Elementary Multiperspective Material Ontology
contributor: Charles Tapley Hoyt
has provider formatter: http://emmo.info/emmo#EMMO_$1
type: Resource
keyword: nfdi4ing
keyword: material science
has prefix: emmo
keyword: communication science
git repository: EMMO
keyword: physics
keyword: industry
description: EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)
keyword: philosophy
has responsible: 0000-0002-1560-809X
is deprecated: false
has URI prefix: http://emmo.info/emmo#EMMO_
keyword: nfdi4cat
is part of: Bioregistry

Plant Phenotype Experiment Ontology
type: Resource
has resource example: GPS location
0000005: GPS_location
is deprecated: false
has provider formatter: http://purl.org/ppeo/PPEO.owl#$1
has responsible: Cyril Pommier
has prefix: ppeo
description: The Plant Phenotyping Experiment Ontology (PPEO) is an implementation of the Minimal Information About Plant Phenotyping Experiment. It lists and organises all the informations necessary to describe and reuse a phenotyping dataset following FAIR principles (Findable Interoperable Accessible Reusable). It has been initiated with experts from Elixir, Emphasis, Bioversity International - CGIAR and RDA.
is part of: Bioregistry
keyword: dataplant
has URI prefix: http://purl.org/ppeo/PPEO.owl#
keyword: life sciences, biology

MetaNetX reaction
has local unique identifier pattern: ^(MNXR\d+|EMPTY)$
is part of: Bioregistry
type: Resource
has prefix: metanetx.reaction
has provider formatter: https://www.metanetx.org/equa_info/$1
has URI prefix: https://www.metanetx.org/equa_info/
has resource example: MNXR101574
description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions.
is deprecated: false
0000005: MNXR101574

Scopus affiliation ID
has prefix: scopus.affiliation
has provider formatter: https://www.scopus.com/affil/profile.uri
is deprecated: false
0000005: 60025709
is part of: Bioregistry
description: identifier for an organisation in author affiliations per Scopus
type: Resource
has resource example: https://www.scopus.com/affil/profile.uri
has URI prefix: https://www.scopus.com/affil/profile.uri

SWEET Ontology Material Aerosol
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: http://sweetontology.net/matrAerosol/$1
keyword: materials
keyword: aerosol
has resource example: Aerosol
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Aerosol
has alternative prefix: somaae
is deprecated: false
has prefix: sweet.maae
0000005: Aerosol
has URI prefix: http://sweetontology.net/matrAerosol/
is part of: Bioregistry
git repository: sweet

SAREF extension for water
has prefix: saref.water
keyword: nfdi4ing
has provider formatter: https://saref.etsi.org/saref4watr/$1
has alternative prefix: s4watr
type: Resource
0000005: AcceptabilityProperty
is deprecated: false
description: This ontology extends the SAREF ontology for the water domain. This work has been developed in the context of the STF 566, which was established with the goal to create three SAREF extensions, one of them for the water domain.
keyword: engineering
keyword: environment
has resource example: AcceptabilityProperty
has URI prefix: https://saref.etsi.org/saref4watr/
is part of: Bioregistry
keyword: iot

Identifiers.org
has part: protonet.cluster
has part: cdd
has part: fairsharing
has part: tair.locus
has part: metlin
has part: mmrrc
has part: homd.seq
has part: lincs.smallmolecule
has part: antibodyregistry
has part: obcs
has part: mobidb
has part: morpheus
0000007: https://identifiers.org/$1:$2
has part: foodb.compound
has part: sgd
has part: chembl
has part: bugbase.protocol
has part: gramene.taxonomy
has part: intact
has part: unipathway.compound
has part: pigqtldb
has part: cbioportal
has part: ird.segment
has part: kegg.metagenome
has part: pazar
has part: nmdc
has part: huge
has part: nucleotide
has part: nemo
has part: vectorbase
has part: miriam.resource
has part: pubchem.substance
has part: sparc.drs
has part: transyt
has part: civic.vid
has part: opl
has part: charprot
has part: bgee.family
has part: cryptodb
has part: pypi
has part: kegg.drug
has part: envipath
has part: tair.protein
has part: apid.interactions
has part: omid
has part: rism
has part: ndc
has part: hinv.transcript
has part: peptideatlas
has part: opb
has part: cabri
has part: funcbase.human
has part: swissregulon
has part: combine.specifications
has part: caps
has part: mi
has part: drsc
has part: homologene
has part: biotools
has part: wb.rnai
has part: ec-code
has part: comptox
has part: covid19
has part: isni
has part: crop2ml
has part: ga4ghdos
has part: nlfff
has part: jaxmice
has part: mex
has part: mmp.db
has part: gcst
has part: rhea
has part: bdsc
has part: mmp.cat
has part: dbd
has part: drugcentral
has part: mir
has part: pocketome
has part: empiar
has part: kegg.genome

LRMI Educational Audience Role Vocabulary
has URI prefix: http://purl.org/dcx/lrmi-vocabs/educationalAudienceRole/
is part of: Bioregistry
has provider formatter: http://purl.org/dcx/lrmi-vocabs/educationalAudienceRole/$1
keyword: open educational resource
contributor: Charles Tapley Hoyt
git repository: lrmi
type: Resource
0000005: mentor
has resource example: mentor
is deprecated: false
description: A concept scheme that defines the primary or intended roles of the audience (beneficiary) of the resource being described.
has prefix: lrmi.educationalaudiencerole
keyword: learning resource

Data Use Ontology
keyword: nfdi4ing
description: DUO is an ontology which represent data use conditions.
keyword: biomedical science
0000005: 0000046
has resource example: DUO_0000046
keyword: computer science
depends on: Basic Formal Ontology
keyword: subject agnostic
has URI prefix: http://purl.obolibrary.org/obo/DUO_
keyword: metadata standardization
keyword: ess
keyword: obo
has provider formatter: http://purl.obolibrary.org/obo/DUO_$1
appears in: Sickle Cell Disease Ontology
keyword: ontology
is deprecated: false
is part of: Bioregistry
depends on: Information Artifact Ontology
has download URL: duo.owl
keyword: nfdi4chem
has responsible: Melanie Courtot
git repository: DUO
has prefix: duo
has local unique identifier pattern: ^\d{7}$
type: Resource

Basic Register of Thesauri, Ontologies & Classifications
has part: https://bartoc.org/en/node/447
has part: https://bartoc.org/en/node/20826
has part: https://bartoc.org/en/node/20715
has part: https://bartoc.org/en/node/20713
has part: https://bartoc.org/en/node/2021
has part: https://bartoc.org/en/node/181
has part: https://bartoc.org/en/node/20697
has part: https://bartoc.org/en/node/20394
has part: https://bartoc.org/en/node/1897
has part: https://bartoc.org/en/node/562
has part: https://bartoc.org/en/node/18206
description: The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).
has part: https://bartoc.org/en/node/14
has part: https://bartoc.org/en/node/1895
has part: https://bartoc.org/en/node/216
has part: https://bartoc.org/en/node/241
has provider formatter: https://bartoc.org/en/node/$1
has part: https://bartoc.org/en/node/18355
has part: https://bartoc.org/en/node/528
has part: https://bartoc.org/en/node/20501
has part: https://bartoc.org/en/node/400
has part: https://bartoc.org/en/node/459
has part: https://bartoc.org/en/node/820
has part: https://bartoc.org/en/node/509
has part: https://bartoc.org/en/node/109
has part: https://bartoc.org/en/node/20686
has part: https://bartoc.org/en/node/20698
has part: https://bartoc.org/en/node/21017
has part: https://bartoc.org/en/node/1237
has part: https://bartoc.org/en/node/581
has part: https://bartoc.org/en/node/1915
has part: https://bartoc.org/en/node/20699
has part: https://bartoc.org/en/node/20428
has part: https://bartoc.org/en/node/20514
has part: https://bartoc.org/en/node/391
has part: https://bartoc.org/en/node/18274
has part: https://bartoc.org/en/node/20712
has part: https://bartoc.org/en/node/2022
has part: https://bartoc.org/en/node/430
has part: https://bartoc.org/en/node/1143
has part: https://bartoc.org/en/node/20825
has part: https://bartoc.org/en/node/17844
has part: https://bartoc.org/en/node/20705
has part: https://bartoc.org/en/node/20510
has part: https://bartoc.org/en/node/17875
has part: https://bartoc.org/en/node/16
has part: https://bartoc.org/en/node/305
has part: https://bartoc.org/en/node/2053
has part: https://bartoc.org/en/node/20703
has responsible: Andreas Ledl
has part: https://bartoc.org/en/node/20716
has part: https://bartoc.org/en/node/20719
has part: https://bartoc.org/en/node/20464
has part: https://bartoc.org/en/node/449
has part: https://bartoc.org/en/node/507
has part: https://bartoc.org/en/node/445
has part: https://bartoc.org/en/node/20684
has part: https://bartoc.org/en/node/571
has part: https://bartoc.org/en/node/20688
has part: https://bartoc.org/en/node/1899
has part: https://bartoc.org/en/node/1884
0000005: 181
type: Registry
has part: https://bartoc.org/en/node/18311
has part: https://bartoc.org/en/node/20702
has part: https://bartoc.org/en/node/20288
has part: https://bartoc.org/en/node/17818
has part: https://bartoc.org/en/node/20052
has part: https://bartoc.org/en/node/18250
has part: https://bartoc.org/en/node/20701
has part: https://bartoc.org/en/node/17815
has part: https://bartoc.org/en/node/20402
has part: https://bartoc.org/en/node/549
has part: https://bartoc.org/en/node/20833
has part: https://bartoc.org/en/node/1940
has part: https://bartoc.org/en/node/20299
has part: https://bartoc.org/en/node/20430
has part: https://bartoc.org/en/node/20710
has part: https://bartoc.org/en/node/558

Zazuko Prefix Server
has part: dcmitype
has part: schema
has part: as
has part: dbo
has part: qudt
has part: time
has part: prov
has part: xsd
has part: sioc
has part: dqv
has part: csvw
has part: dcterms
has part: dcat
has part: earl
has part: qb
has part: ldp
has part: oa
has part: cnt
0000007: https://prefix.zazuko.com/$1:$2
has provider formatter: https://prefix.zazuko.com/prefix/$1:
has part: shsh
has part: exif
has part: vann
has part: log
has part: crm
has part: acl
has part: grddl
has part: og
has part: void
has part: gr
has part: lvont
has part: frbr
has part: skos
has part: sdmx
description: This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from <https://prefix.zazuko.com/about>)
has part: vso
has part: vs
has part: sd
has part: skosxl
has responsible: Adrian Gschwend
has part: vcard
has part: sosa
has part: dcam
has part: xhv
has part: doap
has part: cert
has part: rdfs
has part: ssn
has part: bibo
has part: locn
has part: shex
has part: owl
has part: foaf
type: Registry
has part: sh
has part: gs1
has part: hydra
has part: wdrs
0000005: frbr
has part: dc11
has part: oidc
has part: cc
has part: ical
has part: m4i
has part: xkos
has part: geof
has part: geor
has part: sf
has part: org
has part: geo
has part: wgs
has part: rdfa
has part: https://bioregistry.io/metaregistry/zazuko/resolve/rdf
has part: gn

Biological Collections Ontology
has resource example: BCO_0000081
has provider formatter: http://purl.obolibrary.org/obo/BCO_$1
keyword: metagenomics
keyword: ess
is deprecated: false
has responsible: https://orcid.org/0000-0001-8815-0078
keyword: taxonomy
has URI prefix: http://purl.obolibrary.org/obo/BCO_
0000005: 0000081
keyword: obo
appears in: FuTRES Ontology of Vertebrate Traits
keyword: ontology
keyword: biospecimen
has prefix: bco
keyword: biodiversity
is part of: Bioregistry
keyword: dataplant
keyword: ecology
git repository: bco
has download URL: bco.owl
keyword: sample annotation
description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.
keyword: taxonomic classification
keyword: environmental material
keyword: earth sciences
has local unique identifier pattern: ^\d{7}$
type: Resource

ChemBioSys Project
has resource example: https://data.chembiosys.de/projects/15
has provider formatter: https://data.chembiosys.de/projects/$1
is deprecated: false
has URI prefix: https://data.chembiosys.de/projects/
0000005: 15
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
description: A project in the ChemBioSys data platform
contributor: Charles Tapley Hoyt
has prefix: chembiosys.project
type: Resource

SWEET Ontology Human Technology Readiness
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Technology Readiness
has URI prefix: http://sweetontology.net/humanTechReadiness/
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/humanTechReadiness/$1
0000005: TRL
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: TRL
is deprecated: false
has alternative prefix: sohutr
has prefix: sweet.hutr
keyword: technology readiness
is part of: Bioregistry

NFDI4Ing Resources
has part: Material properties ontology
description: Prefixes for ontologies relevant for the NFDI4Ing
has part: PROV Namespace
has part: Building Topology Ontology
has part: Physics Subject Headings
has part: Ontology of units of Measure
has part: The Software Description Ontology
has part: Smart Applications Reference ontology
has part: The Audio Commons Ontology
has part: Metadata4Ing
has part: Building Ontology
has part: Modern Science Ontology
has part: General Process Ontology
has part: Digital Reference
has part: FIESTA-IoT Ontology
has part: System capabilities, operating ranges, and survival ranges ontology
has part: SAREF4AUTO: an extension of SAREF for the automotive domain
creator: Charles Tapley Hoyt
has part: Core Ontology for Robotics and Automation
has part: IOC: Internet of Construction Ontology
has part: Vehicle Signal Specification Core Ontology
has part: SAREF4LIFT: an extension of SAREF for the Smart Lifts domain
has part: SAREF extension for building devices
has part: SAREF extension for environment
has part: Materials Design Ontology - Full
has part: Basic Formal Ontology
has part: Common Core Ontologies
has part: Big Open Network of Sustainability Assessment Information Ontology
has part: Platform Material Digital Core Ontology
has part: MobiVoc Open Mobility Vocabulary 1.1.4
has part: Standards Ontology
has part: Basisklassifikation
has part: Vocabulary of Materials Tribology Lab at KIT
has part: Ontology Modeling for Intelligent Domotic Environments
has part: ListDB Ontology
has part: EDAM Ontology
has part: International Data Spaces Information Model
has part: Simple Knowledge Organization System (SKOS) version of Materials Data Vocabulary
has part: MathModDB Ontology
has part: SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain
has part: FAIR Vocabulary
has part: The COnCEPT upper-level Design Ontology
has part: Semanticscience Integrated Ontology
has part: Software ontology
has part: Heat Pump Ontology
has part: Sensor, Observation, Sample, and Actuator Ontology
has part: SAREF4INMA: an extension of SAREF for the industry and manufacturing domain
has part: Key Performance Indicator ontology
has part: Base Ontology
has part: Creative Commons Rights Expression Language
has part: FINDEX Bau as a SKOS Thesaurus - Facetted Indexing System for Civil Engineering
has part: SAREF extension for water
has part: Code Ontology
has part: Semantic Web for Earth and Environment Technology Ontology
has part: InfoSecSoS Ontology
has part: Open Energy Ontology
has part: Dublin Core Metadata Initiative Terms
has part: Industrial Data Ontology
has part: Data Use Ontology
has part: Thing Description Ontology
has part: Allotrope Merged Ontology Suite
has part: SAREF4EE: the EEbus/Energy@home extension of SAREF
has part: FINDEX Raum
has part: Tribology Ontology for Artificial Intelligence
has part: Unified Astronomy Thesaurus
has part: Battery Interface Ontology
has part: DFG Classification of Subject Areas Ontology - 2020-2024
has part: Digital Construction Lifecycle (dicl)
has part: Shapes Constraint Language
has part: International Standard for Intelligent Information Request and Delivery Core Ontology
has part: Brick Ontology
has part: FID BAUdigital Subject Headings
has part: Ontology for manufacturing and logistics
has part: Mobility Theme
has part: Semantic Sensor Network Ontology
has part: Information Artifact Ontology
has part: Scientific Evidence and Provenance Information Ontology
has part: The ROSETTA ontology of industrial robotics devices and robotic skills.
has part: Elementary Multiperspective Material Ontology

SWEET Ontology Representation Data Product
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has alternative prefix: sorepdp
0000005: Archive
has provider formatter: http://sweetontology.net/reprDataProduct/$1
is deprecated: false
keyword: representation data product
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Product
has prefix: sweet.repdp
has resource example: Archive
is part of: Bioregistry
has URI prefix: http://sweetontology.net/reprDataProduct/

PubMed Central
type: Resource
has responsible: Jeff Beck
keyword: biomedical science
has resource example: PMC3084216
has alternative prefix: PMC
has provider formatter: http://europepmc.org/articles/$1
has alternative prefix: PMCID
keyword: bibliography
description: PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.
is deprecated: false
keyword: centrally registered identifier
has local unique identifier pattern: ^PMC\d+(\.\d+)?$
has URI prefix: http://europepmc.org/articles/
0000005: PMC3084216
has prefix: pmc
is part of: Bioregistry

Sequencing Initiative Suomi
has prefix: sisu
description: The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.
keyword: preclinical studies
has local unique identifier pattern: ^[0-9]+:[0-9]+$
is part of: Bioregistry
has resource example: variant/17:41223048
type: Resource
keyword: epidemiology
keyword: biomedical science
has URI prefix: http://search.sisuproject.fi/#/variant/
keyword: medicine
has responsible: https://orcid.org/0000-0003-3212-7826
0000005: 17:41223048
is deprecated: false
has provider formatter: http://search.sisuproject.fi/#/variant/$1
keyword: genomics

Human Brain Atlas
has resource example: HBA 4005
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: A controlled vocabulary to support the study of transcription in the human brain
type: Resource
0000005: 4005
git repository: human brain atlas ontology
has download URL: hbao.owl
has prefix: hba
has URI prefix: https://purl.brain-bican.org/ontology/hbao/HBA_
has provider formatter: https://purl.brain-bican.org/ontology/hbao/HBA_$1
keyword: ontology

Plant Ontology
appears in: Genomic Epidemiology Ontology
keyword: life science
keyword: ess
has responsible: Pankaj Jaiswal
keyword: classification
keyword: obo
appears in: Plant Gall Ontology
appears in: An ontology of core ecological entities
keyword: ontology
appears in: Agronomy Ontology
has resource example: PO_0009089
keyword: expression data
description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
is deprecated: false
is part of: Bioregistry
keyword: dataplant
has local unique identifier pattern: ^\d+$
git repository: plant-ontology
keyword: botany
keyword: earth sciences
has prefix: po
has provider formatter: http://purl.obolibrary.org/obo/PO_$1
appears in: Environment Ontology
keyword: life cycle
has URI prefix: http://purl.obolibrary.org/obo/PO_
type: Resource
keyword: structure
has download URL: po.owl
keyword: whole plant development stage
keyword: plant anatomy
0000005: 0009089

Unified Foundational Ontology
has URI prefix: http://purl.org/nemo/gufo#
0000005: Person
description: An _gentle_ implementation of the Unified Foundational Ontology (UFO), which is an upper level ontology like BFO that is concerned with e.g. expressing temporal relationships between events.
has provider formatter: http://purl.org/nemo/gufo#$1
git repository: gufo
contributor: Charles Tapley Hoyt
is part of: Bioregistry
type: Resource
keyword: upper level
has prefix: gufo
has responsible: João Paulo A. Almeida
has resource example: Person
keyword: ontology
keyword: general & upper
keyword: events
is deprecated: false

Secondary Metabolism Collaboratory - biosynthetic gene cluster
has reviewer: https://orcid.org/0000-0001-9439-5346
has provider formatter: https://smc.jgi.doe.gov/bgc/$1
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: https://smc.jgi.doe.gov/bgc/12039302
description: The secondary metabolism collaboratory is a database for secondary metabolite biosynthetic gene clusters. This prefix represents identifiers for individual biosynthetic gene clusters (BGCs) linked to their corresponding bacterial or archaeal source.
0000005: 12039302
type: Resource
contributor: Mufaddal Naguthanawala
has responsible: Daniel W Udwary
has URI prefix: https://smc.jgi.doe.gov/bgc/
has prefix: smc.bgc
is deprecated: false

Broad Fungal Genome Initiative
type: Resource
has resource example: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html
has prefix: broad
description: Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.
has local unique identifier pattern: ^S\d+$
is deprecated: false
has URI prefix: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html
0000005: S7000002168151102
has provider formatter: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html
is part of: Bioregistry

Electron Microscopy Glossary
has provider formatter: https://purls.helmholtz-metadaten.de/emg/EMG_$1
has URI prefix: https://purls.helmholtz-metadaten.de/emg/EMG_
has download URL: ontology.owl
keyword: ontology
has resource example: EMG_00000005
0000005: 00000005
is deprecated: false
has prefix: emg
description: The Electron Microscopy (EM) Glossary is a widespread community effort to harmonize terminology in the electron and ion microscopies. It is created in a not-for profit collaboration between academic and non-university research institutions including domain and metadata experts. It provides harmonized terminology for application level semantic artifacts to source from and align with. [from homepage]
has local unique identifier pattern: ^\d{8}$
is part of: Bioregistry
git repository: em glossary
type: Resource
has responsible: Oonagh Brendike-Mannix
contributor: Charles Tapley Hoyt

BRENDA Ligand
has URI prefix: https://www.brenda-enzymes.de/ligand.php
description: Information for ligands in the BRENDA database.
type: Resource
has prefix: brenda.ligand
has resource example: https://www.brenda-enzymes.de/ligand.php
keyword: structrual bioinformatics
has provider formatter: https://www.brenda-enzymes.de/ligand.php
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
0000005: 278
keyword: chemistry
contributor: Charles Tapley Hoyt

Bioregistry
has part: OrthoDB
has part: NASA Open Science Data Repository Study
has part: National Academic Research and Collaborations Information System
has part: Mammalia Polymorphism Database
has part: MIMIC III Database
has part: GenBase
has part: Saccharomyces Genome Database
has part: Pfam protein family
has part: European Mouse Mutant Archive
has part: ELI Metadata Ontology
has part: Universal Natural Products Database
has part: Allotrope role
has part: CABI Digital Library
has part: Chromosome Ontology
has part: Product Types Ontology
has part: PEPhub
has part: SWEET Ontology Realm Atmospheric Boundary Layer
has part: Vitro Application Ontology
has part: Amphibian gross anatomy
has part: Competence Ontology
has part: KEGG Compound
has part: Progenetix
has part: Digital archive of scholarly articles
has part: SWEET Ontology State Thermodynamic
has part: LinkML
has part: Genitourinary Development Molecular Anatomy Project
has part: SABIO-RK Reaction
has part: OpenAlex
has part: Identifiers.org namespace
has part: PathBank
has part: Encyclopedia of DNA Elements
has part: Mass spectrometry ontology
has part: Minimal Viable Identifier
has part: GenPept
has part: COlleCtion of Open Natural ProdUcTs
has part: SWEET Ontology State Role Geographic
has part: NIF Standard Ontology: Chemical
has part: BDGP insertion DB
has part: Gene Ontology Annotation Database
has part: International Classification of Diseases, 9th Revision
has part: Human Genome Variation Society Nomenclature
type: Registry
has part: Diagnostic and Statistical Manual of Mental Disorders (5th Edition)
has part: SWEET Ontology Representation Scientific Units
has part: Food Classification and Description System (from FSA Food Type identifiers)
has part: Conditions of Access
has part: GnpIS
has part: ICEberg integrative and mobilizable element
has part: Orientation of Proteins in Realistic Lipid Membranes
has part: International Standard for Intelligent Information Request and Delivery Machinery Ontology
has part: SWEET Ontology State Role Biological
has part: Colorectal Cancer Atlas
has part: SWEET Ontology Phenomena System Complexity
has part: BacDive
has part: Bloomington Drosophila Stock Center
has part: SWEET Ontology Human Agriculture
has part: ISO 15926-14
has part: Swiss Personalized Health Network Schema
has part: PRO Research: An ontology for describing RDM-Policies in a structured way
has part: SEED Reactions
has part: Access to Biological Collection Data Schema
has part: DALIA Open Educational Resource
has part: Human Metabolome Database
has part: NCBI Protein
has part: Adverse Event Reporting Ontology
has part: Sharkipedia Species
has part: NFDI Core Ontology
has part: Cross-linker reagents ontology
has part: Ontology for simulation, modelling, and optimization
has part: Molecular Process Ontology
has part: Name Reaction Ontology
has part: SPARQL 1.1 Service Description
has part: ClinGen Allele Registry
has part: DrugBank Salts
has part: Catalogue of Life in Taiwan
has part: DataCite Ontology
has part: Lifestyle Factors Ontology
has part: GlycoNAVI
has part: PRIDE Project
has part: SWAP Logic Ontology

SAREF4SYST: an extension of SAREF for typology of systems and their inter-connections
has alternative prefix: s4syst
has URI prefix: https://saref.etsi.org/saref4syst/
has resource example: Connection
is deprecated: false
description: The present document is the technical specification of SAREF4SYST, a generic extension of [ETSI TS 103 264 SAREF](https://www.etsi.org/deliver/etsi_ts/103200_103299/103264/02.01.01_60/ts_103264v020101p.pdf) that defines an ontology pattern which can be instantiated for different domains. SAREF4SYST defines Systems, Connections between systems, and Connection Points at which systems may be connected. These core concepts can be used generically to define the topology of features of interest, and can be specialized for multiple domains. The topology of features of interest is highly important in many use cases. If a room holds a lighting device, and if it is adjacent with an open window to a room whose luminosity is low, then by turning on the lighting device in the former room one may expect that the luminosity in the latter room will rise. The SAREF4SYST ontology pattern can be instantiated for different domains. For example to describe zones inside a building (systems), that share a frontier (connections). Properties of systems are typically state variables (e.g. agent population, temperature), whereas properties of connections are typically flows (e.g. heat flow). SAREF4SYST has two main aims: on the one hand, to extend SAREF with the capability or representing general topology of systems and how they are connected or interact and, on the other hand, to exemplify how ontology patterns may help to ensure an homogeneous structure of the overall SAREF ontology and speed up the development of extensions. SAREF4SYST consists both of a core ontology, and guidelines to create ontologies following the SAREF4SYST ontology pattern. The core ontology is a lightweight OWL-DL ontology that defines 3 classes and 9 object properties. Use cases for ontology patterns are described extensively in [ETSI TR 103 549 Clauses 4.2 and 4.3](https://www.etsi.org/deliver/etsi_tr/103500_103599/103549/01.01.01_60/tr_103549v010101p.pdf). For the Smart Energy domain: - Electric power systems can…
has prefix: saref.system
has provider formatter: https://saref.etsi.org/saref4syst/$1
is part of: Bioregistry
type: Resource
keyword: iot
keyword: nfdi4ing
0000005: Connection

Tetrahymena Genome Database
has URI prefix: http://ciliate.org/index.php/feature/details/
has local unique identifier pattern: ^TTHERM\_\d+$
description: The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature.
0000005: TTHERM_00648910
has provider formatter: http://ciliate.org/index.php/feature/details/$1
has resource example: TTHERM_00648910
has prefix: tgd
is deprecated: false
is part of: Bioregistry
type: Resource

Alliance of Genome Resources Knowledge Base
has reviewer: Charles Tapley Hoyt
description: The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations. The Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location: - [ZFIN](https://zfin.org) - Zebrafish Information Network - [WormBase](https://wormbase.org) - [MGI](https://www.mgi.org) - Mouse Genome Informatics - [RGD](https://rgd.mcw.edu) - Rat Genome Database - [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database - [FlyBase](https://flybase.org) - [Xenbase](https://www.xenbase.org)
has URI prefix: https://www.alliancegenome.org/accession/
type: Resource
keyword: model organism database
is deprecated: false
has local unique identifier pattern: ^[1-9][0-9]{14}$
has responsible: https://orcid.org/0000-0002-6601-2165
0000005: 100000000000001
has provider formatter: https://www.alliancegenome.org/accession/$1
has prefix: agrkb
is part of: Bioregistry
has resource example: https://www.alliancegenome.org/accession/100000000000001
contributor: Sierra Moxon

BioContext
has part: MOD
has part: ASAP
has part: PANTHER.NODE
has part: RICENETDB.COMPOUND
has part: LPT
has part: APO
has part: ORYZABASE.STAGE
has part: SISU
has part: BGEE.STAGE
has part: T3DB
has part: SUGARBIND
has part: VECTORBASE
has part: SEPIO
has part: KEGG.DISEASE
has part: BIGG.MODEL
has part: PLANA
has part: BDGP.EST
has part: HPA
has part: BIOSYSTEMS
has part: CAPS
has part: VHOG
has part: CHICKENQTLDB
has part: BOLD.TAXONOMY
has part: OBI
has part: MW.PROJECT
has part: EcoGene
has part: APID.INTERACTIONS
has part: METACYC.COMPOUND
has part: WIKIPEDIA.EN
has part: OGI
has part: MIRO
has part: OHD
has part: dictyBase
has part: DUO
has part: NEURONDB
has part: MYCO.TUBER
has part: ASPGD.LOCUS
has part: DRAGONDB.PROTEIN
has part: OBIB
has part: EHDAA2
has part: SGD
has part: RefSeq
has part: CHMO
has part: SIDER.EFFECT
has part: ENSEMBL.PROTIST
has part: FBdv
has part: AOP.STRESSOR
has part: AEO
has part: ENA.EMBL
has part: SO
has part: GXA.GENE
has part: GENO
has part: EPO
has part: LINCS.CELL
has part: PRINTS
has part: GRSDB
has part: IDO
has part: WORMS
has part: METACYC.REACTION
has part: BSPO
has part: CGD
has part: ISSN
has part: BCGO
has part: TAIR.LOCUS
has part: RGD
has part: UNIPROT.ISOFORM
has part: FBbt
has part: BIOTOOLS
has part: CHEMBL.TARGET
has part: GABI
has part: BIOCATALOGUE.SERVICE
has part: HSAPDV
has part: skos
has part: CRO
has part: DRAGONDB.LOCUS
has part: PHYLOMEDB
has provider formatter: https://bioregistry.io/metaregistry/biocontext/$1
has part: UMBBD.PATHWAY
has part: BROAD
has part: NEUROLEX

Database of homology-derived secondary structure of proteins
has URI prefix: https://bioregistry.io/hssp:
has provider formatter: ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2
keyword: sequence
is deprecated: false
keyword: protein
has prefix: hssp
has resource example: 102l.hssp.bz2
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^\w{4}$
0000005: 102l
has responsible: https://orcid.org/0000-0001-6059-6270
keyword: clustering
description: HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.

FAIRSharing
has part: FAIRsharing.b084yh
has part: FAIRsharing.bgkyd7
has part: FAIRsharing.djsbw2
has part: FAIRsharing.IziuCK
has part: FAIRsharing.c23cqq
has part: FAIRsharing.z4agsr
has part: FAIRsharing.we2r5a
has part: FAIRsharing.q9j2e3
has provider formatter: https://fairsharing.org/$1
has part: FAIRsharing.w4tncg
has part: FAIRsharing.2q8c28
has part: FAIRsharing.aSszvY
has part: FAIRsharing.3xwMon
has part: FAIRsharing.rs2815
has part: FAIRsharing.fb99fa
has part: FAIRsharing.m3jtpg
has part: FAIRsharing.9w8ea0
has part: FAIRsharing.7g1bzj
has part: FAIRsharing.mf91p5
has part: FAIRsharing.qv4b3c
has part: FAIRsharing.efv7gw
has part: FAIRsharing.qrrvyk
has part: FAIRsharing.hFLKCn
has part: FAIRsharing.c0bvcy
has part: FAIRsharing.vr52p3
has part: FAIRsharing.9y8f0n
has part: FAIRsharing.dx30m8
has part: FAIRsharing.40j2vd
has part: FAIRsharing.7q4gsz
has part: FAIRsharing.zsgmvd
has part: FAIRsharing.tppk10
has part: FAIRsharing.wwy1ns
has part: FAIRsharing.bxc508
has part: FAIRsharing.4shj9c
has part: FAIRsharing.p77ph9
has part: FAIRsharing.yqn857
has part: FAIRsharing.n8pxvx
has part: FAIRsharing.ex3fqk
has part: FAIRsharing.3zqvaf
has part: FAIRsharing.ca48xs
has part: FAIRsharing.ge1c3p
has part: FAIRsharing.d064y6
has part: FAIRsharing.1413b5
has part: FAIRsharing.ay74mj
has part: FAIRsharing.p58bm4
has part: FAIRsharing.mgxgza
has part: FAIRsharing.910c39
has part: FAIRsharing.p06nme
has part: FAIRsharing.cwx04e
has part: FAIRsharing.mm72as
has part: FAIRsharing.e7skwg
has part: FAIRsharing.fgd5gq
has part: FAIRsharing.f928f1
has part: FAIRsharing.651n9j
has part: FAIRsharing.9gqfpm
has part: FAIRsharing.a8z6gz
has part: FAIRsharing.ap169a
has part: FAIRsharing.mphj4z
has part: FAIRsharing.f0bxfg
has part: FAIRsharing.b97150
has part: FAIRsharing.e4n3an
has part: FAIRsharing.zmx7nn
has part: FAIRsharing.eqgjeq
has part: FAIRsharing.nbfwwv
has part: FAIRsharing.3etvdn
has part: FAIRsharing.j0t0pe
has part: FAIRsharing.y9x8wk
has part: FAIRsharing.ny9vnm
has part: FAIRsharing.97805c
has part: FAIRsharing.cb7086
has part: FAIRsharing.b220d4
has part: FAIRsharing.6xfgaq
has part: FAIRsharing.d88s6e
has part: FAIRsharing.0a674c
has part: FAIRsharing.haxp7g
has part: FAIRsharing.f69084
has part: FAIRsharing.3J6NYn
has part: FAIRsharing.brhpb0
has part: FAIRsharing.4Vs9VM
has part: FAIRsharing.bpxgb6

VMH reaction
has local unique identifier pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$
0000005: HEX1
has prefix: vmhreaction
is deprecated: false
is part of: Bioregistry
has resource example: reaction/HEX1
description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.
has provider formatter: https://www.vmh.life/#reaction/$1
has URI prefix: https://www.vmh.life/#reaction/
type: Resource

OntoBee
has part: ICO
has part: MCO
has part: ONE
has part: NCBITaxon
has part: OMIABIS
has part: PORO
has part: CLYH
has part: NCRO
has part: MFOMD
has part: PR
has part: PO
has part: BMONT
has part: SIO
has part: PSO
has part: EPIO
has part: ORNASEQ
has part: NCIT
has part: ONTOAVIDA
has part: IAO
has part: NGBO
has part: XCO
has part: FYPO
has part: ExO
has part: OAE
has part: OMIT
has part: FAO
has part: CMO
has part: FBbi
has part: FOVT
has part: XAO
has part: OM
has part: OCCO
has part: APO
has part: CDNO
has part: MOD
has part: SWO
has part: HP
has part: EHDAA2
has part: HSO
has part: HOM
has part: NOMEN
has part: OGG
has part: DISDRIV
has part: ENVO
has part: OGI
has part: CTENO
has part: MS
has part: HAO
has part: FBcv
has part: XL
has part: OOSTT
has part: PSDO
has part: CTO
has part: VTO
has part: MPATH
has part: FOBI
has part: AGRO
has responsible: Yongqun Oliver He
has part: CHMO
has part: EDAM
has part: DUO
has part: VariO
type: Registry
has part: FIDEO
has part: PdumDv
has part: MICRO
has part: ARO
has part: OPL
has part: CHEMINF
has part: AfPO
has part: RNAO
has part: VT
has part: ONTONEO
has part: FOODON
has part: MA
has part: PW
has part: BSPO
has part: OHPI
has part: ECOCORE

Morpheus model repository
is part of: Bioregistry
has provider formatter: https://morpheus.gitlab.io/models/$1
has resource example: M0001
has local unique identifier pattern: ^M[0-9]{4,}$
has URI prefix: https://morpheus.gitlab.io/models/
type: Resource
has prefix: morpheus
description: The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software.
is deprecated: false
0000005: M0001

Name-to-Thing
has part: aop.events
has part: piroplasma
has part: vario
has part: mgnify.samp
has part: ubio.namebank
has part: bacmap.map
has part: p3db.site
has part: insdc
has part: umbbd.rule
has part: molbase
has part: kegg
has part: doqcs.pathway
has part: neurondb
has part: isni
has part: iao
has part: zfin
has part: wikidata
has part: ttd.drug
has part: uniprot.isoform
has part: bionumbers
has part: tritrypdb
has part: kegg.disease
has part: corum
has part: ensembl.plant
has part: ensembl.bacteria
has part: napp
has part: arxiv
has part: genpept
has part: stap
has part: hgmd
has part: sasbdb
has part: ngl
has part: mmdb
has part: hcvdb
has part: caps
has part: bitterdb.rec
has part: beetlebase
has part: ms
has part: reactome
has part: soybase
has part: drugbankv4.target
has part: aftol.taxonomy
has part: phenolexplorer
has part: tgd
has part: rgd.qtl
has part: dictybase.gene
has part: omit
has part: sabiork.reaction
has part: tair.locus
has part: grid
has part: massive
has part: ordb
has part: jws
has part: asap
has part: prodom
has part: bugbase.expt
has part: pubchem.substance
has part: treefam
has part: treebase
has part: spdx
has part: biocarta.pathway
has part: aphidbase.transcript
has part: dashr.expression
has part: biomodels.kisao
has part: pmdb
has part: imgt.hla
has part: minid
has part: refseq
has part: intact.molecule
has part: vfdb.gene
has part: oma.protein
has part: yetfasco
has part: isbn
has part: mirbase
has part: viralzone
has part: rebase
has part: otl
has part: peroxibase
has part: glida.gpcr

Dublin Core Elements (1.1)
has alternative prefix: dcelem
keyword: subject agnostic
0000005: contributor
keyword: metadata
keyword: metadata standardization
keyword: life science
has alternative prefix: dc.elements
has alternative prefix: elements
keyword: ontology
keyword: resource metadata
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. **Deprecation Notice**: While the `/elements/1.1/` namespace will be supported indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`) ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3)).
has URI prefix: http://purl.org/dc/elements/1.1/
has alternative prefix: dc11
has download URL: dcelements.owl
has responsible: https://orcid.org/0000-0001-9052-2854
has resource example: contributor
type: Resource
has provider formatter: http://purl.org/dc/elements/1.1/$1
has prefix: dc
keyword: annotation
keyword: biomedical science
is deprecated: true
has alternative prefix: dce

Hymenoptera Anatomy Ontology
description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)
has provider formatter: http://purl.obolibrary.org/obo/HAO_$1
0000005: 0000187
has local unique identifier pattern: ^\d{7}$
keyword: anatomy
keyword: life science
keyword: obo
has responsible: Matt Yoder
has resource example: HAO_0000187
keyword: ontology
has download URL: hao.owl
git repository: hao
is deprecated: false
has prefix: hao
is part of: Bioregistry
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/HAO_

Terminologia Embryologica
has prefix: te
0000005: E5.11.2.0.0.0.4
is deprecated: false
is part of: Bioregistry
description: The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]
type: Resource
contributor: Charles Tapley Hoyt

HUGO Gene Nomenclature Committee
has responsible: Elspeth Bruford
0000005: 16793
keyword: gene
has URI prefix: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/
keyword: life science
description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.
keyword: pseudogene
keyword: ncrna
keyword: classification
has provider formatter: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1
has responsible: Susan Tweedie
has download URL: hgnc.owl.gz
keyword: ontology
is deprecated: false
is part of: Bioregistry
keyword: protein
has prefix: hgnc
has resource example: !/hgnc id/16793
type: Resource
has local unique identifier pattern: ^\d{1,5}$
keyword: gene name

BioGRID Interactions
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has URI prefix: https://thebiogrid.org/interaction/
has responsible: Mike Tyers
contributor: Charles Tapley Hoyt
type: Resource
has prefix: biogrid.interaction
has resource example: https://thebiogrid.org/interaction/2649230
has provider formatter: https://thebiogrid.org/interaction/$1
description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.
0000005: 2649230
is deprecated: false

Art and Architecture Thesaurus
description: The AAT includes generic terms, and associated dates, relationships, and other rich information about concepts related to or required to catalog, discover, and retrieve information about art, architecture, and other visual cultural heritage, including related disciplines such as archaeology and conservation. Visual works include not only visual cultural works classified as "art" according to Western aesthetics, but also utilitarian and ceremonial works. Terminology may be used for work types, roles, materials, styles, cultures, techniques, subject, etc., so long as terms are within the defined scope of AAT. [from https://www.getty.edu/research/tools/vocabularies/aat/aat_faq.html]
has provider formatter: http://vocab.getty.edu/aat/$1
has prefix: getty.att
is deprecated: false
0000005: 300011154
has resource example: http://vocab.getty.edu/aat/300011154
has URI prefix: http://vocab.getty.edu/aat/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

Gene Ontology
keyword: medicine
has download URL: go.owl
appears in: Provisional Cell Ontology
depends on: NCBI Taxonomy
has provider formatter: http://purl.obolibrary.org/obo/GO_$1
keyword: obo
appears in: Medical Action Ontology
appears in: Planarian Phenotype Ontology
contributor: https://orcid.org/0000-0002-8361-2795
appears in: An ontology of core ecological entities
keyword: ontology
keyword: biocuration
appears in: Agronomy Ontology
has alternative prefix: gomf
appears in: Population and Community Ontology
keyword: expression data
is deprecated: false
keyword: protein
keyword: dataplant
keyword: cellular_component
has prefix: go
git repository: go-ontology
appears in: ChEBI Integrated Role Ontology
depends on: Relation Ontology
keyword: molecular_function
keyword: gene functional annotation
description: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
depends on: Cell Ontology
0000005: 0032571
appears in: Xenopus Phenotype Ontology
keyword: sequence annotation
keyword: go-term enrichment data
appears in: Zebrafish Phenotype Ontology
has alternative prefix: goccid
keyword: life sciences, biology
appears in: Environment Ontology
has alternative prefix: gomfid
appears in: Cell Ontology
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/GO_
keyword: knowledge representation
keyword: transcript
appears in: Environmental conditions, treatments and exposures ontology
type: Resource
keyword: gene
keyword: annotation
has resource example: GO_0032571
has responsible: https://orcid.org/0000-0001-6787-2901
depends on: Uber Anatomy Ontology
has alternative prefix: gobpid
has local unique identifier pattern: ^\d{7}$
has alternative prefix: gocc
appears in: Uber Anatomy Ontology
keyword: life science
has alternative prefix: gobp
keyword: biological_process

Library of Congress Format Description Document
0000005: fdd000613
keyword: media type
has prefix: loc.fdd
is deprecated: false
has local unique identifier pattern: ^fdd\d+$
has URI prefix: https://www.loc.gov/preservation/digital/formats/fdd/
has provider formatter: https://www.loc.gov/preservation/digital/formats/fdd/$1
has resource example: https://www.loc.gov/preservation/digital/formats/fdd/fdd000613
keyword: file format
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
description: The digital content format descriptions accessible here provide specific information about individual formats and their characteristics. Each description provides moderately detailed information and citations. Planned for inclusion are a wide variety of formats: file formats, file-format classes, bitstream structures and encodings, and the mechanisms used to compress files or bitstreams. Inclusion of a description for a format does not imply that the format is preferred or acceptable for Library of Congress collections. [from homepage]

Banana Ontology
has provider formatter: https://cropontology.org/rdf/CO_325:$1
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: life science
keyword: food
keyword: ontology
is deprecated: false
keyword: plant phenotypes and traits
keyword: phenotype
has resource example: CO 325:0000519
keyword: agriculture
has responsible: Elizabeth Arnaud
description: The Banana Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
has URI prefix: https://cropontology.org/rdf/CO_325:
is part of: Bioregistry
0000005: 0000519
has prefix: co_325
git repository: Crop-Ontology
has download URL: CO 325.owl

Vehicle Signal Specification Core Ontology
has provider formatter: https://github.com/w3c/vsso-core#$1
is deprecated: false
0000005: VehicleProperty
has resource example: VehicleProperty
keyword: fid move
is part of: Bioregistry
type: Resource
has prefix: vssocore
keyword: nfdi4ing
has URI prefix: https://github.com/w3c/vsso-core#
description: This ontology describes the car's attributes, branches and signals defined in the Vehicle Signal Specification.
keyword: traffic engineering

PROSITE
is part of: Bioregistry
keyword: protein
description: PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
has responsible: Ioannis Xenarios
has provider formatter: https://prosite.expasy.org/$1
has resource example: PS00001
0000005: PS00001
type: Resource
keyword: structure
has local unique identifier pattern: ^PS\d{5}$
has URI prefix: https://prosite.expasy.org/
keyword: biology
is deprecated: false
has prefix: prosite

Oryzabase Stage
has resource example: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/34
description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information.
has provider formatter: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1
is deprecated: false
has prefix: oryzabase.stage
has local unique identifier pattern: ^\d+$
0000005: 34
is part of: Bioregistry
type: Resource
has URI prefix: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/

Open Biomedical Annotations
has prefix: oban
has download URL: oban core.owl
is part of: Bioregistry
type: Resource
description: It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub]
contributor: Charles Tapley Hoyt
has resource example: provenance
has provider formatter: http://purl.org/oban/$1
has URI prefix: http://purl.org/oban/
keyword: ontology
is deprecated: false
0000005: provenance
has local unique identifier pattern: ^\w+$
git repository: OBAN

Document Components Ontology
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has responsible: Silvio Peroni
0000005: Paragraph
has resource example: Paragraph
has prefix: doco
has provider formatter: http://purl.org/spar/doco/$1
type: Resource
keyword: spar
git repository: doco
description: An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix).
keyword: subject agnostic
is deprecated: false
has URI prefix: http://purl.org/spar/doco/

Salmon Ontology
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: https://purl.dataone.org/odo/SALMON_$1
type: Resource
has URI prefix: https://purl.dataone.org/odo/SALMON_
has download URL: salmon.owl
has prefix: salmon
has responsible: Bryce Mecum
has resource example: SALMON_00000674
keyword: ontology
description: An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms.
0000005: 00000674
is deprecated: false

P3DB Protein
description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites.
has prefix: p3db.protein
keyword: small molecule
is deprecated: false
0000005: 70
keyword: protein
is part of: Bioregistry
has provider formatter: http://www.p3db.org/protein.php
has local unique identifier pattern: ^\d+$
has resource example: http://www.p3db.org/protein.php
type: Resource
has URI prefix: https://bioregistry.io/p3db.protein:

Global Biodata Coalition - Global Core Biodata Resources
has part: Orphanet Rare Disease Ontology
has part: HUGO Gene Nomenclature Committee
has part: CIViC Disease
has part: CIViC Source
has part: CIViC variant
has part: PharmGKB Drug
has part: PANTHER Family
description: The [Global Biodata Coalition](https://globalbiodata.org) released a [curated list](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/) of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria [here](https://doi.org/10.5281/zenodo.5845116)). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). Among the databases that don't induce semantic spaces or have simple relationships to prefixes are: - [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.) - [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC) - [GENCODE](https://www.gencodegenes.org/) (uses GenBank) - [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc) - [STRING](https://string-db.org/) (uses UniProt)
has part: Mouse Genome Informatics
has part: PANTHER Pathway
has part: PubMed Central
has part: PharmGKB Disease
has part: Alliance of Genome Resources Knowledge Base
has part: PANTHER Pathway Component
has part: European Nucleotide Archive
has part: CIViC gene
has part: BRENDA Ligand
has part: CIViC Therapy
has part: Orphanet
has part: Global Biodiversity Information Facility
has part: Genome Aggregation Database
has part: PDB Structure
has part: PomBase
has part: UniProt Protein
has part: Ensembl Gene
has part: Rhea reaction
has part: CIViC Assertion
has part: BRENDA Ligand Group
has part: InterPro
has part: Reactome
has part: Saccharomyces Genome Database
has part: BacDive
has part: ProteomeXchange
has part: EcoCyc
has part: BRENDA Tissue Ontology
has part: ChEMBL
has part: Rat Genome Database
has part: CIViC Evidence
has part: FlyBase Gene
has part: PharmGKB pathway
has part: PharmGKB Gene
has part: Chemical Entities of Biological Interest
has part: BRENDA Enzyme
has part: Gene Ontology
has part: VEuPathDB ontology
creator: Charles Tapley Hoyt
type: Collection
has part: Zebrafish Information Network Gene
has part: WormBase
has part: PANTHER Node
has part: UCSC Genome Browser

Dr Paul Schofield
label: Paul Schofield

United States Geological Survey - National Land Cover Database
has prefix: nlcd
keyword: forestry
is deprecated: false
keyword: environment
appears in: Environment Ontology
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
0000005: 12
description: A vocabulary for describing the usage of land cover (e.g., pasture, wetlands, barren, forest, water) extended from the original 16 land cover classes proposed by the [Anderson Level II classification system](https://doi.org/10.3133/pp964) in 1976
type: Resource

PubChem compound
keyword: chemical
has alternative prefix: Pubchem
keyword: metabolite
has resource example: https://pubchem.ncbi.nlm.nih.gov/compound/100101
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/compound/
keyword: epidemiology
type: Resource
has prefix: pubchem.compound
description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.
keyword: structure
0000005: 100101
has responsible: https://orcid.org/0000-0002-5959-6190
has alternative prefix: DSSTox_CID
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/compound/$1
has alternative prefix: PUBCHEM_CID
has alternative prefix: CID
has alternative prefix: pubchem_id
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has alternative prefix: PubChem_Compound_CID
keyword: chemistry
keyword: virology

EBI Ontology Lookup Service
has part: mop
has part: trans
has part: hsapdv
has part: xco
has part: ror
has part: mcro
has part: cido
has part: afo
has part: pride
has part: aeo
has part: rexo
has part: to
has part: taxrank
has part: xpo
has part: rs
has part: symp
has part: fypo
has part: afpo
has part: ico
has part: lipidmaps
has part: nmrcv
has part: hgnc.genegroup
has part: covoc
has part: biolink
has part: om
has part: poro
has part: bspo
has part: ehdaa2
has part: sio
has part: evorao
has part: cheminf
has part: mmusdv
has part: gallont
has part: prefer
has part: gold
has part: dcterms
has part: efo
has part: mesh
has part: rxno
has part: mfmo
has part: ma
has part: ogsf
has part: oio
has part: foodon
has part: bco
has part: gscmixs
has part: dcat
has part: cdao
has part: zp
has part: po
has part: semapv
has part: maxo
has part: xlmod
has part: gsso
has part: colao
has part: upa
has part: edam
has part: dpo
has part: pr
has part: ictv
has part: dmba
has part: aism
has part: ogms
has part: exo
has part: mro
has part: sibo
has part: hp
has part: hgnc
has part: bfo
has part: mmo
has part: ohpi
has part: phipo
has part: micro
has part: exmo
has part: fao
has part: ornaseq
has part: ecocore
has part: slm
has part: ceph
has part: hcao

ArachnoServer
has local unique identifier pattern: ^AS\d{6}$
is part of: Bioregistry
description: ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.
has resource example: http://www.arachnoserver.org/toxincard.html
has responsible: Glenn King
0000005: AS000060
has provider formatter: http://www.arachnoserver.org/toxincard.html
type: Resource
keyword: life science
keyword: drug
contributor: https://orcid.org/0000-0002-1216-4761
has URI prefix: http://www.arachnoserver.org/toxincard.html
is deprecated: false
keyword: protein
has prefix: arachnoserver

Human Unidentified Gene-Encoded
type: Resource
keyword: structure
has prefix: huge
description: The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.
has resource example: KIAA0001
keyword: life science
has provider formatter: https://www.kazusa.or.jp/huge/gfpage/$1
0000005: KIAA0001
is deprecated: false
keyword: dna
keyword: computational biology
keyword: protein
has local unique identifier pattern: ^KIAA\d{4}$
has responsible: https://orcid.org/0000-0002-3328-9571
has URI prefix: https://www.kazusa.or.jp/huge/gfpage/
is part of: Bioregistry

Loggerhead nesting
has prefix: loggerhead
has responsible: Peter Midford
has URI prefix: http://purl.obolibrary.org/obo/LOGGERHEAD_
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/LOGGERHEAD_$1
is deprecated: true
keyword: obo
keyword: ontology
is part of: Bioregistry

Synapse.org external links
has part: Logical Observation Identifiers Names and Codes
has part: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa.
has part: DrugBank
has part: EDAM Ontology
has part: ClinicalTrials.gov
has part: Gramene protein
has part: nextProt
has part: Mouse Genome Informatics
has part: CTD Chemical
has part: ClinVar Record
has part: National Organization for Rare Disorders
has part: NCI Thesaurus
has part: ClinVar Variation
has part: KEGG Reaction
has part: UniProt Archive
has part: Observational Medical Outcomes Partnership
has part: PANTHER Pathway
has part: IntAct protein interaction
has part: PubChem compound
has part: PubMed Central
has part: Open Researcher and Contributor
has part: PANTHER Pathway Component
has part: PharmGKB Disease
has part: Teleost Anatomy Ontology
has part: Alliance of Genome Resources Knowledge Base
has part: ExAC Variant
has part: National Drug File - Reference Terminology
has part: BioSample
has part: Metabolic Encyclopedia of metabolic and other pathways
has part: KEGG Drug
has part: CIViC gene
has part: Internet Standard -- IETF Request for Comments
has part: Integrated Canine Data Commons
has part: arXiv
has part: Plant Experimental Conditions Ontology
has part: Zenodo
has part: Open Science Framework ID
has part: Kyoto Encyclopedia of Genes and Genomes
has part: European Nucleotide Archive
has part: International Classification of Functioning, Disability and Health
has part: DECIPHER CNV Syndromes
has part: Electron Microscopy Data Bank
has part: ArrayExpress
has part: Developing Human Brain Atlas
has part: GeneCards Gene
has part: Chemical Component Dictionary
has part: Global Biodiversity Information Facility
has part: ChEMBL Compound
has part: BRENDA Ligand
has part: COSMIC Cell Lines
has part: IMGT/HLA human major histocompatibility complex sequence database
has part: Human Brain Atlas
has part: BioCyc collection of metabolic pathway databases
has part: Pfam protein clan
has part: CIViC Therapy
has part: PDB Structure
has part: BioPortal
has part: FAIRsharing
has part: Orphanet
has part: bioRxiv
has part: Data Use Ontology
has part: Enzyme Nomenclature
has part: Search Tool for Interactions of Chemicals
has part: Bgee gene
has part: ZINC is not Commercial
has part: Rhea reaction
has part: Brazilian Registry of Clinical Trials
has part: The cBioPortal for Cancer Genomics
has part: Chan Zuckerberg CELLxGENE Collection
has part: PomBase
has part: Mouse Brain Atlas
has part: UniProt Protein
has part: System Science of Biological Dynamics project
has part: InterPro
has part: Ensembl Gene
has part: CIViC Assertion
has part: BRENDA Ligand Group
has part: Sequence Read Archive
has part: NCBI Gene Expression Omnibus
has part: Xenbase

NIF Standard Ontology: Subcellular Entities
0000005: 090803
has reviewer: Charles Tapley Hoyt
contributor: Tom Gillespie
type: Resource
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1
has alternative prefix: nif_subcellular
description: NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO).
is deprecated: false
git repository: NIF-Ontology
has resource example: nlx subcell 090803
has responsible: Tom Gillespie
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
is part of: NIF Standard Ontology: Neurolex
has alternative prefix: NLXSUB
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_subcell_
has prefix: nlx.sub
keyword: cellular components

SWEET Ontology Realm Ocean Floor
git repository: sweet
keyword: realm
has prefix: sweet.reaofl
has URI prefix: http://sweetontology.net/realmOceanFloor/
has alternative prefix: soreaofl
has resource example: AbyssalHill
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Ocean Floor
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: AbyssalHill
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/realmOceanFloor/$1
keyword: ocean floor
type: Resource

Character Set
has identifier space owner: 015em2733
0000005: ASCII
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/CharacterSet#code_
is part of: Bioregistry
has resource example: code ASCII
contributor: Charles Tapley Hoyt
description: Standard set of characters upon which many character encodings are based (Wikipedia).
type: Resource
has prefix: ddi.characterset
has provider formatter: https://vocabularies.cessda.eu/vocabulary/CharacterSet#code_$1

Curated Drug-Drug Interactions Database - Interaction
keyword: chemistry
0000005: 1122888
description: Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety.
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has resource example: http://ddinter.scbdd.com/ddinter/interact/1122888
keyword: drugs
has provider formatter: http://ddinter.scbdd.com/ddinter/interact/$1
has prefix: ddinter.interaction
has responsible: https://orcid.org/0000-0003-3604-3785
keyword: drug-drug interactions
is deprecated: false
has URI prefix: http://ddinter.scbdd.com/ddinter/interact/
has local unique identifier pattern: ^\d+$
keyword: relationships

C. elegans Small Molecule Identifier Database
has URI prefix: https://smid-db.org/smid/
0000005: 137
has alternative prefix: SMID-DB
description: SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications.
is deprecated: false
has prefix: smid
has resource example: https://smid-db.org/smid/137
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://smid-db.org/smid/$1
type: Resource

Docker Hub repository
is deprecated: false
is part of: Bioregistry
description: Docker repository hosted on Docker Hub
contributor: Charles Tapley Hoyt
has URI prefix: https://hub.docker.com/r/
has prefix: dockerhub.repo
type: Resource
has provider formatter: https://hub.docker.com/r/$1
has resource example: gitea
0000005: gitea/gitea

Personal Information Model
description: The PIMO Ontology can be used to express Personal Information Models of individuals. It is based on RDF and NRL, the NEPOMUK Representational Language and other Semantic Web ontologies. This document describes the principle elements of the language and how to use them. (from homepage)
has prefix: nepomuk.pimo
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: http://www.semanticdesktop.org/ontologies/2007/11/01/pimo#
has resource example: Note
0000005: Note
has provider formatter: http://www.semanticdesktop.org/ontologies/2007/11/01/pimo#$1
is deprecated: false

riboCIRC
is deprecated: false
is part of: Bioregistry
has reviewer: https://orcid.org/0000-0001-9439-5346
keyword: peptides
has local unique identifier pattern: ^(hsa|mmu|rno|cel|dme|dre)_ribocirc[A-Za-z0-9.:]+_\d{3}$
has URI prefix: http://www.ribocirc.com/rna_detail.php
type: Resource
has responsible: https://orcid.org/0000-0002-7736-5548
description: Identifiers represent computationally predicted and experimentally verified translatable circular RNAs (circRNAs) across six model species (human, mouse, rat, worm, fly, and zebrafish), including ribosome-associated circRNAs and their encoded peptides with systematic annotation of sequence, structure, and function.
keyword: translation
0000005: hsa_ribocircSCD_001
keyword: ribosome profiling
contributor: Kangho Ji
has provider formatter: http://www.ribocirc.com/rna_detail.php
keyword: circrna
has resource example: http://www.ribocirc.com/rna_detail.php
has prefix: ribocirc

Biocompute Object
has prefix: biocompute
has provider formatter: https://biocomputeobject.org/BCO_$1
git repository: BCO Specification
has URI prefix: https://biocomputeobject.org/BCO_
has resource example: BCO_000001
description: BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication. This pipeline documentation approach has been adopted by a few FDA centers. The goal is to ease the communication burdens between research centers, organizations, and industries. This web portal allows users to build a BioCompute Objects through the interface in a human and machine readable format.
0000005: 000001
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has responsible: https://orcid.org/0000-0001-8823-9945
type: Resource
contributor: Charles Tapley Hoyt

Bloomington Drosophila Stock Center
keyword: fly
has resource example: https://bdsc.indiana.edu/stocks/33607
0000005: 33607
keyword: transposon
keyword: duplication
has provider formatter: https://bdsc.indiana.edu/stocks/$1
keyword: scientist
keyword: mutation
keyword: faseb list
is deprecated: false
keyword: database
keyword: genetic analysis
description: The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.
has URI prefix: https://bdsc.indiana.edu/stocks/
keyword: somatic
keyword: genetic
keyword: deficiency
keyword: sequenced strain
keyword: transposon insertion
has local unique identifier pattern: ^\d+$
has prefix: bdsc
is part of: Bioregistry
keyword: deletion
keyword: insertion
keyword: stock
keyword: disease model
keyword: human disease model
keyword: germline
keyword: invertebrate
keyword: genetic construct
type: Resource
keyword: gene
keyword: protein trap

PeptideAtlas Peptide
has alternative prefix: peptideatlas
0000005: PAp00000009
description: The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools.
is deprecated: false
is part of: Bioregistry
keyword: protein
has prefix: peptideatlas.peptide
keyword: proteomics
has local unique identifier pattern: ^PAp[0-9]{8}$
has resource example: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide
type: Resource
keyword: structure
keyword: mass spectrometry
has provider formatter: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide
has responsible: https://orcid.org/0000-0001-8732-0928
has URI prefix: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide

UniProt Protein
is deprecated: false
has resource example: P0DP23
has responsible: Cathy H. Wu
has local unique identifier pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?(-\d+)?(#PRO_\d+)?$
0000005: P0DP23
keyword: ontology
has download URL: uniprot.owl.gz
has prefix: uniprot
has responsible: https://orcid.org/0000-0003-2148-9135
is part of: Bioregistry
keyword: protein
has alternative prefix: Uniprot ID
keyword: taxonomic classification
has alternative prefix: UniProtKB
has URI prefix: http://purl.uniprot.org/uniprot/
has provider formatter: http://purl.uniprot.org/uniprot/$1
has alternative prefix: SwissProt
has alternative prefix: uniprot/swiss-prot
type: Resource
has responsible: Alex Bateman
has alternative prefix: UniProt
has alternative prefix: UP
contributor: Mufaddal Naguthanawala
keyword: biology
description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information.

Flora Phenotype Ontology
type: Resource
has prefix: flopo
0000005: 0005250
keyword: whole plant development stage
appears in: Plant Gall Ontology
has download URL: flopo.owl
keyword: plant anatomy
keyword: plant cell biology
is deprecated: false
keyword: obo
keyword: ontology
has resource example: FLOPO_0005250
description: Traits and phenotypes of flowering plants occurring in digitized Floras
keyword: biodiversity
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/FLOPO_
keyword: dataplant
has responsible: Robert Hoehndorf
keyword: phenotype
git repository: flopoontology
keyword: horticulture
keyword: botany
has provider formatter: http://purl.obolibrary.org/obo/FLOPO_$1
keyword: life sciences, biology
has local unique identifier pattern: ^\d{7}$
keyword: phenomics

Human Phenotype Ontology
keyword: disease phenotype
description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.
keyword: medicine
keyword: fair data spaces
has download URL: hp.owl
appears in: Medical Action Ontology
keyword: obo
has provider formatter: http://purl.obolibrary.org/obo/HP_$1
appears in: Sickle Cell Disease Ontology
keyword: ontology
keyword: genetics
is deprecated: false
has resource example: HP_0011140
has alternative prefix: hpo
appears in: ChEBI Integrated Role Ontology
has prefix: hp
keyword: omics
0000005: 0011140
git repository: human-phenotype-ontology
keyword: disorder
keyword: phenomics
keyword: life sciences, biology
keyword: preclinical studies
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/HP_
type: Resource
keyword: biomedical science
has responsible: https://orcid.org/0000-0002-5316-1399
keyword: pathology
has local unique identifier pattern: ^\d{7}$

EU Clinical Trials
description: The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.
has alternative prefix: EUCTR
has prefix: euclinicaltrials
has resource example: https://www.clinicaltrialsregister.eu/ctr-search/search
type: Resource
has provider formatter: https://www.clinicaltrialsregister.eu/ctr-search/search
has local unique identifier pattern: ^\d{4}\-\d{6}\-\d{2}$
0000005: 2008-005144-16
has URI prefix: https://www.clinicaltrialsregister.eu/ctr-search/search
is deprecated: false
is part of: Bioregistry

DataCite to DCAT-AP Mapping
0000005: isSupplementedBy
keyword: methods
has prefix: citedcat
has provider formatter: https://w3id.org/citedcat-ap/$1
has resource example: isSupplementedBy
is deprecated: false
has responsible: Andrea Perego
has URI prefix: https://w3id.org/citedcat-ap/
is part of: Bioregistry
keyword: catalogs
type: Resource
contributor: Charles Tapley Hoyt
description: A vocabuarly for describing the background and methodology for the design of the DataCite profile of DCAT-AP (CiteDCAT-AP), as well as the defined mappings.

International Standard Book Number
keyword: bibliography
type: Resource
description: The International Standard Book Number (ISBN) is for identifying printed books.
has alternative prefix: ISBN-13
is deprecated: false
has resource example: https://www.worldcat.org/isbn/9789211613865
0000005: 9789211613865
has URI prefix: https://www.worldcat.org/isbn/
has prefix: isbn
is part of: Bioregistry
has local unique identifier pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$
has alternative prefix: ISBN-10
has provider formatter: https://www.worldcat.org/isbn/$1

Prefix Commons
has part: insdc
has part: kegg.orthology
has part: hogenom
has part: trnadbce
has part: lgicdb
has part: dpvweb
has part: tgma
has part: wormpep
has part: myco.lepra
has part: ccds
has part: flybase.est
has part: compluyeast2dpage
has part: scpd
has part: geo
has part: corum
has part: goa
has part: edam
has part: mpath
has part: evoc
has part: dbest
has part: hcv
has part: biomodels
has part: genatlas
has part: drugbank
has part: doi
has part: vectorbase
has part: protonet.cluster
has part: fao
has part: asrp
has part: pathoplant
has part: otl
has part: protcom
has part: ensembl.bacteria
has part: ena
has part: ncbi.protein
has part: chemspider
has part: mipmod
has part: p3db
has part: pathguide
has part: fbcv
has part: dailymed
has part: opb
has part: modeldb
has part: sgd
has part: teddy
has part: biocyc
has part: omim
has part: vo
has part: topdb
has part: taxonomy
has part: dip
has part: isfinder
has part: 3dmet
has part: gold
has part: prodom
has part: sdap
has part: ncit
has part: imr
has part: pubchem.substance
has part: sheepqtldb
has part: pride
has part: cellimage
has part: apd
has part: mpi
has part: smpdb
has part: alzgene
has part: bold
has part: wikipedia
has part: amoebadb
has part: ensembl.fungi
has part: rnao
has part: rna sstrand
has part: roleo
has part: cl
has part: psi.mi
has part: cgnc
has part: subtiwiki
has part: bactibase
has part: fix
has part: cryptodb

International Classification of Diseases, 9th Revision, Clinical Modification
has resource example: http://icd9cm.chrisendres.com/index.php
keyword: diagnosis
has alternative prefix: ICD9CM_2006
has alternative prefix: IC9CM
keyword: preclinical studies
is part of: Bioregistry
has local unique identifier pattern: ^([\dA-Z]\d{2}(\.\d{1,3}|))|(\d{2}(\.\d{1,2}|))$
contributor: Charles Tapley Hoyt
has URI prefix: http://icd9cm.chrisendres.com/index.php
keyword: epidemiology
has alternative prefix: ICDCM_2005
type: Resource
0000005: 784
description: ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States.
keyword: biomedical science
has provider formatter: http://icd9cm.chrisendres.com/index.php
keyword: health science
keyword: medicine
keyword: ontology
keyword: morbidity
has prefix: icd9cm
is deprecated: false
keyword: disease
has alternative prefix: ICD9CM
has alternative prefix: ICD9CM_2005

EDAM Ontology
keyword: data acquisition
keyword: computer science
keyword: life science
keyword: ess
is deprecated: false
keyword: obo
has prefix: edam
keyword: ontology
has local unique identifier pattern: ^(data|topic|operation|format)\_\d{4}$
description: EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).
has provider formatter: https://www.ebi.ac.uk/ols/ontologies/edam/terms
git repository: edamontology
is part of: Bioregistry
keyword: dataplant
keyword: data transformation
keyword: nfdi4cat
keyword: bioinformatics
has responsible: https://orcid.org/0000-0002-1509-4981
keyword: nfdi4chem
0000005: data_1664
keyword: omics
keyword: earth sciences
keyword: life sciences, biology
type: Resource
keyword: nfdi4ing
has resource example: https://www.ebi.ac.uk/ols/ontologies/edam/terms
keyword: data analysis
has download URL: 1.25-20251112T1620Z-unstable(1.26)
has URI prefix: https://www.ebi.ac.uk/ols/ontologies/edam/terms

Zebrafish Phenotype Ontology
depends on: Gene Ontology
description: The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.
has resource example: ZP_0019030
has provider formatter: http://purl.obolibrary.org/obo/ZP_$1
keyword: obo
depends on: Biological Spatial Ontology
depends on: Basic Formal Ontology
keyword: ontology
has download URL: zp.owl
has responsible: Yvonne Bradford
is deprecated: false
has prefix: zp
git repository: zebrafish-phenotype-ontology
depends on: Zebrafish anatomy and development ontology
depends on: Relation Ontology
0000005: 0019030
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has URI prefix: http://purl.obolibrary.org/obo/ZP_
type: Resource
depends on: Uber Anatomy Ontology
depends on: Phenotype And Trait Ontology

Ontology for Parasite LifeCycle
keyword: life cycle stage
is part of: Bioregistry
keyword: developmental biology
has resource example: OPL_0000319
has provider formatter: http://purl.obolibrary.org/obo/OPL_$1
description: The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc.
has local unique identifier pattern: ^\d{7}$
keyword: life cycle
has responsible: Jie Zheng
has download URL: opl.owl
has prefix: opl
type: Resource
0000005: 0000319
has URI prefix: http://purl.obolibrary.org/obo/OPL_
keyword: host
keyword: anatomy
keyword: life science
is deprecated: false
keyword: obo
git repository: OPL
keyword: ontology

Pfam protein family
has responsible: Alex Bateman
keyword: biology
has URI prefix: https://www.ebi.ac.uk/interpro/entry/pfam/
0000005: PF11779
keyword: domain
keyword: ontology
description: The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.
has download URL: pfam.owl
is deprecated: false
has provider formatter: https://www.ebi.ac.uk/interpro/entry/pfam/$1
is part of: Bioregistry
keyword: protein
has prefix: pfam
has local unique identifier pattern: ^PF\d{5}$
type: Resource
has resource example: PF11779
has alternative prefix: PF

Ontology of Host-Microbiome Interactions
keyword: host
has prefix: ohmi
keyword: life science
has resource example: OHMI_0000460
keyword: obo
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/OHMI_
is deprecated: false
is part of: Bioregistry
has responsible: Yongqun Oliver He
git repository: ohmi
has provider formatter: http://purl.obolibrary.org/obo/OHMI_$1
keyword: microbiome
0000005: 0000460
has download URL: ohmi.owl
has local unique identifier pattern: ^\d{7}$
type: Resource
description: OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.

Ontology of Precision Medicine and Investigation
keyword: omics
git repository: opmi
0000005: 0000101
is part of: Bioregistry
description: OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles.
type: Resource
has responsible: Yongqun Oliver He
keyword: clinical studies
has download URL: opmi.owl
has local unique identifier pattern: ^\d{7}$
has provider formatter: http://purl.obolibrary.org/obo/OPMI_$1
has prefix: opmi
keyword: obo
appears in: clinical LABoratory Ontology
appears in: Sickle Cell Disease Ontology
has resource example: OPMI_0000101
keyword: ontology
is deprecated: false
keyword: disease
has URI prefix: http://purl.obolibrary.org/obo/OPMI_

COlleCtion of Open Natural ProdUcTs
has URI prefix: https://coconut.naturalproducts.net/compound/coconut_id/
type: Resource
keyword: natural producs
has local unique identifier pattern: ^CNP\d{7}(\.\d+)?$
description: COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a "flat" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties.
is deprecated: false
0000005: CNP0171505
keyword: chemistry
has prefix: coconut
contributor: Adriano Rutz
is part of: Bioregistry
keyword: organic chemistry
has provider formatter: https://coconut.naturalproducts.net/compound/coconut_id/$1
has reviewer: Charles Tapley Hoyt
has resource example: CNP0171505

Chemical Book
0000005: CB82546919
has alternative prefix: ChemicalBookNo
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: A hybrid chemical enyclopedia and supplier advertizing system for chemicals.
type: Resource
has URI prefix: https://bioregistry.io/chemicalbook:
has prefix: chemicalbook
has provider formatter: https://www.chemicalbook.com/ChemicalProductProperty_IN_$1.htm
has resource example: ChemicalProductProperty IN CB82546919.htm

Activity Streams
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: ac
type: Resource
description: Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities.
keyword: semantic web
has alternative prefix: as
has URI prefix: http://www.w3.org/ns/activitystreams#
contributor: https://orcid.org/0000-0002-1216-4761
is deprecated: false
has provider formatter: http://www.w3.org/ns/activitystreams#$1
0000005: Add
keyword: social media
has resource example: Add

Peroxibase
has resource example: https://redoxibase.toulouse.inrae.fr/display_perox/view_perox/5282
is part of: Bioregistry
type: Resource
0000005: 5282
keyword: life science
has URI prefix: https://redoxibase.toulouse.inrae.fr/display_perox/view_perox/
keyword: enzyme
has prefix: peroxibase
has responsible: Christophe Dunand
has provider formatter: https://redoxibase.toulouse.inrae.fr/display_perox/view_perox/$1
is deprecated: false
keyword: regulation
keyword: protein
description: Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.
has local unique identifier pattern: ^\d+$

Coconut Ontology
has URI prefix: https://cropontology.org/rdf/CO_326:
0000005: 0000254
has download URL: CO 326.owl
keyword: ontology
has responsible: Elizabeth Arnaud
is part of: Bioregistry
git repository: Crop-Ontology
has resource example: CO 326:0000254
has prefix: co_326
has local unique identifier pattern: ^\d{7}$
type: Resource
has provider formatter: https://cropontology.org/rdf/CO_326:$1
description: Coconut Ontology v1.0 - Coconut trait dictionary started by CIRAD, based on the "Guidelines for collecting coconut germplasm characterisation data during prospecting missions", COGENT (to be published); the "Descriptors for Coconut, (Cocos nucifera L.)", IPGRI (1995); and the "Manual on standardized research techniques in coconut breeding", IPGRI (1996).
is deprecated: false

Germplasm Resources Information Network
0000005: 159787
is part of: Bioregistry
type: Resource
has provider formatter: http://www.ars.usda.gov/research/publications/publications.htm
has reviewer: Charles Tapley Hoyt
keyword: life science
has alternative prefix: grin
has prefix: grin.publication
description: GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections.
has URI prefix: http://www.ars.usda.gov/research/publications/publications.htm
is deprecated: false
has resource example: http://www.ars.usda.gov/research/publications/publications.htm

Glycan Naming and Subsumption Ontology
has download URL: gno.owl
has URI prefix: http://purl.obolibrary.org/obo/GNO_
is part of: Bioregistry
git repository: GNOme
type: Resource
has responsible: https://orcid.org/0000-0001-5168-3196
has resource example: GNO_10004892
has prefix: gno
has provider formatter: http://purl.obolibrary.org/obo/GNO_$1
has local unique identifier pattern: ^(\d{8}|(\w+\d+\w+))$
has alternative prefix: gnome
keyword: obo
description: An ontology for glycans based on GlyTouCan, but organized by subsumption.
keyword: ontology
0000005: 10004892
is deprecated: false

OER Schema
has prefix: oerschema
type: Resource
description: A RDF vocabulary for OER content on the web.
has resource example: InstructionalPattern
git repository: oerschema
keyword: education
keyword: oer
keyword: curricula
has URI prefix: https://oerschema.org/
is deprecated: false
0000005: InstructionalPattern
keyword: oers
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: curriculum
has provider formatter: https://oerschema.org/$1
keyword: open educational resources

SWEET Ontology Phenomena Energy
keyword: phenomena
has resource example: ActiveSolarEnergy
has URI prefix: http://sweetontology.net/phenEnergy/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Energy
is deprecated: false
keyword: energy
has provider formatter: http://sweetontology.net/phenEnergy/$1
is part of: Bioregistry
has prefix: sweet.phen
0000005: ActiveSolarEnergy
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has alternative prefix: sophen

Ensembl Gene
has local unique identifier pattern: ^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$
is part of: Bioregistry
has resource example: ENSG00000139618
type: Resource
has provider formatter: https://www.ensembl.org/id/$1
has alternative prefix: Ensembl
keyword: biomedical science
has prefix: ensembl
keyword: comparative genomics
has URI prefix: https://www.ensembl.org/id/
is deprecated: false
has responsible: Paul Flicek
0000005: ENSG00000139618
description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms.
keyword: genome
keyword: genomics

German Archaeological Institute Thesaurus
has resource example: fe65f286
0000005: _fe65f286
type: Resource
description: A thesaurus of terms useful for digital archaeology
has prefix: dai.thesauri
has provider formatter: http://thesauri.dainst.org/en/concepts/$1
is deprecated: false
is part of: Bioregistry
has URI prefix: http://thesauri.dainst.org/en/concepts/
contributor: Charles Tapley Hoyt

Crystallographic Defect Core Ontology
has resource example: hasDefectComplex
contributor: https://orcid.org/0000-0002-1595-3213
is deprecated: false
git repository: cdco
0000005: hasDefectComplex
has provider formatter: http://purls.helmholtz-metadaten.de/cdos/cdco/$1
keyword: ontology
has responsible: https://orcid.org/0000-0001-7564-7990
description: The Crystallographic Defect Core Ontology (CDCO) defines the common terminology shared across all types of crystallographic defects, providing a unified framework for data integration in materials science.
has URI prefix: http://purls.helmholtz-metadaten.de/cdos/cdco/
is part of: Bioregistry
has reviewer: Charles Tapley Hoyt
has download URL: cdco.owl
has prefix: ocdo
type: Resource

Clinical Trials Ontology
keyword: neurobiology
is deprecated: false
keyword: disease
has responsible: Alpha Tom Kodamullil
has provider formatter: http://purl.obolibrary.org/obo/CTO_$1
0000005: 0000022
has resource example: CTO_0000022
has download URL: cto.owl
keyword: preclinical studies
is part of: Bioregistry
description: The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.
type: Resource
keyword: biomedical science
has URI prefix: http://purl.obolibrary.org/obo/CTO_
has prefix: cto
has local unique identifier pattern: ^\d{7}$
git repository: CTO
keyword: obo
keyword: ontology

Event Venue Registry
has URI prefix: https://cthoyt.com/evr/
type: Resource
contributor: Charles Tapley Hoyt
has prefix: evr
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
description: An open, community-driven registry of conference and event venues. EVR assigns persistent identifiers (PIDs) to make referencing venues FAIR. This is similar to how ORCID assigns PIDs to researchers and ROR assigns PIDs to research organizations. This benefits researchers assembling information about in-person conferences and events by enabling them to refer in an unambiguous way to the venue where it takes place. This repository follows the [Open Data, Open Code, Open Infrastructure (O3) principles](https://www.nature.com/articles/s41597-024-03406-w), meaning that the data and code are all in one repository that anyone can contribute to.
has provider formatter: https://cthoyt.com/evr/$1
git repository: evr
has resource example: https://cthoyt.com/evr/0000001
has responsible: Charles Tapley Hoyt
is deprecated: false
is part of: Bioregistry

Performance Summary Display Ontology
is deprecated: false
has resource example: PSDO_0000055
description: Performance Summary Display Ontology (PSDO) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01). Landis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/PSDO_$1
has local unique identifier pattern: ^\d{7}$
type: Resource
depends on: Basic Formal Ontology
has prefix: psdo
has responsible: https://orcid.org/0000-0002-9117-9338
0000005: 0000055
depends on: The Statistical Methods Ontology
git repository: psdo
keyword: obo
keyword: ontology
depends on: Relation Ontology
has URI prefix: http://purl.obolibrary.org/obo/PSDO_
has download URL: psdo.owl
depends on: Information Artifact Ontology

SWEET Ontology Representation Space
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: soreps
has provider formatter: http://sweetontology.net/reprSpace/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space
has prefix: sweet.reps
type: Resource
has resource example: Space
has URI prefix: http://sweetontology.net/reprSpace/
is deprecated: false
keyword: representation space
0000005: Space
is part of: Bioregistry

Yam Ontology
has resource example: CO 343:0100010
keyword: life science
keyword: food
keyword: ontology
has prefix: co_343
is deprecated: false
keyword: plant phenotypes and traits
keyword: phenotype
keyword: botany
has provider formatter: https://cropontology.org/rdf/CO_343:$1
keyword: agriculture
has responsible: Elizabeth Arnaud
has download URL: CO 343.owl
is part of: Bioregistry
type: Resource
0000005: 0100010
git repository: Crop-Ontology
description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Yam Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
has URI prefix: https://cropontology.org/rdf/CO_343:
has local unique identifier pattern: ^\d{7}$

Human Pluripotent Stem Cell Registry
0000005: BCRTi001-A
keyword: life science
is deprecated: false
has provider formatter: https://hpscreg.eu/cell-line/$1
has resource example: BCRTi001-A
has responsible: https://orcid.org/0000-0002-8411-3226
is part of: Bioregistry
description: hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).
has prefix: hpscreg
has URI prefix: https://hpscreg.eu/cell-line/
type: Resource
has local unique identifier pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$
keyword: biomedical science

Semanticscience Integrated Ontology
has prefix: sio
has provider formatter: https://semanticscience.org/resource/SIO_$1
keyword: biology
keyword: subject agnostic
0000005: 000912
keyword: natural science
keyword: ess
has responsible: https://orcid.org/0000-0003-4727-9435
has resource example: SIO_000912
keyword: ontology
is deprecated: false
is part of: Bioregistry
has download URL: sio-release.owl
keyword: nfdi4chem
has URI prefix: https://semanticscience.org/resource/SIO_
keyword: knowledge representation
git repository: semanticscience
has local unique identifier pattern: ^\d{6}$
type: Resource
keyword: nfdi4ing
description: The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.

NCBI Gene Expression Omnibus
keyword: gene expression
has URI prefix: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
keyword: phenomics
keyword: transcriptomics
type: Resource
has local unique identifier pattern: ^G(PL|SM|SE|DS)\d+$
0000005: GDS1234
has responsible: Tanya Barrett
description: The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.
keyword: comparative genomics
has resource example: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
keyword: life science
keyword: epigenomics
has prefix: geo
keyword: genome
keyword: genomics
is deprecated: false
is part of: Bioregistry
has provider formatter: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
keyword: omics

Microbial Ecophysiological Trait and Phenotype Ontology
has provider formatter: https://w3id.org/metpo/$1
keyword: ontology
is deprecated: false
is part of: Bioregistry
keyword: phenotypes
has local unique identifier pattern: ^\d+$
has URI prefix: https://w3id.org/metpo/
contributor: https://orcid.org/0000-0001-9076-6066
has prefix: metpo
0000005: 1004005
keyword: microbes
has download URL: metpo.owl
type: Resource
has resource example: https://w3id.org/metpo/1004005
has identifier space owner: 02jbv0t02
has reviewer: Charles Tapley Hoyt
git repository: metpo
has responsible: https://orcid.org/0000-0001-9076-6066
description: METPO (Microbial Ecophysiological Trait and Phenotype Ontology) provides standardized terms for describing microbial phenotypes, growth characteristics, and culture conditions. It includes classes for growth media, temperature tolerances, pH tolerances, and relationships like "grows in" and "does not grow in".

Dublin Core Metadata Initiative Abstract Model
keyword: general & upper
has resource example: domainIncludes
is deprecated: false
0000005: domainIncludes
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: metadata model
has URI prefix: http://purl.org/dc/dcam/
description: A metadata model for Dublin Core metadata
keyword: schema
has prefix: dcam
type: Resource
has provider formatter: http://purl.org/dc/dcam/$1
keyword: semantic web

Database of Spatially Interacting Motifs in Proteins
description: The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members.
is deprecated: true
has URI prefix: http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi
keyword: protein
has prefix: imotdb
is part of: Bioregistry
0000005: 53784
has provider formatter: http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi
type: Resource
has resource example: http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi
keyword: interaction
has reviewer: Charles Tapley Hoyt

Cephalopod Ontology
has URI prefix: http://purl.obolibrary.org/obo/CEPH_
has resource example: CEPH_0000109
has provider formatter: http://purl.obolibrary.org/obo/CEPH_$1
is part of: Bioregistry
git repository: cephalopod-ontology
keyword: life cycle
has prefix: ceph
has local unique identifier pattern: ^\d{7}$
type: Resource
has download URL: ceph.owl
0000005: 0000109
keyword: anatomy
keyword: fisheries science
has responsible: https://orcid.org/0000-0002-6601-2165
description: An anatomical and developmental ontology for cephalopods
is deprecated: true
keyword: obo
keyword: ontology
keyword: zoology

Hymenoptera Anatomy Reference
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: http://api.hymao.org/api/ref/
has provider formatter: http://api.hymao.org/api/ref/$1
contributor: Charles Tapley Hoyt
type: Resource
has resource example: http://api.hymao.org/api/ref/98127
0000005: 98127
has responsible: Matt Yoder
has prefix: hao.ref
description: Literature references in the Hymenoptera Anatomy Ontology Portal
is deprecated: false

Semantic Web for Earth and Environment Technology Ontology
has part: SWEET Ontology Property Time Frequency
has part: SWEET Ontology State Visibility
has part: SWEET Ontology Representation Space Direction
has part: SWEET Ontology State Role Impact
has part: SWEET Ontology Phenomena Hydrosphere
keyword: earth science
has part: SWEET Ontology Relationships Physical
has part: SWEET Ontology Process Physical
has part: SWEET Ontology Human Jurisdiction
has part: SWEET Ontology Material Particle
has part: SWEET Ontology Realm Hydrosphere Body
has part: SWEET Ontology Representation Data Format
has part: SWEET Ontology Representation Scientific Model
has part: SWEET Ontology Realm Region
has part: SWEET Ontology Representation Mathematics Function
has part: SWEET Ontology Human Commerce
has part: SWEET Ontology Material Plant
has part: SWEET Ontology Material Natural Resource
has part: SWEET Ontology Phenomena Atmosphere Wind Mesoscale
has part: SWEET Ontology Material Ion
has part: SWEET Ontology Material Instrument
has part: SWEET Ontology Phenomena Heliosphere
has part: SWEET Ontology Relationships Mathematical
has part: SWEET Ontology State System
has part: SWEET Ontology Phenomena Ocean Dynamics
has part: SWEET Ontology Property Dimensionless Ratio
has part: SWEET Ontology Representation Scientific Component
has part: SWEET Ontology Material Element
has part: SWEET Ontology State Chemical
has part: SWEET Ontology Material Rock
has part: SWEET Ontology Material Isotope
has part: SWEET Ontology Representation Time
has part: SWEET Ontology Material Mineral
has part: SWEET Ontology Property Fraction
has part: SWEET Ontology Human Technology Readiness
has part: SWEET Ontology Process State Change
has part: SWEET Ontology Representation Space Reference System
has part: SWEET Ontology Realm Soil
has part: SWEET Ontology Phenomena Energy
has part: SWEET Ontology Material Sediment
has part: SWEET Ontology State Space
has part: SWEET Ontology Realm Geologic Oceanic
has part: SWEET Ontology Material Organic Compound
has part: SWEET Ontology Representation
has part: SWEET Ontology State Role Chemical
has part: SWEET Ontology State Fluid
has part: SWEET Ontology Relationships Human
has part: SWEET Ontology Human Environmental Conservation
has part: SWEET Ontology Phenomena Geologic Tectonic
has part: SWEET Ontology Human Transportation
has part: SWEET Ontology Material Industrial
has part: SWEET Ontology Phenomena Geologic Volcano
has part: SWEET Ontology Material Equipment
has part: SWEET Ontology Phenomena Fluid Dynamics
has part: SWEET Ontology Phenomena Atmosphere Sky
has resource example: GeologicFeature
has part: SWEET Ontology Phenomena Environmental Impact
has part: SWEET Ontology Human Environmental Assessment
keyword: ess
has part: SWEET Ontology Representation Data Service
keyword: geology
has part: SWEET Ontology Representation Time Season
keyword: environmental science
has part: SWEET Ontology Material Water
has part: SWEET Ontology Material Animal
has part: SWEET Ontology State Space Configuration
has prefix: sweet
has part: SWEET Ontology Phenomena System
has part: SWEET Ontology Representation Data Servcie Analysis
has part: SWEET Ontology State Spectral Line
has provider formatter: http://sweetontology.net/human/$1
has part: SWEET Ontology Realm Land Orographic
has part: SWEET Ontology State Time Frequency
has part: SWEET Ontology Phenomena Mixing
has part: SWEET Ontology Representation Space
has part: SWEET Ontology Property Quantity
has part: SWEET Ontology Representation Data Service Geospatial
has part: SWEET Ontology Phenomena Atmosphere Precipitation
has part: SWEET Ontology Realm Hydrosphere
has part: SWEET Ontology Realm Geologic

EcoCyc
keyword: biology
has prefix: ecocyc
0000005: AICARTRANSIMPCYCLO-CPLX
has URI prefix: https://ecocyc.org/gene
has provider formatter: https://ecocyc.org/gene
is deprecated: false
is part of: Bioregistry
description: EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways.
contributor: https://orcid.org/0000-0002-6601-2165
has resource example: https://ecocyc.org/gene
has responsible: https://orcid.org/0000-0002-5876-6418
type: Resource

The Food Ontology
has download URL: foodon.owl
has prefix: foodon
depends on: Ontology for Biomedical Investigations
keyword: botany
keyword: agriculture
depends on: Uber Anatomy Ontology
appears in: Ontology for Nutritional Epidemiology
depends on: Chemical Entities of Biological Interest
has responsible: Damion Dooley
type: Resource
appears in: Food-Biomarker Ontology
appears in: Ontology for Nutritional Studies
depends on: NCBI Taxonomy
appears in: Medical Action Ontology
git repository: foodon
depends on: Basic Formal Ontology
description: FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.
appears in: Agronomy Ontology
keyword: environmental science
keyword: medicine
is deprecated: false
keyword: obo
keyword: food
depends on: Environment Ontology
keyword: ontology
0000005: 03307879
depends on: Relation Ontology
has local unique identifier pattern: ^[0-9]{8}$
keyword: disease
has provider formatter: http://purl.obolibrary.org/obo/FOODON_$1
appears in: Environment Ontology
keyword: sustainability
has resource example: FOODON_03307879
has URI prefix: http://purl.obolibrary.org/obo/FOODON_
is part of: Bioregistry
depends on: Plant Environment Ontology

SWEET Ontology Realm Region
keyword: realm
has provider formatter: http://sweetontology.net/realmRegion/$1
has URI prefix: http://sweetontology.net/realmRegion/
keyword: region
0000005: Austral
has prefix: sweet.rear
has alternative prefix: sorear
is deprecated: false
is part of: Bioregistry
git repository: sweet
has resource example: Austral
type: Resource
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Region

DataCite Ontology
git repository: datacite
keyword: subject agnostic
has URI prefix: http://purl.org/spar/datacite/
0000005: AgentIdentifierScheme
has provider formatter: http://purl.org/spar/datacite/$1
keyword: ontology
has resource example: AgentIdentifierScheme
is deprecated: false
has prefix: datacite
has download URL: datacite.owl
description: An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.
has responsible: Silvio Peroni
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt

RNACentral
is part of: Bioregistry
has URI prefix: https://rnacentral.org/rna/
has provider formatter: https://rnacentral.org/rna/$1
keyword: bioinformatics
git repository: RNAcentral
has alternative prefix: LNCRNADB
has resource example: URS0000759CF4
description: RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases.
has responsible: Blake A Sweeney
type: Resource
0000005: URS0000759CF4
keyword: biology
has local unique identifier pattern: ^URS[0-9A-F]{10}(\_\d+)?$
is deprecated: false
has prefix: rnacentral

MatrixDB Association
is part of: Bioregistry
description: MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations.
type: Resource
has resource example: P00747 P07355
has URI prefix: https://matrixdb.univ-lyon1.fr/association/
is deprecated: false
0000005: P00747__P07355
has provider formatter: https://matrixdb.univ-lyon1.fr/association/$1
has prefix: matrixdb.association
has local unique identifier pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$

H-InvDb Protein
has URI prefix: http://h-invitational.jp/hinv/protein/protein_view.cgi
has resource example: http://h-invitational.jp/hinv/protein/protein_view.cgi
has provider formatter: http://h-invitational.jp/hinv/protein/protein_view.cgi
description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^HIP\d{9}(\.\d+)?$
is deprecated: true
has prefix: hinv.protein
0000005: HIP000030660

Vaccine Ontology
git repository: VO
has download URL: vo.owl
keyword: pathogen
keyword: biological_process
has resource example: VO_0000093
keyword: infectious disease medicine
keyword: obo
keyword: ontology
appears in: Sickle Cell Disease Ontology
keyword: infection process
has URI prefix: http://purl.obolibrary.org/obo/VO_
keyword: immunology
is deprecated: false
keyword: small molecule
has provider formatter: http://purl.obolibrary.org/obo/VO_$1
has prefix: vo
keyword: vaccination
has responsible: Yongqun Oliver He
keyword: pathobiochemistry
0000005: 0000093
keyword: preclinical studies
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
keyword: vaccine
type: Resource
description: The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clinical vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.
keyword: clinical studies
keyword: biomedical science

JWS Online
0000005: achcar11
description: JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.
has local unique identifier pattern: ^\w+$
has URI prefix: https://jjj.bio.vu.nl/models/
keyword: model
has responsible: https://orcid.org/0000-0002-5293-5321
keyword: pathway
is deprecated: false
is part of: Bioregistry
has prefix: jws
has provider formatter: https://jjj.bio.vu.nl/models/$1
has resource example: achcar11
type: Resource

Influenza Ontology
has resource example: FLU_0000404
has local unique identifier pattern: ^\d{7}$
has download URL: flu.owl
type: Resource
0000005: 0000404
has prefix: flu
keyword: obo
is deprecated: true
has responsible: https://orcid.org/0000-0001-9666-6285
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/FLU_
has provider formatter: http://purl.obolibrary.org/obo/FLU_$1
is part of: Bioregistry
description: Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)

GS1 Web Vocabulary
type: Resource
0000005: AllergenTypeCode-3-AMINOPHENOL
has prefix: gs1
description: The initial focus of the GS1 Web Vocabulary is consumer-facing properties for clothing, shoes, food beverage/tobacco and properties common to all products. [from homepage]
is deprecated: false
git repository: WebVoc
is part of: Bioregistry

MIRIAM Legacy Registry Identifier
description: MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.
has prefix: miriam.resource
has provider formatter: https://resolver.api.identifiers.org/resolveMirId/$1
keyword: registry
is part of: Bioregistry
0000005: 00100005
has URI prefix: https://resolver.api.identifiers.org/resolveMirId/
has resource example: https://resolver.api.identifiers.org/resolveMirId/00100005
type: Resource
has local unique identifier pattern: ^001\d{5}$
is deprecated: true

Registry of Research Data Repositories
has part: r3d100010350
has part: r3d100011294
has part: r3d100012902
has part: r3d100010785
has part: r3d100012702
has part: r3d100014517
has part: r3d100012820
has part: r3d100013361
has part: r3d100010795
has part: r3d100010539
has part: r3d100012078
has part: r3d100010671
has part: r3d100011242
0000005: r3d100014165
has part: r3d100013478
has part: r3d100010906
has part: r3d100012688
has part: r3d100011496
has part: r3d100010180
has part: r3d100010372
has part: r3d100011049
has part: r3d100013293
has part: r3d100010648
has part: r3d100011301
has part: r3d100014353
has part: r3d100010285
has part: r3d100012705
has part: r3d100010604
has part: r3d100012197
has part: r3d100010283
has part: r3d100012690
has part: r3d100011373
has part: r3d100013668
has part: r3d100012458
has part: r3d100010921
has part: r3d100012344
has part: r3d100011906
has part: r3d100010617
has part: r3d100010808
has part: r3d100011198
has part: r3d100012630
has provider formatter: https://www.re3data.org/repository/$1
has part: r3d100012725
has part: r3d100013051
has part: r3d100011196
has part: r3d100010880
has part: r3d100012603
has part: r3d100012715
has part: r3d100011285
has part: r3d100013715
has part: r3d100010245
has part: r3d100013432
has part: r3d100011316
has part: r3d100011479
has part: r3d100010776
has part: r3d100010424
has part: r3d100010527
has part: r3d100010741
has part: r3d100012928
has part: r3d100010978
has part: r3d100012152
has part: r3d100012755
has part: r3d100010417
has part: r3d100010626
has part: r3d100013331
has part: r3d100010544
has part: r3d100012171
has part: r3d100010170
has part: r3d100010804
has part: r3d100012535
has part: r3d100000039
has part: r3d100011894
has part: r3d100012362
has part: r3d100013547
has responsible: Michael Witt
has part: r3d100010861
has part: r3d100011556
description: Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines.
has part: r3d100012731
has part: r3d100010137

European Genome-phenome Archive Study
has URI prefix: https://www.ebi.ac.uk/ega/studies/
type: Resource
has provider formatter: https://www.ebi.ac.uk/ega/studies/$1
has local unique identifier pattern: ^EGAS\d{11}$
has resource example: EGAS00000000001
has prefix: ega.study
0000005: EGAS00000000001
is deprecated: false
is part of: Bioregistry
description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.

Scientific Event Ontology
keyword: events
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: Symposium
keyword: academy
type: Resource
description: The Scientific Event Ontology (SEO) is a reference ontology for modeling data about scientific events such as conferences, symposioums, and workshops.
has URI prefix: https://w3id.org/seo#
has prefix: seo
has provider formatter: https://w3id.org/seo#$1
has resource example: Symposium
is deprecated: false

BioDeep Database
type: Resource
has resource example: https://query.biodeep.cn/metabolite/00000000001
0000005: 00000000001
is deprecated: false
has provider formatter: https://query.biodeep.cn/metabolite/$1
is part of: Bioregistry
description: The BioDeep database is a comprehensive database of metabolite information in living organisms: by aggregating metabolite information from multiple public databases and large-scale natural language text mining work, we have built a large scale knowledge network for biological knowledge interpretation. By using the BioDeep database, it is possible to query such large scale metabolic knowledge network.
has prefix: biodeep
has URI prefix: https://query.biodeep.cn/metabolite/
has local unique identifier pattern: ^\d{11}$

SAREF4EE: the EEbus/Energy@home extension of SAREF
type: Resource
keyword: nfdi4ing
is deprecated: false
has alternative prefix: s4ener
keyword: services
keyword: digital planning and construction
has URI prefix: https://saref.etsi.org/saref4ener/
is part of: Bioregistry
keyword: engineering
keyword: environment
description: This is the extension of SAREF for the EEBus and Energy@Home project. The documentation of SAREF4EE is available at http://ontology.tno.nl/SAREF4EE_Documentation_v0.1.pdf. SAREF4EE represents 1) The configuration information exchanged in the use case 'Remote Network Management' according to the EEBus Technical Report, Protocol Specification- Remote Network Management, version 1.0.0.2, 2015-09-19; 2) The scheduling information about power sequences exchanged in the use cases Appliance scheduling through CEM and remote start' and 'Automatic cycle rescheduling', according to the message structures described in General Message Structures, version 0.1.1, 2015-10-07; 3) The monitor and control information exchanged in the use case 'Communicate appliance status and info on manually planned cycles', according to the monitoring and control part of the Energy@Home Data Model, version 1.0; and 4) the event-based data exchanged in the use case 'Demand Response', according to General Message Structures, version 0.1.1, 2015-10-07.
keyword: fid baudigital
has resource example: ActuatorLevel
has provider formatter: https://saref.etsi.org/saref4ener/$1
0000005: ActuatorLevel
has prefix: saref.ener
keyword: nfdi4energy

Metabolic Encyclopedia of metabolic and other pathways
is deprecated: false
keyword: metabolomics
has prefix: metacyc.compound
has provider formatter: https://metacyc.org/compound
has resource example: https://metacyc.org/compound
has local unique identifier pattern: ^[A-Za-z0-9+_.%-:]+$
is part of: Bioregistry
type: Resource
has alternative prefix: MetaCyc
0000005: CPD-10330
description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.
keyword: systems biology
has responsible: https://orcid.org/0000-0002-5876-6418
keyword: life science
has URI prefix: https://metacyc.org/compound

Research Activity Identifier
git repository: ResearchDataServices
has provider formatter: https://raid.org/$1
is deprecated: false
keyword: centrally registered identifier
keyword: resource metadata
has prefix: raid
is part of: Bioregistry
description: RAiD is an identifier and global system, governed by ISO 23527:2022, to uniquely identifiy research projects, collaboratively, collect and publicly share information about them.
keyword: knowledge representation
has URI prefix: https://raid.org/
type: Resource
0000005: 10.26259/0e59e9a5
keyword: fair
keyword: subject agnostic
has local unique identifier pattern: ^102?\.\d+\/.+$
has resource example: https://raid.org/10.26259/0e59e9a5

Encyclopedia of Life
has URI prefix: https://eol.org/pages/
type: Resource
has resource example: https://eol.org/pages/1044544
keyword: biology
keyword: taxonomy
has prefix: eolife
0000005: 1044544
description: A collaborative project intended to create an encyclopedia documenting all living species known to science
is deprecated: false
has local unique identifier pattern: ^\d+$
keyword: biodiversity
is part of: Bioregistry
keyword: ecology
has responsible: EOL Secretariat
has provider formatter: https://eol.org/pages/$1
contributor: Charles Tapley Hoyt

SWEET Ontology Material Isotope
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Isotope
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.mais
has URI prefix: http://sweetontology.net/matrIsotope/
type: Resource
has alternative prefix: somais
keyword: isotope
keyword: materials
has provider formatter: http://sweetontology.net/matrIsotope/$1
has resource example: AlphaParticle
0000005: AlphaParticle
is deprecated: false

Neural ElectroMagnetic Ontology
keyword: electroencephalography
has URI prefix: http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_
keyword: life science
has download URL: nemo.owl
keyword: neuron
keyword: ontology
keyword: imaging
has prefix: nemo2
keyword: neurobiology
has resource example: NEMO_0000196
is deprecated: false
0000005: 0000196
is part of: Bioregistry
keyword: cognition
keyword: brain
description: Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource.
has responsible: https://orcid.org/0000-0003-0612-0970
has provider formatter: http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_$1
keyword: cognitive neuroscience
type: Resource

SWEET Ontology Phenomena Atmosphere Transport
type: Resource
has prefix: sweet.phatmot
0000005: AcidFog
keyword: phenomena
has alternative prefix: sophatmot
keyword: atmosphere transport
has provider formatter: http://sweetontology.net/phenAtmoTransport/$1
has URI prefix: http://sweetontology.net/phenAtmoTransport/
is deprecated: false
is part of: Bioregistry
has resource example: AcidFog
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Transport

SWEET Ontology Phenomena Cryosphere
has provider formatter: http://sweetontology.net/phenCryo/$1
keyword: phenomena
has prefix: sweet.phcr
has URI prefix: http://sweetontology.net/phenCryo/
has alternative prefix: sophcr
keyword: cryosphere
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Cryosphere
has resource example: Accumulation
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
type: Resource
0000005: Accumulation

ProteomicsDB Protein
description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has provider formatter: https://www.proteomicsdb.org/#human/proteinDetails/$1/summary
0000005: 53504
has URI prefix: https://bioregistry.io/proteomicsdb.protein:
has resource example: human/proteinDetails/53504/summary
is deprecated: false
has prefix: proteomicsdb.protein

Protein Structural Change Database
has prefix: pscdb
has resource example: 051.html
is deprecated: false
has responsible: 0000-0001-9090-668X
has provider formatter: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: https://bioregistry.io/pscdb:
0000005: 051
description: The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion.
type: Resource
keyword: life science

Lexvo Ontology
has prefix: lexvo.ontology
keyword: vocabularies
has alternative prefix: lvont
has URI prefix: http://lexvo.org/ontology#
keyword: ontology
is deprecated: false
description: The data model underlying lexvo
has provider formatter: http://lexvo.org/ontology#$1
0000005: Language
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has download URL: ontology
has resource example: Language

International Protein Index
type: Resource
has resource example: http://www.ebi.ac.uk/cgi-bin/dbfetch
has provider formatter: http://www.ebi.ac.uk/cgi-bin/dbfetch
description: IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross references between the primary data sources, it provides minimally redundant but complete sets of proteins for featured species, and it maintains stable and unique identifiers.
is deprecated: true
has URI prefix: https://bioregistry.io/ipi:
0000005: IPI00000001
is part of: Bioregistry
keyword: protein
has prefix: ipi

Plant Genome Network
type: Resource
has provider formatter: http://www.phytozome.net/genePage.php
has alternative prefix: JGI Phytozome
has prefix: phytozome.locus
has resource example: http://www.phytozome.net/genePage.php
has URI prefix: http://www.phytozome.net/genePage.php
0000005: Glyma0021s00410
is deprecated: false
is part of: Bioregistry
description: Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.
has local unique identifier pattern: ^[A-Za-z0-9]+$

The Artificial Intelligence Ontology
is deprecated: false
keyword: computational biology
has provider formatter: https://w3id.org/aio/$1
has responsible: Marcin Pawel Joachimiak
keyword: machine learning
has reviewer: https://orcid.org/0000-0001-9439-5346
description: This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases.
is part of: Bioregistry
keyword: knowledge representation
type: Resource
keyword: artificial intelligence
keyword: natural language processing
has download URL: aio.owl
0000005: Causal_Graphical_Model
has prefix: aio
git repository: artificial-intelligence-ontology
contributor: https://orcid.org/0000-0002-8741-7823
has resource example: Causal Graphical Model
has URI prefix: https://w3id.org/aio/
keyword: ontology

OncoMX Dataset
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: https://data.oncomx.org/OMX_
0000005: 000059
type: Resource
has prefix: omx.dataset
contributor: Charles Tapley Hoyt
has provider formatter: https://data.oncomx.org/OMX_$1
has resource example: OMX_000059
description: OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX.
is deprecated: false

PaxDb Protein
has resource example: !protein/977869
has prefix: paxdb.protein
type: Resource
has URI prefix: http://pax-db.org/#!protein/
0000005: 977869
description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has provider formatter: http://pax-db.org/#!protein/$1

Europe PMC Preprints
keyword: bibliometrics
0000005: PPR103739
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has URI prefix: https://europepmc.org/article/ppr/
description: Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000.
has provider formatter: https://europepmc.org/article/ppr/$1
keyword: preprints
has resource example: PPR103739
contributor: Javier Millán Acosta
has prefix: ppr
has local unique identifier pattern: ^PPR\d+$
is deprecated: false
keyword: publishing
contributor: Tim Vandermeersch

Spectra Hash Code
is deprecated: false
keyword: metabolomics
keyword: proteomics
has local unique identifier pattern: ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$
has prefix: splash
is part of: Bioregistry
has responsible: Oliver Fiehn
keyword: lipidomics
type: Resource
keyword: mass spectrum
has URI prefix: http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/
has provider formatter: http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1
git repository: spectra-hash
description: The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.

DataONE
has URI prefix: https://bioregistry.io/d1id:
has prefix: d1id
is part of: Bioregistry
type: Resource
description: DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.
has local unique identifier pattern: ^\S+$
is deprecated: false
has provider formatter: https://cn.dataone.org/cn/v2/resolve/%7B$1%7D

GnpIS
description: GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest.
has responsible: https://orcid.org/0000-0003-3001-4908
keyword: life science
0000005: AY109603
has prefix: gnpis
is deprecated: false
has provider formatter: https://urgi.versailles.inra.fr/gnpis/
has URI prefix: https://urgi.versailles.inra.fr/gnpis/
has resource example: https://urgi.versailles.inra.fr/gnpis/
has local unique identifier pattern: ^[A-Za-z0-9]+$
is part of: Bioregistry
type: Resource

Metabolomics Standards Initiative Ontology
keyword: omics
has URI prefix: http://purl.obolibrary.org/obo/MSIO_
has provider formatter: http://purl.obolibrary.org/obo/MSIO_$1
is part of: Bioregistry
keyword: life sciences, biology
description: an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.
git repository: MSIO
has prefix: msio
has responsible: Philippe Rocca-Serra
keyword: data analysis
keyword: annotation
keyword: experimental measurement
keyword: mass spectrum
keyword: nmr
has download URL: MSIO-merged-reasoned.owl
has local unique identifier pattern: ^\d{7}$
type: Resource
0000005: 0000111
keyword: nuclear magnetic resonance spectroscopy
keyword: ontology
keyword: functional magnetic resonance imaging
is deprecated: false
keyword: dataplant
keyword: metabolomics
has resource example: MSIO_0000111

BacMap Map
type: Resource
has resource example: index.html
has provider formatter: http://bacmap.wishartlab.com/maps/$1/index.html
description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.
has prefix: bacmap.map
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\w+(\_)?\d+(\.\d+)?$
has URI prefix: https://bioregistry.io/bacmap.map:
0000005: AP011135

Database of Quantitative Cellular Signaling: Model
description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models.
type: Resource
0000005: 57
has responsible: Upinder S. Bhalla
has URI prefix: http://doqcs.ncbs.res.in/template.php
has provider formatter: http://doqcs.ncbs.res.in/template.php
has resource example: http://doqcs.ncbs.res.in/template.php
keyword: model
is deprecated: false
has prefix: doqcs.model
has local unique identifier pattern: ^\d+$
is part of: Bioregistry

Variables relations for Social Sciences research data
contributor: Charles Tapley Hoyt
has identifier space owner: 018afyw53
has provider formatter: https://vocabularies.cessda.eu/vocabulary/Variables-Relations#code_$1
type: Resource
has prefix: gesis.variables-relations
has URI prefix: https://vocabularies.cessda.eu/vocabulary/Variables-Relations#code_
is deprecated: false
0000005: 01
description: As the variable is one of the most relevant entities to enhance data reuse in the Social Sciences, we provide a framework design to better semantics the variables' relations descriptions. These explicit relations between variables enable comparability and facilitate harmonization across waves. We provide a brief textual identification of the relation type, supported by a controlled vocabulary (CV) and an extended description of the relationship. These relations within variables include but are not limited to different versions, derived formats in new waves, new labels and name wording, and alternative response schema through questionnaires and surveys. For instance, a given variable label is changed from one wave to another, even though its concept remains the same. Their values also are subject to change, such as new cardinalities settings, their categorization, or response scheme and scale measurement. They change based on different conditions, e.g., values are updated by any constraints or modified to comply with the study evolution requirements or a new sociological approach. In the Social Sciences, Economics, and Behaviour Sciences, which investigate, for instance, the social structure of the population, political attitudes of voters and candidates, opinions on family, work, religion, politics and society or competencies of adults, those topics are highly subject to change to fit the empirical reality in a constantly changing world. Thus, we propose widening relations descriptions for Social Sciences variables within datasets beginning from the BasedOnObjectType DDI as a first approach.
has resource example: code_01
is part of: Bioregistry

Fungal gross anatomy
description: A structured controlled vocabulary for the anatomy of fungi.
is part of: Bioregistry
keyword: microbiology
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/FAO_
0000005: 0000001
has provider formatter: http://purl.obolibrary.org/obo/FAO_$1
has local unique identifier pattern: ^\d{7}$
keyword: anatomy
keyword: life science
keyword: obo
keyword: ontology
has resource example: FAO_0000001
is deprecated: false
keyword: fungi
git repository: fungal-anatomy-ontology
has download URL: fao.owl
has responsible: Valerie Wood
has prefix: fao

Media Types
has provider formatter: https://www.iana.org/assignments/media-types/$1
keyword: data classification
is deprecated: false
has responsible: Alexey Melnikov
has prefix: iana.mediatype
0000005: application/cdmi-queue
has URI prefix: https://www.iana.org/assignments/media-types/
is part of: Bioregistry
has resource example: cdmi-queue
type: Resource
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^(application|audio|font|haptics|image|message|model|multipart|text|video)(/.*)?$
description: The official list of MIME types, now renamed to media types

The State of Alaska's Salmon and People Ontology
has resource example: SASAP_00000101
type: Resource
description: An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities.
has responsible: Bryce Mecum
keyword: ontology
has URI prefix: https://purl.dataone.org/odo/SASAP_
is deprecated: false
has prefix: sasap
has local unique identifier pattern: ^\d+$
has provider formatter: https://purl.dataone.org/odo/SASAP_$1
is part of: Bioregistry
0000005: 00000101
has download URL: sasap.owl

Online Computer Library Center WorldCat
has URI prefix: https://www.worldcat.org/oclc/
0000005: 634515043
is deprecated: false
has provider formatter: https://www.worldcat.org/oclc/$1
is part of: Bioregistry
has prefix: oclc
has resource example: https://www.worldcat.org/oclc/634515043
type: Resource
has local unique identifier pattern: ^[0-9]+$
description: The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information.

Sorghum Ontology
is part of: Bioregistry
type: Resource
has download URL: CO 324.owl
has prefix: co_324
git repository: Crop-Ontology
has local unique identifier pattern: ^\d{7}$
has resource example: CO 324:0000111
0000005: 0000111
description: The Sorghum Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
keyword: food
keyword: ontology
has URI prefix: https://cropontology.org/rdf/CO_324:
is deprecated: false
keyword: phenotype
keyword: botany
keyword: agriculture
has provider formatter: https://cropontology.org/rdf/CO_324:$1
has responsible: Elizabeth Arnaud

FAIR Cookbook
is part of: Bioregistry
git repository: the-fair-cookbook
has prefix: fcb
has alternative prefix: faircookbook
type: Resource
has URI prefix: https://w3id.org/faircookbook/
has local unique identifier pattern: ^FCB\d{3}$
has provider formatter: https://w3id.org/faircookbook/$1
description: Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).
is deprecated: false
has resource example: FCB005
0000005: FCB005

Potato Ontology
keyword: botany
has URI prefix: https://cropontology.org/rdf/CO_330:
description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
keyword: agriculture
has local unique identifier pattern: ^\d{7}$
type: Resource
has resource example: CO 330:0000106
has download URL: CO 330.owl
keyword: life science
has provider formatter: https://cropontology.org/rdf/CO_330:$1
is deprecated: false
0000005: 0000106
keyword: ontology
has responsible: Elizabeth Arnaud
keyword: plant phenotypes and traits
has prefix: co_330
is part of: Bioregistry
keyword: phenotype
git repository: Crop-Ontology

Soybean Ontology
has download URL: CO 336.owl
keyword: agriculture
has URI prefix: https://cropontology.org/rdf/CO_336:
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
type: Resource
git repository: Crop-Ontology
has resource example: CO 336:0000339
has prefix: co_336
keyword: life science
keyword: food
keyword: ontology
0000005: 0000339
has responsible: Elizabeth Arnaud
is deprecated: false
keyword: plant phenotypes and traits
has provider formatter: https://cropontology.org/rdf/CO_336:$1
description: The Soybean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
keyword: phenotype

SWEET Ontology Human Knowledge Domain
keyword: knowledge domain
has provider formatter: http://sweetontology.net/humanKnowledgeDomain/$1
has prefix: sweet.hukd
is part of: Bioregistry
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
0000005: Anatomy
has alternative prefix: sohukd
has resource example: Anatomy
type: Resource
has URI prefix: http://sweetontology.net/humanKnowledgeDomain/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Knowledge Domain
is deprecated: false

Basic Formal Ontology
appears in: Performance Summary Display Ontology
is deprecated: false
appears in: Alzheimer's Disease Ontology
has prefix: bfo
keyword: dataplant
appears in: Compositional Dietary Nutrition Ontology
has URI prefix: http://purl.obolibrary.org/obo/BFO_
appears in: The Food Ontology
appears in: FuTRES Ontology of Vertebrate Traits
keyword: nfdi4cat
has resource example: BFO_0000001
has responsible: Barry Smith
keyword: foundational ontologies
git repository: BFO
keyword: nfdi4chem
appears in: Xenopus Phenotype Ontology
appears in: Zebrafish Phenotype Ontology
is part of: Bioregistry
type: Resource
appears in: Data Use Ontology
keyword: fairmat
appears in: Ontology for the Anatomy of the Insect SkeletoMuscular system
has download URL: bfo.owl
appears in: Microbial Conditions Ontology
keyword: nfdi4ing
appears in: Health Surveillance Ontology
keyword: data retrieval
appears in: Lepidoptera Anatomy Ontology
0000005: 0000001
keyword: subject agnostic
has local unique identifier pattern: ^\d{7}$
keyword: data identity and mapping
appears in: Uber Anatomy Ontology
has provider formatter: http://purl.obolibrary.org/obo/BFO_$1
appears in: Ontology for Nutritional Studies
appears in: Epilepsy Ontology
appears in: Radiation Biology Ontology
appears in: Provisional Cell Ontology
description: The upper level ontology upon which OBO Foundry ontologies are built.
keyword: obo
appears in: An ontology of core ecological entities
keyword: ontology
appears in: Coleoptera Anatomy Ontology
appears in: Agronomy Ontology
appears in: Population and Community Ontology

BioPortal Prefixes
has part: ONS
has part: MOP
has part: ECOCORE
has part: OBI
has part: MO
has part: TXPO
has part: MONDO
has part: FB-BT
has part: RXNORM
has part: IDO-COVID-19
has part: GRO-CPGA
has part: PHENX
has part: NANDO
has part: UBERON
has part: PECO
has part: PATO
has part: GEXO
has part: OPL
has part: EPIO
has part: CTENO
has part: EDAM
has part: GECKO
has part: CL
has part: BFO
has part: GENO
has part: GO
has part: OARCS
has part: GEO
has part: FLU
has part: ONE
has part: AFO
has part: MIAPA
has part: ENM
has part: OMRSE
has part: WIKIPATHWAYS
has part: VT
has part: CARO
has part: WB-BT
0000005: CHEBI
has part: OVAE
has part: BCIO
has part: ADCAD
has part: HCPCS
has part: CTCAE
has part: LBO
has part: RBO
has part: AEO
has part: BCO
has part: ERO
has part: ICF
has part: SNOMEDCT
has part: CVDO
has part: MMO
has part: DCTERMS
has part: CTO
has part: DCMITYPE
has part: CCO
has part: SSN
has part: SASAP
has part: TADS
has part: CDAO
has part: HPO
has part: PTO
has part: HSAPDV
has part: MF
has part: MAT
has part: EMAP
has part: OCDO
has part: VIDO
has part: MEDDRA
has part: IAO
has part: WB-LS
has part: NDFRT
has part: EHDAA2
has part: MFOMD
has part: PREFER
has part: VBO
has part: OGG
has part: MIRNAO
has part: ZP

ChEMBL database of bioactive drug-like small molecules - Cell lines section
0000005: CHEMBL3307800
has provider formatter: https://www.ebi.ac.uk/chembl/cell_line_report_card/$1
is part of: Bioregistry
type: Resource
has resource example: CHEMBL3307800
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^CHEMBL\d+$
has URI prefix: https://www.ebi.ac.uk/chembl/cell_line_report_card/
has responsible: David Mendez Lopez
keyword: cell lines
has alternative prefix: ChEMBL-Cells
has prefix: chembl.cell
keyword: bioactivities
description: Chemistry resources
is deprecated: false

RiceNetDB Compound
is deprecated: false
has local unique identifier pattern: ^OSC\d{4}$
has prefix: ricenetdb.compound
is part of: Bioregistry
has resource example: http://bis.zju.edu.cn/ricenetdb/compounddetails.php
type: Resource
has provider formatter: http://bis.zju.edu.cn/ricenetdb/compounddetails.php
0000005: OSC1416
description: RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.
has URI prefix: http://bis.zju.edu.cn/ricenetdb/compounddetails.php

Oryza Tag Line
has prefix: otl
has responsible: Emmanuel Guiderdoni
has local unique identifier pattern: ^A[A-Z]+\d+$
has URI prefix: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl
keyword: dna
is part of: Bioregistry
description: Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.
has resource example: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl
type: Resource
0000005: AADB12
has provider formatter: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl
keyword: life science
is deprecated: false

Synthetic Binding Proteins Binding Target
is deprecated: false
has resource example: st00576
has responsible: 0000-0002-1846-639X
is part of: Bioregistry
has local unique identifier pattern: ^st\d+$
has prefix: synbip.bts
has reviewer: https://orcid.org/0000-0001-9439-5346
0000005: st00576
has URI prefix: http://synbip.idrblab.net/data/bts/details/
type: Resource
has provider formatter: http://synbip.idrblab.net/data/bts/details/$1
contributor: Mufaddal Naguthanawala
description: Identifiers for the binding targets of synthetic binding proteins (SBP), describing the specific molecules or complexes that SBPs interact with for their intended applications

Rat Resource and Research Center
keyword: research
keyword: pathogen
keyword: biomedical
0000005: 961
keyword: infectious
keyword: rat model
is deprecated: false
keyword: drug
description: Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. [from RRID]
keyword: cell line
keyword: embryo
keyword: database
keyword: animal
keyword: ovarian
has resource example: https://www.rrrc.us/Strain/
keyword: nuclear
keyword: human
keyword: disease
keyword: strain
is part of: Bioregistry
keyword: genome
keyword: cryopreserved
has local unique identifier pattern: ^\d+$
keyword: hybrid
has prefix: rrrc
keyword: catalog
keyword: germplasma
keyword: protocol
keyword: embryonic stem cell
has URI prefix: https://www.rrrc.us/Strain/
keyword: stem cell
has provider formatter: https://www.rrrc.us/Strain/
keyword: rat
type: Resource
keyword: tissue
keyword: gamete
keyword: inbred
keyword: mutant
keyword: molecular
keyword: reagent
keyword: genotyping

PhylomeDB
keyword: phylogeny
has prefix: phylomedb
keyword: phylogenetics
has responsible: https://orcid.org/0000-0003-0019-1735
keyword: taxonomy
keyword: life science
keyword: phylogenomics
description: PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.
has resource example: http://phylomedb.org/
0000005: Phy000CLXM_RAT
is deprecated: false
keyword: protein
keyword: genome
has URI prefix: http://phylomedb.org/
has local unique identifier pattern: ^\w+$
has provider formatter: http://phylomedb.org/
is part of: Bioregistry
type: Resource

VFDB Gene
has URI prefix: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi
has resource example: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi
is part of: Bioregistry
has prefix: vfdb.gene
type: Resource
description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.
has provider formatter: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi
0000005: VFG2154
is deprecated: false
has local unique identifier pattern: ^\w+$

Illumina Probe Identifier
0000005: ILMN_129894
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^ILMN_\d+$
keyword: transcriptomics
type: Resource
description: Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip.
has prefix: illumina.probe
is deprecated: false

Plant Growth and Development Stage
has prefix: pgdso
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/PGDSO_$1
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/PGDSO_
keyword: obo
is deprecated: true
keyword: ontology

InfoSecSoS Ontology
is deprecated: false
keyword: engineering
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
has URI prefix: http://www.labesc.unirio.br/InfoSecSoS#
has resource example: Accept
has provider formatter: http://www.labesc.unirio.br/InfoSecSoS#$1
description: InfoSecSoS - Ontology for Information Security Management in Systems-of-Systems
has prefix: infosecsos
0000005: Accept

ChEMBL
has local unique identifier pattern: ^CHEMBL\d+$
has prefix: chembl
has responsible: David Mendez Lopez
has provider formatter: https://www.ebi.ac.uk/chembl/id_lookup/$1
type: Resource
0000005: CHEMBL4303805
git repository: GLaDOS
has alternative prefix: chembl
keyword: biochemistry
is deprecated: false
has alternative prefix: ChEMBL_ID
has part: ChEMBL mechanism
description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.
keyword: molecules
keyword: drug discovery
has URI prefix: https://www.ebi.ac.uk/chembl/id_lookup/
keyword: medicinal chemistry
has part: ChEMBL tissue
has alternative prefix: ChEMBL
is part of: Bioregistry
has resource example: CHEMBL4303805
keyword: genomics

Exposure ontology
has resource example: ExO_0000078
appears in: Sickle Cell Disease Ontology
keyword: toxicology
is deprecated: false
keyword: disease
has provider formatter: http://purl.obolibrary.org/obo/ExO_$1
has alternative prefix: ExO
description: ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.
has URI prefix: http://purl.obolibrary.org/obo/ExO_
has download URL: exo.owl
is part of: Bioregistry
appears in: Environmental conditions, treatments and exposures ontology
git repository: exposure-ontology
type: Resource
has responsible: https://orcid.org/0000-0002-2908-3327
keyword: epigenetics
keyword: exposure
has local unique identifier pattern: ^\d{7}$
0000005: 0000078
has prefix: exo
keyword: environmental science
keyword: obo
keyword: ontology

ViolinNet
is deprecated: true
appears in: Ontology of Adverse Events
is part of: Bioregistry
has alternative prefix: violinId
has local unique identifier pattern: ^\d+$
description: Defunct vaccine information source from the He Lab
contributor: Charles Tapley Hoyt
has resource example: http://www.violinet.org/vaxquery/vaccine_detail.php
has provider formatter: http://www.violinet.org/vaxquery/vaccine_detail.php
type: Resource
0000005: 4140
has URI prefix: http://www.violinet.org/vaxquery/vaccine_detail.php
has alternative prefix: violinID
has prefix: violinnet

Merck Millipore (EMD Millipore)
has resource example: SCC111
type: Resource
is deprecated: false
0000005: SCC111
description: Cell line collections (Providers)
is part of: Bioregistry
has URI prefix: https://www.merckmillipore.com/catalogue/item/
has provider formatter: https://www.merckmillipore.com/catalogue/item/$1
has prefix: millipore

NFDI4BIOIMAGE Collection
has part: Medical Subject Headings
has part: Cell Line Ontology
has part: Human Disease Ontology
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4BIOIMAGE
has part: Experimental Factor Ontology
has part: EDAM Ontology
has part: Software ontology
has part: Cell Ontology
has part: Biological Imaging Methods Ontology
has part: Bioregistry
has part: Healthcare metadata - DICOM ontology
has part: Cellular Microscopy Phenotype Ontology
has part: Units of measurement ontology
has part: RSNA Informatics RadLex
has part: Uber Anatomy Ontology
has part: Mouse pathology ontology
has part: Ontology for Biomedical Investigations
has part: SNOMED CT (International Edition)
has part: Mondo Disease Ontology
creator: https://orcid.org/0000-0002-6095-8718
has part: Chemical Entities of Biological Interest
has part: Gene Ontology
type: Collection
has part: NCBI Taxonomy
has part: Mammalian Phenotype Ontology

Medaka fish anatomy and development
has provider formatter: http://purl.obolibrary.org/obo/MFO_$1
has download URL: mfo.owl
has responsible: Thorsten Henrich
is part of: Bioregistry
keyword: fish
keyword: development
has local unique identifier pattern: ^\d{7}$
0000005: 0000001
keyword: anatomy
has resource example: MFO_0000001
type: Resource
description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.
is deprecated: true
keyword: obo
keyword: ontology
has prefix: mfo
has URI prefix: http://purl.obolibrary.org/obo/MFO_

Stemcell Knowledge and Information Portal
0000005: SKIP001214
has local unique identifier pattern: ^SKIP\d+$
has resource example: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail
type: Resource
has URI prefix: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail
has prefix: skip
description: SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine.

Protein Structure and Stability Knowledge Base
contributor: 0009-0008-8406-631X
has URI prefix: https://psskb.org/motif/card/
is deprecated: false
is part of: Bioregistry
has provider formatter: https://psskb.org/motif/card/$1
has reviewer: https://orcid.org/0000-0001-9439-5346
has resource example: 2VM6 A55 A135
type: Resource
0000005: 2VM6_A55_A135
has local unique identifier pattern: ^[A-Za-z0-9_]+$
description: PSSKB allows researchers to model post translational modifications and amino acid substitutions in proteins, providing 3D structural representations. Identifiers represent protein motifs on which PSSKB provides data.
has responsible: https://orcid.org/0000-0003-4472-2016
has prefix: psskb

Ontology for the Anatomy of the Insect SkeletoMuscular system
description: The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.
git repository: aism
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/AISM_$1
depends on: Relation Ontology
is part of: Bioregistry
depends on: Phenotype And Trait Ontology
depends on: Uber Anatomy Ontology
has local unique identifier pattern: ^\d{7}$
0000005: 0000027
appears in: Lepidoptera Anatomy Ontology
type: Resource
has download URL: aism.owl
depends on: Biological Spatial Ontology
has URI prefix: http://purl.obolibrary.org/obo/AISM_
depends on: Basic Formal Ontology
has prefix: aism
contributor: https://orcid.org/0000-0002-1216-4761
appears in: Coleoptera Anatomy Ontology
depends on: Common Anatomy Reference Ontology
is deprecated: false
keyword: obo
has responsible: https://orcid.org/0000-0002-0851-6883
has resource example: AISM_0000027

Ontology for MicroRNA Target
has prefix: omit
description: The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).
has alternative prefix: OMIT
keyword: obo
keyword: mirna
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/OMIT_
git repository: omit
keyword: regulation of gene expression
is part of: Bioregistry
keyword: protein
appears in: Microbial Conditions Ontology
keyword: molecular entity
has responsible: https://orcid.org/0000-0003-2408-2883
has provider formatter: http://purl.obolibrary.org/obo/OMIT_$1
0000005: 0000069
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: prediction and recognition
keyword: gene
keyword: annotation
keyword: molecular interaction
has resource example: OMIT_0000069
keyword: biology
keyword: gene prediction
has download URL: omit.owl
keyword: cell
keyword: life science
is deprecated: false

RxNorm
has local unique identifier pattern: ^[0-9]{1,7}$
contributor: Charles Tapley Hoyt
keyword: biomedical science
description: RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary.
has provider formatter: https://mor.nlm.nih.gov/RxNav/search
keyword: drug
0000005: 221058
has alternative prefix: RXCUI
keyword: ontology
is deprecated: false
keyword: drug name
has prefix: rxnorm
has URI prefix: https://mor.nlm.nih.gov/RxNav/search
is part of: Bioregistry
keyword: preclinical studies
type: Resource
has resource example: https://mor.nlm.nih.gov/RxNav/search

Molecular database for the identification of fungi
keyword: bioinformatics
0000005: UDB000691
has responsible: https://orcid.org/0000-0002-5171-1668
type: Resource
has local unique identifier pattern: ^UDB\d{6}$
keyword: metagenomics
has URI prefix: http://unite.ut.ee/bl_forw.php
keyword: taxonomy
is deprecated: false
has resource example: http://unite.ut.ee/bl_forw.php
has provider formatter: http://unite.ut.ee/bl_forw.php
keyword: biodiversity
description: UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa.
is part of: Bioregistry
keyword: ecology
keyword: genomics
keyword: dna
has prefix: unite

NIF Cell
description: Neuronal cell types
has prefix: nif.cell
type: Resource
is deprecated: true
has responsible: Fahim Imam
has provider formatter: http://purl.obolibrary.org/obo/NIF_CELL_$1
has URI prefix: http://purl.obolibrary.org/obo/NIF_CELL_
keyword: obo
keyword: ontology
is part of: Bioregistry
has download URL: nifcell.owl

Simplified molecular-input line-entry system
keyword: chemistry
keyword: metabolomics
keyword: molecular entity
contributor: Nisha Sharma
is part of: Bioregistry
has URI prefix: https://bioregistry.io/smiles:
git repository: opensmiles
keyword: lipidomics
contributor: Charles Tapley Hoyt
0000005: CC2(C)C\1CCC(C)/C=C/12
type: Resource
keyword: data analysis
has prefix: smiles
has local unique identifier pattern: ^[A-Za-z0-9+\-\*=#$:().>/\\\[\]%]+$
keyword: structure
description: Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions.
keyword: life science
has responsible: Tim Vandermeersch
has provider formatter: https://www.simolecule.com/cdkdepict/depict/bow/svg
is deprecated: false
keyword: bioinformatics

Molecular Interactions Controlled Vocabulary
keyword: miscellaneous
has URI prefix: http://purl.obolibrary.org/obo/MI_
keyword: obo
keyword: ontology
0000005: 0058
has alternative prefix: PSI-MI
is deprecated: false
has local unique identifier pattern: ^\d{4}$
keyword: protein
has resource example: MI_0058
has provider formatter: http://purl.obolibrary.org/obo/MI_$1
has prefix: mi
has download URL: mi.owl
keyword: life sciences, biology
is part of: Bioregistry
description: The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.
git repository: psi-mi-CV
type: Resource
keyword: interaction
keyword: molecular interaction
keyword: molecule
has responsible: https://orcid.org/0000-0001-5084-9000
keyword: protein interactions
keyword: life science

SupraBank Buffer
has provider formatter: https://suprabank.org/buffers/$1
has responsible: https://orcid.org/0000-0002-9676-9839
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: https://suprabank.org/buffers/189
has prefix: suprabank.buffer
keyword: chemical
has URI prefix: https://suprabank.org/buffers/
type: Resource
contributor: Charles Tapley Hoyt
keyword: molecule
description: Identifiers for chemicals used as buffers
0000005: 189

Human Protein Reference Database
has provider formatter: http://www.hprd.org/protein/$1
keyword: protein
0000005: 00001
description: The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
has responsible: https://orcid.org/0000-0001-9943-6127
has prefix: hprd
keyword: structure
has resource example: http://www.hprd.org/protein/00001
is deprecated: true
has URI prefix: http://www.hprd.org/protein/

Drosophila Phenotype Ontology
description: An ontology of commonly encountered and/or high level Drosophila phenotypes.
type: Resource
has download URL: dpo.owl
git repository: drosophila-phenotype-ontology
has responsible: Clare Pilgrim
is deprecated: false
keyword: obo
keyword: ontology
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/FBcv_
has prefix: dpo
has provider formatter: http://purl.obolibrary.org/obo/FBcv_$1
is part of: FlyBase Controlled Vocabulary

Integbio
has part: nbdc00693
has part: nbdc01905
has part: nbdc02433
has part: nbdc00276
has part: nbdc02124
has part: nbdc01207
has part: nbdc00163
has part: nbdc00048
has part: nbdc00375
has part: nbdc00469
has part: nbdc00252
has part: nbdc00136
has part: nbdc02651
has part: nbdc01862
has part: nbdc02671
has part: nbdc02094
has part: nbdc00600
has part: nbdc00613
has part: nbdc01795
has part: nbdc01858
has part: nbdc00064
has part: nbdc02563
has part: nbdc01696
has part: nbdc01041
has part: nbdc00308
has part: nbdc01164
has part: nbdc00438
has part: nbdc00356
has part: nbdc01703
has part: nbdc00004
has part: nbdc00153
has part: nbdc00594
has part: nbdc00818
has part: nbdc00355
description: Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)
has part: nbdc01710
has part: nbdc01422
has part: nbdc00414
has part: nbdc00275
has part: nbdc00420
has part: nbdc00599
has part: nbdc02480
has part: nbdc00220
has part: nbdc00188
has part: nbdc01782
has part: nbdc01815
has part: nbdc02244
has part: nbdc00265
has part: nbdc00908
has part: nbdc01882
has part: nbdc01059
has part: nbdc00273
has part: nbdc02224
has part: nbdc00391
has part: nbdc01698
has part: nbdc02174
has part: nbdc02434
has responsible: Shuichi Kawashima
has part: nbdc00115
has part: nbdc00074
has part: nbdc01764
has part: nbdc00573
has part: nbdc00607
has part: nbdc01174
has part: nbdc00351
has part: nbdc02560
has part: nbdc02566
has part: nbdc02624
has part: nbdc00023
has part: nbdc00103
has part: nbdc00069
has part: nbdc00860
has part: nbdc01630
has part: nbdc00812
has part: nbdc01456
has part: nbdc02191
has part: nbdc00154
has part: nbdc01071
has part: nbdc00206

Web Annotation Ontology
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
0000005: sourceDateStart
keyword: ontology
has download URL: oa.owl
has URI prefix: http://www.w3.org/ns/oa#
is deprecated: false
keyword: quality
has prefix: oa
description: The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture.
has resource example: sourceDateStart
has provider formatter: http://www.w3.org/ns/oa#$1

Vital Sign Ontology
0000005: 0000041
keyword: ontology
is deprecated: false
has provider formatter: https://bioportal.bioontology.org/ontologies/VSO/
is part of: Bioregistry
has responsible: Albert Goldfain
has resource example: https://bioportal.bioontology.org/ontologies/VSO/
keyword: blood
description: The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.
has download URL: vso.owl
keyword: owl
has URI prefix: https://bioportal.bioontology.org/ontologies/VSO/
has prefix: vso
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: biomedical science
keyword: experimental measurement
keyword: health science
keyword: health

Ontology of Vaccine Adverse Events
0000005: 0000609
has download URL: ovae.owl
has prefix: ovae
keyword: obo
description: OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE).
git repository: ovae
keyword: adverse reaction
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/OVAE_
is deprecated: false
has responsible: Yongqun Oliver He
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/OVAE_$1
keyword: vaccine
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: biomedical science
has resource example: OVAE_0000609

CropMRepository
has local unique identifier pattern: ^[0-9]{9}$
has URI prefix: http://www.crop2ml.org/cropmdb/
0000005: 000000001
is deprecated: false
is part of: Bioregistry
has prefix: crop2ml
description: CropMRespository is a database of soil and crop biophysical process models.
has provider formatter: http://www.crop2ml.org/cropmdb/$1
type: Resource
has resource example: http://www.crop2ml.org/cropmdb/000000001

Molecular Process Ontology
has prefix: mop
has responsible: Colin Batchelor
keyword: obo
keyword: ontology
is deprecated: false
keyword: chemistry
keyword: nfdi4cat
description: MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation.
keyword: nfdi4chem
has provider formatter: http://purl.obolibrary.org/obo/MOP_$1
keyword: molecular chemistry
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/MOP_
type: Resource
0000005: 0000079
has resource example: MOP_0000079
git repository: rxno
keyword: reaction data
has download URL: mop.owl
has local unique identifier pattern: ^\d{7}$

UniProt Archive
has resource example: UPI000000000A
is part of: Bioregistry
keyword: protein
description: The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases.
0000005: UPI000000000A
has provider formatter: https://www.uniprot.org/uniparc/$1
has prefix: uniparc
type: Resource
keyword: structure
has responsible: Alex Bateman
is deprecated: false
has URI prefix: https://www.uniprot.org/uniparc/
has local unique identifier pattern: ^UPI[A-F0-9]{10}$

Ion Channel Electrophysiology Ontology
has URI prefix: https://biopragmatics.github.io/providers/icepo/
description: The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools.
is part of: Bioregistry
0000005: 0000002
contributor: Charles Tapley Hoyt
type: Resource
has prefix: icepo
has local unique identifier pattern: ^\d{7}$
has resource example: https://biopragmatics.github.io/providers/icepo/0000002
has responsible: Pascale Gaudet
has download URL: icepo.obo
keyword: ontology
is deprecated: false
has provider formatter: https://biopragmatics.github.io/providers/icepo/$1

Circular double stranded DNA sequences composed
has provider formatter: https://doulix.com/constructs/$1
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^[A-Z0-9]{6,7}$
has URI prefix: https://doulix.com/constructs/
has prefix: dlxc
has resource example: M77F7JM
0000005: M77F7JM
is deprecated: false
description: DOULIX lab-tested standard biological parts, in this case, full length constructs.

ClinVar Record
is deprecated: false
has provider formatter: http://www.ncbi.nlm.nih.gov/clinvar/$1
has URI prefix: http://www.ncbi.nlm.nih.gov/clinvar/
is part of: Bioregistry
0000005: RCV000033555.3
description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.
type: Resource
has resource example: RCV000033555.3
has local unique identifier pattern: ^RCV\d+(\.\d+)?$
has prefix: clinvar.record

Ontology of units of Measure
has URI prefix: http://www.ontology-of-units-of-measure.org/resource/om-2/
keyword: unit
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
has prefix: om
0000005: Dimension
keyword: ess
keyword: units
keyword: physics
has resource example: Dimension
has provider formatter: http://www.ontology-of-units-of-measure.org/resource/om-2/$1
keyword: ontology
is deprecated: false
keyword: nfdi4cat
git repository: OM
has download URL: om.owl
keyword: nfdi4chem
description: The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measures, and dimensions.
keyword: earth sciences
keyword: life sciences, biology

PubChem Classification
has resource example: https://pubchem.ncbi.nlm.nih.gov/classification/
contributor: Charles Tapley Hoyt
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/classification/
0000005: 87
has prefix: pubchem.classification
is deprecated: false
keyword: chemistry
description: The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records.
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/classification/
type: Resource

The Prescription of Drugs Ontology
has URI prefix: http://purl.obolibrary.org/obo/PDRO_
has responsible: Paul Fabry
0000005: 0010039
is part of: Bioregistry
description: An ontology to describe entities related to prescription of drugs
type: Resource
has prefix: pdro
has local unique identifier pattern: ^\d{7}$
git repository: PDRO
keyword: drug
keyword: obo
keyword: ontology
has download URL: pdro.owl
has provider formatter: http://purl.obolibrary.org/obo/PDRO_$1
is deprecated: false
has resource example: PDRO_0010039
keyword: primary health care

Annotated Regulatory Binding Sites
has URI prefix: https://bioregistry.io/abs:
has responsible: https://orcid.org/0000-0001-6261-7370
has provider formatter: http://genome.crg.es/datasets/abs2005/entries/$1.html
description: The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography.
is deprecated: false
keyword: regulation
0000005: A0014
has local unique identifier pattern: ^A\d+$
is part of: Bioregistry
type: Resource
keyword: gene
keyword: interaction
keyword: biology
has prefix: abs
has resource example: A0014.html

EDAM Ontology
has part: data 2658
has part: data 2613
has part: data 2645
has part: data 1035
has part: data 2389
has part: data 2719
has part: data 3856
has part: data 2104
has part: data 2666
has part: data 3264
has part: data 3274
has part: data 2756
has part: data 1161
has part: data 1106
has part: data 1181
0000005: 1004
has part: data 2298
has part: data 2343
has part: data 2632
has part: data 1002
description: EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use.
has part: data 2609
has part: data 2642
has part: data 1182
has part: data 2344
type: Registry
has part: data 1027
has part: data 2578
has part: data 1177
has part: data 2631
has part: data 2619
has part: data 1179
has part: data 1153
has part: data 2657
has part: data 2292
has part: data 1004
has part: data 2356
has part: data 3265
has part: data 3757
has part: data 2367
has part: data 2634
has part: data 1136
has part: data 2773
has part: data 2638
has part: data 1129
has part: data 2787
has part: data 2644
has part: data 1089
has part: data 2741
has part: data 1188
has part: data 2656
has part: data 1128
has part: data 2610
has part: data 1042
has part: data 2651
has part: data 2660
has part: data 2611
has part: data 2716
has part: data 2392
has part: data 2615
has part: data 2629
has part: data 1147
has part: data 1146
has part: data 1133
has part: data 1162
has part: data 2789
has part: data 1174
has part: data 2309
has part: data 1041
has part: data 2628
has part: data 1127
has part: data 1805
has part: data 2302
has part: data 2641
has part: data 2622
has part: data 1098
has part: data 1173
has part: data 2626
has part: data 2652

Web Elements
has provider formatter: https://www.webelements.com/$1
type: Resource
has URI prefix: https://www.webelements.com/
is deprecated: false
description: Browser for the periodic table of the elements
has resource example: chromium
has prefix: webelements
keyword: chemistry
has local unique identifier pattern: ^\w+$
is part of: Bioregistry
0000005: chromium
contributor: Charles Tapley Hoyt

SIDER Drug
0000005: 2244
is deprecated: false
has provider formatter: http://sideeffects.embl.de/drugs/$1
has local unique identifier pattern: ^\d+$
description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.
is part of: Bioregistry
type: Resource
has URI prefix: http://sideeffects.embl.de/drugs/
has prefix: sider.drug
has resource example: http://sideeffects.embl.de/drugs/2244

GlycoMapsDB
has URI prefix: http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php
description: A database of GlycoMaps containing 2585 conformational maps.
has reviewer: Charles Tapley Hoyt
has prefix: glycomapsdb
has resource example: http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php
0000005: 6819
has provider formatter: http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php
is deprecated: false
keyword: small molecule
is part of: Bioregistry
type: Resource

GeoSPARQL
0000005: hasDefaultGeometry
has download URL: geosparql.owl
type: Resource
keyword: nfdi4ing
has URI prefix: http://www.opengis.net/ont/geosparql#
keyword: ess
keyword: fair data spaces
has provider formatter: http://www.opengis.net/ont/geosparql#$1
keyword: ontology
is deprecated: false
is part of: Bioregistry
has resource example: hasDefaultGeometry
description: The OGC GeoSPARQL standard supports representing and querying geospatial data on the Semantic Web. GeoSPARQL defines a vocabulary for representing geospatial data in RDF, and it defines an extension to the SPARQL query language for processing geospatial data. In addition, GeoSPARQL is designed to accommodate systems based on qualitative spatial reasoning and systems based on quantitative spatial computations.
has prefix: geosparql
keyword: earth sciences

Integrated Microbial Genomes Gene
has responsible: Nikos C. Kyrpides
has resource example: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
keyword: gene
has prefix: img.gene
type: Resource
is deprecated: false
keyword: genome
description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information.
has provider formatter: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
has URI prefix: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
0000005: 638309541
is part of: Bioregistry
has local unique identifier pattern: ^\d+$

National Center for Biotechnology Information Registry
has part: TIGRFAM
has part: MedGen
has part: Phytozome
has part: HOMD
has part: PDB
has part: CGD
has part: ViPR
has part: MaizeGDB
has part: GO
type: Registry
has part: UNITE
has part: RAP-DB
has part: dbEST
0000005: ECOCYC
has part: RNAcentral
has part: InterPro
has part: Araport
has part: GABI
has part: ISFinder
has part: MycoBank
has part: EcoGene
description: A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources
has part: SubtiList
has part: LIGM
has part: EPD
has part: TAIR
has part: PFAM
has part: ENSEMBL
has part: TubercuList
has part: NextDB
has part: AntWeb
has part: GOA
has part: BOLD
has responsible: GenBank Support
has part: BEETLEBASE
has part: miRBase
has part: CABRI
has part: Greengenes
has part: HSSP
has part: SoyBase
has part: UniSTS
has part: MGI
has part: GeneID
has part: PomBase
has part: niaEST
has part: HGNC
has part: Xenbase
has part: HPM
has part: GRIN
has part: SEED
has part: ApiDB PlasmoDB
has part: taxon
has part: ECOCYC
has part: ZFIN
has part: RATMAP
has part: RFAM
has part: dictyBase
has part: VBASE2
has part: NMPDR
has part: RGD
has part: WorfDB
has part: NBRC
has part: FBOL
has part: Fungorum
has part: VectorBase
has part: WormBase
has part: JCM
has part: HLA
has part: dbSNP
has part: MIM
has part: FLYBASE
has part: UniProt
has part: dbProbe
has part: SGD
has part: GI
has part: SGN
has part: CDD
has part: ASAP
has part: BDGP EST
has part: GeneDB

SBGN Bricks data and ontology
keyword: ontology
has provider formatter: http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has resource example: BKO:0000204
has responsible: 0000-0002-2118-035X
description: SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way.
has prefix: bko
has reviewer: Charles Tapley Hoyt
type: Resource
0000005: 0000204
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has URI prefix: http://www.sbgnbricks.org/BKO/full/entry/all/BKO:
has download URL: bko.owl

Environmental conditions, treatments and exposures ontology
depends on: Gene Ontology
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
depends on: Chemical Entities of Biological Interest
has prefix: ecto
depends on: Medical Action Ontology
type: Resource
has resource example: ECTO_0000001
depends on: Experimental condition ontology
depends on: NCBI Taxonomy
has URI prefix: http://purl.obolibrary.org/obo/ECTO_
keyword: exposure
has provider formatter: http://purl.obolibrary.org/obo/ECTO_$1
keyword: environmental science
depends on: NCI Thesaurus
is deprecated: false
keyword: obo
depends on: Environment Ontology
keyword: ontology
description: ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).
depends on: Exposure ontology
depends on: Relation Ontology
has download URL: ecto.owl
git repository: environmental-exposure-ontology
is part of: Bioregistry
depends on: Information Artifact Ontology
depends on: Neuro Behavior Ontology
has responsible: https://orcid.org/0000-0002-2908-3327
depends on: Phenotype And Trait Ontology
depends on: Uber Anatomy Ontology

arXiv
has prefix: arxiv
has local unique identifier pattern: ^(\w+(\-\w+)?(\.\w+)?\/?)?\d{4,7}(\.\d+(v\d+)?)?$
keyword: preprints
is deprecated: false
is part of: Bioregistry
keyword: publishing
has provider formatter: https://arxiv.org/abs/$1
has resource example: 0807.4956v1
0000005: 0807.4956v1
type: Resource
description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.
has URI prefix: https://arxiv.org/abs/
keyword: bibliography
contributor: https://orcid.org/0000-0002-1216-4761

InChI
has resource example: https://www.ebi.ac.uk/chebi/advancedSearchFT.do
has local unique identifier pattern: ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$
has responsible: Stephen R. Heller
has URI prefix: https://www.ebi.ac.uk/chebi/advancedSearchFT.do
is deprecated: false
keyword: centrally registered identifier
is part of: Bioregistry
keyword: cheminformatics
keyword: chemical structure image
keyword: chemistry
keyword: molecular entity
0000005: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3
git repository: InChI
has prefix: inchi
keyword: chemical entity
type: Resource
keyword: structure
has provider formatter: https://www.ebi.ac.uk/chebi/advancedSearchFT.do
description: The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier.

Dialnet article ID
type: Resource
0000005: 262393
is deprecated: false
description: identifier of an article in Dialnet
has prefix: dialnet.article
has URI prefix: https://dialnet.unirioja.es/servlet/articulo
has resource example: https://dialnet.unirioja.es/servlet/articulo
has provider formatter: https://dialnet.unirioja.es/servlet/articulo
is part of: Bioregistry
contributor: Charles Tapley Hoyt

UniProt Cross-ref database
has part: DB-0062
has part: DB-0019
has part: DB-0214
has part: DB-0053
has part: DB-0041
has part: DB-0022
has part: DB-0136
has part: DB-0118
has part: DB-0135
has part: DB-0187
has part: DB-0069
has responsible: Alex Bateman
has part: DB-0038
has part: DB-0275
has part: DB-0236
has part: DB-0145
has part: DB-0184
has part: DB-0106
has part: DB-0028
has part: DB-0239
has part: DB-0223
has part: DB-0162
has part: DB-0181
has part: DB-0089
has part: DB-0144
has part: DB-0143
has part: DB-0110
has part: DB-0224
has part: DB-0060
has provider formatter: https://www.uniprot.org/database/$1
has part: DB-0266
has part: DB-0051
has part: DB-0079
has part: DB-0049
has part: DB-0228
has part: DB-0092
has part: DB-0119
has part: DB-0149
has part: DB-0158
has part: DB-0182
has part: DB-0095
description: The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources.
has part: DB-0030
has part: DB-0117
has part: DB-0174
has part: DB-0127
has part: DB-0272
has part: DB-0221
has part: DB-0129
has part: DB-0253
has part: DB-0026
has part: DB-0147
has part: DB-0155
has part: DB-0126
has part: DB-0097
has part: DB-0005
has part: DB-0068
has part: DB-0023
has part: DB-0206
has part: DB-0091
has part: DB-0148
has part: DB-0084
has part: DB-0027
has part: DB-0251
has part: DB-0024
0000005: DB-0174
has part: DB-0072
has part: DB-0113
has part: DB-0044
has part: DB-0031
has part: DB-0037
has part: DB-0241
has part: DB-0042
has part: DB-0226
has part: DB-0160
has part: DB-0177
has part: DB-0058
has part: DB-0046
has part: DB-0152

Common Access to Biological Resources and Information Project
keyword: medical microbiology
keyword: applied microbiology
is part of: Bioregistry
keyword: molecular biology
0000005: dsmz_mutz-id:ACC 291
keyword: virology
has local unique identifier pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$
has URI prefix: https://bioregistry.io/cabri:
type: Resource
keyword: microbiology
has prefix: cabri
has responsible: Paolo Romano
is deprecated: false
description: CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it.
keyword: molecular microbiology
has provider formatter: http://www.cabri.org/CABRI/srs-bin/wgetz

Animal Genome Cattle QTL
has prefix: cattleqtldb
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has provider formatter: https://www.animalgenome.org/QTLdb/q
description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs.
has resource example: https://www.animalgenome.org/QTLdb/q
0000005: 4685
is part of: Animal Genome QTL
has URI prefix: https://www.animalgenome.org/QTLdb/q
is deprecated: false
keyword: genome
keyword: dna

Small Molecule Pathway Database
keyword: pathway
is deprecated: false
0000005: SMP0000219
keyword: chemical
has local unique identifier pattern: ^SMP\d+$
has resource example: SMP0000219
is part of: Bioregistry
has alternative prefix: SMP
keyword: metabolite
has prefix: smpdb
has provider formatter: https://smpdb.ca/view/$1
type: Resource
keyword: life science
has responsible: David Wishart
has URI prefix: https://smpdb.ca/view/
keyword: human
description: The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.

SWEET Ontology Relationships Mathematical
has provider formatter: http://sweetontology.net/relaMath/$1
type: Resource
keyword: mathematical
0000005: averageOver
has resource example: averageOver
is deprecated: false
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sorelm
has URI prefix: http://sweetontology.net/relaMath/
has prefix: sweet.relm
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Mathematical

Mid-level Energy Ontology
is part of: Bioregistry
has responsible: Mirjam Stappel
type: Resource
contributor: Charles Tapley Hoyt
description: The midlevel energy ontology (MENO) is a BFO-based midlevel ontology. It comprises the concepts for energy qualities, energy-based dispositions and energy-driven transformation and transfer processes and their interrelations. It has the goal to provide an upper level structure for these concepts for energy-related domain ontologies.
git repository: midlevel-energy-ontology
has prefix: meno
keyword: ontology
0000005: 01013
has download URL: midlevel-energy.owl
is deprecated: false
has local unique identifier pattern: ^\d+$

ClinGen Curation
is deprecated: false
description: ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides identifiers for curations representing evidence aggregation and expert panel assertions based on standardized evaluation procedures
has provider formatter: https://search.clinicalgenome.org/CCID:$1
has prefix: clingen.curation
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
has local unique identifier pattern: ^\d{6}$
type: Resource
has URI prefix: https://search.clinicalgenome.org/CCID:
has resource example: CCID:004126
contributor: Mufaddal Naguthanawala
0000005: 004126

Reference Sequence Collection
contributor: Sebastian Lobentanzer
has prefix: refseq
description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.
keyword: life science
keyword: rna
has alternative prefix: REFSEQ_PROT
keyword: genetics
is deprecated: false
keyword: computational biology
keyword: protein
has resource example: NP_012345
keyword: dna
has canonical: NCBI Protein
has provider formatter: https://www.ncbi.nlm.nih.gov/protein/$1
has local unique identifier pattern: ^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\d+)|(NZ_[A-Z]{2,4}\d+))(\.\d+)?$
0000005: NP_012345
has responsible: https://orcid.org/0000-0001-7950-1374
is part of: Bioregistry
has URI prefix: https://www.ncbi.nlm.nih.gov/protein/
type: Resource

Coli Genetic Stock Center
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
has responsible: https://orcid.org/0000-0003-1546-6746
keyword: gene
description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.
keyword: life science
is deprecated: true
has URI prefix: http://cgsc.biology.yale.edu/Site.php
has resource example: http://cgsc.biology.yale.edu/Site.php
has prefix: cgsc
0000005: 74
has provider formatter: http://cgsc.biology.yale.edu/Site.php

Drug Central
keyword: drug discovery
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: pharmacology
keyword: drug repositioning
contributor: Charles Tapley Hoyt
has alternative prefix: Drug_Central
has resource example: http://drugcentral.org/drugcard/307
has provider formatter: http://drugcentral.org/drugcard/$1
has prefix: drugcentral
description: DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action.
0000005: 307
type: Resource
has URI prefix: http://drugcentral.org/drugcard/
has download URL: drugcentral.owl
keyword: biomedical science
keyword: drug development
keyword: pharmacy
has responsible: Tudor Oprea
keyword: ontology

Consensus CDS
type: Resource
keyword: gene
description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.
has prefix: ccds
keyword: life science
is deprecated: false
0000005: CCDS12976
is part of: Bioregistry
keyword: protein
has URI prefix: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi
has resource example: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi
has local unique identifier pattern: ^CCDS\d+(\.\d+)?$
has provider formatter: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi
has responsible: Terence D. Murphy

FHIR External Terminologies
has part: RxNorm
has part: Vaccine administered code set
has part: Locus Reference Genomic
has part: SNOMED CT (International Edition)
has part: PharmGKB Gene
has part: HL7 V3 Code System
has part: Sequence types and features ontology
has part: HL7 V2 Code System
has part: COSMIC Gene
has part: Current Procedural Terminology
has part: HUGO Gene Nomenclature Committee
has part: Online Mendelian Inheritance in Man
has part: International Classification of Diseases, 10th Revision
has part: American Type Culture Collection
has part: PubMed
has part: Logical Observation Identifiers Names and Codes
has part: ClinicalTrials.gov
has part: ClinVar Variation
has part: Health Canada Natural Product Number
has part: NCI Thesaurus
has part: Internet Engineering Task Force Language Tag
has part: National Drug File - Reference Terminology
has part: International Classification of Functioning, Disability and Health
has part: Unified Code for Units of Measure
has part: National Uniform Claim Committee Taxonomy
has part: IMGT/HLA human major histocompatibility complex sequence database
has part: Health Canada Drug Identification Number
description: Prefixes mentioned on the _external_ list on the FHIR [Code Systems](https://hl7.org/fhir/terminologies-systems.html) page. This list is mostly complete. Notably, some entries that have not been curated: - HGVS (see discussion at [#460](https://github.com/biopragmatics/bioregistry/issues/460)) - [NUBC](http://www.nubc.org) (National Uniform Billing Committee) - could not find information about the terminology or its entries - [ICPC](http://www.ph3c.org/) (International Classification of Primary Care) _same_ - [GTIN](https://www.gs1.org/standards/id-keys/gtin) (Global Trade Item Number) _same_ - [MDC](https://www.iso.org/standard/37890.html) (Medical Device Codes) since that appears to be part of a larger ISO standard vocabulary that needs further investigation
has part: Ensembl Gene
has part: ISO 3166-1 Country Code
has part: RSNA Informatics RadLex
has part: Reference Sequence Collection
has part: Healthcare metadata - DICOM ontology
creator: Charles Tapley Hoyt
type: Collection
has part: International Classification of Diseases, 9th Revision
has part: Diagnostic and Statistical Manual of Mental Disorders (5th Edition)
has part: dbSNP Reference SNP number
has part: Unique Ingredient Identifier
has part: National Drug Code

Conserved Domain Database at NCBI
description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.
has local unique identifier pattern: ^(cd)?\d{5}$
0000005: cd00400
type: Resource
keyword: structure
has URI prefix: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi
has resource example: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi
has prefix: cdd
is deprecated: false
has provider formatter: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi
is part of: Bioregistry
keyword: protein

SWEET Ontology Representation Scientific Function
is deprecated: false
has URI prefix: http://sweetontology.net/reprSciFunction/
keyword: representation scientific function
has prefix: sweet.repsf
has alternative prefix: sorepsf
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Function
0000005: AdiabaticInvariant
has provider formatter: http://sweetontology.net/reprSciFunction/$1
has resource example: AdiabaticInvariant

GOLD metadata
is part of: Bioregistry
has URI prefix: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi
has canonical: Genomes Online Database
has prefix: gold.meta
type: Resource
description: - DEPRECATION NOTE - Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.
has resource example: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi
0000005: Gm00047
is deprecated: false
has provider formatter: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi
has local unique identifier pattern: ^Gm\d+$

BioAssay Ontology
keyword: cell
keyword: life science
keyword: biochemistry
keyword: biological_process
has alternative prefix: BAO
git repository: BAO
keyword: chemical and environmental engineering
has prefix: bao
0000005: 0002989
keyword: ontology
has download URL: bao complete.owl
is deprecated: false
is part of: Bioregistry
keyword: protein
keyword: dataplant
has URI prefix: http://www.bioassayontology.org/bao#BAO_
keyword: nfdi4cat
keyword: assay
has resource example: BAO_0002989
keyword: molecular entity
keyword: life sciences, biology
description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.
has local unique identifier pattern: ^\d{7}$
keyword: chemical entity
type: Resource
keyword: reagent
keyword: target
keyword: biomedical science
has provider formatter: http://www.bioassayontology.org/bao#BAO_$1

Beta Cell Genomics Ontology
has responsible: Jie Zheng
has download URL: bcgo.owl
keyword: obo
is deprecated: true
0000005: 0000015
keyword: ontology
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/BCGO_
has provider formatter: http://purl.obolibrary.org/obo/BCGO_$1
type: Resource
description: An application ontology built for beta cell genomics studies.
has resource example: BCGO_0000015
git repository: bcgo
has prefix: bcgo
has local unique identifier pattern: ^\d{7}$

Database of Escherichia coli Sequence and Function
has URI prefix: http://www.ecogene.org/gene/
type: Resource
is deprecated: true
has resource example: EG10173
has provider formatter: http://www.ecogene.org/gene/$1
description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.
0000005: EG10173
has local unique identifier pattern: ^EG\d+$
keyword: genome
is part of: Bioregistry
keyword: protein
has prefix: ecogene

Woody Plant Ontology
is deprecated: false
has local unique identifier pattern: ^\d+$
has URI prefix: https://cropontology.org/rdf/CO_357:
has resource example: CO 357:1000290
is part of: Bioregistry
keyword: phenotype
keyword: botany
type: Resource
git repository: Crop-Ontology
has prefix: co_357
0000005: 1000290
keyword: life science
description: The Woody Plant Ontology lists reference variables used for experimentations and observations on woody plants (forest trees and shrubs, and possibly fruit trees). It is an international initiative based on various communities (French, Portuguese and European). Terms are collected from various sources and organized following the Crop Ontology standard which provides harmonized variables composed by a triplet: (i) a trait, the studied character, (ii) a method, the measurement protocol and (iii) a scale, the unit of measurement or scoring scale.
has download URL: CO 357.owl
keyword: ontology
has responsible: Célia Michotey
has provider formatter: https://cropontology.org/rdf/CO_357:$1

SWEET Ontology State Time Geologic
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
0000005: 0MYA
type: Resource
has provider formatter: http://sweetontology.net/stateTimeGeologic/$1
is deprecated: false
has resource example: 0MYA
has prefix: sweet.sttg
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Time Geologic
has alternative prefix: sosttg
is part of: Bioregistry
keyword: state time geologic
has URI prefix: http://sweetontology.net/stateTimeGeologic/
git repository: sweet

USA National Service Center Number
type: Resource
is deprecated: false
has resource example: https://dtp.cancer.gov/dtpstandard/servlet/ChemData
has prefix: nsc
has provider formatter: https://dtp.cancer.gov/dtpstandard/servlet/ChemData
0000005: 27223
description: Identifier used by the Cancer Chemotherapy National Service Center.
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has URI prefix: https://dtp.cancer.gov/dtpstandard/servlet/ChemData

Assembly
has prefix: ncbi.assembly
type: Resource
has resource example: GCF 000005845.2
has URI prefix: https://www.ncbi.nlm.nih.gov/datasets/genome/
has provider formatter: https://www.ncbi.nlm.nih.gov/datasets/genome/$1
0000005: GCF_000005845.2
has local unique identifier pattern: ^[a-zA-Z0-9_\.]+$
description: A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.
is deprecated: false
is part of: Bioregistry

SWEET Ontology State Time Cycle
keyword: state time cycle
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.sttc
type: Resource
is deprecated: false
has provider formatter: http://sweetontology.net/stateTimeCycle/$1
has URI prefix: http://sweetontology.net/stateTimeCycle/
has alternative prefix: sosttc
has resource example: ElNino
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Time Cycle
is part of: Bioregistry
0000005: ElNino

EcoliWiki from EcoliHub
0000005: aaeA
keyword: ontology and terminology
is deprecated: false
keyword: genomics
has prefix: ecoliwiki
has local unique identifier pattern: ^[A-Za-z0-9-]+$
has resource example: aaeA:Gene
keyword: bioinformatics
description: EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes.
is part of: Bioregistry
type: Resource
has URI prefix: https://bioregistry.io/ecoliwiki:
has responsible: https://orcid.org/0000-0002-5876-6418
keyword: life science
has provider formatter: http://ecoliwiki.net/colipedia/index.php/$1:Gene

IntAct protein interaction
has resource example: EBI-2307691
is deprecated: false
contributor: https://orcid.org/0000-0001-7456-0594
keyword: protein
is part of: Bioregistry
description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data.
has local unique identifier pattern: ^EBI\-[0-9]+$
keyword: interaction
keyword: biology
has responsible: 0009-0004-6468-260X
0000005: EBI-2307691
type: Resource
has prefix: intact
has URI prefix: https://www.ebi.ac.uk/intact/interaction/
has responsible: 0000-0003-2534-198X
has identifier space owner: 02catss52
has provider formatter: https://www.ebi.ac.uk/intact/interaction/$1

SNOMED CT (International Edition)
is part of: Bioregistry
has alternative prefix: SNOMECT
has alternative prefix: SNOMEDCTCT
description: SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.
has alternative prefix: SNOMED_CT
has alternative prefix: SNOMEDCT_US_2023_02_28
has alternative prefix: SNOWMEDCT_US_2018_03_01
has alternative prefix: SCTID_2010_1_31
has local unique identifier pattern: ^(\w+)?\d+$
has download URL: http://snomed.info/sct/900000000000207008/version/20251017
has alternative prefix: SNOMEDCTCT_2019_03_01
type: Resource
has alternative prefix: SNOMEDCT_US_2022_09_01
keyword: preclinical studies
has alternative prefix: SNOMEDCT_US_2020_03_01
has alternative prefix: SNOMEDCT_US_2019_03_01
has alternative prefix: SNOMEDCT_US_2024_03_01
has alternative prefix: SNOMEDCT_US_2020_09_01
has resource example: http://purl.bioontology.org/ontology/SNOMEDCT/284196006
has alternative prefix: SNOMEDCT_2005_07_31
keyword: biomedical science
has URI prefix: http://purl.bioontology.org/ontology/SNOMEDCT/
has alternative prefix: SNOMEDCT_US_2019_09_01
has alternative prefix: SNOMEDCT_US_2023_10_01
keyword: health science
has alternative prefix: SNOMEDCT_US_2022_12_31
has alternative prefix: SNOMEDCT_US_2022_07_31
has alternative prefix: SNOMEDCT_US_2023_11_01
has alternative prefix: SCTID
has alternative prefix: SNOMEDCT_US
has alternative prefix: SNOMED_CT_US_2018_03_01
keyword: medicine
has alternative prefix: SNOMEDCT_US_2015_03_01
has alternative prefix: SNOMEDCT_US_2023_03_01
has alternative prefix: SNOMEDCT_US_2018_03_01
has alternative prefix: SNOWMEDCT_US
has alternative prefix: SNOMEDCT_US_2021_03_01
has alternative prefix: SNOMEDCT_US_2018_09_01
has alternative prefix: SNOWMEDCT
has alternative prefix: SNOMEDCTCT_2018_03_01
has alternative prefix: SNOMEDCT
has alternative prefix: SNOMED
has alternative prefix: SNOMEDCT_US_2016_03_01
has alternative prefix: SNOMEDCT_2020_03_01
0000005: 284196006
keyword: ontology
has prefix: snomedct
has provider formatter: http://purl.bioontology.org/ontology/SNOMEDCT/$1
has alternative prefix: SNOMEDCT_US_2023_09_01
has alternative prefix: SNOMEDCT_US_2021_09_01
has alternative prefix: SNOMEDCT_US_2021_07_31
contributor: https://orcid.org/0000-0002-7356-1779
is deprecated: false
has alternative prefix: SNOMEDCT_2010_1_31

COSMIC Gene
has URI prefix: http://cancer.sanger.ac.uk/cosmic/gene/overview
has responsible: https://orcid.org/0000-0002-8315-6574
keyword: genetics
is deprecated: false
is part of: Bioregistry
0000005: BRAF
has provider formatter: http://cancer.sanger.ac.uk/cosmic/gene/overview
0000011: HGNC gene symbol
type: Resource
has alternative prefix: cosmic
description: COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes.
has resource example: http://cancer.sanger.ac.uk/cosmic/gene/overview
keyword: biomedical science
has prefix: cosmic.gene
has local unique identifier pattern: ^[A-Z0-9][A-Z0-9-]*$

ChemDB
has provider formatter: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py
has URI prefix: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py
has responsible: Pierre Baldi
keyword: preclinical studies
type: Resource
keyword: biomedical science
keyword: biochemistry
keyword: systems biology
description: ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.
keyword: life science
is deprecated: false
has resource example: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py
0000005: 3966782
has prefix: chemdb
keyword: small molecule
is part of: Bioregistry
has local unique identifier pattern: ^\d+$

Pathguide
keyword: gene
keyword: interaction
has provider formatter: http://www.pathguide.org/fullrecord.php
has reviewer: Charles Tapley Hoyt
description: Pathguide contains information about 325 biological related resources and molecular interaction related resources.
is deprecated: false
has responsible: https://orcid.org/0000-0003-0185-8861
has URI prefix: http://www.pathguide.org/fullrecord.php
keyword: pathway
keyword: small molecule
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
keyword: protein
has resource example: http://www.pathguide.org/fullrecord.php
0000005: 49
has prefix: pathguide
type: Resource

Aggregation Method
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/AggregationMethod#code_
is part of: Bioregistry
has prefix: ddi.aggregationmethod
contributor: Charles Tapley Hoyt
has provider formatter: https://vocabularies.cessda.eu/vocabulary/AggregationMethod#code_$1
has resource example: code Sum
type: Resource
0000005: Sum
description: Identifies the type of aggregation used to combine related categories, usually within a common branch of a hierarchy, to provide information at a broader level than the level at which detailed observations are taken. (From: The OECD Glossary of Statistical Terms)
has identifier space owner: 015em2733

Name-to-Thing
description: An ARK resolver as well as resolver built with common prefixes as in Identifiers.org
type: Resource
has resource example: chebi:
contributor: Charles Tapley Hoyt
has prefix: n2t
0000005: chebi
has provider formatter: https://n2t.net/$1:
has URI prefix: https://bioregistry.io/n2t:
is deprecated: false
is part of: Bioregistry

Signaling Gateway
keyword: small molecule
is part of: Bioregistry
keyword: protein
has responsible: Kenan Azam
has resource example: http://www.signaling-gateway.org/molecule/query
type: Resource
has URI prefix: http://www.signaling-gateway.org/molecule/query
has local unique identifier pattern: ^A\d{6}$
has provider formatter: http://www.signaling-gateway.org/molecule/query
description: The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.
0000005: A001094
has prefix: signaling-gateway
is deprecated: true
keyword: pathway

AberOWL
has part: ORTH
has part: ITO
has part: PREFER
has part: CDNO
has part: VTO
has part: MIRNAO
has part: WIKIPATHWAYS
has part: ROLEO
has part: OAE
has part: ZFA
has part: VIVO
has part: NMR
has part: XLMOD
has part: ECTO
has part: MESH
has part: IDO-COVID-19
has part: GEOSPARQL
has part: CLO
has part: FaBiO
has part: FB-SP
has part: CTENO
has part: OPMI
has part: RO
has part: SUGARBIND
has part: BIOLINK
has part: PRIDE
has part: ZP
has part: ordo
has part: CCF
has part: OBI
has part: FRAPO
has part: CMO
has part: MAT
has part: OGSF
has part: VT
has part: OBO
has part: OHD
has part: FLU
has part: CHR
has part: APOLLO SV
has part: HOM
has part: EOL
has part: PCO
has part: RDFS
has part: EDDA
has part: BERVO
has part: CCO
has part: ADCAD
has part: DTO
has part: OA
has part: SLSO
has part: PCL
has part: HSO
has part: FPLX
has part: MPIO
has part: MIRO
has part: METPO
has part: LIPRO
has part: ZFS
has part: CLAO
has part: COLAO
has part: ROR
has part: AFO
has part: ICD10CM
has part: CDAO
has part: FIX
has part: OHMI
has part: CTCAE
has part: NDFRT
has part: BTO
has part: HCPCS
has part: OCDO
has part: STY
has part: CRYOEM
has part: UPHENO
has part: FLOPO
has part: FYPO
has part: BCGO
has part: IAO
has part: RADLEX

Microbial Conditions Ontology
depends on: Plant Experimental Conditions Ontology
depends on: Ontology of Microbial Phenotypes
depends on: Cell Ontology
description: Microbial Conditions Ontology is an ontology...
has responsible: Citlalli Mejía-Almonte
has resource example: MCO_0000858
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/MCO_$1
0000005: 0000858
depends on: Ontology for MicroRNA Target
depends on: Uber Anatomy Ontology
depends on: Phenotype And Trait Ontology
depends on: Ontology for Biomedical Investigations
has download URL: mco.owl
depends on: Chemical Entities of Biological Interest
has prefix: mco
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/MCO_
depends on: Zebrafish Experimental Conditions Ontology
depends on: NCBI Taxonomy
keyword: obo
depends on: Cell Line Ontology
depends on: Basic Formal Ontology
depends on: Ontology of Prokaryotic Phenotypic and Metabolic Characters
keyword: ontology
is deprecated: false
depends on: NCI Thesaurus
git repository: microbial-conditions-ontology

Web of Things Thing Model
has prefix: wot.tm
has provider formatter: https://www.w3.org/2022/wot/tm#$1
has URI prefix: https://www.w3.org/2022/wot/tm#
type: Resource
has resource example: model
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: The Thing Model (TM) ontology is an RDF axiomatization of the TM concepts, one of the building blocks of the Web of Things (WoT). Besides providing an alternative to the standard JSON representation format for TM documents, the TM ontology can also be used to process contextual information on Things and for alignments with other WoT-related ontologies. [from homepage]
0000005: model

Cellular Microscopy Phenotype Ontology
has responsible: https://orcid.org/0000-0002-0643-3144
is deprecated: false
has provider formatter: http://www.ebi.ac.uk/cmpo/CMPO_$1
keyword: cellular_component
keyword: microscopy
keyword: phenotype
has download URL: cmpo.owl
git repository: CMPO
0000005: 0000435
is part of: Bioregistry
keyword: phenomics
type: Resource
description: CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.
has resource example: CMPO_0000435
has URI prefix: http://www.ebi.ac.uk/cmpo/CMPO_
keyword: cell
has local unique identifier pattern: ^\d{7}$
keyword: bioimaging
has prefix: cmpo
keyword: imaging
keyword: cell biology
keyword: ontology

KIM German School Types
has URI prefix: https://w3id.org/kim/schularten/
description: This SKOS vocabulary describes types of primary and secondary schools in Germany, such as Grundschule, Gymnasium, and Realschule. This does not include post-secondary education such as universities or hochschulen.
keyword: primary school type
type: Resource
has resource example: s02
keyword: seconary school type
git repository: schularten
keyword: school type
is deprecated: false
0000005: s02
is part of: Bioregistry
has provider formatter: https://w3id.org/kim/schularten/$1
contributor: Charles Tapley Hoyt
has prefix: kim.schularten

DragonDB Locus
is deprecated: true
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.
has local unique identifier pattern: ^\w+$
has URI prefix: https://bioregistry.io/dragondb.locus:
has prefix: dragondb.locus
has provider formatter: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
is part of: Bioregistry
0000005: DEF
has resource example: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
type: Resource

FuncBase Mouse
type: Resource
has prefix: funcbase.mouse
has provider formatter: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1
description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.
is deprecated: false
has URI prefix: http://func.mshri.on.ca/mouse/genes/list_functional_scores/
has resource example: http://func.mshri.on.ca/mouse/genes/list_functional_scores/1351341
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
0000005: 1351341

KEGG gene
has URI prefix: http://www.kegg.jp/entry/
is part of: Bioregistry
keyword: dna
has resource example: bsu:BSU01340
keyword: protein
is part of: Kyoto Encyclopedia of Genes and Genomes
0000005: bsu:BSU01340
description: KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.
has responsible: Minoru Kanehisa
type: Resource
keyword: gene
has prefix: kegg.genes
has provider formatter: http://www.kegg.jp/entry/$1
has local unique identifier pattern: ^\w+:[\w\d\.-]*$
is deprecated: false

PaxDb Organism
description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.
has URI prefix: http://pax-db.org/#!species/
has prefix: paxdb.organism
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
0000005: 9606
has provider formatter: http://pax-db.org/#!species/$1
has resource example: !species/9606

Castor Bean Ontology
has local unique identifier pattern: ^\d{7}$
description: The Castor Bean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data.
keyword: life science
has URI prefix: https://cropontology.org/rdf/CO_347:
keyword: food
has prefix: co_347
keyword: ontology
is deprecated: false
keyword: plant phenotypes and traits
has provider formatter: https://cropontology.org/rdf/CO_347:$1
keyword: phenotype
keyword: botany
keyword: agriculture
has responsible: Elizabeth Arnaud
is part of: Bioregistry
0000005: 0000108
has download URL: CO 347.owl
type: Resource
git repository: Crop-Ontology
has resource example: CO 347:0000108

InterLex
description: InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings.
has prefix: interlex
has responsible: Maryann Elizabeth Martone
keyword: anatomy
has resource example: ilx_0101963
has URI prefix: https://scicrunch.org/scicrunch/interlex/view/ilx_
has local unique identifier pattern: ^[0-9]+$
0000005: 0101963
keyword: imaging
keyword: neurobiology
is deprecated: false
has provider formatter: https://scicrunch.org/scicrunch/interlex/view/ilx_$1
keyword: brain
is part of: Bioregistry
type: Resource
has alternative prefix: ILX
keyword: biomedical science

GeneAnnot: Microarray Gene Annotation
has prefix: genecards.geneannot
is deprecated: false
keyword: gene expression
is part of: Bioregistry
type: Resource
0000005: GSTA1
description: GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match.

AntiFam
is part of: Bioregistry
type: Resource
0000005: ANF00001
has resource example: ANF00001
has provider formatter: https://www.ebi.ac.uk/interpro/entry/antifam/$1
has responsible: Alex Bateman
has reviewer: Charles Tapley Hoyt
has prefix: antifam
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has local unique identifier pattern: ^ANF\d{5}$
description: AntiFam is a database of spurious protein families that have been removed from Pfam due to incorrect hidden Markov model prediction.
has URI prefix: https://www.ebi.ac.uk/interpro/entry/antifam/

Ontology of Biological Attributes
git repository: bio-attribute-ontology
has provider formatter: http://purl.obolibrary.org/obo/OBA_$1
has download URL: oba.owl
keyword: biology
has prefix: oba
has responsible: https://orcid.org/0000-0002-6601-2165
keyword: obo
has local unique identifier pattern: ^(VT)?\d{7}$
description: A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.
keyword: ontology
is deprecated: false
is part of: Bioregistry
appears in: FuTRES Ontology of Vertebrate Traits
0000005: 0000001
type: Resource
has resource example: OBA_0000001
has URI prefix: http://purl.obolibrary.org/obo/OBA_

NIF Standard Ontology: Qualities
contributor: Tom Gillespie
type: Resource
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_qual_
has prefix: nlx.qual
keyword: dispositions
is deprecated: false
git repository: NIF-Ontology
0000005: 100810
has responsible: Tom Gillespie
has resource example: nlx qual 100810
has local unique identifier pattern: ^\d+$
has alternative prefix: NLXQUAL
description: NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO).
is part of: Bioregistry
keyword: qualities
has reviewer: Charles Tapley Hoyt
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1

Ctenophore Ontology
has prefix: cteno
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/CTENO_$1
depends on: Uber Anatomy Ontology
has resource example: CTENO_0000047
has local unique identifier pattern: ^\d{7}$
git repository: ctenophore-ontology
type: Resource
keyword: anatomy
description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
keyword: obo
keyword: ontology
0000005: 0000047
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
has URI prefix: http://purl.obolibrary.org/obo/CTENO_
keyword: developmental biology
has download URL: cteno.owl
depends on: Relation Ontology

Mathematical modeling ontology
has resource example: http://bioportal.bioontology.org/ontologies/MAMO/
has download URL: mamo.owl
has local unique identifier pattern: ^\d{7}$
type: Resource
has responsible: Nicolas Le Novere
has provider formatter: http://bioportal.bioontology.org/ontologies/MAMO/
git repository: mamo-ontology
keyword: systems biology
description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.
0000005: 0000026
is deprecated: true
has prefix: mamo
keyword: obo
keyword: ontology
keyword: computational biology
has URI prefix: http://bioportal.bioontology.org/ontologies/MAMO/
keyword: mathematics
is part of: Bioregistry

TIB Terminology Service
has part: iao
has part: mdv
has part: fibo
has part: obi
has part: meth
has part: ontorxn
has part: cito
has part: saref
has part: cgo
has part: mathmoddb
has part: gc
has part: bont
has part: ofm
has part: sweet
has part: schema
has part: dwcdoe
has part: ets
has part: cidoc
has part: listdb
has part: abcd
has part: chmo
has part: ccrel
has part: s4lift
has part: premis3
has part: ontokin
has part: dsw
has part: wlmo
has part: emdat
has part: sto
has part: dcterms
has part: mv
has part: destf
has part: cao
has part: iirdsmch
has part: mod
has part: dogont
has part: fto
has part: dices
has part: brick
has part: gta
has part: modsci
has part: ftonto
has part: ifc
has part: raum
has part: nmrcv
has part: s4ener
has part: tfsco
has part: ppo
has part: uat
has part: sms
has part: duo
has part: sbo
has part: dot
has part: gemet
has part: hfs
has part: ssn
has part: format
has part: fmi
has part: sosa
has part: stw
has part: m4i
has part: gpo
has part: credit
has part: dcat3
has part: energymarketroles
has part: cob
has part: voc4cat
has part: cco
has part: ontocompchem
has part: efo
has part: tso
has part: agro
has part: mat
has part: openadr
has part: hcrt
has part: ppeo
has part: cto
has part: skosxl
has part: battinfo

Core organization ontology
0000005: ChangeEvent
has provider formatter: http://www.w3.org/ns/org#$1
description: Vocabulary for describing organizational structures, specializable to a broad variety of types of organization.
has resource example: ChangeEvent
has prefix: org
keyword: digital planning and construction
keyword: economics
is deprecated: false
is part of: Bioregistry
keyword: fid baudigital
keyword: w3c rec
keyword: social sciences
has URI prefix: http://www.w3.org/ns/org#
type: Resource

A Systematic Annotation Package for Community Analysis of Genomes
0000005: ABE-0009634
has resource example: http://asap.ahabs.wisc.edu/asap/feature_info.php
keyword: gene expression
is part of: Bioregistry
type: Resource
keyword: comparative genomics
has provider formatter: http://asap.ahabs.wisc.edu/asap/feature_info.php
keyword: life science
is deprecated: true
has prefix: asap
keyword: developmental biology
keyword: genome
has responsible: Jeremy D. Glasner
has local unique identifier pattern: ^[A-Za-z0-9-]+$
has URI prefix: http://asap.ahabs.wisc.edu/asap/feature_info.php
description: ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources.

TogoID
has part: Pmc
has part: Mondo
has part: Pfam
has part: Mirbase
has part: Ncbigene
has part: Taxonomy
has part: Cog
has part: Lrg
has part: Pathbank
has part: PubchemCompound
type: Registry
has part: Prosite
has part: Hgnc
has part: Atc
has part: Lipidmaps
0000005: AffyProbeset
has part: ReactomePathway
has part: Ec
has part: OmaProtein
has part: Cellosaurus
has part: Uniprot
has part: PdbCcd
has part: Sgd
has part: Doid
has part: Clinvar
has part: Rhea
has part: Uberon
has part: Glytoucan
has part: Biosample
has part: InchiKey
has part: PubchemSubstance
has part: Medgen
has part: Intact
has part: HgncSymbol
has part: AffyProbeset
has part: Dbsnp
has part: Vgnc
has part: Smart
has part: ChemblTarget
has part: Pdb
has part: IupharLigand
has part: ChemblCompound
has part: Homologene
has part: UniprotProteome
description: TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)
has part: Interpro
has responsible: https://orcid.org/0000-0003-2391-0384
has part: Chebi
has part: Mp
has part: Ccds
has part: Go
has part: Mesh
has part: Pubmed
has part: Hmdb
has part: Swisslipids
has part: Rgd
has part: Bioproject
has part: Drugbank
has part: Nando
has part: Wikipathways
has part: Meddra
has provider formatter: https://togoid.dbcls.jp/#$1
has part: Togovar
has part: Insdc
has part: UniprotMnemonic

CORDIS Article
0000005: 436605
is deprecated: false
has resource example: https://cordis.europa.eu/article/id/436605
has provider formatter: https://cordis.europa.eu/article/id/$1
description: The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: cordis.article
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: https://cordis.europa.eu/article/id/

Biological Imaging Methods Ontology
has download URL: fbbi.owl
0000005: 00000268
has responsible: https://orcid.org/0000-0002-8841-5870
keyword: life science
is deprecated: true
has URI prefix: http://purl.obolibrary.org/obo/FBbi_
keyword: obo
has resource example: FBbi_00000268
keyword: ontology
keyword: imaging
keyword: experiment
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: assay
has prefix: fbbi
has alternative prefix: FBbi
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/FBbi_$1
git repository: Biological Imaging Methods Ontology
keyword: biomedical science
description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.

Unipathway
has provider formatter: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa
depends on: Relation Ontology
git repository: unipathway
keyword: pathway
has alternative prefix: unipathway
0000005: UCR00513
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-1216-2969
has resource example: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa
description: A manually curated resource for the representation and annotation of metabolic pathways
type: Resource
has download URL: upa.owl
is deprecated: true
has URI prefix: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa
has alternative prefix: UPa
has alternative prefix: unipathway.pathway
has prefix: upa
has local unique identifier pattern: ^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$
keyword: obo
keyword: ontology

GeoNames Ontology
0000005: parentFeature
is deprecated: false
is part of: Bioregistry
description: An ontology used to enable annotating geospatial semantic information to entities in GeoNames
has prefix: geonames.ontology
type: Resource

Linked Open Vocabularies
has part: emmo
has part: qb
has part: doco
has part: sh
has part: dogont
has part: c4o
has part: gufo
has part: geo
has part: skosxl
has part: ssn
has part: frbr
has part: time
has part: xhv
has part: s4bldg
has part: skos
has part: odrl
has part: sdmx
has part: vcard
has part: fabio
has part: pwo
has part: exif
has part: cert
has part: sulo
has part: sdo
has part: premis
has part: sio
has part: grddl
description: A vocabulary in LOV gathers definitions of a set of classes and properties (together simply called terms of the vocabulary), useful to describe specific types of things, or things in a given domain or industry, or things at large but for a specific usage. Terms of vocabularies also provide the links in linked data, in the above case between a Person and a City. The definitions of terms provided by the vocabularies bring clear semantics to descriptions and links, thanks to the formal language they use (some dialect of RDF such as RDFS or OWL). In short, vocabularies provide the semantic glue enabling Data to become meaningful Data. [from https://lov.linkeddata.es/dataset/lov/about]
has part: oa
has part: csvw
has part: frapo
type: Registry
has part: doap
has part: xsd
has part: lvont
has part: biotop
has provider formatter: https://lov.linkeddata.es/dataset/lov/vocabs/$1
has part: oslc
has part: vivo
has part: eli
has part: cnt
0000005: m4i
has part: earl
has part: obo
has part: pav
has part: rdfs
has part: faldo
has part: uniprot
has part: sd
has part: og
has part: adms
has part: rdfa
has part: s4agri
has part: hydra
has part: s4inma
has part: xkos
has part: gr
has part: seo
has part: s4ehaw
has part: s4watr
has part: void
has part: saref
has part: cc
has part: s4syst
has part: swrl
has part: s4ener
has part: modsci
has part: frbrer
has part: edm
has part: sioc
has part: fiesta-iot
has part: s4city
has part: vs
has part: pr
has part: wot
has part: log
has responsible: https://orcid.org/0000-0003-0591-6109
has part: dcam
has part: s4wear

Trade Agreement Ontology
0000005: CustomsUnion
type: Resource
keyword: coypu
has resource example: CustomsUnion
description: An ontology for modeling trade agreements
is deprecated: false
keyword: economics
is part of: Bioregistry
has URI prefix: https://schema.coypu.org/ta#
has provider formatter: https://schema.coypu.org/ta#$1
has prefix: coypu.ta

Zebrafish anatomy and development ontology
type: Resource
keyword: structure
0000005: 0005926
keyword: zebrafish
keyword: anatomy
keyword: morphology
keyword: life science
keyword: obo
keyword: ontology
description: ZFA description.
keyword: life cycle stage
has download URL: zfa.owl
is deprecated: false
git repository: zebrafish-anatomical-ontology
keyword: developmental biology
has resource example: ZFA_0005926
has responsible: https://orcid.org/0000-0002-2244-7917
keyword: life cycle
appears in: Zebrafish Phenotype Ontology
has prefix: zfa
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
has provider formatter: http://purl.obolibrary.org/obo/ZFA_$1
has URI prefix: http://purl.obolibrary.org/obo/ZFA_
has alternative prefix: ZFA_RETIRED

System Science of Biological Dynamics dataset
has provider formatter: https://ssbd.riken.jp/database/dataset/$1
has resource example: https://ssbd.riken.jp/database/dataset/1
has URI prefix: https://ssbd.riken.jp/database/dataset/
is deprecated: false
keyword: molecular dynamics
has responsible: https://orcid.org/0000-0002-8255-1724
keyword: cell biology
0000005: 1
description: Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations.
has prefix: ssbd.dataset
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
keyword: developmental biology
contributor: Charles Tapley Hoyt
type: Resource

Ontology for Nutritional Studies
depends on: Chemical Entities of Biological Interest
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/ONS_$1
0000005: 0000060
appears in: Ontology for Nutritional Epidemiology
keyword: biomedical science
depends on: NCBI Taxonomy
git repository: Ontology-for-Nutritional-Studies
has download URL: ons.owl
depends on: Basic Formal Ontology
has resource example: ONS_0000060
keyword: nutritional science
depends on: The Food Ontology
keyword: obo
has URI prefix: http://purl.obolibrary.org/obo/ONS_
depends on: Environment Ontology
keyword: ontology
depends on: Relation Ontology
is deprecated: false
has prefix: ons
depends on: Ontology for Biomedical Investigations
depends on: Uber Anatomy Ontology
has responsible: Francesco Vitali
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
description: An ontology for description of concepts in the nutritional studies domain.

REPRODUCE-ME Ontology
has responsible: Sheeba Samuel
keyword: nfdi4chem
has URI prefix: https://w3id.org/reproduceme#
0000005: MicrobeamManipulation
is part of: Bioregistry
type: Resource
description: The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility.
keyword: ontology
has resource example: MicrobeamManipulation
has prefix: reproduceme
is deprecated: false
has download URL: reproduce-me.owl
has provider formatter: https://w3id.org/reproduceme#$1

SWEET Ontology Representation Time
has URI prefix: http://sweetontology.net/reprTime/
has provider formatter: http://sweetontology.net/reprTime/$1
0000005: Duration
has alternative prefix: sorept
is deprecated: false
has prefix: sweet.rept
keyword: representation time
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Time
has resource example: Duration
is part of: Bioregistry
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt

NASA Open Science Data Repository Experiment
has resource example: OS-27
is deprecated: false
has reviewer: https://orcid.org/0000-0001-9439-5346
description: Identifiers for space-related data from experiments that investigate biological and health responses of terrestrial life to spaceflight
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-8542-2389
type: Resource
has local unique identifier pattern: ^OS-\d+$
0000005: OS-27
has prefix: nasaosdr.experiment
contributor: Mufaddal Naguthanawala
has URI prefix: https://osdr.nasa.gov/bio/repo/data/experiments/
has provider formatter: https://osdr.nasa.gov/bio/repo/data/experiments/$1

SWEET Ontology Phenomena Mixing
type: Resource
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: phenomena
0000005: Aeration
has resource example: Aeration
keyword: mixing
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Mixing
is deprecated: false
has URI prefix: http://sweetontology.net/phenMixing/
has alternative prefix: sophm
has provider formatter: http://sweetontology.net/phenMixing/$1
has prefix: sweet.phm
is part of: Bioregistry

Biolink Model Registry
has part: XPO
has part: EDAM-FORMAT
description: A modeling paradigm-specific registry of prefixes and their URL expansions
has part: gpi
has part: WIKIDATA PROPERTY
has part: medgen
has part: GOREL
has part: GTOPDB
has part: isbn
has part: biolink
has part: doi
has part: CID
has part: WBbt
has part: KEGG.PATHWAY
has part: fabio
has part: EFO
has part: AGRKB
has part: NLMID
has part: MI
has part: dcid
has part: MSigDB
has part: ResearchID
has responsible: https://orcid.org/0000-0002-3583-7340
has part: FMA
has part: MESH
has part: MAXO
has part: PHARMGKB.VARIANT
has part: RO
has part: PathWhiz
has part: bioschemas
has part: VMC
has part: NCBIGene
has part: WIKIDATA
has part: PomBase
has part: OBAN
has part: EDAM-OPERATION
has part: Xenbase
has part: METPO
has part: CAID
has part: ICD9
has part: ncats.bioplanet
has part: OMIM.PS
has part: LOINC
has part: EDAM-TOPIC
has part: HsapDv
has part: ScopusID
has part: prov
has part: metacyc.reaction
has part: schema
has part: COG
has part: interpro
has part: PHARMGKB.DRUG
has part: orphanet
has part: UniProtKB
has part: foodb.compound
has part: FYECO
has part: GSID
has part: INO
has part: PMC
has part: SPDI
has part: pav
has part: PHARMGKB.PATHWAYS
has part: ncats.drug
has part: WBVocab
has part: SIO
has part: VANDF
has part: dct
has part: wgs
has part: ExO
has part: isni
has part: NDDF
has part: issn
has part: foodb.food
has part: HCPCS
has part: GTEx
has part: mirbase
has part: CTD.DISEASE
has part: CTD.GENE
has part: icd11.foundation

GPCR Natural Variants database
type: Resource
has prefix: gpcrnava
has URI prefix: http://nava.liacs.nl/cgi-bin/nava.py
description: The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans.
keyword: pathway
is deprecated: false
keyword: protein
0000005: 1150
has resource example: http://nava.liacs.nl/cgi-bin/nava.py
is part of: Bioregistry
has provider formatter: http://nava.liacs.nl/cgi-bin/nava.py

Human Disease Ontology
appears in: Sickle Cell Disease Ontology
keyword: ontology
keyword: human
appears in: Cell Line Ontology
keyword: infection process
is deprecated: false
keyword: disease
has local unique identifier pattern: ^\d+$
keyword: disease course
0000005: 0110974
has alternative prefix: do
has responsible: https://orcid.org/0000-0001-8910-9851
is part of: Bioregistry
keyword: genetic disorder
has download URL: doid.owl
type: Resource
description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.
has resource example: DOID_0110974
keyword: biomedical science
git repository: HumanDiseaseOntology
has provider formatter: http://purl.obolibrary.org/obo/DOID_$1
has URI prefix: http://purl.obolibrary.org/obo/DOID_
keyword: disease phenotype
keyword: mental health
keyword: life science
keyword: classification
has prefix: doid
keyword: obo

National Organization for Rare Disorders
has URI prefix: https://rarediseases.org/
has provider formatter: https://rarediseases.org/
appears in: Mondo Disease Ontology
has prefix: nord
has local unique identifier pattern: ^\d+$
is deprecated: false
has resource example: https://rarediseases.org/
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: A website containing information about rare diseases, powered by Wordpress.
0000005: 1693

PhageDive
has responsible: Johannes Wittmann
has provider formatter: https://phagedive.dsmz.de/strain/$1
contributor: Mufaddal Naguthanawala
has prefix: phagedive
is deprecated: false
has URI prefix: https://phagedive.dsmz.de/strain/
description: PhageDive is a database for bacteriophages and archaeal viruses. It provides information regarding taxonomy, host strain, phage morphology, life cycle, origin and genomic data.
has reviewer: https://orcid.org/0000-0001-9439-5346
0000005: 3
has resource example: https://phagedive.dsmz.de/strain/3
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource

NIST Chemistry WebBook
is deprecated: false
description: The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species.
has alternative prefix: NIST Chemistry WebBook
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has prefix: nist
has alternative prefix: NIST

Confidence Information Ontology
keyword: ontology
has responsible: Frédéric Bastian
has provider formatter: http://purl.obolibrary.org/obo/CIO_$1
is deprecated: false
0000005: 0000040
is part of: Bioregistry
has download URL: cio.owl
has resource example: CIO_0000040
has prefix: cio
has local unique identifier pattern: ^\d{7}$
git repository: confidence-information-ontology
type: Resource
description: An ontology to capture confidence information about annotations.
keyword: annotation
keyword: biology
has URI prefix: http://purl.obolibrary.org/obo/CIO_
keyword: obo

DisProt
keyword: protein
has URI prefix: https://disprot.org/
has local unique identifier pattern: ^DP\d{5}$
is part of: Bioregistry
has provider formatter: https://disprot.org/$1
type: Resource
keyword: biomedical science
keyword: structure
keyword: structural biology
keyword: biology
git repository: disprot.github.io
description: DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature.
has responsible: Silvio Tosatto
has resource example: DP00003
has prefix: disprot
0000005: DP00003
has part: DisProt region
is deprecated: false

COVID-19 Surveillance Ontology
0000005: SFB_COVID19_MW286762
description: Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease.
has local unique identifier pattern: ^\w+_COVID19_[-\w]+$
has provider formatter: https://covid19.sfb.uit.no/api/records/$1
has prefix: covid19
has download URL: covid19.owl
has URI prefix: https://covid19.sfb.uit.no/api/records/
keyword: ontology
is deprecated: false
is part of: Bioregistry
type: Resource
has responsible: https://orcid.org/0000-0002-6772-2775
has resource example: SFB COVID19 MW286762

Enzo Life Sciences
type: Resource
keyword: life sciences
has provider formatter: https://www.enzolifesciences.com/$1
has prefix: enzo
has alternative prefix: Enzo Life Sciences
has resource example: ALX-210-175
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: antibodies
description: Enzo Life Sciences is an antibody vendor.
keyword: vendor
has URI prefix: https://www.enzolifesciences.com/
0000005: ALX-210-175

SPARC DRS
has provider formatter: https://services.scicrunch.io/sparc/drs/v1/package/$1
description: The SPARC Data Repository Service (DRS) is an implementation of the Global Alliance for Genomics and Health (GA4GH) DRS specification that provides a standardized API that enables researchers and other data consumers to access and retrieve data objects from various data repositories in a consistent and cloud-agnostic way. This implementation provides information for data objects in the SPARC repository (sparc.science).
has URI prefix: https://services.scicrunch.io/sparc/drs/v1/package/
is deprecated: false
has prefix: sparcdrs
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^(?:[a-zA-Z]+\/)?[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$

ChEBI Data Sources
has part: DrugBank
has part: UM-BBD compound
has part: Protein covalent bond
has part: The Bioinorganic Motif Database
has part: Web Elements
has part: Metabolic Encyclopedia of metabolic and other pathways
has part: KEGG Drug
has part: Chemical Component Dictionary
has part: KNApSAcK
has part: C. elegans Small Molecule Identifier Database
has part: PDB Structure
has part: Alan Wood's Pesticides
has part: European Food Information Resource Network
has part: KEGG Compound
has part: Human Metabolome Database
type: Collection
has part: Yeast Metabolome Database
has part: LIPID MAPS
has part: E. coli Metabolite Database
has part: Chemical Entities of Biological Interest
has part: KEGG Glycan
creator: Charles Tapley Hoyt
description: The data sources used in xrefs in the ChEBI ontology. More information in the "Data Sources" section of [this document](https://docs.google.com/document/d/13_FqP_8qkDdw5RFv5qMYo7xRyfY4xUiuVtLn845A6Io/edit#heading=h.dkfn7xf53tpx).
has part: molbase.sheffield
has part: ChemIDplus
has part: LINCS Small Molecule
has part: Google Patents

Banco de Celulas do Rio de Janeiro
is deprecated: false
description: Cell line collections (Providers)
has prefix: bcrj
has resource example: https://bcrj.org.br/pesquisa/
has local unique identifier pattern: ^\d{4}$
is part of: Bioregistry
type: Resource
0000005: 0278
has URI prefix: https://bcrj.org.br/pesquisa/
has provider formatter: https://bcrj.org.br/pesquisa/

Nematode Expression Pattern DataBase
has prefix: nextdb
has local unique identifier pattern: ^[A-Za-z0-9]+$
keyword: gene expression
type: Resource
0000005: 6b1
description: NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones.
has URI prefix: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php
keyword: life science
has provider formatter: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php
keyword: genome
is deprecated: false
keyword: dna
is part of: Bioregistry
has resource example: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php

SWEET Ontology Property Space Direction
has alternative prefix: sopropsdir
0000005: Angle
is part of: Bioregistry
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
type: Resource
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Direction
has URI prefix: http://sweetontology.net/propSpaceDirection/
has resource example: Angle
has provider formatter: http://sweetontology.net/propSpaceDirection/$1
keyword: space direction
has prefix: sweet.propsdir
is deprecated: false

NEPOMUK Annotation Ontology Specification
has resource example: created
description: The annotation ontology provides vocabulary that enables users to attach custom descriptions, identifiers, tags and ratings to resources on their desktop. Via other properties, the user is also able to make generic relationships between related resources explicit. Some relationships between resources are too general to be included at the domain ontology level. Instead, these properties are also defined in the annotation ontology. Given the high-level status of this ontology, these propreties can be used to link any related resources on the user's desktop, as well as provide custom human-readable textual annotations. (from homepage)
has URI prefix: http://www.semanticdesktop.org/ontologies/2007/08/15/nao#
is deprecated: false
has prefix: nepomuk.nao
has provider formatter: http://www.semanticdesktop.org/ontologies/2007/08/15/nao#$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: created
type: Resource

Protein Model Database
is deprecated: false
0000005: PM0012345
has URI prefix: https://bioinformatics.cineca.it/PMDB/user//search.php
has resource example: https://bioinformatics.cineca.it/PMDB/user//search.php
is part of: Bioregistry
keyword: protein
has local unique identifier pattern: ^PM\d{7}$
description: The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.
type: Resource
keyword: structure
keyword: structural biology
has provider formatter: https://bioinformatics.cineca.it/PMDB/user//search.php
has prefix: pmdb

RNAloops
is part of: Bioregistry
type: Resource
has provider formatter: https://rnaloops.cs.put.poznan.pl/search/details/$1
has reviewer: Charles Tapley Hoyt
has prefix: rnaloops
has responsible: https://orcid.org/0000-0002-5320-2023
description: Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank.
has resource example: https://rnaloops.cs.put.poznan.pl/search/details/91792
keyword: rna
is deprecated: false
0000005: 91792
contributor: https://orcid.org/0000-0001-9439-5346
has local unique identifier pattern: ^\d+$
keyword: structural bioinformatcs
has URI prefix: https://rnaloops.cs.put.poznan.pl/search/details/

TAIR Gene
has resource example: http://arabidopsis.org/servlets/TairObject
is deprecated: false
is part of: Bioregistry
has URI prefix: http://arabidopsis.org/servlets/TairObject
description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus.
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: gene
0000005: 2200934
has provider formatter: http://arabidopsis.org/servlets/TairObject
has prefix: tair.gene
has responsible: 0000-0003-3871-858X

Homosaurus
has prefix: homosaurus
0000005: queerNewspapers
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: An international LGBTQ+ linked data vocabulary
git repository: homosaurus site
appears in: Gender, Sex, and Sexual Orientation Ontology
type: Resource
has responsible: Keahi Kaʻiwalani Adolpho
is deprecated: false
has provider formatter: http://homosaurus.org/terms/$1
has URI prefix: http://homosaurus.org/terms/
has resource example: queerNewspapers

OBO Foundry
has part: nomen
has part: xao
has part: dc cl
has part: bfo
has part: emapa
has part: zfa
has part: hao
has part: hancestro
has part: flopo
has part: vsao
has part: zp
has part: pao
has part: ncbitaxon
has part: po
has part: ontoneo
has part: exo
has part: dinto
has part: ro
has part: fobi
has part: bootstrep
has part: cdao
has part: hom
has part: bila
has part: fypo
has part: bco
has part: zeco
has part: pw
has part: mfomd
has part: fbbi
has part: iao
has part: omo
has part: tgma
has part: swo
has part: mco
has part: zfs
has part: ohpi
has part: zea
has part: clyh
has part: cob
has part: labo
has part: fbsp
has part: gsso
has part: mpio
has part: geo
has part: resid
has part: wbls
has part: oba
has part: bspo
has part: oostt
has part: ev
has part: ico
has part: mod
has part: fma
has part: mfoem
has part: mf
has part: mao
has part: pdro
has part: rnao
has part: occo
has part: ecocore
has part: uo
has part: so
has responsible: https://orcid.org/0000-0002-6601-2165
has part: ido
has part: omrse
has part: ohmi
has part: eco
has part: ontoavida
has part: ero
has part: afpo
has part: ehdaa
has part: mop
has part: vo
has part: upheno
has part: ecto
has part: ohd
has part: vario
has part: ppo
has part: foodon
has part: idomal

FuncBase Yeast
0000005: 2701
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has provider formatter: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1
type: Resource
has prefix: funcbase.yeast
has resource example: http://func.mshri.on.ca/yeast/genes/list_functional_scores/2701
has URI prefix: http://func.mshri.on.ca/yeast/genes/list_functional_scores/
is deprecated: false
description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.

The ALlele FREquency Database
keyword: genome
is part of: Bioregistry
0000005: LO362836C
description: ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases.
has resource example: https://alfred.med.yale.edu/alfred/recordinfo.asp
has URI prefix: https://alfred.med.yale.edu/alfred/recordinfo.asp
type: Resource
is deprecated: true
has reviewer: Charles Tapley Hoyt
contributor: https://orcid.org/0000-0002-1216-4761
has prefix: alfred
keyword: classification
has provider formatter: https://alfred.med.yale.edu/alfred/recordinfo.asp

NCBI Data Repository Service
type: Resource
has local unique identifier pattern: ^[0-9a-fA-F]{32}$
has prefix: ncbidrs
has provider formatter: https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/$1
description: This is the namespace for the archive of sequence and other files provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in the sequencing data model managed under the insdc.sra namespace.
is deprecated: false
has URI prefix: https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/
is part of: Bioregistry

Toxic Process Ontology
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/TXPO_
has provider formatter: http://purl.obolibrary.org/obo/TXPO_$1
is deprecated: false
git repository: TXPO
description: Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. The TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms. In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp
has responsible: Yuki Yamagata
is part of: Bioregistry
type: Resource
has download URL: txpo.owl
has local unique identifier pattern: ^\d{7}$
has resource example: TXPO_0002066
0000005: 0002066
keyword: obo
has prefix: txpo

Yeast Intron Database v4.3
has provider formatter: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl
has local unique identifier pattern: ^[A-Z0-9]+$
is deprecated: false
has resource example: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl
has prefix: yeastintron
is part of: Bioregistry
has URI prefix: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl
description: The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].
type: Resource
0000005: SNR17A

SWEET Ontology Property Mass
has URI prefix: http://sweetontology.net/propMass/
is part of: Bioregistry
has prefix: sweet.propm
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sopropm
has provider formatter: http://sweetontology.net/propMass/$1
type: Resource
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Mass
0000005: BulkDensity
keyword: mass
is deprecated: false
has resource example: BulkDensity

Platynereis stage ontology
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/PD_ST_$1
keyword: obo
has prefix: pd_st
is deprecated: true
keyword: ontology
has responsible: Thorsten Henrich
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/PD_ST_

Interlinking Ontology for Biological Concepts
has URI prefix: http://purl.jp/bio/4/id/
description: Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: "Interlinking Ontology for Biological Concepts © National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International".
has resource example: http://purl.jp/bio/4/id/200906038218908385
keyword: ontology
has prefix: iobc
is deprecated: false
is part of: Bioregistry
git repository: IOBC
0000005: 200906038218908385
type: Resource
has provider formatter: http://purl.jp/bio/4/id/$1
has download URL: iobc.owl
has responsible: Tatsuya Kushida

SHACL Node Expression
has prefix: shnex
has URI prefix: http://www.w3.org/ns/shacl-node-expr#
has provider formatter: http://www.w3.org/ns/shacl-node-expr#$1
0000005: instancesOf
type: Resource
contributor: Charles Tapley Hoyt
git repository: data-shapes
description: A vocabulary used in tandem with SHACL for representing node shapes
has resource example: instancesOf
is deprecated: false
is part of: Bioregistry

ChEMBL tissue
description: Tissues used to annotate cells and cell lines, cross-referenced to EFO, BTO, UBERON, and CALOHA
type: Resource
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^CHEMBL\d+$
has responsible: David Mendez Lopez
has prefix: chembl.tissue
0000005: CHEMBL3559721
is part of: ChEMBL
is deprecated: false
is part of: Bioregistry

Virus Pathogen Resource
has local unique identifier pattern: ^[A-Za-z 0-9]+$
keyword: proteomics
has prefix: vipr
0000005: BeAn 70563
is part of: Bioregistry
has URI prefix: https://bioregistry.io/vipr:
keyword: epidemiology
type: Resource
keyword: biomedical science
has provider formatter: http://www.viprbrc.org/brc/viprStrainDetails.do
keyword: life science
git repository: VirusBRC
has responsible: Richard Scheuermann
keyword: immunology
is deprecated: false
description: The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.
keyword: genomics
keyword: virology

Mouse Tumor Biology Database
has provider formatter: http://tumor.informatics.jax.org/mtbwi/strainDetails.do
keyword: dna
is part of: Bioregistry
has resource example: http://tumor.informatics.jax.org/mtbwi/strainDetails.do
has URI prefix: http://tumor.informatics.jax.org/mtbwi/strainDetails.do
keyword: gene expression
description: The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors.
type: Resource
0000005: 1374
has reviewer: Charles Tapley Hoyt
has prefix: mtbd
is deprecated: false

Cellosaurus Registry
has part: Cell Biolabs
has part: IGSR
has part: VBO
has part: MMRRC
has part: Cell Model Passport
has part: ColonAtlas
has part: KYinno
has part: Ximbio
has part: Abcam
has part: Cellosaurus
has part: Millipore
has part: CLO
has part: NCIt
has part: DrugBank
has part: IGRhCellID
has part: WiCell
has part: RCB
has part: CCRID
has part: Kerafast
has part: dbSNP
has part: VGNC
has part: PRIDE
has part: Horizon Discovery
has part: ABCD
has part: ICLDB
has part: CLDB
has part: NRFC
has part: SKIP
has part: CBA
has part: HIVReagentProgram
has part: MeSH
has part: dbGAP
has part: FlyBase Cell line
has responsible: https://orcid.org/0000-0003-2826-6444
has part: dbMHC
has part: HLA
has part: LiGeA
has part: TNGB
0000005: 4DN
has part: CGNC
has part: Sigma-Aldrich
has part: HipSci
has part: LIMORE
has part: ENCODE
has part: KCLB
has part: UniProtKB
has part: TKG
has part: BioSamples
has part: MGI
has part: HGNC
has part: Coriell
has part: ChEMBL-Cells
has part: IHW
has part: CL
has part: ArrayExpress
has part: ABM
has part: DGRC
has part: PubMed
has part: FCS-free
has part: ChEMBL-Targets
has part: 4DN
has part: GEO
has part: CelloPub
has part: SLKBase
has part: DSMZCellDive
has part: UBERON
has part: MetaboLights
has part: BEI Resources
has part: BCGO
has part: Imanis
has part: Lonza
has part: DepMap
has part: ESTDAB
has part: PubChem
has part: AddexBio
has part: Progenetix
has part: LINCS LDP
has part: NIHhESC
has part: JCRB

Ontology for Biomarkers of Clinical Interest
has prefix: obci
0000005: 000000001
keyword: ontology
has responsible: https://orcid.org/0000-0001-5809-9523
has URI prefix: http://purl.obolibrary.org/obo/OBCI_
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has resource example: OBCI_000000001
description: The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects.
has reviewer: https://orcid.org/0000-0001-9439-5346
contributor: https://orcid.org/0000-0001-5809-9523
type: Resource
has download URL: obci.owl
has provider formatter: http://purl.obolibrary.org/obo/OBCI_$1

ClinicalTrials.gov
has alternative prefix: clinicaltrial
has alternative prefix: ctgov
has local unique identifier pattern: ^NCT\d{8}$
type: Resource
has resource example: NCT00222573
has URI prefix: https://www.clinicaltrials.gov/study/
keyword: drug
has prefix: clinicaltrials
0000005: NCT00222573
description: ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries
keyword: human
keyword: ontology
has alternative prefix: NCT
is deprecated: false
keyword: disease
is part of: Bioregistry
has download URL: clinicaltrials.owl.gz
has provider formatter: https://www.clinicaltrials.gov/study/$1

Multiple alignment
keyword: ontology
has resource example: MAO_0000061
0000005: 0000061
keyword: sequence
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/MAO_
has provider formatter: http://purl.obolibrary.org/obo/MAO_$1
has local unique identifier pattern: ^\d{7}$
type: Resource
description: An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment.
has prefix: mao
is deprecated: true
keyword: obo
keyword: alignment

Molecular Modeling Database
0000005: 50885
is deprecated: false
keyword: dna
keyword: small molecule
keyword: protein
description: The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.
has URI prefix: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-1707-4167
has prefix: mmdb
has provider formatter: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi
type: Resource
has local unique identifier pattern: ^\d{1,5}$
keyword: structure
keyword: interaction
has resource example: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi

OMA Protein
has provider formatter: https://omabrowser.org/oma/vps/$1
type: Resource
has local unique identifier pattern: ^[A-Z0-9]{5}\d+$
has resource example: HUMAN16963
is deprecated: false
has URI prefix: https://omabrowser.org/oma/vps/
description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.
is part of: Bioregistry
has prefix: oma.protein
0000005: HUMAN16963

Immune Epitope Database MHC Restrictions
keyword: life science
contributor: Mufaddal Naguthanawala
keyword: immunology
has prefix: iedb.mhc
is deprecated: false
is part of: Bioregistry
has resource example: https://www.iedb.org/mhc/86
has local unique identifier pattern: ^\d+$
keyword: bioinformatics
has provider formatter: https://www.iedb.org/mhc/$1
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.iedb.org/mhc/
type: Resource
0000005: 86
description: Identifiers for Major Histocompatibility Complex (MHC) restrictions of immune cells, detailing genetic factors that influence immune recognition.
has responsible: https://orcid.org/0000-0001-8957-7612

Sanger Cell Model Passports
type: Resource
has prefix: cell_model_passport
has provider formatter: https://cellmodelpassports.sanger.ac.uk/passports/$1
has resource example: SIDM01262
description: Cell line databases/resources
0000005: SIDM01262
is deprecated: false
has URI prefix: https://cellmodelpassports.sanger.ac.uk/passports/
is part of: Bioregistry

Common Anatomy Reference Ontology
type: Resource
description: The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies.
has prefix: caro
has provider formatter: http://purl.obolibrary.org/obo/CARO_$1
keyword: annotation
has URI prefix: http://purl.obolibrary.org/obo/CARO_
has responsible: https://orcid.org/0000-0001-9114-8737
has local unique identifier pattern: ^\d{7}$
has resource example: CARO_0000000
keyword: anatomy
keyword: life science
appears in: Lepidoptera Anatomy Ontology
0000005: 0000000
is deprecated: true
appears in: Plant Gall Ontology
keyword: obo
has download URL: caro.owl
keyword: ontology
appears in: Population and Community Ontology
appears in: Coleoptera Anatomy Ontology
git repository: caro
appears in: Human developmental anatomy, abstract
is part of: Bioregistry
appears in: Ontology for the Anatomy of the Insect SkeletoMuscular system

Tohoku University cell line catalog
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has provider formatter: http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html
has prefix: tkg
0000005: 0221
type: Resource
description: Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells.
is deprecated: false
has resource example: 0221.html
has URI prefix: https://bioregistry.io/tkg:

Brassica Ontology
has prefix: co_348
keyword: ontology
has responsible: Elizabeth Arnaud
is deprecated: false
keyword: plant phenotypes and traits
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: phenotype
keyword: botany
keyword: agriculture
has URI prefix: https://cropontology.org/rdf/CO_348:
type: Resource
git repository: Crop-Ontology
description: Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Brassica Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
has download URL: CO 348.owl
has provider formatter: https://cropontology.org/rdf/CO_348:$1
has resource example: CO 348:1100107
0000005: 1100107
keyword: life science

Database of Macromolecular Interactions
has resource example: 2GC4
is part of: Bioregistry
type: Resource
has provider formatter: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1
has URI prefix: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/
0000005: 2GC4
is deprecated: true
has local unique identifier pattern: ^[0-9][A-Za-z0-9]{3}$
description: DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.
has prefix: dommino

Developing Human Brain Atlas
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://purl.brain-bican.org/ontology/dhbao/DHBA_$1
has resource example: DHBA_10153
description: A controlled vocabulary to support the study of transcription in the developing human brain
type: Resource
has URI prefix: https://purl.brain-bican.org/ontology/dhbao/DHBA_
git repository: developing human brain atlas ontology
0000005: 10153
has prefix: dhba
has download URL: dhbao.owl
keyword: ontology
is deprecated: false
has local unique identifier pattern: ^\d+$

SAREF4AUTO: an extension of SAREF for the automotive domain
has resource example: AcousticSensor
description: This ontology extends the SAREF ontology for the automotive domain. This work has been developed in the context of the STF 566, which was established with the goal to create four SAREF extensions, one of them for the automotive domain.
keyword: traffic engineering
has alternative prefix: s4auto
has URI prefix: https://saref.etsi.org/saref4auto/
is deprecated: false
keyword: engineering
0000005: AcousticSensor
keyword: fid move
has prefix: saref.auto
is part of: Bioregistry
type: Resource
has provider formatter: https://saref.etsi.org/saref4auto/$1
keyword: nfdi4ing

ASTD
keyword: alternative splicing
has provider formatter: http://www.ebi.ac.uk/astd/geneview.html
is deprecated: true
description: Identifier of an object from the ASTD database.
has URI prefix: http://www.ebi.ac.uk/astd/geneview.html
0000011: Ensembl Gene
has prefix: astd
is part of: Bioregistry
keyword: transcript
type: Resource
keyword: gene
has reviewer: Charles Tapley Hoyt
0000005: ENSG00000136147
has resource example: http://www.ebi.ac.uk/astd/geneview.html

European Genome-phenome Archive Dataset
has URI prefix: https://www.ebi.ac.uk/ega/datasets/
is deprecated: false
keyword: genomics
description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.
is part of: Bioregistry
keyword: phenomics
type: Resource
has local unique identifier pattern: ^EGAD\d{11}$
keyword: clinical studies
keyword: biomedical science
has identifier space owner: 02catss52
keyword: biology
has prefix: ega.dataset
has provider formatter: https://www.ebi.ac.uk/ega/datasets/$1
has responsible: Thomas Keane
0000005: EGAD00000000001
has resource example: EGAD00000000001

GoodRelations
has URI prefix: http://purl.org/goodrelations/v1#
is deprecated: false
has prefix: gr
description: A vocabulary for e-commerce
keyword: ebusiness
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: category
has provider formatter: http://purl.org/goodrelations/v1#$1
0000005: category
type: Resource

SWEET Ontology Realm Ocean
is deprecated: false
has resource example: Abyss
has alternative prefix: soreao
has provider formatter: http://sweetontology.net/realmOcean/$1
has URI prefix: http://sweetontology.net/realmOcean/
is part of: Bioregistry
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: ocean
contributor: Charles Tapley Hoyt
keyword: realm
0000005: Abyss
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Ocean
has prefix: sweet.reao

Coleoptera Anatomy Ontology
type: Resource
0000005: 0000000
description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.
git repository: colao
depends on: Biological Spatial Ontology
depends on: Basic Formal Ontology
has download URL: colao.owl
depends on: Common Anatomy Reference Ontology
has resource example: COLAO_0000000
has provider formatter: http://purl.obolibrary.org/obo/COLAO_$1
keyword: obo
has responsible: https://orcid.org/0000-0002-0851-6883
has prefix: colao
keyword: ontology
depends on: Relation Ontology
depends on: Ontology for the Anatomy of the Insect SkeletoMuscular system
is deprecated: false
is part of: Bioregistry
depends on: Uber Anatomy Ontology
depends on: Phenotype And Trait Ontology
has URI prefix: http://purl.obolibrary.org/obo/COLAO_
has local unique identifier pattern: ^\d{7}$

Zebrafish Experimental Conditions Ontology
keyword: developmental biology
description: Ontology of Zebrafish Experimental Conditions
keyword: genomics
keyword: phenotype
keyword: disease course
is part of: Bioregistry
git repository: zebrafish-experimental-conditions-ontology
has prefix: zeco
type: Resource
appears in: Microbial Conditions Ontology
keyword: gene
has provider formatter: http://purl.obolibrary.org/obo/ZECO_$1
has local unique identifier pattern: ^\d{7}$
keyword: mutation
keyword: model organisms
has URI prefix: http://purl.obolibrary.org/obo/ZECO_
has resource example: ZECO_0000171
keyword: allele
0000005: 0000171
keyword: obo
keyword: ontology
keyword: animal physiology
keyword: genome
keyword: genetics
has download URL: zeco.owl
has responsible: Yvonne Bradford
keyword: expression data
is deprecated: false

Metabolite and Tandem Mass Spectrometry Database
0000005: 1455
is part of: Bioregistry
has local unique identifier pattern: ^\d{4}$
has provider formatter: http://metlin.scripps.edu/metabo_info.php
has URI prefix: http://metlin.scripps.edu/metabo_info.php
type: Resource
has prefix: metlin
has resource example: http://metlin.scripps.edu/metabo_info.php
is deprecated: true
description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry.

PIR Superfamily Classification System
has responsible: Cathy H. Wu
has resource example: https://pir.georgetown.edu/cgi-bin/ipcSF
is deprecated: false
description: The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.
is part of: Bioregistry
keyword: protein
0000005: PIRSF000100
has URI prefix: https://pir.georgetown.edu/cgi-bin/ipcSF
keyword: proteomics
type: Resource
has prefix: pirsf
keyword: structure
has local unique identifier pattern: ^PIRSF\d{6}$
keyword: life science
has provider formatter: https://pir.georgetown.edu/cgi-bin/ipcSF

SwissRegulon
type: Resource
has local unique identifier pattern: ^[A-Za-z0-9]+$
has provider formatter: http://swissregulon.unibas.ch/query/$1
keyword: life science
has resource example: AHR
description: A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form.
has prefix: swissregulon
has URI prefix: http://swissregulon.unibas.ch/query/
has responsible: https://orcid.org/0000-0001-6338-1312
is deprecated: false
is part of: Bioregistry
0000005: AHR

NFDI4DS Ontology
is deprecated: false
has resource example: City
description: The NFDI4DS ontology (nfdi4dso) is an ontology describing various resources all resources (datasets, data providers, persons, projects and other entities) within the domain of NFDI4DataScience. nfdi4dso is a module that builds upon the NFDIcore Ontology (https://ise-fizkarlsruhe.github.io/nfdicore/2.0.0/) and maintains alignment with the Basic Formal Ontology (BFO). [from homepage]
has provider formatter: https://nfdi.fiz-karlsruhe.de/nfdi4dso/$1
has URI prefix: https://nfdi.fiz-karlsruhe.de/nfdi4dso/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: City
type: Resource
has prefix: nfdi4dso

SWEET Ontology Phenomena Cycle Material
is part of: Semantic Web for Earth and Environment Technology Ontology
type: Resource
has prefix: sweet.phcm
keyword: cycle material
keyword: phenomena
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Cycle Material
is deprecated: false
has resource example: BiogeochemicalCycle
has provider formatter: http://sweetontology.net/phenCycleMaterial/$1
0000005: BiogeochemicalCycle
has URI prefix: http://sweetontology.net/phenCycleMaterial/
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
has alternative prefix: sophcm

Damage Topology Ontology
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
0000005: Causation
has prefix: tib.dot
description: The Damage Topology Ontology (DOT) allows the definition of damage representations and their relations with other damages and affected construction components. The ontology supports a generic damage modeling approach and therefore could be applied for any type of degradation as well as for any construction type (e.g. buildings or bridges). Damage representations can be modeled either as damaged areas (dot:DamageArea) or elementary damage elements (dot:DamageElement). Thereby, instances of dot:DamageElement should be aggregated in a dot:DamageArea, however significant damages e.g. large cracks could be modelled as dot:DamageElement without dot:DamageArea. For grouping multiple coherent damages, a damage pattern could be defined by using dot:DamagePattern as third type for damage representation. Besides the topological damage classes, damage can also be categorized acording to a certain damage type using subclasses of dot:ClassifiedDamage as defined in extensions of DOT. A division between structural and non-structural damage is made by using the dot:StructuralDamage or dot:Defect classes. In addition to the topology, damage documentation that is commonly created during inspections and damage assessment can be linked to the damages as well as to the damaged components.
has provider formatter: https://w3id.org/dot#$1
has URI prefix: https://w3id.org/dot#
is deprecated: false
keyword: engineering
has resource example: Causation

Cancer Cell Line Encyclopedia Cells
contributor: Charles Tapley Hoyt
has prefix: ccle
has alternative prefix: ccle.cell
keyword: cancer cell line
type: Resource
0000005: BT20_BREAST
has provider formatter: https://www.cbioportal.org/patient
keyword: cell
description: Datasets around different cancer cell lines generated by the Broad Institute and Novartis
keyword: cell line
has resource example: https://www.cbioportal.org/patient
has responsible: https://orcid.org/0000-0002-3539-9803
keyword: ontology
has URI prefix: https://www.cbioportal.org/patient
is deprecated: false
is part of: Bioregistry
has download URL: ccle.owl

Human Reference Atlas Common Coordinate Framework Ontology
has local unique identifier pattern: ^\S+$
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
keyword: ontology
has resource example: https://bioportal.bioontology.org/ontologies/CCF/
is part of: Bioregistry
has URI prefix: https://bioportal.bioontology.org/ontologies/CCF/
0000005: extraction_set
has reviewer: Charles Tapley Hoyt
git repository: ccf-ontology
description: The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage—making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA.
type: Resource
has download URL: ccf.owl
has provider formatter: https://bioportal.bioontology.org/ontologies/CCF/
has responsible: Katy Börner
has prefix: ccf

ChEBI Integrated Role Ontology
has download URL: chiro.owl
is part of: Bioregistry
depends on: Human Phenotype Ontology
depends on: Uber Anatomy Ontology
has provider formatter: http://purl.obolibrary.org/obo/chiro#$1
depends on: Chemical Entities of Biological Interest
depends on: Gene Ontology
depends on: Protein Ontology
type: Resource
depends on: NCBI Taxonomy
git repository: chiro
depends on: Mammalian Phenotype Ontology
keyword: obo
keyword: ontology
is deprecated: false
description: CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.
keyword: chemistry
has URI prefix: http://purl.obolibrary.org/obo/chiro#
has prefix: chiro
keyword: nfdi4chem
has responsible: https://orcid.org/0000-0001-5208-3432

Metathesaurus Names
appears in: Unified Medical Language System Concept Unique Identifier
has local unique identifier pattern: ^U\d+$
has alternative prefix: umls.mth
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: https://uts.nlm.nih.gov/uts/umls/vocabulary/MTH/
has provider formatter: https://uts.nlm.nih.gov/uts/umls/vocabulary/MTH/$1
appears in: Mondo Disease Ontology
has prefix: mth
0000005: U001388
has resource example: U001388
description: The Unified Medical Language System® (UMLS®) Metathesaurus (MTH) was developed and is maintained by the U.S. National Library of Medicine (NLM). MTH contains concept names, attributes, relationships, and other data that were created by NLM to facilitate construction of the UMLS Metathesaurus.
is deprecated: false

CohesinDB gene
type: Resource
keyword: gene
contributor: https://orcid.org/0009-0000-6974-6386
has URI prefix: https://cohesindb.iqb.u-tokyo.ac.jp/browsegene/eachgene/
has reviewer: Charles Tapley Hoyt
0000005: CDBG00009781
description: Contains identifiers for genes that are part of cohesin regulated CRMs (cis-regulatory modules) from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each identifier represents a single cohesin-related CRM. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information.
is deprecated: false
has provider formatter: https://cohesindb.iqb.u-tokyo.ac.jp/browsegene/eachgene/$1
has responsible: Ryuichiro Nakato
has prefix: cohesindb.gene
has resource example: CDBG00009781
is part of: Bioregistry
has local unique identifier pattern: ^CDBG000\d{5}$

Network Data Exchange
has prefix: ndex
keyword: life science
description: The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge.
git repository: ndexbio
is deprecated: false
has URI prefix: https://www.ndexbio.org/viewer/networks/
is part of: Bioregistry
has provider formatter: https://www.ndexbio.org/viewer/networks/$1
keyword: microbiology
keyword: epidemiology
type: Resource
contributor: Charles Tapley Hoyt
has responsible: Rudolf T. Pillich

Population and Community Ontology
has provider formatter: http://purl.obolibrary.org/obo/PCO_$1
keyword: biodiversity
is part of: Bioregistry
keyword: ecology
keyword: dataplant
keyword: evolution
has resource example: PCO_0000021
has download URL: pco.owl
depends on: Phenotype And Trait Ontology
keyword: social sciences
0000005: 0000021
appears in: Environment Ontology
has prefix: pco
depends on: Gene Ontology
has local unique identifier pattern: ^\d{7}$
keyword: life sciences, biology
type: Resource
keyword: community care
git repository: pco
depends on: NCBI Taxonomy
depends on: Basic Formal Ontology
depends on: Common Anatomy Reference Ontology
keyword: social and behavioural science
has responsible: https://orcid.org/0000-0001-8815-0078
keyword: obo
depends on: Environment Ontology
appears in: An ontology of core ecological entities
depends on: Relation Ontology
keyword: ontology
description: The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.
keyword: population genetics
has URI prefix: http://purl.obolibrary.org/obo/PCO_
depends on: Information Artifact Ontology
is deprecated: false

Pfam protein clan
0000005: CL0192
has resource example: CL0192
has responsible: Alex Bateman
keyword: ontology
keyword: protein family
is deprecated: false
has provider formatter: https://www.ebi.ac.uk/interpro/set/pfam/$1
has download URL: pfam.clan.owl
has prefix: pfam.clan
is part of: Bioregistry
has URI prefix: https://www.ebi.ac.uk/interpro/set/pfam/
type: Resource
contributor: Charles Tapley Hoyt
description: Higher order grouping of Pfam families
has local unique identifier pattern: ^CL\d+$

The SEED
has reviewer: Charles Tapley Hoyt
type: Resource
has URI prefix: https://pubseed.theseed.org/SubsysEditor.cgi
0000005: Histidinol dehydrogenase (EC 1.1.1.23)
is deprecated: false
has prefix: seed.role
contributor: https://orcid.org/0000-0002-7674-5194
has provider formatter: https://pubseed.theseed.org/SubsysEditor.cgi
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
git repository: TheSEED
description: With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [Fellowship for Interpretation of Genomes (FIG)](http://thefig.info/) as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. This prefix provides identifiers for molecular roles that describe the function of one or more proteins in microbes and plants.

Minimum Anformation About a Phylogenetic Analysis Ontology
keyword: phylogeny
keyword: phylogenetics
has local unique identifier pattern: ^\d{7}$
keyword: life science
description: The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.
has download URL: miapa.owl
keyword: obo
has resource example: MIAPA_0000010
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/MIAPA_
is deprecated: false
has prefix: miapa
0000005: 0000010
has responsible: Hilmar Lapp
has provider formatter: http://purl.obolibrary.org/obo/MIAPA_$1
git repository: miapa
is part of: Bioregistry
type: Resource

DOME Registry
has resource example: dfyn1yvtz3
is part of: Bioregistry
type: Resource
has responsible: Silvio Tosatto
has URI prefix: https://registry.dome-ml.org/review/
0000005: dfyn1yvtz3
is deprecated: false
has provider formatter: https://registry.dome-ml.org/review/$1
has prefix: dome
description: The DOME registry is a curated set of papers related to machine learning methods in biology, each with its own unique DOME identifier.
has local unique identifier pattern: ^[a-z0-9]{10}$
has reviewer: https://orcid.org/0000-0001-9439-5346
contributor: 0009-0008-8406-631X

Nanbyo Disease Ontology
has resource example: NANDO:1200031
has URI prefix: https://nanbyodata.jp/disease/NANDO:
keyword: ontology
is deprecated: false
description: Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan.
has provider formatter: https://nanbyodata.jp/disease/NANDO:$1
0000005: 1200031
has prefix: nando
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has download URL: nando.owl

Wikidata Entity
has part: Q113009139
has part: Q2082879
has part: Q114677953
has part: Q21039006
has part: Q114677837
has part: Q113012663
has part: Q81661625
has part: Q6972354
has part: Q107698738
has part: Q113014439
has part: Q113014431
has part: Q113012668
has part: Q11801904
has part: Q55118319
has part: Q4836352
has part: Q81661674
has part: Q48460
has part: Q81661681
has part: Q113009193
has part: Q81661598
has part: Q55118439
has part: Q1406710
has part: Q83428681
has part: Q55118544
has part: Q56328412
has part: Q111274068
has part: Q81661585
has part: Q112972813
has part: Q81661781
has part: Q902623
has part: Q81661843
has part: Q1502787
has part: Q7095051
has part: Q17027854
has part: Q50018
has part: Q114677908
has part: Q81661837
has part: Q55118646
has part: Q113012672
has part: Q109302681
has part: Q29123382
has part: Q81661727
has part: Q114677952
has part: Q17052437
has part: Q2860403
has part: Q203250
has part: Q81661673
has part: Q113014440
has part: Q604063
has part: Q55118328
has part: Q824258
has part: Q114677881
has part: Q4783563
has part: Q81661832
has part: Q81661692
has part: Q81661845
has part: Q114677888
has part: Q81661821
has part: Q6983890
has part: Q81661853
has part: Q65057180
has part: Q113014432
has part: Q55118575
has part: Q114677892
has part: Q6826947
has part: Q104225190
has part: Q55118561
has part: Q81661752
has part: Q55118285
has part: Q31110555
has part: Q55118402
has part: Q4651693
has part: Q113989515
has part: Q81661774
has part: Q81661736
has part: Q113009128
has part: Q81661586
has part: Q15304508
has part: Q81661827

The Drug-Drug Interactions Ontology
keyword: ontology
has prefix: dinto
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/DINTO_
type: Resource
is deprecated: true
has download URL: dinto.owl
git repository: DINTO
has provider formatter: http://purl.obolibrary.org/obo/DINTO_$1
keyword: obo
description: A formal represention for drug-drug interactions knowledge.

Ontology of Biological and Clinical Statistics
has provider formatter: http://purl.obolibrary.org/obo/OBCS_$1
keyword: biomedical science
keyword: biology
has responsible: Jie Zheng
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: medicine
has resource example: OBCS_0000121
keyword: obo
has download URL: obcs.owl
keyword: ontology
keyword: medical informatics
description: OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)
is deprecated: false
0000005: 0000121
keyword: statistics
git repository: obcs
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/OBCS_
keyword: vaccine
has prefix: obcs

Database of Complete Genome Homologous Genes Families
keyword: sequence
is deprecated: false
is part of: Bioregistry
0000005: HOMO_3.PE998
has URI prefix: http://hogenom.univ-lyon1.fr/query_sequence
has prefix: hogenom
has resource example: http://hogenom.univ-lyon1.fr/query_sequence
type: Resource
has provider formatter: http://hogenom.univ-lyon1.fr/query_sequence
keyword: phylogeny
keyword: phylogenetics
description: HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.
keyword: life science
has local unique identifier pattern: ^[A-Z][A-Z0-9_]+\.PE\d+$
keyword: classification
has responsible: Guy Perrière

Terminology for Description of Dynamics
has URI prefix: https://www.ebi.ac.uk/ols/ontologies/teddy/terms
has provider formatter: https://www.ebi.ac.uk/ols/ontologies/teddy/terms
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
keyword: neurophysiology
type: Resource
has prefix: biomodels.teddy
git repository: teddy.md
has responsible: Michael Hucka
keyword: systems biology
0000005: 0000066
has resource example: https://www.ebi.ac.uk/ols/ontologies/teddy/terms
keyword: ontology
has download URL: teddy-inferred.owl
is deprecated: false
has alternative prefix: teddy
keyword: synthetic biology
description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.

Crop Ontology Curation Tool
has part: CO 343
has part: CO 323
has part: CO 358
0000005: CO_325
description: The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms
has part: CO 337
has part: CO 370
has part: CO 320
has part: CO 357
has part: CO 326
has part: CO 360
has part: CO 366
has part: CO 331
has part: CO 348
has part: CO 336
has part: CO 346
has part: CO 338
has part: CO 347
has part: CO 334
has part: CO 341
has part: CO 356
has part: CO 330
0000007: https://cropontology.org/term/$1:$2
has responsible: Elizabeth Arnaud
has part: CO 321
has part: CO 335
has part: CO 324
has provider formatter: https://cropontology.org/ontology/$1
type: Registry
has part: CO 322
has part: CO 345
has part: CO 340
has part: CO 367
has part: CO 333
has part: CO 339
has part: CO 350
has part: CO 365
has part: CO 359
has part: CO 325
has part: CO 327

UCSC Genome Browser
has URI prefix: ftp://hgdownload.cse.ucsc.edu/goldenPath/
description: The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.
has provider formatter: ftp://hgdownload.cse.ucsc.edu/goldenPath/$1
is part of: Bioregistry
0000005: uc001rvw.5
contributor: Charles Tapley Hoyt
type: Resource
has responsible: Maximilian Haeussler
is deprecated: false
has resource example: uc001rvw.5
has prefix: ucsc

GESIS Knowledge Graph Schema
description: Predicates that are used to construct the GESIS Knowledge Graph, a bibliometrics KG.
has provider formatter: https://data.gesis.org/gesiskg/schema/$1
0000005: linkContext
is deprecated: false
is part of: Bioregistry
has URI prefix: https://data.gesis.org/gesiskg/schema/
has prefix: gesiskg
has resource example: linkContext
keyword: nfdi
type: Resource
contributor: Charles Tapley Hoyt
keyword: data schema

Genderal Ontology for Linguistic Description
contributor: Charles Tapley Hoyt
has resource example: class-goldTerm.html
is deprecated: true
has URI prefix: https://bioregistry.io/linguist.gold:
0000005: Term
has provider formatter: https://lambdamusic.github.io/ontospy-examples/gold-2010owl/class-gold$1.html
is part of: Bioregistry
has prefix: linguist.gold
type: Resource

ModelDB concept
has provider formatter: https://modeldb.science/modellist/$1
0000005: 3639
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: https://modeldb.science/modellist/3639
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: https://modeldb.science/modellist/
description: Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models.
has prefix: modeldb.concept

TopFind
0000005: Q9UKQ2
type: Resource
has responsible: Christopher M. Overall
description: TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.
keyword: life science
has URI prefix: http://clipserve.clip.ubc.ca/topfind/proteins/
is deprecated: false
has prefix: topfind
has resource example: Q9UKQ2
0000011: UniProt Protein
is part of: Bioregistry
has provider formatter: http://clipserve.clip.ubc.ca/topfind/proteins/$1
has local unique identifier pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$

NCI Metathesaurus
is deprecated: false
description: NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical.
has provider formatter: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp
0000005: C0026339
has resource example: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp
has local unique identifier pattern: ^C\d+$
is part of: Bioregistry
has prefix: ncim
has identifier space owner: 040gcmg81
type: Resource
has URI prefix: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp

Amphibian gross anatomy
has prefix: aao
is part of: Bioregistry
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/AAO_$1
has resource example: AAO_0000138
has local unique identifier pattern: ^\d{7}$
0000005: 0000138
keyword: anatomy
has responsible: David Blackburn
has URI prefix: http://purl.obolibrary.org/obo/AAO_
keyword: obo
is deprecated: true
keyword: ontology
description: A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon.

Coriell Institute for Medical Research
is part of: Bioregistry
has prefix: coriell
has URI prefix: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx
has resource example: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx
description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.
0000005: GM17027
type: Resource
has provider formatter: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx
has local unique identifier pattern: ^[A-Z]{2}\d+$
is deprecated: false

Gene Ontology Registry
has part: ENA
has part: DDANAT
has part: CORUM
has part: SO
has part: PlasmoDB
has part: ECO
has part: IUPHAR RECEPTOR
has part: UBERON
has part: SABIO-RK
description: A database-specific registry supporting curation in the Gene Ontology
has part: UniRule
has part: HGNC
has part: COG Pathway
has part: RESID
has part: OMIM
has part: KEGG ENZYME
has part: UniPathway
has part: BioCyc
has part: AspGD LOCUS
has part: PDB
has part: OBI
has part: GO REF
has part: SGN
has part: MeSH
has part: KEGG PATHWAY
has part: BRENDA
has part: DOI
type: Registry
has part: REBASE
has part: DisProt
has part: FBbt
has part: gomodel
has part: GOREL
has part: Rfam
has part: RNAmods
has part: MaizeGDB Locus
has part: JSTOR
has part: EcoCyc
has part: PO
has part: ENSEMBL
has part: COG Cluster
has part: BTO
has part: EchoBASE
has part: SEED
has part: GRIN
has part: RGD
has part: PharmGKB
has part: WBls
has part: ISBN
has part: ASAP
has part: Reactome
has part: HAMAP
has part: dbSNP
has part: WBbt
has part: MA
has part: FMA
has part: MGI
has part: IMGT HLA
has part: CAS
has part: CL
has part: NIF Subcellular
has part: Prosite
has part: Wikipedia
has part: HPA
has part: CGD
has part: PubChem BioAssay
has part: SGD
has part: PomBase
has part: TGD
has part: CASSPC
has part: Xenbase
has part: BFO
has part: PubChem Compound
has part: UM-BBD enzymeID
has part: PIRSF
has part: UM-BBD ruleID
has part: KEGG REACTION
has part: BIOMD
has part: CDD

Costal and Marine Ecological Classification Standard
type: Resource
has download URL: cmecs.owl
has resource example: 595.html
keyword: ontology
0000005: 595
git repository: cmecs
is deprecated: false
has provider formatter: https://cmecscatalog.org/cmecs/classification/unit/$1.html
keyword: ecology
has URI prefix: https://bioregistry.io/cmecs:
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
keyword: marine ecology
has prefix: cmecs
description: Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.

Asteraceae Genome Database - Genome
has prefix: asteraceaegd.genome
description: The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collection refers to the genomic data of Asteraceae species.
type: Resource
0000005: 0002
has provider formatter: https://cbcb.cdutcm.edu.cn/AGD/genome/details/
contributor: Mufaddal Naguthanawala
is deprecated: false
has responsible: Wei Chen
has URI prefix: https://cbcb.cdutcm.edu.cn/AGD/genome/details/
has reviewer: https://orcid.org/0000-0001-9439-5346
has resource example: https://cbcb.cdutcm.edu.cn/AGD/genome/details/
is part of: Bioregistry
has local unique identifier pattern: ^\d{4}$

Human developmental anatomy, abstract version
keyword: development
has provider formatter: http://purl.obolibrary.org/obo/EHDAA_$1
has responsible: Jonathan Bard
keyword: anatomy
description: A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.
is deprecated: true
keyword: obo
keyword: human
keyword: ontology
has local unique identifier pattern: ^\d+$
has URI prefix: http://purl.obolibrary.org/obo/EHDAA_
0000005: 1
has resource example: EHDAA 1
is part of: Bioregistry
type: Resource
has download URL: ehdaa.obo
has prefix: ehdaa

JRC Data Catalogue
has URI prefix: http://data.europa.eu/89h/
has provider formatter: http://data.europa.eu/89h/$1
type: Resource
0000005: jrc-eurl-ecvam-chemagora
has prefix: eu89h
is deprecated: false
has resource example: jrc-eurl-ecvam-chemagora
description: The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.
has local unique identifier pattern: ^[a-z0-9\-_]+$
is part of: Bioregistry

IUPHAR family
has resource example: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward
is deprecated: false
has local unique identifier pattern: ^\d+$
has prefix: iuphar.family
is part of: Bioregistry
0000005: 78
type: Resource
has URI prefix: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward
has provider formatter: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward
description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits.
has alternative prefix: IUPHARfam

Intrinsically Disordered Proteins Ontology
description: IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR.
keyword: protein structure
is deprecated: false
has local unique identifier pattern: ^\d{5}$
git repository: idpo
keyword: proteomics
has responsible: Federica Quaglia
has prefix: idpo
keyword: protein analysis
keyword: proteins
keyword: structural biochemistry
has resource example: IDPO:00056
is part of: Bioregistry
has provider formatter: https://www.disprot.org/idpo/IDPO:$1
0000005: 00056
type: Resource
contributor: Charles Tapley Hoyt
keyword: structural bioinformatics
keyword: structural biology
has URI prefix: https://www.disprot.org/idpo/IDPO:

Probability Distribution Ontology
keyword: systems biology
0000005: c0000005
is deprecated: false
keyword: computational biology
keyword: mathematics
description: ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities.
has prefix: probonto
keyword: statistics
has URI prefix: http://www.probonto.org/ontology#PROB_
git repository: ontology
has responsible: 0000-0003-4614-562X
is part of: Bioregistry
has provider formatter: http://www.probonto.org/ontology#PROB_$1
has resource example: PROB c0000005
type: Resource
has local unique identifier pattern: ^(c|k)\d{7}$

KNApSAcK
type: Resource
has alternative prefix: KNApSAcK
0000005: C00000001
has URI prefix: http://www.knapsackfamily.com/knapsack_core/information.php
has provider formatter: http://www.knapsackfamily.com/knapsack_core/information.php
has resource example: http://www.knapsackfamily.com/knapsack_core/information.php
is deprecated: false
has local unique identifier pattern: ^C\d{8}$
is part of: Bioregistry
description: KNApSAcK provides information on metabolites and the taxonomic class with which they are associated.
has prefix: knapsack

Rice Ontology
has prefix: co_320
keyword: life science
has download URL: CO 320.owl
is deprecated: false
has resource example: CO 320:0000618
keyword: food
keyword: ontology
keyword: plant phenotypes and traits
is part of: Bioregistry
has responsible: Jeffrey A. Detras
0000005: 0000618
keyword: phenotype
git repository: Crop-Ontology
keyword: botany
has provider formatter: https://cropontology.org/rdf/CO_320:$1
keyword: agriculture
description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The IBP Rice Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Based on SES, Rice Descriptor and IRIS DB.
has local unique identifier pattern: ^\d{7}$
type: Resource
has URI prefix: https://cropontology.org/rdf/CO_320:

OASIS Open Services for Lifecycle Collaboration Core Vocabulary
0000005: Property
is part of: Bioregistry
has provider formatter: http://open-services.net/ns/core#$1
type: Resource
contributor: Charles Tapley Hoyt
has URI prefix: http://open-services.net/ns/core#
keyword: plm
has responsible: Jim Amsden
description: Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains.
has prefix: oslc
has resource example: Property
is deprecated: false

SWEET Ontology Realm Soil
has alternative prefix: soreas
has prefix: sweet.reas
has provider formatter: http://sweetontology.net/realmSoil/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Soil
has resource example: A Horizon
is deprecated: false
has URI prefix: http://sweetontology.net/realmSoil/
is part of: Bioregistry
keyword: soil
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
0000005: A_Horizon
keyword: realm
is part of: Semantic Web for Earth and Environment Technology Ontology

NeuroVault Image
has provider formatter: https://neurovault.org/images/$1
has URI prefix: https://neurovault.org/images/
has prefix: neurovault.image
has resource example: https://neurovault.org/images/58788
is deprecated: false
0000005: 58788
is part of: Bioregistry
description: Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images.
type: Resource
has local unique identifier pattern: ^[1-9][0-9]*$

SWEET Ontology Property Quantity
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/propQuantity/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Quantity
0000005: BalanceEquation
type: Resource
has prefix: sweet.propq
keyword: quantity
is deprecated: false
has resource example: BalanceEquation
has URI prefix: http://sweetontology.net/propQuantity/
has alternative prefix: sopropq
is part of: Bioregistry
contributor: Charles Tapley Hoyt

Digital archive of scholarly articles
0000005: 3075966
type: Resource
has prefix: jstor
is deprecated: false
has resource example: http://www.jstor.org/stable/3075966
has URI prefix: http://www.jstor.org/stable/
description: JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.
has local unique identifier pattern: ^\d+$
has provider formatter: http://www.jstor.org/stable/$1
is part of: Bioregistry

NCI Pathway Interaction Database: Pathway
has alternative prefix: pid
type: Resource
has provider formatter: http://pid.nci.nih.gov/search/pathway_landing.shtml
keyword: gene
is deprecated: true
has local unique identifier pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$
keyword: life science
has download URL: pid.pathway.owl
has responsible: Carl F. Schaefer
has URI prefix: http://pid.nci.nih.gov/search/pathway_landing.shtml
has prefix: pid.pathway
description: The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information.
keyword: ontology
has resource example: http://pid.nci.nih.gov/search/pathway_landing.shtml
keyword: pathway
keyword: small molecule
is part of: Bioregistry
keyword: protein

Open Biological and Biomedical Ontologies
description: The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies.
0000005: uberon
keyword: health
has URI prefix: http://purl.obolibrary.org/obo/
keyword: ontology and terminology
keyword: ontology
has responsible: https://orcid.org/0000-0002-7356-1779
is deprecated: false
has download URL: obo.owl
has provider formatter: http://purl.obolibrary.org/obo/$1
has resource example: uberon
git repository: OBOFoundry.github.io
is part of: Bioregistry
type: Resource
has prefix: obo
keyword: biology

Minimum Information about a Tailoring Enzyme data repository
type: Resource
has reviewer: Charles Tapley Hoyt
git repository: mite data
contributor: https://orcid.org/0000-0001-6534-6609
has provider formatter: https://mite.bioinformatics.nl/repository/$1
has prefix: mite
is deprecated: false
has URI prefix: https://mite.bioinformatics.nl/repository/
description: MITE (Minimum Information about a Tailoring Enzyme) is a data repository and associated data standard designed to capture the reaction- and substrate-specificities of tailoring enzymes. Community-driven and fully expert-reviewed, it represents enzymatic reactions using reaction SMARTS and links to established resources such as UniProt, NCBI GenPept, Rhea, and MIBiG. MITE serves as a knowledgebase for enzyme and pathway annotation, in silico biosynthesis, and machine learning applications.
has reviewer: https://orcid.org/0000-0001-9439-5346
has responsible: https://orcid.org/0000-0001-6534-6609
is part of: Bioregistry
has resource example: MITE0000001
0000005: MITE0000001
has local unique identifier pattern: ^MITE\d{7}$

Candida Genome Database
keyword: nucleotide
is part of: Bioregistry
has URI prefix: http://www.candidagenome.org/cgi-bin/locus.pl
type: Resource
0000005: CAL0003079
has responsible: Gavin Sherlock
keyword: life science
description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.
keyword: eukaryotic
has local unique identifier pattern: ^CAL\d{7}$
keyword: genome
is deprecated: false
has provider formatter: http://www.candidagenome.org/cgi-bin/locus.pl
has resource example: http://www.candidagenome.org/cgi-bin/locus.pl
has prefix: cgd

SNP500Cancer
0000005: TP53-47
is part of: Bioregistry
type: Resource
has URI prefix: http://snp500cancer.nci.nih.gov/snp.cfm
has provider formatter: http://snp500cancer.nci.nih.gov/snp.cfm
description: The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer.
has reviewer: Charles Tapley Hoyt
has resource example: http://snp500cancer.nci.nih.gov/snp.cfm
is deprecated: true
has prefix: snp500cancer
keyword: dna

Global Natural Products Social Molecular Networking Task
is part of: Bioregistry
contributor: https://orcid.org/0000-0002-6601-2165
description: GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS)
has local unique identifier pattern: ^[a-f0-9]+$
type: Resource
has reviewer: Charles Tapley Hoyt
has resource example: https://gnps.ucsd.edu/ProteoSAFe/status.jsp
has prefix: gnps.task
has provider formatter: https://gnps.ucsd.edu/ProteoSAFe/status.jsp
has responsible: Mingxun Wang
has URI prefix: https://gnps.ucsd.edu/ProteoSAFe/status.jsp
is deprecated: false

Joint FAO/WHO Expert Committee on Food Additives
has prefix: jecfa
is deprecated: false
has reviewer: https://orcid.org/0000-0001-9439-5346
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
0000005: 2116
description: JECFA provides identifiers for flavors, food additives, contaminants, toxicants, and veterinary drugs. Each entry includes chemical details, acceptable or tolerable intake limits, and links to related reports and monographs.
contributor: Mufaddal Naguthanawala

SoyBase
description: SoyBase is a repository for curated genetics, genomics and related data resources for soybean.
keyword: development
keyword: plant breeding
keyword: comparative genomics
keyword: spider
has prefix: soybase
has provider formatter: https://legacy.soybase.org/sbt/search/search_results.php
keyword: life science
has local unique identifier pattern: ^\w+(\-)?\w+(\-)?\w+$
keyword: obo
0000005: BARC-013845-01256
has responsible: Jacqueline Campbell
has URI prefix: https://legacy.soybase.org/sbt/search/search_results.php
is deprecated: false
is part of: Bioregistry
keyword: phenotype
keyword: agriculture
type: Resource
has resource example: https://legacy.soybase.org/sbt/search/search_results.php

Medical Subject Headings
has alternative prefix: MESHPP
has alternative prefix: MESH
has alternative prefix: meshUID
has download URL: mesh.owl.gz
has alternative prefix: MESH_SUPPLEMENTAL_RECORD_UI
keyword: literature curation
0000005: C063233
has local unique identifier pattern: ^(C|D|Q)\d+$
is part of: Bioregistry
type: Resource
keyword: data retrieval
keyword: biomedical science
has URI prefix: https://meshb.nlm.nih.gov/record/ui
has alternative prefix: MSH2010_2010_02_22
has alternative prefix: MESHCS
keyword: life science
description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.
keyword: classification
has alternative prefix: MESHA
keyword: ontology
has alternative prefix: MESH_DESCRIPTOR_UI
keyword: metascience
keyword: topics
has alternative prefix: MESHC
has alternative prefix: MESHD
contributor: https://orcid.org/0000-0001-5246-9351
has prefix: mesh
has alternative prefix: MSH
is deprecated: false
has provider formatter: https://meshb.nlm.nih.gov/record/ui
has resource example: https://meshb.nlm.nih.gov/record/ui
keyword: bioinformatics
has alternative prefix: MeSH

MHC Restriction Ontology
keyword: obo
keyword: ontology
keyword: immunology
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/MRO_
0000005: 0000634
has prefix: mro
has provider formatter: http://purl.obolibrary.org/obo/MRO_$1
has download URL: mro.owl
is part of: Bioregistry
has resource example: MRO_0000634
type: Resource
keyword: immune system
keyword: major histocompatibility complex
has local unique identifier pattern: ^\d{7}$
has responsible: Bjoern Peters
description: The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.
git repository: MRO

SWEET Ontology Representation Scientific Law
has prefix: sweet.repsl
0000005: BernoulliTheorem
has URI prefix: http://sweetontology.net/reprSciLaw/
is part of: Bioregistry
has alternative prefix: sorepsl
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Law
has provider formatter: http://sweetontology.net/reprSciLaw/$1
type: Resource
has resource example: BernoulliTheorem
keyword: representation scientific law
is deprecated: false

Numeric Type
has identifier space owner: 015em2733
has URI prefix: https://vocabularies.cessda.eu/vocabulary/NumericType#code_
is deprecated: false
is part of: Bioregistry
has provider formatter: https://vocabularies.cessda.eu/vocabulary/NumericType#code_$1
has prefix: ddi.numerictype
contributor: Charles Tapley Hoyt
description: Specifies the type of numeric data.
type: Resource
has resource example: code Integer
0000005: Integer

Data Catalog
has resource example: Dataset
type: Resource
contributor: Charles Tapley Hoyt
has download URL: dcat3
description: DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web
keyword: computer science
has responsible: https://orcid.org/0000-0001-9052-2854
keyword: subject agnostic
keyword: data management
has provider formatter: http://www.w3.org/ns/dcat#$1
keyword: ess
has URI prefix: http://www.w3.org/ns/dcat#
keyword: ontology
0000005: Dataset
is deprecated: false
has prefix: dcat
keyword: w3c rec
git repository: dxwg
is part of: Bioregistry

BioLegend
keyword: life sciences
0000005: 3403
is deprecated: false
is part of: Bioregistry
keyword: reagents
has local unique identifier pattern: ^\d+$
keyword: antibodies
contributor: Charles Tapley Hoyt
has provider formatter: https://www.biolegend.com/Default.aspx
description: BioLegend is a life sciences supply vendor.
has resource example: https://www.biolegend.com/Default.aspx
keyword: vendor
keyword: assays
type: Resource
has prefix: biolegend
has URI prefix: https://www.biolegend.com/Default.aspx

Beta Cell Biology Consortium
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: functional genomics
keyword: protocol
keyword: embryonic stem cell
keyword: gene expression
keyword: pancreatic development
keyword: mouse strain
keyword: cell replacement
keyword: pancreatic islet development
type: Resource
has provider formatter: https://scicrunch.org/resolver/RRID:BCBC_$1
keyword: gene
keyword: pancreatic islet
keyword: beta cell
keyword: antibody
keyword: pancreatic islet function
has prefix: bcbc
keyword: mouse embryonic stem cell line
has resource example: RRID:BCBC 4623
keyword: basic science
keyword: cell regeneration
keyword: cell reprogramming
0000005: 4623
keyword: cell line
description: One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage]
keyword: data sharing
has URI prefix: https://scicrunch.org/resolver/RRID:BCBC_
keyword: data set
keyword: adenovirus
keyword: basic research
keyword: mouse
keyword: pancreas
keyword: embryonic stem cell line
keyword: genomics
is deprecated: false

SWEET Ontology Property Energy
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has URI prefix: http://sweetontology.net/propEnergy/
type: Resource
0000005: AvailablePotentialEnergy
has alternative prefix: soprope
has prefix: sweet.prope
has provider formatter: http://sweetontology.net/propEnergy/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Energy
is deprecated: false
is part of: Bioregistry
keyword: energy
has resource example: AvailablePotentialEnergy
contributor: Charles Tapley Hoyt

SWEET Ontology Relationships Physical
type: Resource
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Physical
has prefix: sweet.relph
is deprecated: false
keyword: physical
has URI prefix: http://sweetontology.net/relaPhysical/
has resource example: colderThan
0000005: colderThan
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/relaPhysical/$1
has alternative prefix: sorelph

ISO 3166-1 Country Code
type: Resource
0000005: 554
has resource example: https://data.who.int/countries/554
is deprecated: false
has provider formatter: https://data.who.int/countries/$1
has prefix: iso.3166
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: An identifier for a country in numeric format per ISO 3166-1
contributor: Charles Tapley Hoyt
has URI prefix: https://data.who.int/countries/

SWEET Ontology State Role Representative
0000005: RepresentativeRole
has URI prefix: http://sweetontology.net/stateRoleRepresentative/
is deprecated: false
has prefix: sweet.strr
is part of: Bioregistry
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Representative
keyword: state role representative
type: Resource
git repository: sweet
has alternative prefix: sostrr
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/stateRoleRepresentative/$1
has resource example: RepresentativeRole

Database of small human noncoding RNAs
has URI prefix: http://lisanwanglab.org/DASHR/entry/
has alternative prefix: dashr
has provider formatter: http://lisanwanglab.org/DASHR/entry/$1
type: Resource
has resource example: hsa-mir-200a
has prefix: dashr.rna
has local unique identifier pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
0000005: hsa-mir-200a
has responsible: https://orcid.org/0000-0002-3684-0031
keyword: life science
description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.
is deprecated: false
is part of: Bioregistry

UMLS Semantic Types Ontology
has resource example: T039
has prefix: sty
has provider formatter: https://uts.nlm.nih.gov/uts/umls/semantic-network/$1
keyword: ontology
is deprecated: false
description: UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types.
has responsible: https://orcid.org/0000-0003-4769-4217
has download URL: sty.owl
0000005: T039
has alternative prefix: umls.st
has alternative prefix: UMLSSG
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
contributor: https://orcid.org/0000-0003-2473-2313
has URI prefix: https://uts.nlm.nih.gov/uts/umls/semantic-network/
has local unique identifier pattern: ^T\d{3}$
has alternative prefix: umls.sty

Indian Crop Phenome Database Project
description: This resource is about projects in the Indian Crop Phenome Database (ICPD). The ICPD is a domain of the Indian Biological Data Center (IBDC), Regional Centre for Biotechnology, Faridabad, developed for the digitization of crop phenome data. Being the global agricultural powerhouse, the bulk of biological data generated in India is associated with agricultural trials. Ironically most of the trial data has been inaccessible to other researchers, and remains unpublished, and is lost as time passes. Therefore, ICPD would act as single-stop user-friendly platform for freely archiving, organizing, analyzing, and sharing the multi-crop phenome data following FAIR (Findable, Accessible, Interoperable and Re-usable) data principles. [from homepage]
has prefix: icpd.project
is deprecated: false
0000005: PPJ_100024
has responsible: Sonia Balyan
is part of: Bioregistry
type: Resource
contributor: Sonia Balyan
has reviewer: Charles Tapley Hoyt
has local unique identifier pattern: ^PPJ_\d+$

Imanis Life Sciences cell line products
type: Resource
has prefix: imanis
0000005: CL070
has provider formatter: https://www.imanislife.com/
has resource example: https://www.imanislife.com/
is deprecated: false
description: Cell line collections (Providers)
is part of: Bioregistry
has URI prefix: https://www.imanislife.com/

SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain
has download URL: s4ehaw.owl
has alternative prefix: s4ehaw
keyword: ontology
0000005: Activity
is deprecated: false
is part of: Bioregistry
keyword: engineering
has URI prefix: https://saref.etsi.org/saref4ehaw/
has resource example: Activity
description: The objective of SAREF4EHAW is to extend SAREF ontology for the eHealth/Ageing-well (EHAW) vertical. Clause 4.1 of the present document shortly introduces a high level view of the envisioned SAREF4EHAW semantic model and modular ontology, with the retained concepts (i.e. classes) and their relations. SAREF4EHAW extension has been specified and formalised by investigating EHAW domain related resources, as reported in ETSI TR 103 509, such as: potential stakeholders, standardization initiatives, alliances/associations, European projects, EC directives, existing ontologies, and data repositories. Therefore, SAREF4EHAW modular ontology shall both: - Allow the implementation of a limited set of typical EHAW related use cases already identified in ETSI TR 103 509, i.e. - Use case 1 ?elderly at home monitoring and support?, - Use case 2 ?monitoring and support of healthy lifestyles for citizens?, - Use case 3 ?Early Warning System (EWS) and Cardiovascular Accidents detection?. - Fulfil the eHealth Ageing Well related requirements provided in ETSI TR 103 509, mainly the ontological ones that were mostly taken as input for the ontology specification. SAREF4EHAW mainly reuses the following existing ontologies: SAREF, ETSI SmartBAN reference model, SAREF 4 Environment extension and W3C SSN System module. The following figure presents the high level view of SAREF4EHAW ontology. ![SAREF4SYST overview](diagrams/SAREF4EHAW_Model.jpg) For semantic interoperability handling purposes, an ontology based solution, combined with sensing-as-a-service and WoT strategies, is retained for SAREF4EHAW. Therefore, an upper level ontology, at service level, shall also behas been fully modelled (Service class and sub-classes depicted in the previous figure). For embedded semantic analytics purposes, SAREF4EHAW shall behas been designed using the modularity principle (see ETSI TR 103 509) and can thus be mainly described by the following self-contained knowledge sub-ontologies (or modules): Healt…
type: Resource
has prefix: saref.ehaw
keyword: iot
keyword: nfdi4ing
has provider formatter: https://saref.etsi.org/saref4ehaw/$1

FINDEX Raum
has provider formatter: https://terminology.fraunhofer.de/voc/raum#$1
has prefix: findex.raum
keyword: civil engineering
is deprecated: false
has resource example: R00000000000 3
keyword: digital planning and construction
is part of: Bioregistry
keyword: fid baudigital
keyword: earth sciences
has URI prefix: https://terminology.fraunhofer.de/voc/raum#
0000005: R00000000000_3
type: Resource
description: SKOS-Modellierung des Thesaurus FINDEX Raum des Fraunhofer-Informationszentrums Raum und Bau IRB
keyword: nfdi4ing

Berkeley Drosophila Genome Project EST database
type: Resource
description: The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI).
has prefix: bdgp.est
has URI prefix: https://www.ncbi.nlm.nih.gov/nucest/
has canonical: EST database maintained at the NCBI.
has resource example: EY223054.1
0000005: EY223054.1
has local unique identifier pattern: ^\w+(\.)?(\d+)?$
is deprecated: false
has provider formatter: https://www.ncbi.nlm.nih.gov/nucest/$1
keyword: genome
is part of: Bioregistry

Zebrafish developmental stages ontology
0000005: 0000050
keyword: life cycle
has local unique identifier pattern: ^\d{7}$
git repository: zebrafish-anatomical-ontology
description: Developmental stages of the Zebrafish
type: Resource
has prefix: zfs
has resource example: ZFS_0000050
has URI prefix: http://purl.obolibrary.org/obo/ZFS_
has download URL: zfs.owl
has provider formatter: http://purl.obolibrary.org/obo/ZFS_$1
keyword: anatomy
is deprecated: false
keyword: obo
keyword: zoology
keyword: ontology
keyword: marine biology
is part of: Bioregistry
keyword: developmental biology
keyword: aging
has responsible: https://orcid.org/0000-0002-2244-7917

MultiCellDS Digital snapshot
type: Resource
has resource example: MCDS S 0000000001
is part of: MultiCellDS
has URI prefix: http://multicellds.org/MultiCellDB/
0000005: MCDS_S_0000000001
is deprecated: false
has local unique identifier pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$
has provider formatter: http://multicellds.org/MultiCellDB/$1
description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.
is part of: Bioregistry
has prefix: multicellds.snapshot

Wikidata Entity
0000005: Q42
has provider formatter: http://www.wikidata.org/entity/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: http://www.wikidata.org/entity/
has prefix: wikidata.entity
type: Resource
is part of: Wikidata
is deprecated: false
has local unique identifier pattern: ^Q\d+$
has resource example: Q42
description: Entity in Wikidata

Non-Coding RNA Ontology
has local unique identifier pattern: ^\d{7}$
type: Resource
has resource example: NCRO_0002927
has provider formatter: http://purl.obolibrary.org/obo/NCRO_$1
has URI prefix: http://purl.obolibrary.org/obo/NCRO_
keyword: ncrna
0000005: 0002927
keyword: obo
keyword: ontology
has download URL: ncro.owl
keyword: genomics
is deprecated: false
is part of: Bioregistry
description: An ontology for non-coding RNA, both of biological origin, and engineered.
has prefix: ncro
has responsible: https://orcid.org/0000-0003-2408-2883
git repository: ncro

Virus' miRNA target
has provider formatter: http://vita.mbc.nctu.edu.tw/search.php
is part of: Bioregistry
keyword: gene expression
has resource example: http://vita.mbc.nctu.edu.tw/search.php
keyword: structure
has URI prefix: http://vita.mbc.nctu.edu.tw/search.php
has prefix: vita
type: Resource
0000005: AB016785
keyword: rna
is deprecated: false
description: ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons.

PRO Research: An ontology for describing RDM-Policies in a structured way
has prefix: pror
has URI prefix: http://w3id.org/nfdi4ing/pro-research#
has provider formatter: http://w3id.org/nfdi4ing/pro-research#$1
is part of: Bioregistry
keyword: nfdi4ing
has responsible: Tobias Hamann
type: Resource
has resource example: isReferencedByPolicy
0000005: isReferencedByPolicy
description: PRO Research: An ontology for describing RDM-Policies in a structured way
is deprecated: false
keyword: engineering

FactGrid
has prefix: factgrid
has local unique identifier pattern: ^Q\d+$
description: A wikibase for linguistic knowledge
is deprecated: false
is part of: Bioregistry
0000005: Q24708
has resource example: Q24708
has responsible: https://orcid.org/0000-0001-9230-4666
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: https://database.factgrid.de/viewer/item/$1
has URI prefix: https://database.factgrid.de/viewer/item/

BacMap Biography
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: http://bacmap.wishartlab.com/organisms/1050
type: Resource
has prefix: bacmap.biog
has provider formatter: http://bacmap.wishartlab.com/organisms/$1
has URI prefix: http://bacmap.wishartlab.com/organisms/
0000005: 1050
description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.
is deprecated: false

Toxin and Toxin Target Database
has prefix: t3db
is part of: Bioregistry
0000005: T3D0001
has resource example: T3D0001
type: Resource
keyword: biomedical science
keyword: molecule
has responsible: David Wishart
keyword: life science
has provider formatter: http://www.t3db.org/toxins/$1
has local unique identifier pattern: ^T3D\d+$
is deprecated: false
keyword: protein
description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.
has URI prefix: http://www.t3db.org/toxins/

Human BioMolecular Atlas Program Sample
type: Resource
has URI prefix: https://portal.hubmapconsortium.org/browse/sample/
has responsible: Katy Börner
has prefix: hubmap.sample
is deprecated: false
description: The samples subsection of HuBMAP provides metadata about individual tissue samples collected from donors, and are the downstream experimental datasets for scRNA sequencing. Each sample has a unique identifier that links it to donor information, anatomical source, and related datasets.
has reviewer: https://orcid.org/0000-0001-9439-5346
has local unique identifier pattern: ^[a-f0-9]{32}$
contributor: 0009-0008-8406-631X
is part of: Bioregistry
has provider formatter: https://portal.hubmapconsortium.org/browse/sample/$1

Human Protein Atlas tissue profile information
has responsible: Mathias Uhlen
0000005: ENSG00000026508
description: The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers.
keyword: systems biology
has URI prefix: http://www.proteinatlas.org/
has provider formatter: http://www.proteinatlas.org/$1
is deprecated: false
keyword: protein
has resource example: ENSG00000026508
has prefix: hpa
keyword: proteomics
is part of: Bioregistry
keyword: transcriptomics
type: Resource
keyword: biomedical science
keyword: structure
has local unique identifier pattern: ^ENSG\d{11}$

Measurement method ontology
has prefix: mmo
keyword: life science
has responsible: https://orcid.org/0000-0002-6443-9376
has resource example: MMO_0000574
keyword: model organisms
has provider formatter: http://purl.obolibrary.org/obo/MMO_$1
keyword: obo
keyword: ontology
0000005: 0000574
is deprecated: false
is part of: Bioregistry
keyword: dataplant
git repository: MMO-Measurement-Method-Ontology
keyword: phenotype
has local unique identifier pattern: ^\d{7}$
keyword: preclinical studies
type: Resource
has download URL: mmo.owl
description: A representation of the variety of methods used to make clinical and phenotype measurements.
keyword: biomedical science
has URI prefix: http://purl.obolibrary.org/obo/MMO_

Molecule role (INOH Protein name/family name ontology)
keyword: obo
is deprecated: true
keyword: ontology
keyword: small molecule
has resource example: IMR_0000001
is part of: Bioregistry
keyword: protein
0000005: 0000001
description: MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data.
has local unique identifier pattern: ^\d{7}$
type: Resource
has prefix: imr
has provider formatter: http://purl.obolibrary.org/obo/IMR_$1
has URI prefix: http://purl.obolibrary.org/obo/IMR_

REBASE Enzyme Number
is deprecated: false
keyword: dna
keyword: small molecule
keyword: protein
has URI prefix: https://bioregistry.io/rebase:
has provider formatter: http://rebase.neb.com/rebase/enz/$1.html
has responsible: Richard John Roberts
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has resource example: 101.html
keyword: structure
has prefix: rebase
keyword: life science
keyword: enzyme
description: REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.
keyword: rna
0000005: 101
keyword: genome

KEGG Drug
has provider formatter: https://www.kegg.jp/entry/$1
has local unique identifier pattern: ^D\d+$
is deprecated: false
0000005: D00123
has alternative prefix: KEGG DRUG
has URI prefix: https://www.kegg.jp/entry/
keyword: small molecule
is part of: Bioregistry
has resource example: D00123
has prefix: kegg.drug
is part of: Kyoto Encyclopedia of Genes and Genomes
has alternative prefix: KEGG.DRUG
has responsible: Minoru Kanehisa
description: KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.
type: Resource

Creative Biolabs protein
has prefix: creativebiolabs.protein
contributor: Mufaddal Naguthanawala
is deprecated: false
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
type: Resource
description: Creative Biolabs Protein provides identifiers for protein-related entities, including therapeutic proteins, proteolytic enzymes, antibody-like scaffold proteins, soluble T cell receptors, and tetramers.
0000005: VS-0724-CJ1
has local unique identifier pattern: ^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$

Ontology for Biobanking
keyword: biobank
keyword: health science
has prefix: obib
git repository: biobanking
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/OBIB_$1
is deprecated: false
has download URL: obib.owl
is part of: Bioregistry
0000005: 0000389
has resource example: OBIB_0000389
has URI prefix: http://purl.obolibrary.org/obo/OBIB_
has local unique identifier pattern: ^\d{7}$
type: Resource
description: The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology.
has responsible: https://orcid.org/0009-0003-4268-6207

International Classification of Diseases, 10th Revision
has alternative prefix: ICD10
has provider formatter: https://icd.who.int/browse10/2019/en#/$1
keyword: ontology
has local unique identifier pattern: ^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\.[0-9]))?))$
is deprecated: false
keyword: disease
has alternative prefix: ICD10WHO
keyword: diagnosis
0000005: C34
has download URL: icd10.owl
has alternative prefix: ICD-10
contributor: https://orcid.org/0000-0002-2906-7319
contributor: https://orcid.org/0000-0002-7356-1779
keyword: global health
is part of: Bioregistry
has prefix: icd10
contributor: Charles Tapley Hoyt
has URI prefix: https://icd.who.int/browse10/2019/en#/
keyword: epidemiology
type: Resource
keyword: biomedical science
has alternative prefix: ICD
description: The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases. Note that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States.
keyword: health science
keyword: taxonomy
keyword: classification
has resource example: C34

The Natural Products Atlas
0000005: NPA000001
has responsible: Roger Linington
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.npatlas.org/explore/compounds/
is part of: Bioregistry
has local unique identifier pattern: ^NPA\d{6}$
has provider formatter: https://www.npatlas.org/explore/compounds/$1
type: Resource
has prefix: npatlas
description: Identifiers for microbially derived natural products that contains compound structures, producing organism taxonomy, biosynthetic and chemical properties.
contributor: Mufaddal Naguthanawala
has resource example: NPA000001
is deprecated: false

GlycoNAVI
keyword: life science
has provider formatter: https://glyconavi.org/hub/
git repository: doc
description: GlycoNAVI is a website for carbohydrate research. It consists of the "GlycoNAVI Database" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the "GlycoNAVI tools" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools.
has resource example: https://glyconavi.org/hub/
keyword: glycomics
is deprecated: false
is part of: Bioregistry
has prefix: glyconavi
keyword: chemistry
has local unique identifier pattern: ^GN_[A-Za-z0-9_:]+$
0000005: GN_G03681DA
has URI prefix: https://glyconavi.org/hub/
has responsible: 0000-0001-9504-189X
keyword: organic chemistry
type: Resource

Dengue Fever Ontology
has responsible: Elvira Mitraka
keyword: medicine
has download URL: idoden.owl
description: An ontology for dengue fever.
keyword: ontology
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: idoden
has local unique identifier pattern: ^\d{7}$
0000005: 0003463
type: Resource
has resource example: IDODEN_0003463
has provider formatter: http://purl.bioontology.org/ontology/IDODEN_$1
has URI prefix: http://purl.bioontology.org/ontology/IDODEN_

UM-BBD compound
is part of: Bioregistry
type: Resource
has alternative prefix: UM-BBD_compID
has local unique identifier pattern: ^c\d+$
description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.
has provider formatter: http://eawag-bbd.ethz.ch/servlets/pageservlet
0000005: c0001
is deprecated: false
has resource example: http://eawag-bbd.ethz.ch/servlets/pageservlet
has prefix: umbbd.compound
has URI prefix: http://eawag-bbd.ethz.ch/servlets/pageservlet

ChemBioSys Publication
has prefix: chembiosys.publication
is deprecated: false
has provider formatter: https://data.chembiosys.de/publications/$1
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
description: A publication in the ChemBioSys data platform
contributor: Charles Tapley Hoyt
0000005: 157
has URI prefix: https://data.chembiosys.de/publications/
has resource example: https://data.chembiosys.de/publications/157
type: Resource

Tick Anatomy Ontology
keyword: ontology
has resource example: TADS_0000547
description: The anatomy of the Tick, Families: Ixodidae, Argassidae
has responsible: Daniel Sonenshine
is part of: Bioregistry
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/TADS_$1
has prefix: tads
keyword: anatomy
has local unique identifier pattern: ^\d{7}$
0000005: 0000547
keyword: life science
has download URL: tads.owl
has URI prefix: http://purl.obolibrary.org/obo/TADS_
is deprecated: true
keyword: obo
git repository: TADS

Virtual Contact File
has download URL: ns
type: Resource
has provider formatter: http://www.w3.org/2006/vcard/ns#$1
has responsible: Renato Iannella
has resource example: Agent
0000005: Agent
description: vCard is a specification developed by the Internet Engineering Task Force (IETF) for the description of people and organisations
keyword: ontology
has prefix: vcard
is deprecated: false
is part of: Bioregistry
has URI prefix: http://www.w3.org/2006/vcard/ns#
contributor: Charles Tapley Hoyt
keyword: people

Plant Transcription Factor Database
0000005: Ath_AT1G01030.1
is deprecated: false
has local unique identifier pattern: ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$
has responsible: https://orcid.org/0000-0001-6470-8815
has provider formatter: http://planttfdb.cbi.pku.edu.cn/tf.php
keyword: rna
description: The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors.
keyword: small molecule
keyword: dna
keyword: regulation
is part of: Bioregistry
keyword: protein
has URI prefix: http://planttfdb.cbi.pku.edu.cn/tf.php
type: Resource
keyword: gene
has prefix: planttfdb
has resource example: http://planttfdb.cbi.pku.edu.cn/tf.php
keyword: life science

Mouse gross anatomy and development, timed
type: Resource
description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).
keyword: development
keyword: anatomy
has resource example: EMAP 1
is deprecated: true
keyword: obo
has download URL: emap.owl
keyword: ontology
keyword: mouse
has responsible: https://orcid.org/0000-0002-0956-8634
has local unique identifier pattern: ^\d+$
has prefix: emap
has provider formatter: http://purl.obolibrary.org/obo/EMAP_$1
0000005: 1
has URI prefix: http://purl.obolibrary.org/obo/EMAP_
is part of: Bioregistry

AmoebaDB
keyword: model organism
has provider formatter: https://amoebadb.org/amoeba/app/record/gene/$1
has responsible: Omar S. Harb
0000005: EDI_244000
contributor: https://orcid.org/0000-0002-1216-4761
has local unique identifier pattern: ^EDI_\d+$
keyword: genomics
is deprecated: false
has URI prefix: https://amoebadb.org/amoeba/app/record/gene/
has resource example: EDI_244000
keyword: functional genomics
description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
is part of: Bioregistry
type: Resource
has prefix: amoebadb

ClinVar Variation
has resource example: https://www.ncbi.nlm.nih.gov/clinvar/variation/12345
has alternative prefix: clinvar.variant
has provider formatter: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1
keyword: preclinical studies
has alternative prefix: clinvar
type: Resource
keyword: clinical studies
keyword: biomedical science
has responsible: https://orcid.org/0000-0001-7451-4467
description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.
0000005: 12345
is deprecated: false
is part of: Bioregistry
keyword: genomics
has local unique identifier pattern: ^\d+$
has URI prefix: https://www.ncbi.nlm.nih.gov/clinvar/variation/
has prefix: clinvar.variation

Mutant Mouse Resource and Research Centers
keyword: embryonic stem cell line
is deprecated: false
has responsible: https://orcid.org/0000-0002-3070-8224
keyword: cryopreserved
has prefix: mmrrc
0000005: 70
has URI prefix: http://www.mmrrc.org/catalog/getSDS.php
has provider formatter: http://www.mmrrc.org/catalog/getSDS.php
keyword: transgenic
keyword: mutant mouse strain
has resource example: http://www.mmrrc.org/catalog/getSDS.php
keyword: embryonic stem cell
keyword: mouse strain
keyword: stem cell
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: mutant
type: Resource
keyword: biology
description: The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections.
keyword: faseb list
keyword: database

Croissant Format Specification
0000005: FileObject
has prefix: croissant
type: Resource
contributor: Charles Tapley Hoyt
keyword: artificial intelligence
description: A data model describing machine learning experiments
has resource example: FileObject
has provider formatter: http://mlcommons.org/croissant/$1
has URI prefix: http://mlcommons.org/croissant/
is deprecated: false
is part of: Bioregistry
keyword: machine learning

TreeBASE
is part of: Bioregistry
has prefix: treebase
has URI prefix: https://bioregistry.io/treebase:
has local unique identifier pattern: ^TB[1,2]?:[A-Z][a-z]?\d+$
has provider formatter: http://purl.org/phylo/treebase/phylows/study/$1
has resource example: http://purl.org/phylo/treebase/phylows/study/TB2:S1000
has responsible: https://orcid.org/0000-0001-9254-7318
type: Resource
git repository: issues
is deprecated: true
keyword: phylogenetics
keyword: classification
keyword: phylogenomics
description: TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc.
0000005: TB2:S1000

PathBank
has responsible: David Wishart
keyword: systems biology
keyword: human genetics
keyword: molecular microbiology
has resource example: SMP0000219
keyword: cell biology
keyword: medical informatics
keyword: ontology
keyword: endocrinology
keyword: genetics
is deprecated: false
0000005: SMP0000219
keyword: cheminformatics
keyword: molecular biology
keyword: bioinformatics
keyword: metabolomics
has download URL: pathbank.owl.gz
keyword: proteomics
has URI prefix: https://pathbank.org/view/
has local unique identifier pattern: ^(SMP|PW)\d+$
keyword: database management
has prefix: pathbank
keyword: plant genetics
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: microbiology
keyword: transcriptomics
type: Resource
keyword: animal genetics
keyword: drug metabolism
keyword: biology
has provider formatter: https://pathbank.org/view/$1
description: PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana.

BEI Resources
has provider formatter: https://www.beiresources.org/Catalog/cellBanks/$1.aspx
contributor: Charles Tapley Hoyt
has resource example: MRA-253.aspx
0000005: MRA-253
has prefix: beiresources
type: Resource
keyword: cell lines
has URI prefix: https://bioregistry.io/beiresources:
has alternative prefix: BEI_Resources
is deprecated: false
description: Cell line collections (Providers)
is part of: Bioregistry

European Mouse Mutant Archive
keyword: mouse
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
keyword: mutant mouse strain
has provider formatter: https://www.infrafrontier.eu/emma/strain-search/straindetails/
0000005: 11478
has prefix: imsr_em
type: Resource
keyword: mutant mouse repository
keyword: mutant strain
has resource example: https://www.infrafrontier.eu/emma/strain-search/straindetails/
has URI prefix: https://www.infrafrontier.eu/emma/strain-search/straindetails/
has responsible: https://orcid.org/0000-0002-5836-9850
description: Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. [from RRID]
is deprecated: false

Academic Event Ontology
is part of: Bioregistry
type: Resource
has responsible: https://orcid.org/0000-0002-1595-3213
keyword: history
has reviewer: Charles Tapley Hoyt
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
keyword: educational science
has URI prefix: http://purl.obolibrary.org/obo/AEON_
keyword: miscellaneous
description: The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page).
keyword: ontology
has resource example: AEON_0000001
is deprecated: false
has download URL: aeon.owl
contributor: https://orcid.org/0000-0002-1595-3213
has prefix: aeon
has provider formatter: http://purl.obolibrary.org/obo/AEON_$1
keyword: social sciences
git repository: aeon

EST database maintained at the NCBI.
is part of: Bioregistry
description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
has URI prefix: https://www.ncbi.nlm.nih.gov/nucest/
type: Resource
has resource example: BP100000
0000005: BP100000
keyword: life science
has prefix: dbest
is deprecated: false
has responsible: Todd M Lowe
keyword: dna
has local unique identifier pattern: ^([A-Z]+)?\d+(\.\d+)?$
has provider formatter: https://www.ncbi.nlm.nih.gov/nucest/$1
keyword: bioinformatics

Nucleotide Sequence Database
has resource example: X58356
type: Resource
has URI prefix: https://www.ebi.ac.uk/ena/data/view/
0000005: X58356
has provider formatter: https://www.ebi.ac.uk/ena/data/view/$1
is deprecated: false
keyword: dna
has prefix: insdc
is part of: Bioregistry
description: The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.
has local unique identifier pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4,6}\d{8,10}|[A-J][A-Z]{2}\d{5})(\.\d+)?$

Ontology for manufacturing and logistics
keyword: engineering
has resource example: Anthropomorphic Robot
description: Ontology for manufacturing and logistics
git repository: OFM
type: Resource
keyword: nfdi4ing
0000005: Anthropomorphic_Robot
has prefix: tib.ofm
has URI prefix: http://www.ontologies.com/Ontology3197.owl#
is deprecated: false
has provider formatter: http://www.ontologies.com/Ontology3197.owl#$1
is part of: Bioregistry

SciProfiles ID
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: person
keyword: researcher
has URI prefix: https://sciprofiles.com/profile/
type: Resource
has provider formatter: https://sciprofiles.com/profile/$1
description: numerical identifier for an author in SciProfiles by MDPI
is deprecated: false
0000005: 118021
has resource example: https://sciprofiles.com/profile/118021
has local unique identifier pattern: ^[1-9]\d*$
has prefix: sciprofiles

Basisklassifikation
keyword: fid move
keyword: earth sciences
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
has resource example: http://uri.gbv.de/terminology/bk/0
has provider formatter: http://uri.gbv.de/terminology/bk/$1
keyword: ess
has prefix: tib.bk
is deprecated: false
keyword: digital planning and construction
keyword: fid baudigital
description: The (Dutch) Basic Classification (nl Nederlandse basisclassificatie), BK or NBC is a hierarchical classification system developed by Dutch libraries specifically for scientific works. The classification system was introduced at the end of the 1980s under the direction of the Royal Library of the Netherlands and has been in use since 1990. Since then it has been continually revised. The BK is mainly used in the Netherlands and in the Common Library Network (GBV).
0000005: 0
has URI prefix: http://uri.gbv.de/terminology/bk/

LOTUS Initiative for Open Natural Products Research
keyword: chemistry
has provider formatter: https://lotus.naturalproducts.net/compound/lotus_id/$1
description: LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry.
contributor: Adriano Rutz
has resource example: LTS0004651
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^LTS\d{7}$
keyword: drugs
has reviewer: Charles Tapley Hoyt
has URI prefix: https://lotus.naturalproducts.net/compound/lotus_id/
has responsible: Adriano Rutz
has prefix: lotus
0000005: LTS0004651
is deprecated: false
keyword: metabolites

StoreDB Study
type: Resource
description: Study inside StoreDB at University of Cambridge
0000005: 1174
is deprecated: false
has provider formatter: https://www.storedb.org/store_v3/study.jsp
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: storedb.study
contributor: Charles Tapley Hoyt
has resource example: https://www.storedb.org/store_v3/study.jsp
has URI prefix: https://www.storedb.org/store_v3/study.jsp

FIESTA-IoT Ontology
type: Resource
keyword: iot
keyword: nfdi4ing
description: The FIESTA-IoT ontology takes inspiration from the well-known Noy et al. methodology for reusing and interconnecting existing ontologies. To build the ontology, we leverage a number of core concepts from various mainstream ontologies and taxonomies, such as Semantic Sensor Network (SSN), M3-lite (a lite version of M3 ontology), WGS84, IoT-lite, Time, and DUL ontology.
has prefix: fiesta.iot
is deprecated: false
has provider formatter: http://purl.org/iot/ontology/fiesta-iot#$1
has URI prefix: http://purl.org/iot/ontology/fiesta-iot#
git repository: ontology
keyword: engineering
is part of: Bioregistry

SAGE Social Science Thesaurus
0000005: -LHR8P7WS-K
type: Resource
description: The SAGE Social Science Thesaurus is a multidisciplinary vocabulary of the most important concepts in the social sciences. SAGE uses this vocabulary as its principal keyword vocabulary for automated tagging of content on SAGE Knowledge and SAGE Research Methods. You are welcome to browse, download, use and transform the vocabulary for any non-commercial purpose. The majority of concepts in the thesaurus have been mined from headwords in SAGE encyclopedias and other reference works. Relationships between concepts have been inferred from implicit structures in those works, for example subject indexes and readers' guides. As such, the thesaurus is a structured representation of what the editors of those reference works consider to be the most important concepts in the social sciences. Additional scraping work has extracted and structured concept-specific metadata, such as dates (for events and people) and definitions. In addition to broader-narrower relationships, concepts are grouped by type: concepts, people, organizations, events, methods, theories or laws.
has prefix: sage.socialsciencethesaurus
is deprecated: false
has provider formatter: http://data.loterre.fr/ark:/67375/N9J$1
is part of: Bioregistry
has resource example: N9J-LHR8P7WS-K
contributor: Charles Tapley Hoyt
has URI prefix: http://data.loterre.fr/ark:/67375/N9J

GeoSPARQL Function
is part of: Bioregistry
type: Resource
description: Functions for GeoSPARQL
has prefix: geosparql.function
is deprecated: false
0000005: sfEquals

The Extensible Observation Ontology
has download URL: oboe.owl
keyword: environmental science
has prefix: oboe
contributor: https://orcid.org/0000-0002-1595-3213
keyword: observations
keyword: ess
is deprecated: false
keyword: fair data spaces
has responsible: Bryce Mecum
keyword: ontology
git repository: oboe
keyword: biodiversity
has URI prefix: http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#
is part of: Bioregistry
keyword: ecology
keyword: nfdi4chem
description: The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations.
has provider formatter: http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#$1
has resource example: Characteristic
has reviewer: Charles Tapley Hoyt
type: Resource
0000005: Characteristic

Climate and Forecast Standard Names
is part of: Bioregistry
has prefix: bodc.cf
has resource example: MIKUZ25U
0000005: MIKUZ25U
keyword: earth sciences
type: Resource
has provider formatter: http://vocab.nerc.ac.uk/collection/P07/current/$1
description: Ontology representation of the Climate and Forecast (CF) standard names parameter vocabulary, which is intended for use with climate and forecast data in the atmosphere, surface and ocean domains. Every CF parameter is captured as a SKOS concept.This vocabulary is a simplified version of the CF vocabulary P07 from the NERC Vocabulary Server (NVS), National Oceanography Centre - British Oceanographic Data Centre (BODC), https://vocab.nerc.ac.uk.
has URI prefix: http://vocab.nerc.ac.uk/collection/P07/current/
is deprecated: false
keyword: ess

PRINTS compendium of protein fingerprints
has alternative prefix: sprint
has local unique identifier pattern: ^PR\d{5}$
keyword: protein
has responsible: https://orcid.org/0000-0003-2409-4235
is part of: Bioregistry
has provider formatter: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi
type: Resource
has resource example: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi
has URI prefix: https://bioregistry.io/prints:
keyword: structural biology
keyword: biology
has prefix: prints
description: PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.
is deprecated: true
keyword: domain
0000005: PR00001

Anatomical Therapeutic Chemical Classification System
keyword: ontology
has URI prefix: http://www.whocc.no/atc_ddd_index/
keyword: chemical biology
is part of: Bioregistry
keyword: pharmacology
has provider formatter: http://www.whocc.no/atc_ddd_index/
description: The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.
keyword: chemical
has alternative prefix: ATC_code
has local unique identifier pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$
type: Resource
0000005: A10BA02
keyword: biomedical science
keyword: approved drug
has resource example: http://www.whocc.no/atc_ddd_index/
has alternative prefix: ATTC
is deprecated: false
keyword: drug
keyword: pharmacological family classification
has prefix: atc
keyword: atc code

CIViC variant
has resource example: https://civicdb.org/links/variant/12
has URI prefix: https://civicdb.org/links/variant/
is deprecated: false
is part of: Bioregistry
has provider formatter: https://civicdb.org/links/variant/$1
has responsible: Malachi Griffith
0000005: 12
type: Resource
has prefix: civic.vid
has local unique identifier pattern: ^[0-9]+$
has alternative prefix: civic.variant
description: CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.

SWEET Ontology Representation Representation Scientific Methodology
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: representation representation scientific methodology
has prefix: sweet.repsme
has alternative prefix: sorepsme
has provider formatter: http://sweetontology.net/reprSciMethodology/$1
0000005: AerialPhotography
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Representation Scientific Methodology
has resource example: AerialPhotography
has URI prefix: http://sweetontology.net/reprSciMethodology/
is part of: Bioregistry
type: Resource
git repository: sweet

AgroPortal
has part: EDAM
has part: DSW
has part: CO 338
has part: SIO
has part: CO 346
type: Registry
has part: RO
has part: SSN
has part: GO
has part: FOODEX2
has part: CO 339
has part: CO 356
has part: OM
0000005: ENVO
has part: GEMET
has part: CO 350
has part: ENVO
has part: CO 320
has part: EOL
has part: CL
has part: TAXRANK
has part: SOSA
has part: ATOL
has part: CO 337
has part: CO 359
has part: PECO
has provider formatter: http://agroportal.lirmm.fr/ontologies/$1
has part: FOBI
has part: CO 336
has part: EO
has part: VT
has part: CDNO
has part: FOODON
has part: CO 357
has part: TO
has part: CO 345
has part: GALLONT
has part: CO 340
has part: CO 341
has part: FLOPO
has part: BFO
has part: CO 347
has part: PR
has part: CDAO
has part: VBO
has part: PPEO
has part: BCO
has part: CO 321
has part: CO 358
has part: AGROVOC
has part: CO 324
has part: EFO
has part: LPT
has part: CO 330
has part: ECTO
has part: PCO
has part: SIREN
has part: CO 327
has part: SAREF
has part: ADW
has part: PO
description: A vocabulary and ontology repository for agronomy and related domains.
has part: ONS
has part: OBOE
has part: PPO
has part: CO 365
has part: FALDO
has part: STY
has part: CO 360
has responsible: https://orcid.org/0000-0002-2404-1582
has part: CO 335
has part: PATO
has part: TAX
has part: CO 370
has part: CO 326
has part: CO 333
has part: CO 331
has part: CO 348
has part: VARIO

Search Tool for Interactions of Chemicals
has prefix: stitch
0000005: BQJCRHHNABKAKU
has responsible: 0000-0002-2627-833X
has provider formatter: http://stitch.embl.de/interactions/$1
keyword: small molecule
is deprecated: false
keyword: protein
has local unique identifier pattern: ^\w{14}$
has URI prefix: http://stitch.embl.de/interactions/
description: STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.
has resource example: BQJCRHHNABKAKU
is part of: Bioregistry
type: Resource
keyword: interaction
keyword: life science

Semantically-Interlinked Online Communities Core Ontology
has resource example: Item
is part of: Bioregistry
0000005: Item
type: Resource
contributor: Charles Tapley Hoyt
description: Semantically-Interlinked Online Communities, or SIOC, is an attempt to link online community sites, to use Semantic Web technologies to describe the information that communities have about their structure and contents, and to find related information and new connections between content items and other community objects. SIOC is based around the use of machine-readable information provided by these sites.
has provider formatter: http://rdfs.org/sioc/ns#$1
keyword: society
has URI prefix: http://rdfs.org/sioc/ns#
has prefix: sioc.core
is deprecated: false
has alternative prefix: sioc

Metabolic Atlas Reaction
has prefix: metatlas.reaction
keyword: reactions
contributor: Mihail Anton
has local unique identifier pattern: ^MAR\d{5}$
has provider formatter: https://metabolicatlas.org/identifier/MetabolicAtlas/$1
is part of: Bioregistry
keyword: chemistry
is part of: Metabolic Atlas
has reviewer: Charles Tapley Hoyt
description: A subspace of Metabolic Atlas for reactions.
type: Resource
has responsible: Mihail Anton
has URI prefix: https://metabolicatlas.org/identifier/MetabolicAtlas/
has resource example: MAR11851
is deprecated: false
0000005: MAR11851

Dictyostelium discoideum anatomy
has local unique identifier pattern: ^\d{7}$
has provider formatter: http://purl.obolibrary.org/obo/DDANAT_$1
type: Resource
has prefix: ddanat
has responsible: https://orcid.org/0000-0002-4532-2703
keyword: cell
keyword: anatomy
keyword: life science
is deprecated: false
description: A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum.
0000005: 0000006
has resource example: DDANAT_0000006
keyword: obo
keyword: ontology
keyword: slime-mould
has download URL: ddanat.owl
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/DDANAT_
git repository: migration-data

GiardiaDB
keyword: eukaryotic
has responsible: Omar S. Harb
has prefix: giardiadb
keyword: genome
is deprecated: false
has resource example: GL50803_102438
keyword: genomics
has local unique identifier pattern: ^\w+$
is part of: Bioregistry
has provider formatter: https://giardiadb.org/giardiadb/app/record/gene/$1
type: Resource
has URI prefix: https://giardiadb.org/giardiadb/app/record/gene/
description: GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
0000005: GL50803_102438

miRBase pre-miRNA
has responsible: Sam Griffiths-Jones
keyword: biology
has URI prefix: http://www.mirbase.org/cgi-bin/mirna_entry.pl
description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).
is deprecated: false
keyword: rna
keyword: ontology
is part of: Bioregistry
has download URL: mirbase.owl
0000005: MI0026471
has resource example: http://www.mirbase.org/cgi-bin/mirna_entry.pl
has local unique identifier pattern: ^MI\d{7}$
has prefix: mirbase
has provider formatter: http://www.mirbase.org/cgi-bin/mirna_entry.pl
type: Resource
keyword: gene

SWEET Ontology Phenomena Atmosphere Wind
has resource example: AgeostrophicWind
is part of: Bioregistry
0000005: AgeostrophicWind
git repository: sweet
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Wind
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: atmosphere wind
type: Resource
has prefix: sweet.phatmow
keyword: phenomena
has alternative prefix: sophatmow
has URI prefix: http://sweetontology.net/phenAtmoWind/
has provider formatter: http://sweetontology.net/phenAtmoWind/$1
is deprecated: false

National Academic Research and Collaborations Information System
description: NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases.
has resource example: oai:cwi.nl:4725
type: Resource
keyword: subject agnostic
has prefix: narcis
has provider formatter: http://www.narcis.nl/publication/RecordID/$1
0000005: oai:cwi.nl:4725
has URI prefix: http://www.narcis.nl/publication/RecordID/
has local unique identifier pattern: ^oai\:cwi\.nl\:\d+$
is deprecated: false
is part of: Bioregistry

SWEET Ontology State
has provider formatter: http://sweetontology.net/state/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State
0000005: BinaryState
is deprecated: false
has resource example: BinaryState
has URI prefix: http://sweetontology.net/state/
has alternative prefix: sost
is part of: Bioregistry
keyword: state
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.st

Digital Construction Occupancy
has resource example: AcousticComfort
description: Digital Construction Occupancy ontology represents those aspects of construction and renovation projects that concern the comfort, safety and health of occupants, including visual and thermal comfort, indoor air quality and building acoustics, as well as related sensor observations.
is deprecated: false
keyword: digital planning and construction
has provider formatter: https://w3id.org/digitalconstruction/0.5/Occupancy#$1
keyword: fid baudigital
has URI prefix: https://w3id.org/digitalconstruction/0.5/Occupancy#
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
keyword: civil engineering
has prefix: digitalconstruction.occupancy
0000005: AcousticComfort

Orientation of Proteins in Realistic Lipid Membranes
has provider formatter: https://oprlm.org/proteins/$1
has resource example: https://oprlm.org/proteins/6782
has reviewer: https://orcid.org/0000-0001-9439-5346
description: Orientations of Proteins in Realistic Lipid Membranes (OPRLM) is a database for visualizing proteins in realistic lipid membranes. It includes the classification of proteins into types, superfamilies, and families, and also provides information on intracellular localizations of the proteins. Identifiers represent proteins.
type: Resource
has local unique identifier pattern: ^\d*$
0000005: 6782
has prefix: oprlm
has URI prefix: https://oprlm.org/proteins/
is deprecated: false
has responsible: Wonpil Im
contributor: 0009-0008-8406-631X
is part of: Bioregistry

PharmacoDB Datasets
has resource example: https://pharmacodb.ca/datasets/1
has URI prefix: https://pharmacodb.ca/datasets/
has provider formatter: https://pharmacodb.ca/datasets/$1
is deprecated: false
has local unique identifier pattern: ^\d+$
has prefix: pharmacodb.dataset
0000005: 1
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset.

MGnify Study
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^MGYS\d{8}$
has prefix: mgnifystudy
has provider formatter: https://www.ebi.ac.uk/metagenomics/studies/$1
0000005: MGYS00006794
description: The free-to-use MGnify platform provides assembly, analysis and archiving of microbiome-derived nucleic acid sequence data from a wide range of biomes, with analysis results providing taxonomic and functional profiles. The platform also includes MGnify Proteins, a database of protein sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes, a resource of biome-specific catalogues of microbial genomes, including extensive functional annotations.
type: Resource
has resource example: MGYS00006794
has URI prefix: https://www.ebi.ac.uk/metagenomics/studies/

Research Organization Registry
description: ROR (Research Organization Registry) is a global, community-led registry of open persistent identifiers for research organizations. ROR is jointly operated by California Digital Library, Crossref, and Datacite.
is deprecated: false
has responsible: https://orcid.org/0000-0002-2916-3423
git repository: ror-community
0000005: 03yrm5c26
has resource example: 03yrm5c26
is part of: Bioregistry
type: Resource
has download URL: ror.owl.gz
has provider formatter: https://ror.org/$1
has prefix: ror
has local unique identifier pattern: ^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$
keyword: data management
keyword: ontology
has URI prefix: https://ror.org/

Physico-chemical process
keyword: obo
has provider formatter: http://purl.obolibrary.org/obo/REX_$1
has responsible: https://orcid.org/0000-0001-8123-5351
keyword: ontology
has resource example: REX_0000512
keyword: chemistry
has prefix: rex
has URI prefix: http://purl.obolibrary.org/obo/REX_
is part of: Bioregistry
type: Resource
keyword: enzymatic reaction
0000005: 0000512
keyword: reaction data
has local unique identifier pattern: ^\d{7}$
description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.
has download URL: rex.owl
keyword: life science
keyword: biochemistry
is deprecated: true

Yongqun Oliver He
label: Yongqunh He

Applied Biological Materials cell line products
0000005: T0599
has prefix: abm
is deprecated: false
description: Cell line collections (Providers)
contributor: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.abmgood.com/search
has provider formatter: https://www.abmgood.com/search
is part of: Bioregistry
type: Resource
has resource example: https://www.abmgood.com/search

CABI Digital Library
description: Research and learning in agriculture, the environment and the applied life sciences
has resource example: https://www.cabi.org/cabebooks/ebook/20000614040
0000005: 20000614040
has prefix: cabi
is deprecated: false
has local unique identifier pattern: ^\d+$
has provider formatter: https://www.cabi.org/cabebooks/ebook/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: https://www.cabi.org/cabebooks/ebook/
type: Resource

Open Energy Ontology
keyword: nfdi4energy
0000005: 00030015
has provider formatter: https://openenergyplatform.org/ontology/oeo/OEO_$1
has URI prefix: https://openenergyplatform.org/ontology/oeo/OEO_
has responsible: Mirjam Stappel
has download URL: oeo-full.owl
type: Resource
keyword: nfdi4ing
description: OEO is a domain reference ontology for energy system modeling.
has reviewer: Charles Tapley Hoyt
git repository: ontology
contributor: Mirjam Stappel
keyword: ontology
is deprecated: false
keyword: energy
keyword: engineering
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: OEO_00030015
has prefix: oeo
keyword: mechanical engineering, energy technology
keyword: energy engineering

Japan Registry of Clinical Trials
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://jrct.niph.go.jp/en-latest-detail/$1
type: Resource
has URI prefix: https://jrct.niph.go.jp/en-latest-detail/
is deprecated: false
has local unique identifier pattern: ^jRCT\w?\d+$
has resource example: jRCTs041220087
description: This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring Safety of Regenerative Medicine, etc.' It is a system for performing notification procedures such as In addition, based on the clinical research practice standards stipulated in the same law, we disclose information that the World Health Organization (WHO) requires to be disclosed, information that ensures the transparency of the research process, and information that contributes to the selection of participation in clinical research by the public. (translated from website)
has prefix: jrct
0000005: jRCTs041220087

Plant Environment Ontology
is deprecated: true
description: The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.
keyword: obo
keyword: ontology
git repository: plant-environment-ontology
appears in: The Food Ontology
has provider formatter: http://purl.obolibrary.org/obo/EO_$1
has prefix: eo
has download URL: peco.owl
keyword: plant
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
type: Resource
has resource example: EO_0007404
0000005: 0007404
has URI prefix: http://purl.obolibrary.org/obo/EO_
has responsible: Pankaj Jaiswal

National Science Foundation Award
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
0000005: 1458400
has resource example: https://www.nsf.gov/awardsearch/showAward
description: Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research.
has provider formatter: https://www.nsf.gov/awardsearch/showAward
has URI prefix: https://www.nsf.gov/awardsearch/showAward
type: Resource
has prefix: nsf.award

Chemical Methods Ontology
has resource example: CHMO_0002902
keyword: electron microscopy
has local unique identifier pattern: ^\d{7}$
type: Resource
has prefix: chmo
description: CHMO, the chemical methods ontology, describes methods used to
has responsible: Colin Batchelor
has download URL: chmo.owl
keyword: mass spectrometry assay
keyword: chromatography
appears in: Radiation Biology Ontology
0000005: 0002902
has provider formatter: http://purl.obolibrary.org/obo/CHMO_$1
keyword: obo
appears in: Sickle Cell Disease Ontology
keyword: ontology
is deprecated: false
git repository: rsc-cmo
has URI prefix: http://purl.obolibrary.org/obo/CHMO_
is part of: Bioregistry
keyword: dataplant
keyword: chemistry
keyword: nfdi4cat
keyword: assay
keyword: nfdi4chem

ChecklistBank
type: Resource
has prefix: clb
is deprecated: false
0000005: 1010
has URI prefix: https://www.checklistbank.org/dataset/
is part of: Bioregistry
description: ChecklistBank is an index and repository for taxonomic and nomenclatural datasets
has provider formatter: https://www.checklistbank.org/dataset/$1
has local unique identifier pattern: ^[0-9]+(LR)?$
has resource example: https://www.checklistbank.org/dataset/1010

Phenoscape Publication
description: Documentation of the Phenoscape Curation Workflow
is deprecated: false
is part of: Bioregistry
has prefix: pspub
contributor: Charles Tapley Hoyt
type: Resource

Functional Requirements for Bibliographic Records Entity-Relationship Model
has URI prefix: http://iflastandards.info/ns/fr/frbr/frbrer/
description: This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)
has provider formatter: http://iflastandards.info/ns/fr/frbr/frbrer/$1
keyword: frbr
is deprecated: false
is part of: Bioregistry
0000005: 1001
contributor: Charles Tapley Hoyt
has resource example: http://iflastandards.info/ns/fr/frbr/frbrer/1001
type: Resource
has prefix: frbrer

KEGG Environ
description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.
0000005: ev:E00032
type: Resource
has prefix: kegg.environ
is deprecated: true
has provider formatter: http://www.kegg.jp/entry/$1
has URI prefix: http://www.kegg.jp/entry/
has alternative prefix: KEGG.EDRUG
has local unique identifier pattern: ^(ev\:)?E\d+$
has resource example: ev:E00032
is part of: Bioregistry
is part of: Kyoto Encyclopedia of Genes and Genomes

SAREF4INMA: an extension of SAREF for the industry and manufacturing domain
has prefix: saref.industry
description: SAREF4INMA is an extension of SAREF for the industry and manufacturing domain. SAREF4INMA focuses on extending SAREF for the industry and manufacturing domain to solve the lack of interoperability between various types of production equipment that produce items in a factory and, once outside the factory, between different organizations in the value chain to uniquely track back the produced items to the corresponding production equipment, batches, material and precise time in which they were manufactured. SAREF4INMA is specified and published by ETSI in the TS 103 410-5 associated to this ontology file. SAREF4INMA was created to be aligned with related initiatives in the smart industry and manufacturing domain in terms of modelling and standardization, such as the Reference Architecture Model for Industry 4.0 (RAMI), which combines several standards used by the various national initiatives in Europe that support digitalization in manufacturing. The full list of use cases, standards and requirements that guided the creation of SAREF4INMA are described in the associated ETSI TR 103 507.
keyword: industry
0000005: Area
has URI prefix: https://saref.etsi.org/saref4inma/
has alternative prefix: s4inma
is deprecated: false
is part of: Bioregistry
has provider formatter: https://saref.etsi.org/saref4inma/$1
keyword: engineering
type: Resource
keyword: iot
has resource example: Area
keyword: nfdi4ing

SWEET Ontology Property
has URI prefix: http://sweetontology.net/prop/
has provider formatter: http://sweetontology.net/prop/$1
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.prop
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property
type: Resource
git repository: sweet
has alternative prefix: soprop
0000005: Accuracy
keyword: property
has resource example: Accuracy

Biological Spatial Ontology
git repository: biological-spatial-ontology
has URI prefix: http://purl.obolibrary.org/obo/BSPO_
keyword: ontology
has resource example: BSPO_0000029
keyword: physiology
appears in: Coleoptera Anatomy Ontology
is deprecated: false
is part of: Bioregistry
0000005: 0000029
appears in: FuTRES Ontology of Vertebrate Traits
keyword: phenotype
appears in: Zebrafish Phenotype Ontology
has prefix: bspo
keyword: phenomics
has download URL: bspo.owl
keyword: functional domain
description: An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.
has local unique identifier pattern: ^\d{7}$
type: Resource
appears in: Ontology for the Anatomy of the Insect SkeletoMuscular system
has provider formatter: http://purl.obolibrary.org/obo/BSPO_$1
appears in: Uber Anatomy Ontology
keyword: anatomy
appears in: Lepidoptera Anatomy Ontology
keyword: systems biology
keyword: life science
has responsible: https://orcid.org/0000-0002-6601-2165
keyword: obo

Allotrope Merged Ontology Suite
description: Allotrope Merged Ontology Suite
is part of: Bioregistry
has provider formatter: http://purl.allotrope.org/ontologies/$1
has part: Allotrope role
type: Resource
has responsible: Allotrope Foundation
keyword: nfdi4ing
has part: Allotrope process
has part: Allotrope result
has URI prefix: http://purl.allotrope.org/ontologies/
has resource example: AFR_10001055
keyword: ontology
has part: Allotrope quality
0000005: result#AFR_10001055
has download URL: merged-without-qudt-and-inferred
is deprecated: false
keyword: chemistry
keyword: nfdi4cat
keyword: nfdi4chem
has prefix: afo

Open Tree of Life
has URI prefix: https://tree.opentreeoflife.org/taxonomy/browse
has resource example: https://tree.opentreeoflife.org/taxonomy/browse
has provider formatter: https://tree.opentreeoflife.org/taxonomy/browse
contributor: https://orcid.org/0000-0003-2699-3066
is deprecated: false
description: Identifier for an entity in open tree of life
has local unique identifier pattern: ^[1-9]\d*$
is part of: Bioregistry
0000005: 3905431
type: Resource
has prefix: otol
has reviewer: Charles Tapley Hoyt

Complex Portal
has local unique identifier pattern: ^CPX-[0-9]+$
has responsible: 0009-0004-6468-260X
has responsible: https://orcid.org/0000-0001-7456-0594
has URI prefix: https://www.ebi.ac.uk/complexportal/complex/
has prefix: complexportal
keyword: ontology
is deprecated: false
has provider formatter: https://www.ebi.ac.uk/complexportal/complex/$1
has alternative prefix: ComplexPortal
0000005: CPX-263
has download URL: complexportal.owl
has resource example: CPX-263
description: A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.
is part of: Bioregistry
type: Resource
keyword: protein complex

NIST/CODATA ID
is part of: Bioregistry
has prefix: nist.codata
type: Resource
0000005: c
is deprecated: false
description: identifier for a physical constant
has URI prefix: https://physics.nist.gov/cgi-bin/cuu/Value
has resource example: https://physics.nist.gov/cgi-bin/cuu/Value
has provider formatter: https://physics.nist.gov/cgi-bin/cuu/Value

MathModDB Ontology
keyword: nfdi4ing
has prefix: mathmoddb
keyword: computer science
has provider formatter: https://mardi4nfdi.de/mathmoddb#$1
is deprecated: false
has resource example: ComputationalTask
has URI prefix: https://mardi4nfdi.de/mathmoddb#
0000005: ComputationalTask
keyword: mathematics
is part of: Bioregistry
git repository: MathModDB
keyword: engineering
description: This is the MathModDB Ontology for documenting mathematical models.
type: Resource

TIB Terminology Service
description: An instance of the EBI Lookup Service deployed by TIB
has provider formatter: https://terminology.tib.eu/ts/ontologies/$1
is deprecated: false
is part of: Bioregistry
0000005: abcd
has responsible: https://orcid.org/0000-0001-5246-9351
type: Resource
contributor: Charles Tapley Hoyt
has prefix: tib.ts
has resource example: abcd
has URI prefix: https://terminology.tib.eu/ts/ontologies/

A Semantic Web Rule Language Combining OWL and RuleML
has provider formatter: http://www.w3.org/2003/11/swrl#$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
description: SWRL enables Horn-like rules to be combined with an OWL knowledge base.
has URI prefix: http://www.w3.org/2003/11/swrl#
0000005: Variable
keyword: vocabularies
has prefix: swrl
has resource example: Variable
is deprecated: false

Kinetic Simulation Algorithm Ontology
is deprecated: false
has resource example: KISAO_0000057
keyword: bioinformatics
has alternative prefix: biomodels.kisao
has URI prefix: http://purl.obolibrary.org/obo/KISAO_
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment.
git repository: KiSAO
has prefix: biomodels.kisao
has provider formatter: http://purl.obolibrary.org/obo/KISAO_$1
keyword: algorithm
keyword: computer science
has alternative prefix: kisao
0000005: 0000057
has download URL: kisao.owl
type: Resource
keyword: obo
keyword: ontology
has responsible: Jonathan Karr

General Formal Ontology
description: The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas.
type: Resource
keyword: life science
keyword: ontology
is deprecated: false
keyword: engineering
keyword: foundational ontologies
has URI prefix: http://www.onto-med.de/ontologies/gfo.owl#
is part of: Bioregistry
0000005: projects_to
has resource example: projects to
contributor: Charles Tapley Hoyt
keyword: biomedical science
has download URL: gfo.owl
has prefix: gfo
has provider formatter: http://www.onto-med.de/ontologies/gfo.owl#$1

Common Terminology Criteria for Adverse Events
keyword: biomedical science
has local unique identifier pattern: ^E\d+$
appears in: Ontology of Adverse Events
is deprecated: false
has resource example: E12768
keyword: ontology
has download URL: ctcae.owl
has URI prefix: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae5.owl#
is part of: Bioregistry
keyword: disease
0000005: E12768
has provider formatter: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae5.owl#$1
contributor: Charles Tapley Hoyt
has responsible: Yongqun Oliver He
description: The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI).
type: Resource
keyword: cancer
has prefix: ctcae
has alternative prefix: CTCAE

Wikidata Property
has part: P7471
has part: P3406
has part: P3606
has part: P2646
has part: P11931
has part: P1925
has part: P938
has part: P232
has part: P356
has part: P233
has part: P685
has part: P4550
has part: P591
has part: P6049
has part: P1578
has part: P638
has part: P11199
has part: P1154
has part: P496
has part: P8697
has part: P1579
has part: P4033
has part: P3088
has part: P593
has part: P2576
has part: P683
has part: P2275
has part: P4901
has part: P235
has part: P2106
has part: P3890
has part: P2062
has part: P11089
has part: P1930
has responsible: WikiData Support
has part: P1748
has part: P11198
has part: P11955
has part: P493
has part: P2871
has part: P661
has part: P6689
has part: P8159
has part: P1053
has part: P11956
has part: P299
has part: P1694
has part: P1929
has part: P5039
has part: P4338
has part: P4229
has part: P492
has part: P5806
has part: P213
has part: P1153
has part: P7238
has part: P665
has part: P2798
has part: P4317
has part: P494
has part: P5501
has part: P1294
has part: P2926
has part: P2796
has part: P353
has part: P893
has part: P2410
has part: P227
has part: P4495
has part: P3841
has part: P6634
has part: P8656
has part: P2057
has part: P686
has part: P6861
has part: P3519
has part: P10538
has part: P351
has part: P5299
has part: P7893

Rat Strain Ontology
keyword: obo
keyword: ontology
0000005: 0001807
has provider formatter: http://purl.obolibrary.org/obo/RS_$1
has download URL: rat strain.owl
keyword: strain
is deprecated: false
has prefix: rs
has resource example: RS_0001807
has URI prefix: http://purl.obolibrary.org/obo/RS_
is part of: Bioregistry
git repository: RS-Rat-Strain-Ontology
type: Resource
has responsible: https://orcid.org/0000-0001-5256-8683
has local unique identifier pattern: ^\d{7}$
keyword: mutation
keyword: life science
description: Ontology of rat strains

Darwin Core Terms
has responsible: John Wieczorek
keyword: geographic location
has prefix: dwc
has URI prefix: http://rs.tdwg.org/dwc/terms/
keyword: life science
is deprecated: false
0000005: Dataset
has resource example: Dataset
keyword: biodiversity
is part of: Bioregistry
git repository: dwc
contributor: Charles Tapley Hoyt
description: Darwin Core is a vocabulary standard for transmitting information about biodiversity. This document lists all terms in namespaces currently used in the vocabulary.
keyword: sample annotation
keyword: taxonomic classification
type: Resource
has provider formatter: http://rs.tdwg.org/dwc/terms/$1

SupraBank Molecule
contributor: Charles Tapley Hoyt
type: Resource
0000005: 2196
description: Identifiers for molecules in SupraBank
keyword: molecule
has prefix: suprabank.molecule
has provider formatter: https://suprabank.org/molecules/$1
is deprecated: false
has URI prefix: https://suprabank.org/molecules/
has responsible: https://orcid.org/0000-0002-9676-9839
keyword: chemical
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has resource example: https://suprabank.org/molecules/2196

FlyBase Gene
has URI prefix: https://flybase.org/reports/
keyword: anatomy
keyword: blast
keyword: life science
keyword: faseb list
is deprecated: false
has responsible: Victoria K. Jenkins
keyword: genotype
keyword: image
keyword: bio.tools
has download URL: flybase.owl
keyword: allele
keyword: movie
has prefix: flybase
keyword: ontology
has local unique identifier pattern: ^FB\w{2}\d{7}$
keyword: drosophilidae
keyword: genetics
keyword: rna-seq
keyword: sequence
keyword: genome
keyword: genomics
keyword: dna
0000005: FBgn0011293
has provider formatter: https://flybase.org/reports/$1
is part of: Bioregistry
keyword: molecular biology
keyword: stock
keyword: bioinformatics
keyword: phenotype
has alternative prefix: FlyBase
keyword: video resource
keyword: functional genomics
keyword: image collection
type: Resource
keyword: life-cycle
keyword: mutant
keyword: gene
keyword: controlled term
has resource example: FBgn0011293
keyword: interaction
keyword: molecular genetics
description: FlyBase is the database of the Drosophila Genome Projects and of associated literature.
keyword: comparative genomics
keyword: expression
has alternative prefix: FB

SWEET Ontology Representation Mathematics Operation
has alternative prefix: sorepmo
has prefix: sweet.repmo
0000005: AreaIntegral
has resource example: AreaIntegral
keyword: representation mathematics operation
is part of: Bioregistry
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Operation
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/reprMathOperation/$1
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
has URI prefix: http://sweetontology.net/reprMathOperation/

Lepidoptera Anatomy Ontology
depends on: Basic Formal Ontology
keyword: ontology
0000005: 0000005
depends on: Common Anatomy Reference Ontology
is deprecated: false
has prefix: lepao
git repository: lepao
has resource example: LEPAO_0000005
depends on: Relation Ontology
depends on: Ontology for the Anatomy of the Insect SkeletoMuscular system
description: The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research.
is part of: Bioregistry
type: Resource
has responsible: https://orcid.org/0000-0002-9136-9932
depends on: Phenotype And Trait Ontology
depends on: Uber Anatomy Ontology
has local unique identifier pattern: ^\d{7}$
has download URL: lepao.owl
has URI prefix: http://purl.obolibrary.org/obo/LEPAO_
has provider formatter: http://purl.obolibrary.org/obo/LEPAO_$1
keyword: obo
depends on: Biological Spatial Ontology

Coronavirus Infectious Disease Ontology
has resource example: CIDO_0000005
keyword: drug interaction
has local unique identifier pattern: ^\d{7}$
git repository: cido
has provider formatter: http://purl.obolibrary.org/obo/CIDO_$1
keyword: drug
has download URL: cido.owl
keyword: obo
keyword: ontology
has prefix: cido
keyword: drug discovery
keyword: covid-19
keyword: infection process
0000005: 0000005
is deprecated: false
keyword: disease
has URI prefix: http://purl.obolibrary.org/obo/CIDO_
keyword: drug repositioning
keyword: bioinformatics
keyword: virology
is part of: Bioregistry
description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.
type: Resource
keyword: epidemiology
has responsible: Yongqun Oliver He

MycoBrowser leprae
keyword: genome
has local unique identifier pattern: ^ML\w+$
is deprecated: false
has URI prefix: https://mycobrowser.epfl.ch/genes/
is part of: Bioregistry
type: Resource
0000005: ML0224
description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.
has provider formatter: https://mycobrowser.epfl.ch/genes/$1
is part of: MycoBrowser
has prefix: myco.lepra
has resource example: ML0224
keyword: sequence

Bibliometric Data Ontology
description: An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF.
keyword: subject agnostic
git repository: bido
is deprecated: false
has resource example: CategorialBibliometricData
has prefix: bido
0000005: CategorialBibliometricData
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has responsible: Silvio Peroni
has provider formatter: http://purl.org/spar/bido/$1
type: Resource
has URI prefix: http://purl.org/spar/bido/

Protein modification
is part of: Bioregistry
keyword: protein
keyword: dataplant
keyword: chemistry
0000005: 01467
keyword: nfdi4chem
keyword: proteomics
keyword: life sciences, biology
has prefix: mod
type: Resource
has download URL: mod.owl
keyword: post-translational protein modification
keyword: enzymatic reaction
keyword: structure
keyword: molecule
has URI prefix: http://purl.obolibrary.org/obo/MOD_
description: The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications.
keyword: life science
has resource example: MOD_01467
keyword: obo
git repository: psi-mod-CV
has alternative prefix: PSI-MOD
has responsible: Pierre-Alain Binz
keyword: ontology
has local unique identifier pattern: ^\d{5}$
has provider formatter: http://purl.obolibrary.org/obo/MOD_$1
keyword: chemical biology
is deprecated: false

Kyoto Encyclopedia of Genes and Genomes
0000005: hsa00190
has part: KEGG Disease
has part: KEGG Orthology
has prefix: kegg
has alternative prefix: KEGG
has part: KEGG Compound
type: Resource
has part: KEGG genome
is deprecated: true
description: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
has part: KEGG Module
has part: KEGG LIGAND
has part: KEGG Glycan
has part: KEGG gene
has provider formatter: http://www.kegg.jp/entry/$1
has URI prefix: http://www.kegg.jp/entry/
has local unique identifier pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$
has part: KEGG Metagenome
has part: KEGG Drug Group
has part: KEGG Environ
has part: KEGG Reaction
has part: kegg.rclass
is part of: Bioregistry
has part: KEGG Enzyme
has resource example: hsa00190
has part: KEGG Drug

Human Ancestry Ontology
keyword: human genetics
keyword: obo
keyword: ontology
keyword: population genetics
description: Human ancestry ontology for the NHGRI GWAS Catalog
is deprecated: false
has local unique identifier pattern: ^\d{4}$
is part of: Bioregistry
has responsible: https://orcid.org/0000-0003-1058-2668
0000005: 0290
has resource example: HANCESTRO_0290
keyword: demographics
has download URL: hancestro.owl
has provider formatter: http://purl.obolibrary.org/obo/HANCESTRO_$1
type: Resource
git repository: ancestro
has URI prefix: http://purl.obolibrary.org/obo/HANCESTRO_
keyword: genome-wide association study
has identifier space owner: 02catss52
has prefix: hancestro

AphidBase Transcript
0000005: ACYPI000159
is part of: Bioregistry
keyword: genome
has URI prefix: http://bipaa.genouest.org/apps/grs-2.3/grs
type: Resource
has provider formatter: http://bipaa.genouest.org/apps/grs-2.3/grs
has responsible: https://orcid.org/0000-0002-6472-4839
has resource example: http://bipaa.genouest.org/apps/grs-2.3/grs
description: AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.
is deprecated: false
has local unique identifier pattern: ^ACYPI\d{6}(-RA)?$
has prefix: aphidbase.transcript

ArrayExpress Platform
is part of: Bioregistry
0000005: A-GEOD-50
type: Resource
has provider formatter: https://www.ebi.ac.uk/arrayexpress/arrays/$1
has resource example: A-GEOD-50
is deprecated: false
has prefix: arrayexpress.platform
has URI prefix: https://www.ebi.ac.uk/arrayexpress/arrays/
has local unique identifier pattern: ^[AEP]-\w{4}-\d+$
description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results.

International Standard Name Identifier
has URI prefix: http://www.isni.org/isni/
is deprecated: false
0000005: 000000012281955X
has provider formatter: http://www.isni.org/isni/$1
is part of: Bioregistry
has resource example: 000000012281955X
description: ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC. The mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described.
has local unique identifier pattern: ^[0-9]{15}[0-9X]{1}$
type: Resource
has prefix: isni

DrugBank Condition
has prefix: drugbank.condition
description: Indications and other conditions in drugbank
0000005: DBCOND0066902
is deprecated: false
has URI prefix: https://go.drugbank.com/indications/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: DBCOND0066902
type: Resource
has provider formatter: https://go.drugbank.com/indications/$1
has responsible: David Wishart
has local unique identifier pattern: ^DBCOND\d+$

Yeast Intron Database v3
0000005: SNR17A
has resource example: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb
type: Resource
has prefix: yid
has URI prefix: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb
has local unique identifier pattern: ^[A-Z0-9]+$
description: The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].
is deprecated: true
is part of: Bioregistry
has provider formatter: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb

Open Science Framework ID
has URI prefix: https://osf.io/
has resource example: 2u4tf
has prefix: osf
keyword: work
keyword: paper
0000005: 2u4tf
is deprecated: false
description: ID in osf.io
has provider formatter: https://osf.io/$1
keyword: author
keyword: person
is part of: Bioregistry
keyword: researcher
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^[a-z0-9]{5}$
type: Resource

SWEET Ontology Relationships Human
has alternative prefix: sorelh
has provider formatter: http://sweetontology.net/relaHuman/$1
has resource example: hasAttribute
keyword: human
has URI prefix: http://sweetontology.net/relaHuman/
0000005: hasAttribute
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Human
git repository: sweet
type: Resource
has prefix: sweet.relh

PharmacoDB Tissues
has prefix: pharmacodb.tissue
has URI prefix: https://pharmacodb.ca/tissues/
is deprecated: false
description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has resource example: https://pharmacodb.ca/tissues/13
has provider formatter: https://pharmacodb.ca/tissues/$1
0000005: 13

Metadata4Ing
0000005: Method
has URI prefix: http://w3id.org/nfdi4ing/metadata4ing#
type: Resource
has prefix: m4i
keyword: nfdi4ing
has provider formatter: http://w3id.org/nfdi4ing/metadata4ing#$1
keyword: engineering science
has responsible: Dorothea Iglezakis
keyword: metadata
is deprecated: false
has resource example: Method
has local unique identifier pattern: ^[A-Za-z_0-9]*$
keyword: digital planning and construction
is part of: Bioregistry
keyword: engineering
has identifier space owner: 05qj6w324
keyword: nfdi4cat
keyword: fid baudigital
contributor: Giacomo Lanza
git repository: metadata4ing
description: The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a thorough framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the information contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. "Inheritance" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method × object of research.
has reviewer: Charles Tapley Hoyt
keyword: academy

German Federal Ministry of Education and Research Glossary
has resource example: G1.html
has provider formatter: https://www.datenportal.bmbf.de/portal/de/$1.html
has prefix: bmbf.glossary
0000005: G1
description: A german-language glossary provides you with definitions of the terms used in the portal in the fields of education, science, research and innovation and is updated regularly.
has URI prefix: https://bioregistry.io/bmbf.glossary:
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

BiGG Reaction
keyword: ontology
has prefix: bigg.reaction
has resource example: 13GS
has download URL: bigg.reaction.owl
is part of: Bioregistry
has responsible: https://orcid.org/0000-0003-1238-1499
description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions.
has local unique identifier pattern: ^[a-z_A-Z0-9]+$
has provider formatter: http://bigg.ucsd.edu/models/universal/reactions/$1
type: Resource
has URI prefix: http://bigg.ucsd.edu/models/universal/reactions/
0000005: 13GS
is deprecated: false
keyword: reaction

SWEET Ontology Property Time
has alternative prefix: sopropti
has prefix: sweet.propti
keyword: time
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Time
has URI prefix: http://sweetontology.net/propTime/
is deprecated: false
is part of: Bioregistry
has provider formatter: http://sweetontology.net/propTime/$1
has resource example: Age
is part of: Semantic Web for Earth and Environment Technology Ontology
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
0000005: Age

DrugBank Reaction
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: Reactions in drugbank
has URI prefix: https://go.drugbank.com/reactions/
has provider formatter: https://go.drugbank.com/reactions/$1
contributor: Charles Tapley Hoyt
has responsible: David Wishart
type: Resource
has prefix: drugbank.reaction
0000005: 1537
has resource example: https://go.drugbank.com/reactions/1537

DBLP author ID
has prefix: dblp.author
description: identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/)
has provider formatter: https://dblp.org/pid/$1
0000005: 199/2168
is part of: Bioregistry
type: Resource
has URI prefix: https://dblp.org/pid/
has resource example: https://dblp.org/pid/199/2168
is deprecated: false

IMGT/HLA human major histocompatibility complex sequence database
keyword: rna
keyword: immunology
is part of: Bioregistry
keyword: dna
has alternative prefix: IPD-IMGT/HLA
description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature.
keyword: protein
keyword: immunogenetics
has responsible: Steven G. E. Marsh
0000005: A*01:01:01:01
has resource example: https://www.ebi.ac.uk/ipd/imgt/hla/alleles/
has URI prefix: https://bioregistry.io/imgt.hla:
type: Resource
has prefix: imgt.hla
keyword: biomedical science
has provider formatter: https://www.ebi.ac.uk/ipd/imgt/hla/alleles/?query=eq(name,%22$1%22)
has identifier space owner: 02catss52
is deprecated: false
has local unique identifier pattern: ^[A-Z0-9*:]+$

Uber Anatomy Ontology
depends on: Phenotype And Trait Ontology
appears in: The Echinoderm Anatomy and Development Ontology
appears in: Health Surveillance Ontology
appears in: Porifera Ontology
has alternative prefix: Uberon
keyword: life sciences, biology
depends on: Gene Ontology
0000005: 2005080
depends on: Chemical Entities of Biological Interest
appears in: Lepidoptera Anatomy Ontology
depends on: Protein Ontology
type: Resource
appears in: Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology
appears in: Genomic Epidemiology Ontology
appears in: Provisional Cell Ontology
appears in: Ontology for Nutritional Studies
appears in: Gene Ontology
depends on: NCBI Taxonomy
has alternative prefix: UBERON
appears in: Medical Action Ontology
appears in: Ctenophore Ontology
depends on: Biological Spatial Ontology
depends on: Basic Formal Ontology
appears in: An ontology of core ecological entities
appears in: Mammalian Feeding Muscle Ontology
has resource example: UBERON_2005080
has URI prefix: http://purl.obolibrary.org/obo/UBERON_
has download URL: uberon.owl
keyword: anatomy
appears in: Coleoptera Anatomy Ontology
has prefix: uberon
keyword: taxonomy
appears in: Cell Line Ontology
keyword: life science
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
keyword: obo
appears in: FuTRES Ontology of Vertebrate Traits
has provider formatter: http://purl.obolibrary.org/obo/UBERON_$1
appears in: The Food Ontology
appears in: Clytia hemisphaerica Development and Anatomy Ontology
depends on: Environment Ontology
appears in: ChEBI Integrated Role Ontology
keyword: ontology
depends on: Cell Ontology
description: Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
depends on: Relation Ontology
appears in: Zebrafish Phenotype Ontology
appears in: Environment Ontology
git repository: uberon
is part of: Bioregistry
keyword: developmental biology
keyword: dataplant
appears in: The Amphioxus Development and Anatomy Ontology
has local unique identifier pattern: ^\d+$
has alternative prefix: Uber-anatomy ontology
depends on: OBO Metadata Ontology
appears in: Environmental conditions, treatments and exposures ontology
depends on: Neuro Behavior Ontology
appears in: Cell Ontology
appears in: Microbial Conditions Ontology
appears in: Ontology for the Anatomy of the Insect SkeletoMuscular system

Minimal Viable Identifier
has local unique identifier pattern: ^[A-Za-z0-9]+$
has prefix: minid
has URI prefix: https://hdl.handle.net/hdl:20.500.12582/
type: Resource
keyword: data retrieval
has resource example: b97957
has provider formatter: https://hdl.handle.net/hdl:20.500.12582/$1
description: Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.
keyword: subject agnostic
is deprecated: false
has part: MINID Test
is part of: Bioregistry
has responsible: https://orcid.org/0000-0003-2129-5269
0000005: b97957

NeXusOntology
has provider formatter: http://purl.org/nexusformat/definitions/NeXusOntology#$1
has URI prefix: http://purl.org/nexusformat/definitions/NeXusOntology#
has resource example: version
0000005: version
keyword: physics
description: NeXusOntology: Machine-readable ontology of the NeXus definitions
is deprecated: false
has prefix: nexus
is part of: Bioregistry
keyword: fairmat
type: Resource

Novus Biologicals
description: A vendor of antibodies and other biologics
is deprecated: false
has resource example: nb100-56351
is part of: Bioregistry
0000005: nb100-56351
contributor: Charles Tapley Hoyt
has provider formatter: https://www.novusbio.com/products/$1
has prefix: novus
has URI prefix: https://www.novusbio.com/products/
type: Resource

SWEET Ontology Phenomena Fluid Dynamics
has alternative prefix: sophfd
is part of: Semantic Web for Earth and Environment Technology Ontology
0000005: Anticyclone
keyword: phenomena
has URI prefix: http://sweetontology.net/phenFluidDynamics/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Fluid Dynamics
has resource example: Anticyclone
has provider formatter: http://sweetontology.net/phenFluidDynamics/$1
is deprecated: false
is part of: Bioregistry
keyword: fluid dynamics
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
has prefix: sweet.phfd

U.S. Education Level Vocabulary
description: This vocabulary defines education levels for pre-kindergarten through grade 12 for the United States. It also defines general categories for post-secondary education (vocational, professional and life-long learning).
contributor: Charles Tapley Hoyt
0000005: Pre-K
has responsible: https://orcid.org/0000-0002-3511-2892
has URI prefix: http://purl.org/ASN/scheme/ASNEducationLevel/
keyword: open educational resources
type: Resource
has resource example: Pre-K
is deprecated: false
has provider formatter: http://purl.org/ASN/scheme/ASNEducationLevel/$1
is part of: Bioregistry
keyword: education level
has prefix: ans.educationlevel

ChemBioSys Model
has local unique identifier pattern: ^\d+$
description: A model in the ChemBioSys data platform
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: chembiosys.model
has provider formatter: https://data.chembiosys.de/models/$1
has resource example: https://data.chembiosys.de/models/11
type: Resource
0000005: 11
has URI prefix: https://data.chembiosys.de/models/
is deprecated: false

Teleost taxonomy ontology
type: Resource
0000005: 1058367
has download URL: tto.owl
has URI prefix: http://purl.obolibrary.org/obo/TTO_
keyword: life science
is deprecated: false
keyword: obo
keyword: ontology
git repository: teleost-taxonomy-ontology
is part of: Bioregistry
description: An ontology covering the taxonomy of teleosts (bony fish)
has local unique identifier pattern: ^\d+$
has responsible: https://orcid.org/0000-0002-8688-6599
keyword: taxonomic classification
keyword: phenotype
has prefix: tto
has provider formatter: http://purl.obolibrary.org/obo/TTO_$1
has resource example: TTO_1058367
keyword: fish

Cell Line Ontology [derivative]
has resource example: ThoracicArtery
has provider formatter: http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1
has URI prefix: http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#
is deprecated: true
keyword: ontology
0000005: ThoracicArtery
is part of: Bioregistry
description: Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.
has prefix: mcc
type: Resource
has responsible: Usha Mahadevan

Malaria Ontology
is part of: Bioregistry
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/IDOMAL_
has download URL: idomal.owl
keyword: molecular infection biology
keyword: intervention design
keyword: biomedical science
keyword: malaria
has prefix: idomal
keyword: pathogen
has resource example: IDOMAL_0002350
keyword: life science
keyword: obo
is deprecated: true
has provider formatter: http://purl.obolibrary.org/obo/IDOMAL_$1
appears in: Sickle Cell Disease Ontology
keyword: ontology
has responsible: Pantelis Topalis
0000005: 0002350
keyword: disease
description: An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.
git repository: IDOMAL
has local unique identifier pattern: ^(5?)\d{7}$

Current Procedural Terminology
contributor: 0000-0003-2975-882X
description: Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]
is part of: Bioregistry
has download URL: cpt.owl
has local unique identifier pattern: ^\d+$
type: Resource
contributor: Sierra Moxon
keyword: biomedical science
has URI prefix: https://www.aapc.com/codes/cpt-codes/
has reviewer: Charles Tapley Hoyt
keyword: health science
0000005: 00103
has provider formatter: https://www.aapc.com/codes/cpt-codes/$1
keyword: medicine
has prefix: cpt
has alternative prefix: ama-cpt
keyword: ontology
is deprecated: false
has resource example: https://www.aapc.com/codes/cpt-codes/00103
has responsible: American Medical Association

American Type Culture Collection
description: The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.
has prefix: atcc
is deprecated: false
has alternative prefix: ATCC(dna)
keyword: virology
has resource example: https://www.atcc.org/products/11303
has URI prefix: https://www.atcc.org/products/
is part of: Bioregistry
keyword: epidemiology
type: Resource
has provider formatter: https://www.atcc.org/products/$1
has local unique identifier pattern: ^([a-zA-Z]+-)?\d+(\.\d)?$
0000005: 11303
has alternative prefix: ATCC(in host)
has alternative prefix: ATCC number
keyword: life science
has alternative prefix: ATCC

Cellosaurus Registry
keyword: registry
has resource example: 4DN
has provider formatter: https://bioregistry.io/metaregistry/cellosaurus/$1
is deprecated: false
0000005: 4DN
is part of: Bioregistry
keyword: cells
type: Resource
has URI prefix: https://bioregistry.io/metaregistry/cellosaurus/
contributor: Charles Tapley Hoyt
description: The set of prefixes used in the Cellosaurus resource
keyword: cell lines
has prefix: cellosaurus.resource

TransportDB
is part of: Bioregistry
keyword: protein
has URI prefix: http://www.membranetransport.org/protein.php
description: TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.
type: Resource
has reviewer: Charles Tapley Hoyt
has resource example: http://www.membranetransport.org/protein.php
is deprecated: false
has prefix: transportdb
has provider formatter: http://www.membranetransport.org/protein.php
0000005: MMP0523

eNanoMapper ontology
0000005: 8000221
has prefix: enm
has resource example: ENM_8000221
keyword: health science
type: Resource
has URI prefix: http://purl.enanomapper.org/onto/ENM_
has responsible: Tim Vandermeersch
keyword: ontology
description: The eNanoMapper project (https://www.enanomapper.net/), NanoCommons project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/) are creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO.
is deprecated: false
keyword: chemistry
has download URL: enanomapper.owl
keyword: nfdi4chem
keyword: nanosafety
keyword: nanoparticle
is part of: Bioregistry
keyword: chemical entity
has local unique identifier pattern: ^\d+$
has provider formatter: http://purl.enanomapper.org/onto/ENM_$1

XML Web of Trust Ontology
description: he WOT, or Web Of Trust, schema is designed to facilitate the use of Public Key Cryptography tools such as PGP or GPG to sign RDF documents and document these signatures.
has URI prefix: http://xmlns.com/wot/0.1/
has resource example: EncryptedDocument
is deprecated: false
is part of: Bioregistry
keyword: quality
keyword: security
0000005: EncryptedDocument
has provider formatter: http://xmlns.com/wot/0.1/$1
type: Resource
has prefix: wot
contributor: Charles Tapley Hoyt

SubstrateDB
0000005: 1915
description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.
has prefix: pmap.substratedb
keyword: reaction
keyword: domain
has responsible: https://orcid.org/0000-0003-2023-4608
has resource example: http://substrate.burnham.org/protein/annotation/1915/html
is deprecated: false
keyword: protein
has provider formatter: http://substrate.burnham.org/protein/annotation/$1/html
has URI prefix: https://bioregistry.io/pmap.substratedb:
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource

German University Subject Classification System
type: Resource
git repository: hochschulfaechersystematik
has URI prefix: https://w3id.org/kim/hochschulfaechersystematik/
has provider formatter: https://w3id.org/kim/hochschulfaechersystematik/$1
has resource example: n2
keyword: educational science
has prefix: kim.hochschulfaechersystematik
0000005: n2
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: educational resources
description: A classification of subjects in Hochschule (universities of applied sciences)

Environmental Molecular Sciences Laboratory Project
contributor: 0009-0007-1862-833X
has URI prefix: https://sc-data.emsl.pnnl.gov/
is deprecated: false
has prefix: emsl.project
has resource example: https://sc-data.emsl.pnnl.gov/
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: https://orcid.org/0000-0002-6601-2165
has reviewer: Charles Tapley Hoyt
0000005: 60141
has provider formatter: https://sc-data.emsl.pnnl.gov/
description: As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website. Project pages provide details including: - Research team and institution - The EMSL project DOI - Link to project data available in EMSLs Data Portal - Project type
type: Resource
has responsible: https://orcid.org/0000-0002-8683-0050

NASC code
has URI prefix: http://arabidopsis.info/StockInfo
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^(\w+)?\d+$
has prefix: nasc
has resource example: http://arabidopsis.info/StockInfo
keyword: life science
0000005: N1899
is deprecated: false
keyword: genome
has responsible: Sean May
has provider formatter: http://arabidopsis.info/StockInfo
description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.

Occupation Ontology
type: Resource
has prefix: occo
description: This Occupaton Ontology (OccO) is an ontology in the domain of human occupaitons. Current OccO version is developed based on the US Bureau of Labor Statistics Standard Occupation Classification (SOC) and the related O*Net System. The OccO development follows the principles of the Open Biological and Biomedical (OBO) Foundry.
has URI prefix: http://purl.obolibrary.org/obo/OCCO_
0000005: 00000001
keyword: obo
has download URL: occo.owl
keyword: ontology
has local unique identifier pattern: ^\d+$
is deprecated: false
git repository: OccO
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/OCCO_$1
has responsible: Jie Zheng

Ontology of RNA Sequencing
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/ORNASEQ_$1
description: An application ontology designed to annotate next-generation sequencing experiments performed on RNA.
is deprecated: false
has download URL: ornaseq.owl
keyword: rna-seq assay
has URI prefix: http://purl.obolibrary.org/obo/ORNASEQ_
0000005: 0000010
is part of: Bioregistry
keyword: transcriptomics
type: Resource
keyword: single cell rna-seq
git repository: ornaseq
has resource example: ORNASEQ_0000010
has local unique identifier pattern: ^\d{7}$
has responsible: Stephen Fisher
keyword: single cell
has prefix: ornaseq
keyword: obo

SWEET Ontology Representation Space Geometry 3D
is part of: Bioregistry
git repository: sweet
type: Resource
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has prefix: sweet.repsg3
has alternative prefix: sorepsg3
has resource example: AirSpace
has URI prefix: http://sweetontology.net/reprSpaceGeometry3D/
has provider formatter: http://sweetontology.net/reprSpaceGeometry3D/$1
is deprecated: false
0000005: AirSpace
keyword: representation space geometry 3d
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space Geometry 3D

TriTrypDB
has responsible: Omar S. Harb
has resource example: http://tritrypdb.org/tritrypdb/showRecord.do
is deprecated: false
keyword: genomics
is part of: Bioregistry
type: Resource
has provider formatter: http://tritrypdb.org/tritrypdb/showRecord.do
has URI prefix: http://tritrypdb.org/tritrypdb/showRecord.do
keyword: comparative genomics
0000005: Tb927.8.620
has prefix: tritrypdb
description: TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
keyword: infectious disease medicine
has local unique identifier pattern: ^\w+(\.)?\w+(\.)?\w+$

RiceNetDB Gene
type: Resource
has prefix: ricenetdb.gene
has resource example: http://bis.zju.edu.cn/ricenetdb/genedetails.php
description: RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.
0000005: LOC_Os01g49190.1
has URI prefix: http://bis.zju.edu.cn/ricenetdb/genedetails.php
has provider formatter: http://bis.zju.edu.cn/ricenetdb/genedetails.php
has local unique identifier pattern: ^LOC\_Os\d{1,2}g\d{5}\.\d$
is deprecated: false
is part of: Bioregistry

Protein Model Portal
has prefix: pmp
0000011: UniProt Protein
is part of: Bioregistry
has responsible: 0000-0003-2715-335X
keyword: protein
keyword: prediction
has resource example: Q0VCA6
has provider formatter: http://www.proteinmodelportal.org/query/uniprot/$1
has local unique identifier pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$
type: Resource
description: The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers.
keyword: structure
0000005: Q0VCA6
is deprecated: true
has URI prefix: http://www.proteinmodelportal.org/query/uniprot/

GeoNames Feature Code
has download URL: geonames.feature.owl
has responsible: Marc Wick
keyword: ontology
has URI prefix: https://bioregistry.io/geonames.feature:
is deprecated: false
has resource example: ADM1
is part of: Bioregistry
has prefix: geonames.feature
keyword: geography
0000005: ADM1
has provider formatter: https://www.geonames.org/recent-changes/featurecode/$1/
contributor: Charles Tapley Hoyt
type: Resource
description: All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes.

Metadata Management and distribution system for Multiple GNSS Networks
type: Resource
has provider formatter: https://gnss-metadata.eu/MOID/$1
has local unique identifier pattern: ^[a-zA-Z0-9]+\.[a-f0-9]{24}$
has URI prefix: https://gnss-metadata.eu/MOID/
has prefix: moid
has resource example: station.6051b2f8b9142a5b8c676342
description: M3G stands for “Metadata Management and distribution system for Multiple GNSS Networks”. M3G allows to upload, validate, and distribute GNSS station metadata such as IGS-style site logs, information about local networks, DOIs, nominal data provision, data licenses attached to the daily RINEX data, etc...
is deprecated: false
0000005: station.6051b2f8b9142a5b8c676342
is part of: Bioregistry

BioSchemas
type: Resource
description: Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]
has URI prefix: https://bioschemas.org/profiles/
has alternative prefix: bioschema
is deprecated: false
has resource example: Dataset
has provider formatter: https://bioschemas.org/profiles/$1
0000005: Dataset
git repository: specifications
has alternative prefix: bioschemas_draft
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: bioschemas

Ligand Expo
type: Resource
keyword: nucleic acid
keyword: structure
keyword: interaction
has provider formatter: http://ligand-depot.rutgers.edu/pyapps/ldHandler.py
description: Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.
keyword: life science
is deprecated: false
has prefix: ligandexpo
has local unique identifier pattern: ^(\w){3}$
has resource example: http://ligand-depot.rutgers.edu/pyapps/ldHandler.py
is part of: Bioregistry
keyword: protein
has URI prefix: https://bioregistry.io/ligandexpo:
has responsible: John Westbrook
keyword: chemical
0000005: ABC

Mungbean Ontology
keyword: food
description: The Mungbean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data.
keyword: ontology
has provider formatter: https://cropontology.org/rdf/CO_346:$1
is deprecated: false
keyword: plant phenotypes and traits
has URI prefix: https://cropontology.org/rdf/CO_346:
0000005: 0000199
keyword: phenotype
keyword: agriculture
has responsible: Elizabeth Arnaud
is part of: Bioregistry
has resource example: CO 346:0000199
type: Resource
git repository: Crop-Ontology
has prefix: co_346
has local unique identifier pattern: ^\d{7}$
keyword: life science
has download URL: CO 346.owl

Online Mendelian Inheritance in Man
is part of: Bioregistry
has prefix: omim
keyword: disease course
0000005: 603903
keyword: phenotype
keyword: gene expression
keyword: genetic disorder
type: Resource
keyword: gene
keyword: biomedical science
has resource example: MIM:603903
has URI prefix: https://omim.org/MIM:
has provider formatter: https://omim.org/MIM:$1
is deprecated: false
keyword: genotype
has alternative prefix: mim
keyword: ontology
has responsible: https://orcid.org/0000-0002-1780-5230
description: Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.
has alternative prefix: OMIM
keyword: disease
has local unique identifier pattern: ^\d+$

Oryzabase Gene
has URI prefix: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/
type: Resource
0000005: 117
has prefix: oryzabase.gene
has provider formatter: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1
description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.
has resource example: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/117
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry

Infectious Disease Ontology
git repository: infectious-disease-ontology
has local unique identifier pattern: ^\d{7}$
keyword: preclinical studies
type: Resource
keyword: biomedical science
keyword: molecular infection biology
has prefix: ido
has resource example: IDO_0000504
has URI prefix: http://purl.obolibrary.org/obo/IDO_
is deprecated: false
keyword: classification
keyword: obo
0000005: 0000504
appears in: Sickle Cell Disease Ontology
keyword: ontology
has download URL: ido.owl
description: Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.
keyword: disease
has responsible: Lindsay Cowell
is part of: Bioregistry
contributor: Yohann Paris
has provider formatter: http://purl.obolibrary.org/obo/IDO_$1
keyword: disease course

SWEET Ontology Material Instrument
has alternative prefix: somains
0000005: Anemometer
keyword: instrument
has URI prefix: http://sweetontology.net/matrInstrument/
is deprecated: false
is part of: Bioregistry
has resource example: Anemometer
has prefix: sweet.mains
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/matrInstrument/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Instrument
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
keyword: materials

SWEET Ontology Material Compound
has resource example: ChemicalCompound
keyword: compound
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Compound
has provider formatter: http://sweetontology.net/matrCompound/$1
is part of: Bioregistry
0000005: ChemicalCompound
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: materials
has alternative prefix: somac
has prefix: sweet.mac
has URI prefix: http://sweetontology.net/matrCompound/

SWEET Ontology Phenomena ElectroMagnetic
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/phenElecMag/$1
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.phel
has URI prefix: http://sweetontology.net/phenElecMag/
keyword: phenomena
0000005: CurrentSheet
is deprecated: false
has resource example: CurrentSheet
keyword: electromagnetic
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena ElectroMagnetic
has alternative prefix: sophel

Insect Resistance Ontology
0000005: 0000008
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
type: Resource
contributor: Charles Tapley Hoyt
has prefix: iro
has provider formatter: https://legacy.vectorbase.org/ontology-browser
has URI prefix: https://legacy.vectorbase.org/ontology-browser
is deprecated: true
has resource example: https://legacy.vectorbase.org/ontology-browser

The International Harmonization of Nomenclature and Diagnostic criteria
contributor: Charles Tapley Hoyt
type: Resource
keyword: biomedical science
has prefix: inhand
keyword: toxicity
has responsible: https://orcid.org/0000-0003-4682-0824
is deprecated: false
keyword: disease
description: The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.
is part of: Bioregistry

SWEET Ontology Material Animal
is part of: Bioregistry
has prefix: sweet.man
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/matrAnimal/$1
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: materials
has URI prefix: http://sweetontology.net/matrAnimal/
has resource example: AcornWorm
keyword: animal
has alternative prefix: soman
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Animal
is deprecated: false
0000005: AcornWorm

Dr. Duke's Phytochemical and Ethnobotanical Databases chemical
has URI prefix: https://phytochem.nal.usda.gov/phytochem/chemicals/show/
is deprecated: false
description: identifier for chemicals linked to information on occurrence in plants
is part of: Bioregistry
has provider formatter: https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1
has resource example: https://phytochem.nal.usda.gov/phytochem/chemicals/show/19
type: Resource
0000005: 19
has prefix: drduke

Electron Microscopy Public Image Archive
has identifier space owner: 02catss52
0000005: 10595
is deprecated: false
has resource example: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10595
description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure
has provider formatter: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1
has responsible: https://orcid.org/0000-0001-7663-9028
has URI prefix: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: bioinformatics
contributor: Charles Tapley Hoyt
has prefix: empiar
type: Resource
keyword: biology

Summary Statistic Type
has provider formatter: https://vocabularies.cessda.eu/vocabulary/SummaryStatisticType#code_$1
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has prefix: ddi.summarystatistictype
has identifier space owner: 015em2733
has resource example: code ArithmeticMean
0000005: ArithmeticMean
description: Specifies the type of summary statistic. Summary statistics are a single number representation of the characteristics of a set of values.
has URI prefix: https://vocabularies.cessda.eu/vocabulary/SummaryStatisticType#code_

Mouse Genome Informatics
keyword: pathology
keyword: expression
keyword: life science
keyword: blast
keyword: image
keyword: genotype
keyword: orthology
keyword: data analysis service
keyword: tumor
has prefix: mgi
has provider formatter: http://www.informatics.jax.org/accession/MGI:$1
keyword: ontology
keyword: ontology and terminology
keyword: model
keyword: pathway
keyword: genome
keyword: genetics
keyword: function
is deprecated: false
keyword: strain
keyword: recombinase
keyword: sequence
0000005: 6017782
has resource example: MGI:6017782
keyword: gold standard
keyword: phenotype
keyword: molecular neuroanatomy resource
keyword: animal model
has URI prefix: http://www.informatics.jax.org/accession/MGI:
keyword: gene expression
keyword: human disease
has local unique identifier pattern: ^\d+$
description: The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.
has download URL: mgi.owl.gz
is part of: Bioregistry
keyword: single nucleotide polymorphism
type: Resource
keyword: gene
has responsible: https://orcid.org/0000-0003-3342-5753
has alternative prefix: MGD
keyword: human health
has alternative prefix: MGI

The Statistical Methods Ontology
keyword: data analysis
keyword: graph
keyword: experimental measurement
has prefix: stato
has URI prefix: http://purl.obolibrary.org/obo/STATO_
keyword: ess
keyword: study design
keyword: obo
has provider formatter: http://purl.obolibrary.org/obo/STATO_$1
0000005: 0000288
appears in: Ontology for Avida digital evolution platform
appears in: Sickle Cell Disease Ontology
keyword: ontology
keyword: data visualization
is deprecated: false
appears in: Performance Summary Display Ontology
is part of: Bioregistry
has resource example: STATO_0000288
keyword: dataplant
keyword: statistics
keyword: omics
has responsible: Philippe Rocca-Serra
has download URL: stato.owl
git repository: stato
description: STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.
has local unique identifier pattern: ^\d{7}$
type: Resource

Pseudomonas Genome Database
description: The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.
is part of: Bioregistry
has local unique identifier pattern: ^P\w+$
has prefix: pseudomonas
has URI prefix: http://www.pseudomonas.com/feature/show/
has resource example: http://www.pseudomonas.com/feature/show/
type: Resource
has provider formatter: http://www.pseudomonas.com/feature/show/
0000005: PSEEN0001
is deprecated: false

KIM License
description: A vocabulary describing licenses for data and code
has prefix: kim.license
0000005: nonCommercial
git repository: license
has URI prefix: https://w3id.org/kim/license/
is deprecated: false
has provider formatter: https://w3id.org/kim/license/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
keyword: license
has resource example: nonCommercial

Epidemiology Ontology
description: An ontology designed to support the semantic annotation of epidemiology resources
contributor: https://orcid.org/0000-0002-7276-9009
has URI prefix: http://purl.obolibrary.org/obo/EPO_
has prefix: epo
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/EPO_$1
is part of: Bioregistry
type: Resource
has download URL: epo.owl
is deprecated: true

International Classification of Diseases, 9th Revision
has alternative prefix: ICD9_2005
has prefix: icd9
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^((\d\d\d|V\d\d|E[8-9]\d\d)(\.\d{1,2})?)|(\d{1,3}-\d{1,3})$
has provider formatter: http://www.icd9data.com/getICD9Code.ashx
description: The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics.
has alternative prefix: ICD9
has URI prefix: http://www.icd9data.com/getICD9Code.ashx
0000005: 277.9
type: Resource
has alternative prefix: MTHICD9_2006
has resource example: http://www.icd9data.com/getICD9Code.ashx
is deprecated: false

FlyBase Reference Report
has local unique identifier pattern: ^\d{7}$
type: Resource
contributor: Charles Tapley Hoyt
0000005: 0187632
has prefix: fbrf
description: FlyBase internal citation identifiers
has resource example: FBrf0187632
has provider formatter: https://flybase.org/reports/FBrf$1
has URI prefix: https://flybase.org/reports/FBrf
is deprecated: false
is part of: Bioregistry

SWEET Ontology Human
is deprecated: false
has provider formatter: http://sweetontology.net/human/$1
has resource example: Behavior
has alternative prefix: sohu
keyword: human
has prefix: sweet.hu
0000005: Behavior
is part of: Bioregistry
has URI prefix: http://sweetontology.net/human/
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
type: Resource

DrugBank Drug Category
keyword: topics
is part of: Bioregistry
keyword: chemistry
contributor: Charles Tapley Hoyt
description: Close to 5K Categorizations for drugs, similar to ATCC.
has local unique identifier pattern: ^DBCAT\d+$
type: Resource
has responsible: David Wishart
has URI prefix: https://www.drugbank.ca/categories/
0000005: DBCAT000600
has prefix: drugbank.category
keyword: drugs
is deprecated: false
has provider formatter: https://www.drugbank.ca/categories/$1
keyword: metascience
has resource example: DBCAT000600

Mention Typing Ontology
keyword: nlp
has responsible: https://orcid.org/0009-0006-3139-1667
has provider formatter: http://purl.org/spar/mito/$1
is deprecated: false
description: An ontology with predicates to formalization of the concept of mentions. The mentions may be either explicit (e.g. as when well stated into an article "Dr. Johnson's groundbreaking research on climate change") or implicit (e.g. such as discussing "seminal studies in the field"). MiTO contains the object property mito:mentions and its inverse mito:isMentionedBy.
has prefix: mito
keyword: ontology
has URI prefix: http://purl.org/spar/mito/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: mito
keyword: text mining
keyword: ner
0000005: MentionType
type: Resource
has resource example: MentionType
keyword: mentions
keyword: natural language processing

iNaturalist Taxonomy
has prefix: inaturalist.taxon
0000005: 21723
has URI prefix: https://www.inaturalist.org/taxa/
has resource example: https://www.inaturalist.org/taxa/21723
description: Identifier for a species in iNaturalist
has local unique identifier pattern: ^[1-9]\d{0,6}$
type: Resource
has provider formatter: https://www.inaturalist.org/taxa/$1
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt

Evidence and Conclusion Ontology
keyword: assay
keyword: sample annotation
keyword: evidence
0000005: 0007807
has prefix: eco
keyword: literature curation
has URI prefix: http://purl.obolibrary.org/obo/ECO_
keyword: text mining
has local unique identifier pattern: ^\d{7}$
type: Resource
has responsible: https://orcid.org/0000-0001-7628-5565
has download URL: eco.owl
contributor: https://orcid.org/0000-0003-3035-6940
has provider formatter: http://purl.obolibrary.org/obo/ECO_$1
keyword: life science
git repository: evidenceontology
keyword: study design
is deprecated: false
keyword: obo
has resource example: ECO_0007807
keyword: ontology
keyword: biocuration
description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.
keyword: curated information
keyword: computational biology
keyword: digital curation
keyword: resource metadata
is part of: Bioregistry

LRMI Educational Use Vocabulary
is deprecated: false
keyword: learning resource
has prefix: lrmi.eduse
description: A concept scheme that enumerates the educational uses of a learning resource.
is part of: Bioregistry
git repository: lrmi
type: Resource
keyword: open educational resource
contributor: Charles Tapley Hoyt
0000005: instruction
has URI prefix: http://purl.org/dcx/lrmi-vocabs/educationalUse/
has provider formatter: http://purl.org/dcx/lrmi-vocabs/educationalUse/$1
has resource example: instruction

Spectral Database for Organic Compounds
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
description: The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra.
has provider formatter: https://sdbs.db.aist.go.jp/CompoundView.aspx
has URI prefix: https://sdbs.db.aist.go.jp/CompoundView.aspx
0000005: 4544
has resource example: https://sdbs.db.aist.go.jp/CompoundView.aspx
is deprecated: false
has prefix: sdbs

Catalogue of Life
has URI prefix: https://www.checklistbank.org/dataset/3LR/taxon/
has local unique identifier pattern: ^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$
has provider formatter: https://www.checklistbank.org/dataset/3LR/taxon/$1
is deprecated: false
description: Identifier of a taxon or synonym in the Catalogue of Life
0000005: 4QHKG
is part of: Bioregistry
type: Resource
has prefix: col
has resource example: 4QHKG

Library of Congress Control Number
description: LCCN Permalinks are persistent URLs for bibliographic records in the LC Catalog and authority records in LC Authorities. These links are constructed using the record's LCCN (or Library of Congress Control Number), an identifier assigned by the Library of Congress to bibliographic and authority records. LCCN Permalinks are also available for citation records in the Handbook for Latin American Studies (HLAS). [from homepage]
has URI prefix: https://lccn.loc.gov/
has provider formatter: https://lccn.loc.gov/$1
type: Resource
contributor: Charles Tapley Hoyt
has resource example: https://lccn.loc.gov/2011488555
is deprecated: false
0000005: 2011488555
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: lccn

Alzheimer Gene Database
keyword: gene
has responsible: 0000-0002-0108-124X
has provider formatter: http://www.alzgene.org/geneoverview.asp
has URI prefix: http://www.alzgene.org/geneoverview.asp
is deprecated: false
has prefix: alzgene
is part of: Bioregistry
description: The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data.
has resource example: http://www.alzgene.org/geneoverview.asp
has reviewer: Charles Tapley Hoyt
0000005: 88
type: Resource

eVOC (Expressed Sequence Annotation for Humans)
keyword: anatomy
is deprecated: true
keyword: obo
keyword: experiment
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/EV_
has resource example: EV_0100011
appears in: Cell Ontology
is part of: Bioregistry
has responsible: eVOC mailing list
has prefix: ev
0000005: 0100011
type: Resource
description: Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.
keyword: development
has provider formatter: http://purl.obolibrary.org/obo/EV_$1
keyword: cell
has local unique identifier pattern: ^\d{7}$

Langua aLimentaria Thesaurus
is deprecated: false
has provider formatter: https://www.langual.org/langual_thesaurus.asp
has local unique identifier pattern: ^B\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
0000005: B2067
has prefix: langual
has URI prefix: https://www.langual.org/langual_thesaurus.asp
description: Langual stands for "langua alimentaria" or "language of food". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases
has resource example: https://www.langual.org/langual_thesaurus.asp

Xenopus Anatomy Ontology
is deprecated: false
keyword: developmental biology
has download URL: xao.owl
has responsible: https://orcid.org/0000-0002-9611-1279
has provider formatter: http://purl.obolibrary.org/obo/XAO_$1
git repository: xao
appears in: Xenopus Phenotype Ontology
keyword: life cycle
is part of: Bioregistry
type: Resource
keyword: structure
description: XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.
has resource example: XAO_0004486
has local unique identifier pattern: ^\d{7}$
keyword: anatomy
keyword: morphology
keyword: life science
keyword: obo
0000005: 0004486
has URI prefix: http://purl.obolibrary.org/obo/XAO_
keyword: ontology
has prefix: xao
keyword: life cycle stage

Cell Signaling Technology Antibody
has alternative prefix: cst.ab
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products.
0000005: 3305
has URI prefix: https://bioregistry.io/cst.antibody:
has prefix: cst.antibody
has provider formatter: http://www.cellsignal.com/products/$1.html
is deprecated: false
keyword: pathway
has resource example: 3305.html

Pan African Clinical Trials Registry
has prefix: pactr
description: The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. The registry is an African initiative serving the needs of Africans. It provides an open-access platform where clinical trials can be registered free of charge. The PACTR aims to increase clinical trial registration in Africa by developing awareness of the need to register trials and supporting trialists during registration. (from homepage)
is deprecated: false
has local unique identifier pattern: ^PACTR\d+$
0000005: PACTR202304525632216
contributor: Charles Tapley Hoyt
is part of: Bioregistry
type: Resource

Recommendation Ontology
keyword: rec
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: The Recommendation Ontology specification provides basic concepts and properties for describing recommendations on/for the Semantic Web.
has URI prefix: http://purl.org/ontology/rec/core#
has download URL: recommendationontology.owl
type: Resource
0000005: Recommendation
has prefix: rec
is deprecated: false
has provider formatter: http://purl.org/ontology/rec/core#$1
keyword: ontology
has resource example: Recommendation

LINCS Data
0000005: LDS-1110
has URI prefix: http://lincsportal.ccs.miami.edu/datasets/#/view/
has resource example: view/LDS-1110
description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).
has prefix: lincs.data
is deprecated: false
has local unique identifier pattern: ^[EL]D[SG]-\d+$
is part of: Bioregistry
has provider formatter: http://lincsportal.ccs.miami.edu/datasets/#/view/$1
type: Resource

Lonza
has URI prefix: https://knowledge.lonza.com/cell
0000005: 968
description: Contains information about cells and data sheets related to transfection.
has provider formatter: https://knowledge.lonza.com/cell
is deprecated: false
has resource example: https://knowledge.lonza.com/cell
is part of: Bioregistry
has prefix: lonza
has local unique identifier pattern: ^\d+$
type: Resource
contributor: Charles Tapley Hoyt

Phenol-Explorer
0000005: 75
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis.
has provider formatter: http://phenol-explorer.eu/foods/$1
type: Resource
has URI prefix: http://phenol-explorer.eu/foods/
has resource example: http://phenol-explorer.eu/foods/75
has prefix: phenolexplorer

HMS LINCS Compound
0000005: 10001-101
has provider formatter: https://lincs.hms.harvard.edu/db/sm/$1
is part of: Bioregistry
has alternative prefix: hmsl_id
contributor: Charles Tapley Hoyt
type: Resource
has local unique identifier pattern: ^1\d{4}-\d{3}$
has prefix: hms.lincs.compound
has resource example: https://lincs.hms.harvard.edu/db/sm/10001-101
description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.
has URI prefix: https://lincs.hms.harvard.edu/db/sm/
has alternative prefix: HMS-LINCS
is deprecated: false

NCBI Probe database Public registry of nucleic acid reagents
has URI prefix: https://www.ncbi.nlm.nih.gov/probe/
description: The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.
is deprecated: true
has provider formatter: https://www.ncbi.nlm.nih.gov/probe/
has prefix: dbprobe
0000005: 1000000
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: nucleotide
has resource example: https://www.ncbi.nlm.nih.gov/probe/
type: Resource

Feature Annotation Location Description Ontology
keyword: binding site
keyword: nucleic acid sequence
keyword: sequence feature
has resource example: ForwardStrandPosition
git repository: FALDO
keyword: ontology
keyword: gene feature
0000005: ForwardStrandPosition
keyword: genetics
is deprecated: false
has URI prefix: http://biohackathon.org/resource/faldo#
is part of: Bioregistry
has download URL: faldo.owl
contributor: Charles Tapley Hoyt
keyword: geography
keyword: sequence annotation
description: It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources
has provider formatter: http://biohackathon.org/resource/faldo#$1
has responsible: FALDO group
has prefix: faldo
type: Resource

DataPLANT Biology Ontology
is deprecated: false
has URI prefix: https://purl.org/nfdi4plants/ontology/dpbo/DPBO_
contributor: https://orcid.org/0000-0002-0476-9699
keyword: dataplant
has prefix: dpbo
has resource example: DPBO_0010015
keyword: life sciences, biology
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
has provider formatter: https://purl.org/nfdi4plants/ontology/dpbo/DPBO_$1
git repository: nfdi4plants ontology
has reviewer: Charles Tapley Hoyt
has responsible: https://orcid.org/0000-0002-8000-0400
has responsible: https://orcid.org/0000-0002-9905-4011
description: With the DataPLANT biology ontology (DPBO), DataPLANT provides an intermediate ontology that acts as a broker and bridge between the individual researcher/domain experts and main ontology providers. DPBO enables easy and agile collection of missing vocabulary as well as relationships between terms for (meta)data annotation using DataPLANT’s Swate tool.
has download URL: dpbo.obo
0000005: 0010015
keyword: ontology

Common Entity Data Standards - Domain Entity Schema
has provider formatter: https://ceds.ed.gov/element/$1
0000005: 000254
has URI prefix: https://ceds.ed.gov/element/
has prefix: ceds.element
is deprecated: false
has local unique identifier pattern: ^\d+$
description: The Common Entity Data Standards (CEDS) Domain Entity Schema (DES) provides a hierarchy of domains, entities, categories, and elements. It is intended for use primarily by people as an index to search, map, and organize elements in a logical way. [from homepage]
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: https://ceds.ed.gov/element/000254
type: Resource

Plant Stress Ontology
keyword: botany
depends on: Relation Ontology
description: The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.
has URI prefix: http://purl.obolibrary.org/obo/PSO_
is part of: Bioregistry
keyword: life sciences, biology
git repository: plant-stress-ontology
keyword: agronomy
has resource example: PSO_0000013
has local unique identifier pattern: ^\d{7}$
type: Resource
has responsible: Laurel Cooper
has prefix: pso
keyword: obo
keyword: ontology
0000005: 0000013
has download URL: pso.owl
is deprecated: false
keyword: dataplant
has provider formatter: http://purl.obolibrary.org/obo/PSO_$1

Identifiers.org namespace
is part of: Bioregistry
has prefix: miriam
0000005: pubmed
keyword: biomedical science
has URI prefix: https://registry.identifiers.org/registry/
has local unique identifier pattern: ^[0-9a-z_:\.-]+$
has provider formatter: https://registry.identifiers.org/registry/$1
keyword: life science
description: Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain.
keyword: biochemistry
type: Resource
has responsible: Nicolas Le Novere
has resource example: pubmed
has alternative prefix: identifiers.namespace
is deprecated: false

PhosphoPoint Phosphoprotein
is deprecated: true
description: PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information.
has provider formatter: http://kinase.bioinformatics.tw/showall.jsp
has resource example: http://kinase.bioinformatics.tw/showall.jsp
has local unique identifier pattern: ^\w+$
has URI prefix: https://bioregistry.io/phosphopoint.protein:
is part of: Bioregistry
type: Resource
has prefix: phosphopoint.protein
0000005: AURKA

ShiBASE
is part of: Bioregistry
has URI prefix: http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi
0000005: SDY2614
has provider formatter: http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi
has resource example: http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi
type: Resource
has reviewer: Charles Tapley Hoyt
has prefix: shibase
is deprecated: true
keyword: genome
description: The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format.

MicroScope
has responsible: MEDIGUE Claudine
description: MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.
keyword: comparative genomics
keyword: life science
has provider formatter: http://www.genoscope.cns.fr/agc/microscope/mage/info.php
has resource example: http://www.genoscope.cns.fr/agc/microscope/mage/info.php
has prefix: microscope
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
0000005: 5601141
has URI prefix: http://www.genoscope.cns.fr/agc/microscope/mage/info.php
type: Resource

Diagnostic and Statistical Manual of Mental Disorders (4th Edition)
has local unique identifier pattern: ^\d+\.\d+$
type: Resource
0000005: 315.1
is deprecated: false
has alternative prefix: dsm-iv
has prefix: dsm4
description: A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]
is part of: Bioregistry
contributor: Charles Tapley Hoyt

HoloFood sample
has provider formatter: https://www.holofooddata.org/sample/$1
has responsible: https://orcid.org/0000-0002-5805-7195
has URI prefix: https://www.holofooddata.org/sample/
has reviewer: https://orcid.org/0000-0001-9439-5346
type: Resource
0000005: SAMEA10104908
has local unique identifier pattern: ^SAMEA\d{8}$
contributor: 0009-0008-8406-631X
has prefix: holofood.sample
description: The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the samples semantic space represent samples derived from animals in HoloFood trials.
has resource example: SAMEA10104908
is deprecated: false
is part of: Bioregistry

NIF Standard Ontology: Investigations
is part of: Bioregistry
type: Resource
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1
keyword: data analysis
has reviewer: Charles Tapley Hoyt
has prefix: nlx.inv
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_inv_
contributor: Tom Gillespie
has resource example: nlx inv 90901
has alternative prefix: NLXINV
description: NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis.
is deprecated: false
git repository: NIF-Ontology
0000005: 90901
keyword: funding agencies
has responsible: Tom Gillespie
has local unique identifier pattern: ^\d+$

Tissue List
has prefix: uniprot.tissue
description: The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified.
is part of: Bioregistry
has provider formatter: https://www.uniprot.org/tissues/$1
0000005: TS-0285
type: Resource
has responsible: Alex Bateman
is deprecated: false
has local unique identifier pattern: ^TS-\d{4}$
has URI prefix: https://www.uniprot.org/tissues/
has resource example: TS-0285

Flybase Cell Line
has prefix: fbtc
contributor: Charles Tapley Hoyt
has provider formatter: https://flybase.org/reports/FBtc$1
has alternative prefix: FlyBase_Cell_line
has local unique identifier pattern: ^\d{7}$
type: Resource
has URI prefix: https://flybase.org/reports/FBtc
has resource example: FBtc0000190
description: The cell line vocabulary inside FlyBase
is deprecated: false
is part of: Bioregistry
0000005: 0000190

Kidney and Urinary Pathway Ontology
type: Resource
is deprecated: true
0000005: 0001009
has prefix: kupo
appears in: Cell Ontology
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^\d{7}$

Mosquito insecticide resistance
is part of: Bioregistry
has resource example: MIRO_40000617
type: Resource
has download URL: miro.owl
has prefix: miro
keyword: mutation
keyword: life science
is deprecated: true
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/MIRO_$1
git repository: MIRO
has responsible: https://orcid.org/0000-0003-2497-2210
has URI prefix: http://purl.obolibrary.org/obo/MIRO_
keyword: phenotype
has local unique identifier pattern: ^\d{8}$
description: Application ontology for entities related to insecticide resistance in mosquitos
0000005: 40000617

IRD Segment Sequence
0000005: CY077097
has prefix: ird.segment
is deprecated: false
keyword: protein
has resource example: http://www.fludb.org/brc/fluSegmentDetails.do
has responsible: Richard Scheuermann
has URI prefix: http://www.fludb.org/brc/fluSegmentDetails.do
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^\w+(\_)?\d+(\.\d+)?$
description: Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).
keyword: gene
has provider formatter: http://www.fludb.org/brc/fluSegmentDetails.do

International Standard Classification of Education, 2013 Edition
description: ISCED is designed to serve as a framework to classify educational activities as defined in programmes and the resulting qualifications into internationally agreed categories. The basic concepts and definitions of ISCED are therefore intended to be internationally valid and comprehensive of the full range of education systems.
has provider formatter: https://w3id.org/kim/isced-2013/$1
has URI prefix: https://w3id.org/kim/isced-2013/
is deprecated: false
keyword: education level
has prefix: isced2013
keyword: educational resources
keyword: open educational resources
has resource example: n0021
is part of: Bioregistry
0000005: n0021
type: Resource
contributor: Charles Tapley Hoyt

SWEET Ontology Material Water
0000005: BlackWater
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Water
is deprecated: false
has prefix: sweet.maw
has URI prefix: http://sweetontology.net/matrWater/
has resource example: BlackWater
has provider formatter: http://sweetontology.net/matrWater/$1
is part of: Bioregistry
keyword: water
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
keyword: materials
has alternative prefix: somaw

Enzyme Nomenclature
keyword: biochemistry
has URI prefix: https://www.enzyme-database.org/query.php
has download URL: ec.owl
is deprecated: false
keyword: classification
has alternative prefix: EC-CODE
keyword: enzyme
keyword: ontology
has provider formatter: https://www.enzyme-database.org/query.php
0000005: 1.1.1.1
has resource example: https://www.enzyme-database.org/query.php
keyword: centrally registered identifier
is part of: Bioregistry
has local unique identifier pattern: ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.[nB]\d{1,3}|\.-\.-\.-|\.\d{1,3}\.-\.-|\.\d{1,3}\.\d{1,3}\.-)?$
has alternative prefix: intenz
has prefix: ec
description: The Enzyme Nomenclature (also known as the Enzyme Commission Code) is a species-agnostic controlled vocabulary for specific enzymes and an associated hierarchical classification into 7 main categories. The Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/) of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html). There are few notable resources providing access to the Enzyme Nomenclature: Website Homepage Notes ExplorEnz https://www.enzyme-database.org This is the resource officially recommended by IUBMB IUBMB (via by Queen Mary) https://iubmb.qmul.ac.uk/enzyme This is a web-based version of the 1992 publication. IntEnz https://www.ebi.ac.uk/intenz Shutdown in 2024 ExPaSy https://enzyme.expasy.org EnzymePortal https://www.ebi.ac.uk/enzymeportal
has alternative prefix: ECCODE
has responsible: Kristian Axelsen
has alternative prefix: EC number
has alternative prefix: EC
has alternative prefix: EC_CODE
keyword: enzymology
has alternative prefix: eccode
keyword: enzyme commission number
type: Resource
has identifier space owner: 00910ay07
has alternative prefix: ec-code

Proteoform Atlas
has URI prefix: http://repository.topdownproteomics.org/proteoforms/
has prefix: pfr
description: Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets.
is deprecated: false
has alternative prefix: TDR
has local unique identifier pattern: ^\d+$
has provider formatter: http://repository.topdownproteomics.org/proteoforms/$1
is part of: Bioregistry
0000005: 1001
contributor: Charles Tapley Hoyt
type: Resource
has resource example: http://repository.topdownproteomics.org/proteoforms/1001

snoDB
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^snoDB\d{4}$
0000005: snoDB0001
has prefix: snodb
contributor: https://orcid.org/0009-0000-6974-6386
has responsible: Michelle S Scott
keyword: rna
has provider formatter: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/detailed_view/$1
description: Contains identifiers for human small nucleolar RNAs (snoRNAs) from snoDB, an interactive database of human small nucleolar RNAs (snoRNAs) that includes up-to-date information on snoRNA features, genomic location, conservation, host gene, snoRNA–RNA targets and snoRNA abundance and provides links to other resources.
is deprecated: false
keyword: snorna-protein
has URI prefix: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/detailed_view/
has resource example: snoDB0001
has reviewer: https://orcid.org/0000-0001-9439-5346
keyword: human nucleolar rna

GWAS Central Phenotype
description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype.
has URI prefix: https://www.gwascentral.org/phenotype/
has local unique identifier pattern: ^HGVPM\d+$
has resource example: HGVPM623
keyword: condition
has prefix: gwascentral.phenotype
is deprecated: false
keyword: disease
is part of: Bioregistry
keyword: phenotype
has responsible: https://orcid.org/0000-0002-0292-7972
0000005: HGVPM623
type: Resource
keyword: symptom
has provider formatter: https://www.gwascentral.org/phenotype/$1

4D Nucleome Data Portal Experiment Replicate
has resource example: 4DNESWX1J3QU
0000005: 4DNESWX1J3QU
has provider formatter: https://data.4dnucleome.org/experiment-set-replicates/$1
is deprecated: false
has URI prefix: https://data.4dnucleome.org/experiment-set-replicates/
has prefix: _4dn.replicate
is part of: Bioregistry
has alternative prefix: 4dn.replicate
description: Database portal containing replicate experiments of different assays and samples
type: Resource
contributor: Charles Tapley Hoyt
contributor: https://orcid.org/0000-0001-5130-7705
contributor: https://orcid.org/0000-0002-6240-9325
contributor: 0000-0002-5798-662X

NeuroVault Collection
has prefix: neurovault.collection
description: Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images.
is deprecated: false
is part of: Bioregistry
has provider formatter: https://neurovault.org/collections/$1
0000005: 3304
has resource example: https://neurovault.org/collections/3304
has local unique identifier pattern: ^[1-9][0-9]*$
type: Resource
has URI prefix: https://neurovault.org/collections/

Heat Pump Ontology
has prefix: tib.hpont
description: The Heat Pump Ontology (HPOnt) aims to formalize and represent all the relevant information of Heat Pumps. The HPOnt has been developed as part of the REACT project which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 824395.
is deprecated: false
keyword: engineering
is part of: Bioregistry
has resource example: HeatPumpOperatingMode
0000005: HeatPumpOperatingMode
git repository: REACT-ONTOLOGY
type: Resource
has URI prefix: https://w3id.org/hpont#
keyword: nfdi4ing
has provider formatter: https://w3id.org/hpont#$1

Human developmental anatomy, abstract
keyword: ontology
keyword: life cycle stage
depends on: Common Anatomy Reference Ontology
has alternative prefix: HDAA2
has URI prefix: http://purl.obolibrary.org/obo/EHDAA2_
depends on: Anatomical Entity Ontology
depends on: Cell Ontology
has download URL: ehdaa2.owl
is part of: Bioregistry
type: Resource
has responsible: Jonathan Bard
git repository: human-developmental-anatomy-ontology
keyword: biomedical science
has prefix: ehdaa2
has local unique identifier pattern: ^\d{7}$
has provider formatter: http://purl.obolibrary.org/obo/EHDAA2_$1
description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human.
keyword: anatomy
0000005: 0000000
has alternative prefix: RETIRED_EHDAA2
has resource example: EHDAA2_0000000
is deprecated: true
keyword: obo
keyword: animal organ development
has alternative prefix: EHDAA2_RETIRED

European Science Vocabulary
type: Resource
keyword: computer science
is deprecated: false
description: European Science Vocabulary (EuroSciVoc) is the taxonomy of fields of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with fields of science categories extracted from CORDIS content through a semi-automatic process developed with Natural Language Processing (NLP) techniques. (from homepage)
has prefix: euroscivoc
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: http://data.europa.eu/8mn/euroscivoc/$1
keyword: educational resources
has URI prefix: http://data.europa.eu/8mn/euroscivoc/

Bgee gene
is deprecated: false
has prefix: bgee.gene
has responsible: 0000-0003-3947-488X
description: Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee.
is part of: Bioregistry
has resource example: FBgn0000015
has provider formatter: https://www.bgee.org/gene/$1
0000005: FBgn0000015
has local unique identifier pattern: ^[A-Za-z0-9]+$
keyword: gene expression
has URI prefix: https://www.bgee.org/gene/
contributor: 0000-0003-3947-488X
type: Resource

Discourse Elements Ontology
has provider formatter: http://purl.org/spar/deo/$1
git repository: deo
has resource example: Reference
is deprecated: false
is part of: Bioregistry
description: An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO.
has responsible: Silvio Peroni
contributor: Charles Tapley Hoyt
keyword: spar
type: Resource
0000005: Reference
has prefix: deo
has URI prefix: http://purl.org/spar/deo/
keyword: subject agnostic

PANTHER Pathway
has local unique identifier pattern: ^P\d{5}$
is deprecated: false
has prefix: panther.pathway
0000005: P00024
is part of: Bioregistry
type: Resource
has resource example: http://www.pantherdb.org/pathway/pathwayDiagram.jsp
description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components.
has URI prefix: http://www.pantherdb.org/pathway/pathwayDiagram.jsp
has provider formatter: http://www.pantherdb.org/pathway/pathwayDiagram.jsp

SWEET Ontology Phenomena Atmosphere Pressure
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: AtmosphericAnticyclone
has provider formatter: http://sweetontology.net/phenAtmoPressure/$1
keyword: phenomena
has prefix: sweet.phatmops
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Pressure
0000005: AtmosphericAnticyclone
has URI prefix: http://sweetontology.net/phenAtmoPressure/
is deprecated: false
keyword: atmosphere pressure
is part of: Bioregistry
has alternative prefix: sophatmops

Reactome
has local unique identifier pattern: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$
0000005: R-BTA-418592
has provider formatter: https://reactome.org/content/detail/$1
has alternative prefix: RE
has alternative prefix: REACT
has URI prefix: https://reactome.org/content/detail/
has responsible: 0000-0002-5494-626X
is deprecated: false
has prefix: reactome
keyword: reaction
has alternative prefix: Reactome
has alternative prefix: reactome.pathway
keyword: human
keyword: ontology
keyword: pathway
is part of: Bioregistry
description: The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.
contributor: Sierra Moxon
has resource example: R-BTA-418592
type: Resource
has download URL: reactome.owl.gz

Unified Medical Language System Concept Unique Identifier
has URI prefix: https://uts.nlm.nih.gov/uts/umls/concept/
0000005: C2584994
is deprecated: false
has alternative prefix: UMLS
has responsible: https://orcid.org/0000-0003-4769-4217
has provider formatter: https://uts.nlm.nih.gov/uts/umls/concept/$1
has local unique identifier pattern: ^C\d+$
is part of: Bioregistry
has prefix: umls
has alternative prefix: umls.cui
type: Resource
keyword: biomedicine
has alternative prefix: UMLS CUI
has alternative prefix: UMLS_CUI
has resource example: https://uts.nlm.nih.gov/uts/umls/concept/C2584994
description: The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.

Creative Commons Schema
keyword: license
is deprecated: true
0000005: License
has prefix: cc.legacy
description: A precursor that was later replaced with the Creative Commons Rights Expression Language (ccREL)
has URI prefix: http://web.resource.org/cc/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: schema
has provider formatter: http://web.resource.org/cc/$1
has resource example: License
type: Resource

NIF Standard Ontology: Brain Regions
type: Resource
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_br_
has alternative prefix: NLXBR
keyword: brain regions
is deprecated: false
git repository: NIF-Ontology
description: NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999).
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_br_$1
has responsible: Tom Gillespie
is part of: Bioregistry
has prefix: nlx.br
has local unique identifier pattern: ^\d+$
has resource example: nlx br 145
keyword: neuroscience
has reviewer: Charles Tapley Hoyt
0000005: 145
keyword: anatomy
contributor: Tom Gillespie

MEROPS Family
has responsible: Neil D Rawlings
has provider formatter: https://www.ebi.ac.uk/merops/cgi-bin/famsum
has local unique identifier pattern: ^[SCTAGMNU]\d+$
type: Resource
0000005: S1
has prefix: merops.family
has URI prefix: https://www.ebi.ac.uk/merops/cgi-bin/famsum
description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families.
has resource example: https://www.ebi.ac.uk/merops/cgi-bin/famsum
is deprecated: false
is part of: Bioregistry

Science Data Discovery Ontology
keyword: ontology
is deprecated: false
0000005: 3000001
has URI prefix: http://purl.obolibrary.org/obo/SDDO_
description: The Science Data Discovery Ontology (sddo) is being developed to provide a semantic foundation for the discovery of information managed by NASA's Science Mission Directorate. This information spans many scientific disciplines, fields and subfields, including heliophysics, earth science, planetary science, astrophysics, biology, astrobiology, and physical science. [from repository]
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
contributor: Charles Tapley Hoyt
has resource example: SDDO_3000001
type: Resource
has responsible: Daniel C. Berrios
has provider formatter: http://purl.obolibrary.org/obo/SDDO_$1
has prefix: sddo
git repository: sddo
has download URL: sddo.owl

IEEE Xplore author ID
0000005: 37271072100
has URI prefix: https://ieeexplore.ieee.org/author/
has local unique identifier pattern: ^[1-9]\d*$
keyword: person
is part of: Bioregistry
keyword: researcher
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: https://ieeexplore.ieee.org/author/$1
description: identifier for an author in IEEE Xplore
has prefix: ieee.author
is deprecated: false
has resource example: https://ieeexplore.ieee.org/author/37271072100

Common Bean Ontology
description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Common Bean Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
0000005: 0000189
keyword: food
keyword: ontology
has responsible: Elizabeth Arnaud
is deprecated: false
is part of: Bioregistry
has URI prefix: https://cropontology.org/rdf/CO_335:
has prefix: co_335
keyword: botany
keyword: agriculture
has local unique identifier pattern: ^\d{7}$
has download URL: CO 335.owl
type: Resource
git repository: Crop-Ontology
has resource example: CO 335:0000189
has provider formatter: https://cropontology.org/rdf/CO_335:$1

Mouse Developmental Stages
keyword: obo
has URI prefix: http://purl.obolibrary.org/obo/MmusDv_
0000005: 0000066
has prefix: mmusdv
keyword: ontology
has alternative prefix: MmusDv
keyword: life cycle stage
is deprecated: false
keyword: embryology
keyword: developmental biology
has download URL: mmusdv.owl
has responsible: Frédéric Bastian
is part of: Bioregistry
type: Resource
git repository: developmental-stage-ontologies
description: Life cycle stages for Mus Musculus
has provider formatter: http://purl.obolibrary.org/obo/MmusDv_$1
has resource example: MmusDv_0000066
has local unique identifier pattern: ^\d{7}$
keyword: anatomy

C. elegans development ontology
type: Resource
keyword: life science
keyword: obo
keyword: ontology
keyword: worm
keyword: life cycle stage
has responsible: https://orcid.org/0000-0001-9076-6015
is deprecated: false
keyword: developmental biology
description: Ontology about the development and life stages of the C. elegans
has URI prefix: http://purl.obolibrary.org/obo/WBls_
has provider formatter: http://purl.obolibrary.org/obo/WBls_$1
keyword: life cycle
is part of: Bioregistry
has prefix: wbls
has download URL: wbls.owl
has resource example: WBls_0000690
has alternative prefix: WBls
0000005: 0000690
keyword: development
git repository: c-elegans-development-ontology
has local unique identifier pattern: ^\d{7}$

SWEET Ontology State Role Impact
has prefix: sweet.stri
has URI prefix: http://sweetontology.net/stateRoleImpact/
has provider formatter: http://sweetontology.net/stateRoleImpact/$1
has alternative prefix: sostri
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: state role impact
type: Resource
has resource example: Catastrophic
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Impact
is deprecated: false
0000005: Catastrophic

Chemical Information Ontology
description: Contains entries for various database identifiers
has part: CHEMINF_000446
has part: CHEMINF_000140
has part: CHEMINF_000406
has part: CHEMINF_000447
has part: CHEMINF_000566
has part: CHEMINF_000412
has part: CHEMINF_000405
has part: CHEMINF_000407
has part: CHEMINF_000565
has provider formatter: https://semanticscience.org/resource/CHEMINF_$1
has part: CHEMINF_000141
has part: CHEMINF_000409
has part: CHEMINF_000304
has part: CHEMINF_000411
has part: CHEMINF_000408
has part: CHEMINF_000563
type: Registry
has responsible: Tim Vandermeersch
has part: CHEMINF_000569
0000005: 000140
has part: CHEMINF_000564

PANTHER Node
has local unique identifier pattern: ^PTN\d{9}$
has resource example: http://www.pantree.org/node/annotationNode.jsp
has provider formatter: http://www.pantree.org/node/annotationNode.jsp
is part of: Bioregistry
0000005: PTN000000026
description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes.
has prefix: panther.node
type: Resource
is deprecated: false
has URI prefix: http://www.pantree.org/node/annotationNode.jsp

CODATA Research Data Management Terminology
description: The goal of the CODATA Research Data Management Terminology is to gather the key terms needed for a common understanding of the research data management domain. The RDMT was revised by the CODATA RDM Terminology Working Group, shared for public review, and then confirmed and finalised in 2023. The RDMT grew out of the CASRAI Research Data Management Glossary, which was intended as a practical reference for individuals and groups concerned with the improvement of research data management (RDM). In 2020, CASRAI requested that CODATA assume responsibility for the curation of this valued resource. To that end, the RDM Terminology Working Group uses a lightweight and pragmatic biennial process to review the resource now restructured as the CODATA RDM Terminology and suggest any edits, additions and removals that are required in order to develop and improve this important reference resource.
contributor: Charles Tapley Hoyt
0000005: aggregated-data
type: Resource
has provider formatter: https://terms.codata.org/rdmt/$1
has prefix: codata.rdmt
has responsible: Laura Molloy
is deprecated: false
has URI prefix: https://terms.codata.org/rdmt/
has resource example: aggregated-data
is part of: Bioregistry

EuroVoc
keyword: food
keyword: employment
keyword: international relations
keyword: political science
description: EuroVoc is the EU's multilingual and multidisciplinary thesaurus. It contains keywords, organized in 21 domains and 127 sub-domains, which are used to describe the content of documents in EUR-Lex. [from homepage]
is deprecated: false
keyword: forest management
keyword: economics
keyword: social science
0000005: 1837
keyword: geography
keyword: business administration
keyword: social policy
keyword: transport
has resource example: http://eurovoc.europa.eu/1837
keyword: energy engineering
keyword: agriculture
keyword: linguistics
keyword: public finance
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: transportation planning
contributor: Charles Tapley Hoyt
keyword: trade
has URI prefix: http://eurovoc.europa.eu/
has prefix: eurovoc
has provider formatter: http://eurovoc.europa.eu/$1
keyword: environmental science
keyword: fisheries science
type: Resource

Gene Normal Tissue Expression
type: Resource
has resource example: http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl
description: GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E.
is deprecated: false
has provider formatter: http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl
0000005: GC06M052656
is part of: Bioregistry
has prefix: genecards.genenote
has URI prefix: https://bioregistry.io/genecards.genenote:
keyword: gene expression

Metabolome Express
is deprecated: false
has URI prefix: https://www.metabolome-express.org/datasetview.php
has provider formatter: https://www.metabolome-express.org/datasetview.php
description: A public place to process, interpret and share GC/MS metabolomics datasets.
has prefix: mex
has local unique identifier pattern: ^\d+$
has resource example: https://www.metabolome-express.org/datasetview.php
is part of: Bioregistry
type: Resource
0000005: 36

Software Package Data Exchange License
0000005: CC-BY-1.0
has local unique identifier pattern: ^[0-9A-Za-z\-.\+]+$
has URI prefix: https://spdx.org/licenses/
has provider formatter: https://spdx.org/licenses/$1
has resource example: CC-BY-1.0
keyword: ontology
description: The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception.
is deprecated: false
has alternative prefix: spdx.license
has download URL: spdx.owl
has prefix: spdx
git repository: license-list-data
is part of: Bioregistry
has alternative prefix: spdx.licenses
type: Resource
keyword: license

Taxonomic rank vocabulary
has URI prefix: http://purl.obolibrary.org/obo/TAXRANK_
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
type: Resource
has resource example: TAXRANK_0000001
git repository: taxrank
has prefix: taxrank
has provider formatter: http://purl.obolibrary.org/obo/TAXRANK_$1
keyword: taxonomy
description: A vocabulary of taxonomic ranks (species, family, phylum, etc)
keyword: life science
is deprecated: false
keyword: obo
keyword: ontology
has download URL: taxrank.owl
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-8688-6599
keyword: taxonomic classification

Rebuilding a Kidney
has URI prefix: https://www.rebuildingakidney.org/id/
has provider formatter: https://www.rebuildingakidney.org/id/$1
keyword: cell biology
has local unique identifier pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
has resource example: Q-2958
is deprecated: false
git repository: Create-citable-datasets
keyword: developmental biology
keyword: genomics
keyword: molecular biology
has prefix: rbk
has responsible: Leif Oxburgh
is part of: Bioregistry
0000005: Q-2958
description: (Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function.
type: Resource

Relation Ontology
keyword: life sciences, biology
appears in: Environmental conditions, treatments and exposures ontology
appears in: Cell Ontology
type: Resource
appears in: Ontology for the Anatomy of the Insect SkeletoMuscular system
appears in: The Echinoderm Anatomy and Development Ontology
appears in: Collembola Anatomy Ontology
appears in: Health Surveillance Ontology
has local unique identifier pattern: ^(HOM)?\d{7}$
git repository: obo-relations
appears in: Porifera Ontology
has URI prefix: http://purl.obolibrary.org/obo/RO_
appears in: Uber Anatomy Ontology
has resource example: RO_0002533
appears in: Lepidoptera Anatomy Ontology
keyword: subject agnostic
appears in: Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology
appears in: Radiation Biology Ontology
appears in: Genomic Epidemiology Ontology
has provider formatter: http://purl.obolibrary.org/obo/RO_$1
has alternative prefix: obo_rel
appears in: Provisional Cell Ontology
has download URL: ro.owl
appears in: Ontology for Nutritional Studies
has prefix: ro
0000005: 0002533
appears in: Gene Ontology
appears in: Medical Action Ontology
appears in: Planarian Phenotype Ontology
appears in: Plant Gall Ontology
keyword: obo
appears in: Ctenophore Ontology
description: The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.
appears in: An ontology of core ecological entities
has alternative prefix: oborel
appears in: Ontology for Avida digital evolution platform
appears in: Agronomy Ontology
keyword: ontology
appears in: Population and Community Ontology
appears in: Process Chemistry Ontology
appears in: Coleoptera Anatomy Ontology
appears in: Unipathway
appears in: Performance Summary Display Ontology
is deprecated: false
keyword: dataplant
has responsible: https://orcid.org/0000-0002-6601-2165
appears in: FuTRES Ontology of Vertebrate Traits
has alternative prefix: RO_proposed_relation
appears in: Compositional Dietary Nutrition Ontology
appears in: The Food Ontology
appears in: Clytia hemisphaerica Development and Anatomy Ontology
keyword: relations
keyword: nfdi4chem
keyword: foundational ontologies
appears in: Plant Stress Ontology
appears in: Xenopus Phenotype Ontology
appears in: Environment Ontology
appears in: Zebrafish Phenotype Ontology
is part of: Bioregistry

Gene Expression Ontology
has responsible: Martin Kuiper
keyword: life science
description: Gene Expression Ontology
keyword: ontology
keyword: expression data
is deprecated: false
is part of: Bioregistry
has prefix: gexo
has download URL: gexo.owl
keyword: gene expression
type: Resource

Curated Drug-Drug Interactions Database - Drug
has URI prefix: http://ddinter.scbdd.com/ddinter/drug-detail/
has responsible: https://orcid.org/0000-0003-3604-3785
has local unique identifier pattern: ^DDInter\d+$
is part of: Bioregistry
keyword: relationships
keyword: chemistry
contributor: Sierra Moxon
description: Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety.
has reviewer: Charles Tapley Hoyt
0000005: DDInter20
type: Resource
has prefix: ddinter.drug
has resource example: DDInter20
keyword: drugs
is deprecated: false
has provider formatter: http://ddinter.scbdd.com/ddinter/drug-detail/$1

KIM School Subjects
has URI prefix: http://w3id.org/kim/schulfaecher/
description: A vocabulary describing subjects taught in German primary and secondary school (not university/hochschulen), such as German, math, and art.
has resource example: s1000
git repository: schulfaecher
type: Resource
keyword: subject
is deprecated: false
has prefix: kim.schulfaecher
keyword: school subject
has provider formatter: http://w3id.org/kim/schulfaecher/$1
keyword: discipline
is part of: Bioregistry
0000005: s1000
contributor: Charles Tapley Hoyt

ProteomeXchange
has provider formatter: http://proteomecentral.proteomexchange.org/cgi/GetDataset
is part of: Bioregistry
type: Resource
has prefix: px
has resource example: http://proteomecentral.proteomexchange.org/cgi/GetDataset
has URI prefix: http://proteomecentral.proteomexchange.org/cgi/GetDataset
description: The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination.
0000005: PXD000500
is deprecated: false
has local unique identifier pattern: ^(R)?PXD\d{6}$

SNP to Transcription Factor Binding Sites
has provider formatter: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi
description: SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome.
is deprecated: false
is part of: Bioregistry
has prefix: snp2tfbs
0000011: dbSNP Reference SNP number
has local unique identifier pattern: ^rs[0-9]+$
has URI prefix: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi
type: Resource
0000005: rs11603840
has resource example: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi

Homology Ontology
keyword: homologous
keyword: life cycle stage
is deprecated: false
has resource example: HOM_0000049
keyword: molecular entity
has responsible: Frédéric Bastian
is part of: Bioregistry
type: Resource
has prefix: hom
has download URL: hom.owl
keyword: anatomy
description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.
has local unique identifier pattern: ^\d{7}$
keyword: life science
has URI prefix: http://purl.obolibrary.org/obo/HOM_
has provider formatter: http://purl.obolibrary.org/obo/HOM_$1
0000005: 0000049
keyword: obo
keyword: ontology
git repository: homology-ontology

BRENDA Tissue Ontology
keyword: life sciences, biology
is part of: Bioregistry
has resource example: BTO_0000590
type: Resource
keyword: enzymology
0000005: 0000590
keyword: tissue
keyword: experimental measurement
has provider formatter: http://purl.obolibrary.org/obo/BTO_$1
keyword: cell
has local unique identifier pattern: ^\d{7}$
has alternative prefix: BTO
keyword: medicine
keyword: anatomy
keyword: life science
keyword: enzyme
keyword: obo
keyword: ontology
keyword: organ
keyword: cell biology
git repository: BTO
is deprecated: false
description: The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
keyword: dataplant
keyword: genomics
has prefix: bto
keyword: sample annotation
has URI prefix: http://purl.obolibrary.org/obo/BTO_
has download URL: bto.owl
keyword: nfdi4chem
keyword: omics
keyword: proteomics
has responsible: Christian-Alexander Dudek

Quantities, Units, Dimensions, and Types Ontology
keyword: ontology
keyword: quantification
is deprecated: false
has provider formatter: http://qudt.org/schema/qudt#$1
has download URL: qudt.owl
is part of: Bioregistry
keyword: unit
contributor: Charles Tapley Hoyt
description: Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.
git repository: qudt-public-repo
keyword: experimental measurement
has URI prefix: http://qudt.org/schema/qudt#
type: Resource
keyword: measurement systems
has resource example: baseDimensionEnumeration
0000005: baseDimensionEnumeration
keyword: methods
has prefix: qudt
keyword: units

Sustainable Development Goals Interface Ontology
git repository: sdgio
type: Resource
has resource example: SDGIO_00020134
keyword: environmental science
is deprecated: false
has responsible: Pier Luigi Buttigieg
has local unique identifier pattern: ^\d{8}$
keyword: ontology
description: The Sustainable Development Goals Interface Ontology (SDGIO) aims to provide a semantic bridge between 1) the Sustainable Development Goals, their targets, and indicators and 2) the large array of entities they refer to. SDGIO will reuse existing ontologies where appropriate.
keyword: sustainability
is part of: Bioregistry
0000005: 00020134
has provider formatter: http://purl.unep.org/sdg/SDGIO_$1
has prefix: sdgio
has download URL: sdgio.owl
has URI prefix: http://purl.unep.org/sdg/SDGIO_

Functional Mock-up Interface Ontology
type: Resource
has prefix: udsaes.fmi
has URI prefix: https://purl.org/fmi-ontology#
git repository: fmi2rdf
description: An ontology transcription of definitions in the Functional Mock-up Interface (FMI) standard document from https://fmi-standard.org/ that enables representing Functional Mock-up Units (FMUs) in RDF
0000005: FMU
is deprecated: false
is part of: Bioregistry
has provider formatter: https://purl.org/fmi-ontology#$1
keyword: mechanical engineering, energy technology
has resource example: FMU
keyword: nfdi4energy

GrainGenes symbol
contributor: Charles Tapley Hoyt
has provider formatter: http://wheat.pw.usda.gov/report
description: A database for Triticeae and Avena gene symbols.
type: Resource
0000005: 1-FEH+w3
has prefix: graingenes.symbol
has URI prefix: http://wheat.pw.usda.gov/report
is deprecated: false
has resource example: http://wheat.pw.usda.gov/report
is part of: Bioregistry

Integrated Taxonomic Information System
description: Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world.
0000005: 589462
keyword: biodiversity
is deprecated: false
has resource example: https://www.itis.gov/servlet/SingleRpt/SingleRpt
has download URL: itis.owl.gz
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has prefix: itis
contributor: Charles Tapley Hoyt
has URI prefix: https://www.itis.gov/servlet/SingleRpt/SingleRpt
has provider formatter: https://www.itis.gov/servlet/SingleRpt/SingleRpt
keyword: taxonomy
type: Resource
keyword: life science
has responsible: https://orcid.org/0000-0002-4972-3782
keyword: ontology

Digital Construction Lifecycle (dicl)
has resource example: BLCS Framework
is deprecated: false
keyword: digital planning and construction
is part of: Bioregistry
has URI prefix: https://w3id.org/digitalconstruction/0.5/Lifecycle#
has provider formatter: https://w3id.org/digitalconstruction/0.5/Lifecycle#$1
keyword: fid baudigital
description: An ontology to represent the enhancement of building data throughout the construction lifecycle stages
has prefix: digitalconstruction.lifecycle
type: Resource
keyword: nfdi4ing
0000005: BLCS_Framework
keyword: civil engineering

NCBI Gene
keyword: genetics
has URI prefix: https://www.ncbi.nlm.nih.gov/gene/
has alternative prefix: EntrezGene
keyword: genome
keyword: genomics
keyword: dna
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has responsible: Terence D. Murphy
has alternative prefix: NCBI_GeneID
contributor: Rhiannon Cameron
has alternative prefix: EGID
type: Resource
has resource example: https://www.ncbi.nlm.nih.gov/gene/100010
description: Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis.
keyword: gene
has alternative prefix: entrez gene/locuslink
has provider formatter: https://www.ncbi.nlm.nih.gov/gene/$1
0000005: 100010
has alternative prefix: NCBIGene
has prefix: ncbigene
has identifier space owner: 02meqm098
is deprecated: false
has alternative prefix: GeneID
has alternative prefix: entrez
has alternative prefix: nihgeneid

DataPLANT Resources
has part: Agronomy Ontology
has part: Population and Community Ontology
has part: Basic Formal Ontology
has part: DataPLANT Biology Ontology
has part: Plant Trait Ontology
has part: EDAM Ontology
has part: NCI Thesaurus
has part: Experimental Factor Ontology
has part: Software ontology
has part: Plant Phenology Ontology
has part: Biological Collections Ontology
has part: Plant Stress Ontology
has part: Plant Experimental Conditions Ontology
has part: The Statistical Methods Ontology
has part: Ontology of Microbial Phenotypes
has part: Environment Ontology
has part: Relation Ontology
has part: BioAssay Ontology
has part: Units of measurement ontology
has part: Mass spectrometry ontology
has part: Plant Phenotype Experiment Ontology
has part: Phenotype And Trait Ontology
type: Collection
has part: Ontology for Biomedical Investigations
has part: BRENDA Tissue Ontology
has part: Core Ontology for Biology and Biomedicine
has part: Uber Anatomy Ontology
has part: Measurement method ontology
has part: Metabolomics Standards Initiative Ontology
has part: Gene Ontology
has part: Chemical Entities of Biological Interest
has part: Protein modification
description: Prefixes for ontologies relevant for the DataPLANT (i.e. the NFDI consortium for plants)
creator: Charles Tapley Hoyt
has part: Flora Phenotype Ontology
has part: Chemical Methods Ontology
has part: Plant Ontology

National Uniform Claim Committee Taxonomy
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA. The taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct "Levels" including Provider Grouping, Classification, and Area of Specialization. - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc. - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology. - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards.
0000005: 207LH0002X
has prefix: nucc.taxonomy
has local unique identifier pattern: ^\d{3}\w(\w|\d_)\d{4}X$
is deprecated: false

Publishing Workflow Ontology
is deprecated: false
has resource example: Workflow
has prefix: pwo
description: An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity.
0000005: Workflow
is part of: Bioregistry
git repository: pwo
has provider formatter: http://purl.org/spar/pwo/$1
type: Resource
contributor: Charles Tapley Hoyt
keyword: spar
has responsible: Silvio Peroni
keyword: subject agnostic
has URI prefix: http://purl.org/spar/pwo/

Tree of Life Web Project
type: Resource
has URI prefix: http://tolweb.org/
contributor: https://orcid.org/0000-0003-2699-3066
description: The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). Each page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.
is deprecated: false
0000005: 98034
has provider formatter: http://tolweb.org/$1
has prefix: tol
has resource example: http://tolweb.org/98034
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has alternative prefix: tol.webproj

Ensembl Plants
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes.
is part of: Bioregistry
type: Resource
0000005: AT1G73965
has resource example: AT1G73965
has provider formatter: https://plants.ensembl.org/id/$1
has URI prefix: https://plants.ensembl.org/id/
has local unique identifier pattern: ^\w+(\.\d+)?(\.\d+)?$
has prefix: ensembl.plant
keyword: genome
is deprecated: false

Pigeon Pea Ontology
has URI prefix: https://cropontology.org/rdf/CO_341:
keyword: food
keyword: ontology
has provider formatter: https://cropontology.org/rdf/CO_341:$1
0000005: 0000140
has download URL: CO 341.owl
is deprecated: false
keyword: plant phenotypes and traits
description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Pigeon Pea Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
has prefix: co_341
keyword: phenotype
keyword: botany
keyword: agriculture
has responsible: Elizabeth Arnaud
is part of: Bioregistry
git repository: Crop-Ontology
has resource example: CO 341:0000140
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: life science

Collembola Anatomy Ontology
type: Resource
has responsible: https://orcid.org/0000-0002-9136-9932
has prefix: clao
git repository: Collembola
has local unique identifier pattern: ^\d{7}$
0000005: 0000088
keyword: obo
has resource example: CLAO_0000088
has download URL: clao.owl
has provider formatter: http://purl.obolibrary.org/obo/CLAO_$1
keyword: ontology
is deprecated: false
description: CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).
depends on: Relation Ontology
has URI prefix: http://purl.obolibrary.org/obo/CLAO_
is part of: Bioregistry

NIF Standard Ontology: Molecules
keyword: proteins
has responsible: Tom Gillespie
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1
description: NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
keyword: neuroscience
0000005: 90806
keyword: biology
has reviewer: Charles Tapley Hoyt
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_mol_
contributor: Tom Gillespie
has alternative prefix: NLXMOL
has resource example: nlx mol 90806
has prefix: nlx.mol
is deprecated: false
git repository: NIF-Ontology
keyword: chemistry

ELI Metadata Ontology
contributor: Charles Tapley Hoyt
has provider formatter: http://data.europa.eu/eli/ontology#$1
has URI prefix: http://data.europa.eu/eli/ontology#
0000005: InForce
keyword: frbr
keyword: contracts
is deprecated: false
has resource example: InForce
is part of: Bioregistry
has prefix: eli
description: An ontology to describe legislation, based on the FRBR model, that encodes the ELI metadata fields.
type: Resource

NCBI Registry
has URI prefix: https://bioregistry.io/metaregistry/ncbi/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: ECOCYC
description: A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources
0000005: ECOCYC
has provider formatter: https://bioregistry.io/metaregistry/ncbi/$1
type: Resource
is deprecated: false
has prefix: ncbi.resource

Physiologically-Based Pharmacokinetic Ontology
git repository: pbpko
has prefix: pbpko
description: An ontology for modeling and understanding of pharmacokinetics in biological systems.
has responsible: https://orcid.org/0000-0003-0593-2598
has URI prefix: http://purl.obolibrary.org/obo/PBPKO_
is deprecated: false
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/PBPKO_$1
is part of: Bioregistry
has download URL: pbpko.owl
type: Resource
0000005: 10008

Cluster of orthologous genes
has URI prefix: https://www.ncbi.nlm.nih.gov/research/cog/cog/
has local unique identifier pattern: ^COG\d+$
keyword: life science
has responsible: Michael Y Galperin
description: COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.
has provider formatter: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1
has alternative prefix: cog
0000005: COG0001
is deprecated: false
has alternative prefix: COG_Cluster
is part of: Bioregistry
keyword: protein
keyword: genome
contributor: Charles Tapley Hoyt
has resource example: COG0001
has prefix: cog.cluster
type: Resource

Linear double stranded DNA sequences
has URI prefix: https://doulix.com/biomodules/
has prefix: dlxb
is deprecated: false
is part of: Bioregistry
has provider formatter: https://doulix.com/biomodules/$1
0000005: 6VDC956
description: DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences.
has local unique identifier pattern: ^[A-Z0-9]{6,7}$
has resource example: 6VDC956
type: Resource

SWEET Ontology Phenomena Reaction
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
has URI prefix: http://sweetontology.net/phenReaction/
keyword: phenomena
has alternative prefix: sophr
0000005: Activation
keyword: reaction
has resource example: Activation
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Reaction
has provider formatter: http://sweetontology.net/phenReaction/$1
has prefix: sweet.phr
is deprecated: false
is part of: Bioregistry

SWEET Ontology Representation Data Model
is deprecated: false
has prefix: sweet.repdm
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: Array
0000005: Array
keyword: representation data model
has URI prefix: http://sweetontology.net/reprDataModel/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Model
has provider formatter: http://sweetontology.net/reprDataModel/$1
has alternative prefix: sorepdm

Statistical Torsional Angles Potentials
is part of: Bioregistry
type: Resource
0000005: 1a24
has resource example: http://psb.kobic.re.kr/STAP/refinement1/result.php
keyword: life science
has URI prefix: http://psb.kobic.re.kr/STAP/refinement1/result.php
is deprecated: true
has local unique identifier pattern: ^[0-9][A-Za-z0-9]{3}$
description: STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB).
has provider formatter: http://psb.kobic.re.kr/STAP/refinement1/result.php
has responsible: Bong Hyun Sung
has prefix: stap
keyword: statistics

SupraBank Additive
contributor: Charles Tapley Hoyt
has prefix: suprabank.additive
has URI prefix: https://suprabank.org/additives/
keyword: molecule
0000005: 10
description: Identifiers for chemicals used as additives
has responsible: https://orcid.org/0000-0002-9676-9839
is deprecated: false
is part of: Bioregistry
has resource example: https://suprabank.org/additives/10
has provider formatter: https://suprabank.org/additives/$1
keyword: chemical
type: Resource

MycoBrowser smegmatis
description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.
has resource example: MSMEG 3769
has local unique identifier pattern: ^MSMEG\w+$
keyword: sequence
has prefix: myco.smeg
keyword: genome
has URI prefix: https://mycobrowser.epfl.ch/genes/
is part of: Bioregistry
type: Resource
has provider formatter: https://mycobrowser.epfl.ch/genes/$1
is part of: MycoBrowser
is deprecated: false
0000005: MSMEG_3769

MIPModDB
0000005: HOSAPI0399
has provider formatter: http://bioinfo.iitk.ac.in/MIPModDB/result.php
has prefix: mipmod
has responsible: Ramasubbu Sankararamakrishnan
is deprecated: false
keyword: protein
has local unique identifier pattern: ^\w+$
is part of: Bioregistry
has resource example: http://bioinfo.iitk.ac.in/MIPModDB/result.php
type: Resource
has URI prefix: http://bioinfo.iitk.ac.in/MIPModDB/result.php
keyword: structure
description: MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.

Curation of Neurodegeneration Supporting Ontology
is deprecated: false
has local unique identifier pattern: ^CONSO\d{5}$
has URI prefix: https://pharmacome.github.io/conso/
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
keyword: neuroscience
keyword: biology
has resource example: CONSO00010
description: An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases.
keyword: neurodegeneration
0000005: CONSO00010
keyword: life science
has prefix: conso
keyword: ontology
has provider formatter: https://pharmacome.github.io/conso/$1
has responsible: Charles Tapley Hoyt

PathoPlant®
has reviewer: Charles Tapley Hoyt
has provider formatter: http://www.pathoplant.de/detail.php
has prefix: pathoplant
is deprecated: false
has resource example: http://www.pathoplant.de/detail.php
0000005: MO000027
keyword: pathway
keyword: small molecule
is part of: Bioregistry
keyword: protein
has URI prefix: http://www.pathoplant.de/detail.php
description: PathoPlant® is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant® also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment.
keyword: gene expression
type: Resource
keyword: interaction

Mammalian Phenotype Ontology
keyword: phenotype
appears in: ChEBI Integrated Role Ontology
has download URL: mp.owl
has URI prefix: http://purl.obolibrary.org/obo/MP_
keyword: behavior
git repository: mammalian-phenotype-ontology
is part of: Bioregistry
type: Resource
keyword: mammalian
has resource example: MP_0005452
has local unique identifier pattern: ^\d{7}$
has prefix: mp
keyword: life science
has responsible: Sue Bello
keyword: obo
description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.
0000005: 0005452
appears in: Sickle Cell Disease Ontology
keyword: ontology
keyword: physiology
is deprecated: false
keyword: developmental biology
has provider formatter: http://purl.obolibrary.org/obo/MP_$1

Semantic Web Applications in Neuromedicine
description: SWAN ontology consists in a collection of ontologies used to create, manage and share scientific knowledge bases.
is part of: Bioregistry
has prefix: swan
type: Resource
has download URL: swan.owl
contributor: Charles Tapley Hoyt
git repository: swan-ontology
is deprecated: true
keyword: ontology

SWEET Ontology Realm Astrophysical Body
has alternative prefix: soreaab
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
keyword: realm
is part of: Semantic Web for Earth and Environment Technology Ontology
0000005: Asteroid
type: Resource
has provider formatter: http://sweetontology.net/realmAstroBody/$1
has resource example: Asteroid
has URI prefix: http://sweetontology.net/realmAstroBody/
keyword: astrophysical body
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Astrophysical Body
is deprecated: false
has prefix: sweet.reaab

PANTHER Pathway Component
type: Resource
is deprecated: false
0000005: P00266
has URI prefix: http://www.pantherdb.org/pathway/pathCatDetail.do
has local unique identifier pattern: ^(G|P|U|C|S)\d{5}$
is part of: Bioregistry
has resource example: http://www.pantherdb.org/pathway/pathCatDetail.do
has prefix: panther.pthcmp
description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.
has provider formatter: http://www.pantherdb.org/pathway/pathCatDetail.do

AntiBodies Chemically Defined database
has URI prefix: https://web.expasy.org/abcd/ABCD_
is deprecated: false
has provider formatter: https://web.expasy.org/abcd/ABCD_$1
keyword: immunology
is part of: Bioregistry
keyword: molecular biology
contributor: Charles Tapley Hoyt
has resource example: ABCD AD834
has responsible: Pierre Cosson
0000005: AD834
type: Resource
description: The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies
has prefix: abcd
contributor: https://orcid.org/0000-0002-1216-4761

Open Data for Access and Mining
0000005: frim1
description: Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed.
is deprecated: false
has provider formatter: http://pmb-bordeaux.fr/getdata/json/$1/datapackage
is part of: Bioregistry
has prefix: odam
has resource example: http://pmb-bordeaux.fr/getdata/json/frim1/datapackage
has local unique identifier pattern: ^[A-Za-z0-9]+$
type: Resource
has URI prefix: https://bioregistry.io/odam:

SWEET Ontology State Role Geographic
has resource example: Barrier
type: Resource
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Geographic
is deprecated: false
has prefix: sweet.strg
0000005: Barrier
has provider formatter: http://sweetontology.net/stateRoleGeographic/$1
keyword: state role geographic
is part of: Bioregistry
has alternative prefix: sostrg
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has URI prefix: http://sweetontology.net/stateRoleGeographic/

Shape Expression Vocabulary
is deprecated: false
has URI prefix: http://www.w3.org/ns/shex#
keyword: rdf
has local unique identifier pattern: ^\w+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces.
has provider formatter: http://www.w3.org/ns/shex#$1
0000005: TripleExpression
type: Resource
has prefix: shex
git repository: shexspec.github.io
has resource example: TripleExpression
keyword: semantic web
keyword: metadata

SWEET Ontology Phenomena Ocean
has alternative prefix: sopho
has provider formatter: http://sweetontology.net/phenOcean/$1
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Ocean
type: Resource
keyword: ocean
keyword: phenomena
has URI prefix: http://sweetontology.net/phenOcean/
has resource example: OceanPhenomena
has prefix: sweet.pho
is deprecated: false
is part of: Bioregistry
0000005: OceanPhenomena

Veterans Health Administration (VHA) unique identifier
has prefix: vuid
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
0000005: 4007166
is deprecated: false
description: The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year.

Interaction Network Ontology
is deprecated: false
keyword: obo
keyword: ontology
git repository: ino
has prefix: ino
has URI prefix: http://purl.obolibrary.org/obo/INO_
is part of: Bioregistry
has responsible: Yongqun Oliver He
0000005: 0000003
has provider formatter: http://purl.obolibrary.org/obo/INO_$1
has resource example: INO_0000003
has local unique identifier pattern: ^\d{7}$
description: he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.
type: Resource
keyword: molecular interaction
has download URL: ino.owl
keyword: life science

Conditions of Access
has resource example: no login.html
keyword: open educational resources
has local unique identifier pattern: ^login|no_login$
0000005: no_login
keyword: open educational resource
contributor: Martin Voigt
type: Resource
has reviewer: Charles Tapley Hoyt
has URI prefix: https://bioregistry.io/kim.conditionsofaccess:
description: Identifiers describing conditions of access to an object (login) as defined by the [OER metadata group](https://oerworldmap.org/resource/urn:uuid:fd06253e-fe67-4910-b923-51db9d27e59f).
keyword: learning materials
has prefix: kim.conditionsofaccess
is deprecated: false
has provider formatter: https://skohub.io/dini-ag-kim/value-lists/heads/main/w3id.org/kim/conditionsOfAccess/$1.html
is part of: Bioregistry
keyword: learning material

Allergome
has URI prefix: http://www.allergome.org/script/dettaglio.php
type: Resource
0000005: 1948
keyword: biomedical science
keyword: allergen
contributor: https://orcid.org/0000-0002-1216-4761
keyword: health science
keyword: medicine
keyword: life science
has provider formatter: http://www.allergome.org/script/dettaglio.php
is deprecated: false
has resource example: http://www.allergome.org/script/dettaglio.php
description: Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources.
has prefix: allergome
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has responsible: https://orcid.org/0000-0002-9137-1442

CALIPHO Group Ontology of Human Anatomy
0000005: TS-0001
keyword: anatomy
git repository: controlled-vocabulary
description: This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins.
keyword: ontology
has local unique identifier pattern: ^TS-\d+$
keyword: human
keyword: physiology
is deprecated: false
has prefix: caloha
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-0819-0473
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: https://www.nextprot.org/term/$1
has download URL: caloha.obo
has URI prefix: https://www.nextprot.org/term/
has resource example: TS-0001

LiceBase
has provider formatter: https://licebase.org/
has URI prefix: https://licebase.org/
description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.
is part of: Bioregistry
type: Resource
has resource example: https://licebase.org/
has local unique identifier pattern: ^[A-Za-z0-9\-\/]+$
0000005: EMLSAT00000003403
keyword: life science
has responsible: https://orcid.org/0000-0003-4110-0748
has prefix: licebase
is deprecated: false

Vertebrate trait ontology
has download URL: vt.owl
keyword: biology
has local unique identifier pattern: ^\d{7}$
keyword: trait
type: Resource
keyword: morphology
has responsible: Carissa Park
keyword: obo
keyword: ontology
keyword: animal physiology
appears in: Sickle Cell Disease Ontology
keyword: physiology
0000005: 0000685
is deprecated: false
keyword: developmental biology
has URI prefix: http://purl.obolibrary.org/obo/VT_
has resource example: VT_0000685
description: The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.
has provider formatter: http://purl.obolibrary.org/obo/VT_$1
keyword: phenotype
has prefix: vt
git repository: vertebrate-trait-ontology
keyword: vertebrate
is part of: Bioregistry

TTD Target
type: Resource
has prefix: ttd.target
description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.
0000005: t59328
has URI prefix: https://db.idrblab.net/ttd/data/target/details/
is deprecated: false
has provider formatter: https://db.idrblab.net/ttd/data/target/details/$1
has local unique identifier pattern: ^t\d+$
has resource example: t59328
is part of: Bioregistry

Rat Genome Database
keyword: human
keyword: genetic
keyword: ontology
keyword: marker
keyword: immunology
keyword: physiology
has prefix: rgd
keyword: pathway
keyword: mouse
has alternative prefix: RGD
keyword: disease
has URI prefix: http://rgd.mcw.edu/rgdweb/report/gene/main.html
keyword: strain
keyword: sequence
keyword: recombinant inbred rat
is part of: Bioregistry
keyword: genome
keyword: genomics
keyword: function
keyword: dna
keyword: gold standard
keyword: phenotype
keyword: translational medicine
keyword: proteomics
keyword: behavior
keyword: est
keyword: qtl
keyword: phenomics
type: Resource
keyword: rat
has local unique identifier pattern: ^\d{4,}$
keyword: inbred rat strain
keyword: map
keyword: mutant
keyword: gene
has provider formatter: http://rgd.mcw.edu/rgdweb/report/gene/main.html
keyword: biomedical science
has download URL: rgd.owl.gz
0000005: 7499841
keyword: comparative genomics
keyword: model organism
keyword: knockout
keyword: veterinary medicine
has responsible: https://orcid.org/0000-0002-6443-9376
keyword: organism supplier
is deprecated: false
keyword: variation
keyword: faseb list
keyword: genomic
keyword: genotype
has resource example: http://rgd.mcw.edu/rgdweb/report/gene/main.html
keyword: quantitative genetics
description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes.
keyword: molecular medicine
keyword: data analysis service
keyword: congenic rat

SWEET Ontology Representation Time Day
has alternative prefix: soreptd
has prefix: sweet.reptd
keyword: representation time day
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: Dawn
has URI prefix: http://sweetontology.net/reprTimeDay/
type: Resource
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Time Day
0000005: Dawn
has provider formatter: http://sweetontology.net/reprTimeDay/$1
is deprecated: false

Date Type
has URI prefix: https://vocabularies.cessda.eu/vocabulary/DateType#code_
type: Resource
has provider formatter: https://vocabularies.cessda.eu/vocabulary/DateType#code_$1
has identifier space owner: 015em2733
has resource example: code DateTime
has prefix: ddi.datetype
is deprecated: false
0000005: DateTime
is part of: Bioregistry
description: Specifies the type of date.
contributor: Charles Tapley Hoyt

SugarBind
keyword: biomedical science
has resource example: http://sugarbind.expasy.org/lectins/172
has provider formatter: http://sugarbind.expasy.org/$1
has URI prefix: http://sugarbind.expasy.org/
description: The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands.
has local unique identifier pattern: ^[A-Za-z]+\/[0-9]+$
keyword: ontology
has responsible: Frederique Lisacek
has download URL: sugarbind.owl
has prefix: sugarbind
keyword: glycomics
0000005: lectins/172
is deprecated: false
is part of: Bioregistry
type: Resource

Database of Genomic Structural Variation - Variant
is deprecated: false
has prefix: dbvar.variant
0000005: nsv3875336
description: Variants in dbVar.
is part of: Bioregistry
type: Resource
has URI prefix: https://www.ncbi.nlm.nih.gov/dbvar/variants/
contributor: Charles Tapley Hoyt
has resource example: nsv3875336
has provider formatter: https://www.ncbi.nlm.nih.gov/dbvar/variants/$1
has alternative prefix: dbvar.variants

Ontology for genetic interval
has local unique identifier pattern: ^\d{7}$
has URI prefix: http://purl.obolibrary.org/obo/OGI_
is deprecated: true
has provider formatter: http://purl.obolibrary.org/obo/OGI_$1
keyword: obo
keyword: ontology
has download URL: ogi.owl
has prefix: ogi
is part of: Bioregistry
0000005: 0000019
type: Resource
has responsible: https://orcid.org/0000-0002-5379-5359
has alternative prefix: OGI.owl
has resource example: OGI_0000019
description: An ontology that formalizes the genomic element by defining an upper class genetic interval

SWEET Ontology Realm Climate Zone
type: Resource
keyword: realm
0000005: A
has prefix: sweet.reacz
is deprecated: false
keyword: climate zone
has resource example: http://sweetontology.net/realmClimateZone/A
is part of: Bioregistry
has URI prefix: http://sweetontology.net/realmClimateZone/
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: soreacz
has provider formatter: http://sweetontology.net/realmClimateZone/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Climate Zone

ImMunoGeneTics database covering immunoglobulins and T-cell receptors
has prefix: imgt.ligm
type: Resource
has local unique identifier pattern: ^M\d+$
has provider formatter: http://www.imgt.org/ligmdb/view
has resource example: http://www.imgt.org/ligmdb/view
description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.
has responsible: https://orcid.org/0000-0003-0116-9353
has URI prefix: http://www.imgt.org/ligmdb/view
is deprecated: false
is part of: Bioregistry
keyword: dna
0000005: M94112

SABIO-RK Compound
has resource example: http://sabiork.h-its.org/newSearch
is deprecated: false
has provider formatter: http://sabiork.h-its.org/newSearch
description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information.
0000005: 75
has URI prefix: http://sabiork.h-its.org/newSearch
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has prefix: sabiork.compound

Fossilworks Taxon
has prefix: fossilworks.taxon
is part of: Bioregistry
type: Resource
description: Identifier for an animal, plant, or microorganism from the fossilworks website
has URI prefix: http://www.fossilworks.org/cgi-bin/bridge.pl
has local unique identifier pattern: ^[1-9]\d{0,5}$
has reviewer: Charles Tapley Hoyt
has resource example: http://www.fossilworks.org/cgi-bin/bridge.pl
contributor: https://orcid.org/0000-0003-2699-3066
0000005: 40565
is deprecated: false
has provider formatter: http://www.fossilworks.org/cgi-bin/bridge.pl

Chan Zuckerberg CELLxGENE Dataset
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: cellxgene.dataset
description: Assigns identifiers to datasets indexed by CELLxGENE, such those resulting from scRNA-seq experiments
type: Resource
has provider formatter: https://cellxgene.cziscience.com/e/$1
has responsible: Ambrose Carr
is deprecated: false
has URI prefix: https://cellxgene.cziscience.com/e/

Destatis subject classification
is deprecated: false
has resource example: https://onto.tib.eu/destf/cs/01
has provider formatter: https://onto.tib.eu/destf/cs/$1
has URI prefix: https://onto.tib.eu/destf/cs/
0000005: 01
is part of: Bioregistry
type: Resource
keyword: subject
keyword: educational science
has prefix: destatis.subject
keyword: miscellaneous
description: A vocabulary of university course subjects
git repository: destatis faecherklassifikation

RNA ontology
keyword: life science
has resource example: RNAO_0000128
is deprecated: true
keyword: obo
keyword: ontology
has download URL: rnao.owl
git repository: rnao
is part of: Bioregistry
type: Resource
0000005: 0000128
keyword: structure
keyword: rna secondary structure
has provider formatter: http://purl.obolibrary.org/obo/RNAO_$1
has URI prefix: http://purl.obolibrary.org/obo/RNAO_
has local unique identifier pattern: ^\d{7}$
keyword: sequence motif
has prefix: rnao
description: Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.
keyword: biochemistry
keyword: ribonucleic acid
has responsible: Colin Batchelor

SWEET Ontology Realm Landform
keyword: landform
0000005: CentralCreekCrater
has prefix: sweet.real
is deprecated: false
has resource example: CentralCreekCrater
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Landform
has URI prefix: http://sweetontology.net/realmLandform/
has provider formatter: http://sweetontology.net/realmLandform/$1
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
keyword: realm
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: soreal

Cross-linker reagents ontology
has provider formatter: http://purl.obolibrary.org/obo/XL_$1
has prefix: xl
has URI prefix: http://purl.obolibrary.org/obo/XL_
type: Resource
is deprecated: true
is part of: Bioregistry

Bioregistry Metaregistry
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
description: The Bioregistry's meta-registry
has resource example: Identifiers.org
has URI prefix: https://bioregistry.io/metaregistry/
keyword: registry
has responsible: Charles Tapley Hoyt
is deprecated: false
has provider formatter: https://bioregistry.io/metaregistry/$1
keyword: metaregistry
keyword: data science
has prefix: bioregistry.registry
keyword: data integration
0000005: miriam

Chemical Information Ontology
keyword: structure
has responsible: Tim Vandermeersch
description: The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.
0000005: 000410
appears in: Process Chemistry Ontology
keyword: biochemistry
keyword: life science
is deprecated: false
has provider formatter: http://purl.obolibrary.org/obo/CHEMINF_$1
has download URL: cheminf.owl
keyword: obo
has prefix: cheminf
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/CHEMINF_
is part of: Bioregistry
keyword: chemistry
keyword: nfdi4cat
keyword: nfdi4chem
keyword: molecular entity
git repository: semanticchemistry
has local unique identifier pattern: ^\d{6}$
has resource example: CHEMINF_000410
type: Resource

Radiation Biology Ontology
has download URL: rbo.owl
keyword: ontology
is deprecated: false
has prefix: rbo
depends on: Environment Ontology
git repository: RBO
depends on: Relation Ontology
has provider formatter: http://purl.obolibrary.org/obo/RBO_$1
has local unique identifier pattern: ^\d{6,8}$
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/RBO_
depends on: Units of measurement ontology
type: Resource
depends on: Phenotype And Trait Ontology
depends on: Ontology for Biomedical Investigations
has resource example: RBO_00000105
has responsible: Daniel C. Berrios
depends on: Chemical Methods Ontology
keyword: obo
0000005: 00000105
depends on: Basic Formal Ontology
description: RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.

Authenticus ID
has local unique identifier pattern: ^[A-Z]-[0-9A-Z]{3}-[0-9A-Z]{3}$
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: https://www.authenticus.pt/
keyword: person
has provider formatter: https://www.authenticus.pt/$1
keyword: researcher
type: Resource
0000005: P-008-GD6
has prefix: authenticus
has resource example: P-008-GD6
description: ID of a researcher in Authenticus website

Drug Target Ontology
appears in: Protein Ontology
git repository: DTO
keyword: drug target
keyword: ontology
keyword: drug discovery
is deprecated: false
keyword: disease
has URI prefix: http://www.drugtargetontology.org/dto/DTO_
keyword: protein
description: DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.
has resource example: DTO_90000018
has prefix: dto
0000005: 90000018
has provider formatter: http://www.drugtargetontology.org/dto/DTO_$1
has download URL: dto.owl
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
contributor: Charles Tapley Hoyt
keyword: biomedical science

Aclame
has provider formatter: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi
0000005: 2
keyword: gene
has prefix: mge
keyword: life science
is deprecated: true
keyword: genome
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi
description: ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.
has resource example: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi
has alternative prefix: aclame
type: Resource

National Drug File - Reference Terminology
0000005: N0000001662
keyword: ontology
keyword: physiology
is deprecated: false
is part of: Bioregistry
keyword: drug name
contributor: Charles Tapley Hoyt
has alternative prefix: ndf-rt
description: NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction].
has URI prefix: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp
keyword: chemical entity
has alternative prefix: NUI
has local unique identifier pattern: ^N[0-9]{10}$
type: Resource
keyword: biomedical science
has prefix: ndfrt
keyword: health science
has resource example: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp
has provider formatter: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp
keyword: medicine

Ontology for Biomedical Investigations
git repository: obi
keyword: life sciences, biology
has download URL: obi.owl
has local unique identifier pattern: ^\d{7}$
type: Resource
appears in: Microbial Conditions Ontology
keyword: reagent
has responsible: Bjoern Peters
keyword: biomedical science
appears in: Health Surveillance Ontology
appears in: Ontology for Nutritional Epidemiology
has resource example: OBI_0400109
appears in: Radiation Biology Ontology
has prefix: obi
keyword: life science
keyword: study design
description: The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).
appears in: Ontology for Nutritional Studies
keyword: obo
appears in: Medical Action Ontology
appears in: Plant Gall Ontology
appears in: clinical LABoratory Ontology
keyword: device
appears in: Sickle Cell Disease Ontology
keyword: ontology
appears in: Agronomy Ontology
appears in: Process Chemistry Ontology
is deprecated: false
keyword: data transformation
0000005: 0400109
has URI prefix: http://purl.obolibrary.org/obo/OBI_
has provider formatter: http://purl.obolibrary.org/obo/OBI_$1
is part of: Bioregistry
keyword: dataplant
keyword: nfdi4cat
keyword: assay
appears in: The Food Ontology
keyword: nfdi4chem
keyword: functional genomics

Simple Knowledge Organization System eXtension for Labels
has alternative prefix: skos-xl
keyword: computer science
keyword: semantic web
keyword: metadata
has URI prefix: http://www.w3.org/2008/05/skos-xl#
keyword: skos
keyword: data model
keyword: miscellaneous
description: The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web. SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.This document provides a brief description of the SKOS-XL vocabulary.
0000005: literalForm
has prefix: skosxl
is deprecated: false
keyword: w3c rec
has resource example: literalForm
is part of: Bioregistry
has provider formatter: http://www.w3.org/2008/05/skos-xl#$1
type: Resource
contributor: Charles Tapley Hoyt
has alternative prefix: skos.xl

tsRNADisease
has reviewer: https://orcid.org/0000-0001-9439-5346
has local unique identifier pattern: ^TRD\d{5}$
type: Resource
keyword: cancer
has provider formatter: http://118.178.132.53/tsRNADisease/detail.php
has responsible: https://orcid.org/0000-0002-6782-0316
description: Identifiers correspond to curated associations between diseases and tRNA-derived small RNAs (tsRNAs) in the tsRNADisease database.
has prefix: tsrnadisease
is deprecated: false
keyword: disease
is part of: Bioregistry
keyword: tsrna
has URI prefix: http://118.178.132.53/tsRNADisease/detail.php
0000005: TRD00001
contributor: Kangho Ji
has resource example: http://118.178.132.53/tsRNADisease/detail.php

The Drug Ontology
keyword: approved drug
has URI prefix: http://purl.obolibrary.org/obo/DRON_
0000005: 00023232
keyword: drug
git repository: dron
keyword: obo
has resource example: DRON_00023232
has responsible: William Hogan
appears in: Sickle Cell Disease Ontology
keyword: ontology
has prefix: dron
keyword: small molecule
is deprecated: false
has provider formatter: http://purl.obolibrary.org/obo/DRON_$1
has local unique identifier pattern: ^\d{8}$
is part of: Bioregistry
description: An ontology to support comparative effectiveness researchers studying claims data.
has download URL: dron.owl
type: Resource
keyword: biomedical science

Common Greenhouse Ontology
has prefix: tib.cgo
keyword: horticulture
keyword: earth sciences
is part of: Bioregistry
0000005: AbioticStressTrait
has provider formatter: https://www.tno.nl/agrifood/ontology/common-greenhouse-ontology#$1
has URI prefix: https://www.tno.nl/agrifood/ontology/common-greenhouse-ontology#
type: Resource
keyword: ess
has resource example: AbioticStressTrait
description: This ontology describes concepts related to greenhouses. It mainly describes Dutch greenhouses, but can also be applied to greenhouses outside of The Netherlands. The ontology describes multiple aspects of the domain of greenhouses.
keyword: chemical and environmental engineering
is deprecated: false

Bioregistry Schema
has prefix: bioregistry.schema
has provider formatter: https://bioregistry.io/schema/#$1
has responsible: Charles Tapley Hoyt
keyword: registry
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: Schema for the export of the Bioregistry as RDF
has local unique identifier pattern: ^\d{7}$
0000005: 0000001
has URI prefix: https://bioregistry.io/schema/#
type: Resource
has resource example: Resource

SWEET Ontology Phenomena Ocean Dynamics
type: Resource
keyword: ocean dynamics
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: phenomena
has provider formatter: http://sweetontology.net/phenOceanDynamics/$1
has prefix: sweet.phod
has resource example: BoundaryCurrent
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Ocean Dynamics
is deprecated: false
0000005: BoundaryCurrent
has alternative prefix: sophod
has URI prefix: http://sweetontology.net/phenOceanDynamics/
is part of: Bioregistry

India Clinical Trials Registry
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
0000005: CTRI/2023/04/052053
has provider formatter: https://trialsearch.who.int/Trial2.aspx
description: The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage) Note that the identifier in this semantic space is not the one used in the webpages
has resource example: https://trialsearch.who.int/Trial2.aspx
has prefix: ctri
has local unique identifier pattern: ^CTRI/\d{4}/\d{2,3}/\d+$
is deprecated: false
has URI prefix: https://trialsearch.who.int/Trial2.aspx

CAS Registry Number
keyword: chemical
is part of: Bioregistry
has alternative prefix: CAS_RN
keyword: chemical entity
type: Resource
has alternative prefix: CASID
keyword: structure
has URI prefix: https://commonchemistry.cas.org/detail
0000005: 50-00-0
has responsible: https://orcid.org/0000-0001-9316-9400
has prefix: cas
has alternative prefix: cas_id
description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.
has local unique identifier pattern: ^\d{1,7}\-\d{2}\-\d$
has provider formatter: https://commonchemistry.cas.org/detail
has alternative prefix: SECONDARY_CAS_RN
keyword: physical chemistry
is deprecated: false
has resource example: https://commonchemistry.cas.org/detail

SWEET Ontology Property Count
has provider formatter: http://sweetontology.net/propCount/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: AtomicNeutralNumberDensity
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: AtomicNeutralNumberDensity
has alternative prefix: sopropcou
keyword: count
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Count
has URI prefix: http://sweetontology.net/propCount/
has prefix: sweet.propcou
is deprecated: false

Xenopus Phenotype Ontology
depends on: Relation Ontology
is part of: Bioregistry
depends on: Information Artifact Ontology
has local unique identifier pattern: ^\d+$
depends on: Xenopus Anatomy Ontology
0000005: 0100002
type: Resource
depends on: Phenotype And Trait Ontology
has download URL: xpo.owl
depends on: Gene Ontology
depends on: Chemical Entities of Biological Interest
has prefix: xpo
has provider formatter: http://purl.obolibrary.org/obo/XPO_$1
git repository: xenopus-phenotype-ontology
keyword: obo
depends on: Basic Formal Ontology
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/XPO_
is deprecated: false
description: XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.
has resource example: XPO_0100002
has responsible: https://orcid.org/0000-0002-9611-1279
depends on: Cell Ontology

Groundnut Ontology
has local unique identifier pattern: ^\d{7}$
type: Resource
has prefix: co_337
keyword: life science
is deprecated: false
has resource example: CO 337:0000054
has provider formatter: https://cropontology.org/rdf/CO_337:$1
0000005: 0000054
keyword: food
has responsible: https://orcid.org/0000-0002-0091-7981
keyword: ontology
keyword: plant phenotypes and traits
is part of: Bioregistry
has URI prefix: https://cropontology.org/rdf/CO_337:
description: The Groundnut Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
has download URL: CO 337.owl
git repository: Crop-Ontology
keyword: phenotype
keyword: botany
keyword: agriculture

Clinical Trial Registries
has part: Korean Clinical Research Information Service
has part: ClinicalTrials.gov
has part: University hospital Medical Information Network Clinical Trial Registry
has part: Lebanon Clinical Trials Registry
has part: Sri Lanka Clinical Trials Registry
has part: Japan Registry of Clinical Trials
has part: Brazilian Registry of Clinical Trials
has part: Thai Clinical Trials Registry
has part: EU Clinical Trials
has part: Philippine Health Research Registry
has part: German Clinical Trials Register
type: Collection
has part: Iranian Registry of Clinical Trials
has part: Pan African Clinical Trials Registry
has part: Swiss National Clinical Trials Portal
has part: Cuban Registry of Clinical Trials
has part: International Clinical Trials Registry Platform
has part: India Clinical Trials Registry
has part: Australian New Zealand Clinical Trials Registry
has part: International Traditional Medicine Clinical Trial Registry
has part: Clinical Trials Information System
creator: Charles Tapley Hoyt
description: A collection of clinical trial registries appearing in the World Health Organization's [International Clinical Trials Registry Platform (ICTRP)](https://trialsearch.who.int/)
has part: Peruvian Clinical Trial Registry
has part: Chinese Clinical Trial Registry
has part: Health Canada Clinical Trials Database

EasyChair Topic
has URI prefix: https://easychair.org/cfp/topic.cgi
has resource example: https://easychair.org/cfp/topic.cgi
0000005: 27106865
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
type: Resource
description: Call for paper topics in EasyChair
has provider formatter: https://easychair.org/cfp/topic.cgi
keyword: metascience
keyword: topics
has prefix: easychair.topic
is deprecated: false

SWEET Ontology Material Equipment
is deprecated: false
has resource example: Aircraft
0000005: Aircraft
is part of: Bioregistry
has URI prefix: http://sweetontology.net/matrEquipment/
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Equipment
has provider formatter: http://sweetontology.net/matrEquipment/$1
keyword: equipment
type: Resource
has alternative prefix: somaeq
keyword: materials
has prefix: sweet.maeq

Bacillus subtilis genome sequencing project
description: SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.
has URI prefix: http://genolist.pasteur.fr/SubtiList/genome.cgi
0000005: BG11523
is deprecated: true
has local unique identifier pattern: ^BG\d+$
has prefix: subtilist
has responsible: Antoine Danchin
keyword: genome
keyword: dna
keyword: protein
has provider formatter: http://genolist.pasteur.fr/SubtiList/genome.cgi
is part of: Bioregistry
has resource example: http://genolist.pasteur.fr/SubtiList/genome.cgi
type: Resource

UniRef
has resource example: UniRef90 P00750
description: The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.
has URI prefix: https://www.uniprot.org/uniref/
is deprecated: false
has provider formatter: https://www.uniprot.org/uniref/$1
0000005: UniRef90_P00750
has prefix: uniref
has local unique identifier pattern: ^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$
is part of: Bioregistry
type: Resource
has responsible: Alex Bateman

Pathogen Host Interaction Phenotype Ontology
has responsible: Alayne Cuzick
git repository: phipo
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/PHIPO_
has download URL: phipo.owl
description: Ontology of species-neutral phenotypes observed in pathogen-host interactions.
is part of: Bioregistry
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/PHIPO_$1
depends on: Phenotype And Trait Ontology
has prefix: phipo
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
has resource example: PHIPO_0000001
keyword: obo
keyword: ontology

NIF Standard Ontology: Cell Types
has prefix: nlx.cell
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_cell_
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1
has reviewer: Charles Tapley Hoyt
keyword: cell lines
contributor: Tom Gillespie
keyword: cell types
0000005: 091005
has responsible: Tom Gillespie
has alternative prefix: NLXCELL
description: NLXCELL conatins cell types with a focus on neuron types.
is deprecated: false
has local unique identifier pattern: ^\d+$
git repository: NIF-Ontology
is part of: Bioregistry
has resource example: nlx cell 091005
keyword: cells
type: Resource
keyword: neuroscience

SWEET Ontology Representation Data Service Validation
has provider formatter: http://sweetontology.net/reprDataServiceValidation/$1
has resource example: Acceptance
is deprecated: false
0000005: Acceptance
has URI prefix: http://sweetontology.net/reprDataServiceValidation/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Service Validation
has prefix: sweet.repdsv
keyword: representation data service validation
is part of: Bioregistry
has alternative prefix: sorepdsv
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology

Ontology of Physics for Biology
keyword: ontology
is deprecated: false
keyword: concentration
contributor: https://orcid.org/0000-0001-9439-5346
0000005: 00573
has prefix: opb
has local unique identifier pattern: ^\d+$
has URI prefix: https://bioportal.bioontology.org/ontologies/OPB/
is part of: Bioregistry
description: The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.
has provider formatter: https://bioportal.bioontology.org/ontologies/OPB/
has resource example: https://bioportal.bioontology.org/ontologies/OPB/
keyword: structure
has download URL: opb.owl
has responsible: https://orcid.org/0000-0002-2390-6572
type: Resource
keyword: life science
keyword: physics

Scopus Researcher
is deprecated: false
has prefix: scopus
has resource example: https://www.scopus.com/authid/detail.uri
has provider formatter: https://www.scopus.com/authid/detail.uri
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has alternative prefix: scopus.author
type: Resource
0000005: 56305849200
contributor: Charles Tapley Hoyt
description: Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. Delivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts and humanities, Scopus features smart tools to track, analyze and visualize research.
has URI prefix: https://www.scopus.com/authid/detail.uri
keyword: subject agnostic

Library of Congress Subject Headings - Genre Forms
has prefix: lcsh.genreforms
type: Resource
has resource example: gf2018026088
has URI prefix: http://id.loc.gov/authorities/genreForms/
has provider formatter: http://id.loc.gov/authorities/genreForms/$1
description: A subset of Library of Congress (LOC) subject headings
is deprecated: false
is part of: Library of Congress Subject Headings
is part of: Bioregistry
0000005: gf2018026088
contributor: Charles Tapley Hoyt

Cellosaurus
description: The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.
0000005: 0440
has provider formatter: https://www.cellosaurus.org/CVCL_$1
keyword: controlled vocabularies
type: Resource
has download URL: cellosaurus.obo
has resource example: CVCL_0440
has alternative prefix: CVCL
keyword: cell lines
keyword: life science
keyword: ontologies
keyword: ontology
has URI prefix: https://www.cellosaurus.org/CVCL_
git repository: cellosaurus
has responsible: https://orcid.org/0000-0003-2826-6444
has prefix: cellosaurus
keyword: thesaurus
is deprecated: false
has local unique identifier pattern: ^[A-Z0-9]{4}$
is part of: Bioregistry

Variation Ontology
has provider formatter: http://purl.obolibrary.org/obo/VariO_$1
has prefix: vario
is deprecated: true
keyword: sequence variant
keyword: ribonucleic acid
keyword: obo
keyword: ontology
keyword: chromosome structure variation
0000005: 0376
keyword: genetics
has local unique identifier pattern: ^\d+$
has download URL: vario.owl
is part of: Bioregistry
keyword: protein
description: The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level.
has resource example: VariO_0376
has responsible: Mauno Vihinen
keyword: deoxyribonucleic acid
has URI prefix: http://purl.obolibrary.org/obo/VariO_
type: Resource

EndlessForms Studio Unit
is deprecated: false
has provider formatter: https://graphics.endlessforms.info/unit
0000005: HUMAN0000304
is part of: Bioregistry
has resource example: https://graphics.endlessforms.info/unit
contributor: Charles Tapley Hoyt
has responsible: Melissa D Clarkson
has prefix: endlessforms.unit
type: Resource
has URI prefix: https://graphics.endlessforms.info/unit
description: A unit of a vector graphic for an anatomical entity useful for biological and biomedical informatics applications.

LipidBank
keyword: molecule
has prefix: lipidbank
keyword: life science
has local unique identifier pattern: ^\w+\d+$
0000005: BBA0001
is deprecated: true
description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
has responsible: https://orcid.org/0000-0003-1898-4426
has URI prefix: https://bioregistry.io/lipidbank:
has provider formatter: https://lipidbank.jp/data/$1.cdx
is part of: Bioregistry
type: Resource
keyword: lipid
keyword: structure
has resource example: BBA0001.cdx

Plant Phenology Ontology
keyword: life cycle
git repository: PPO
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/PPO_$1
type: Resource
keyword: phenology
0000005: 0002058
has local unique identifier pattern: ^\d{7}$
description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.
keyword: obo
keyword: ontology
has resource example: PPO_0002058
is deprecated: false
has responsible: https://orcid.org/0000-0001-8815-0078
keyword: dataplant
has download URL: ppo.owl
has prefix: ppo
has URI prefix: http://purl.obolibrary.org/obo/PPO_
keyword: phenotype
keyword: botany
keyword: life sciences, biology

SWEET Ontology Phenomena Atmosphere Wind Mesoscale
has prefix: sweet.phatmowm
is deprecated: false
has resource example: AnabaticWind
has URI prefix: http://sweetontology.net/phenAtmoWindMesoscale/
is part of: Bioregistry
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Wind Mesoscale
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: phenomena
has provider formatter: http://sweetontology.net/phenAtmoWindMesoscale/$1
keyword: atmosphere wind mesoscale
has alternative prefix: sophatmowm
0000005: AnabaticWind

Comparative Data Analysis Ontology
has local unique identifier pattern: ^\d{7}$
keyword: evolutionary biology
type: Resource
description: a formalization of concepts and relations relevant to evolutionary comparative analysis
keyword: biomedical science
0000005: 0000072
has provider formatter: http://purl.obolibrary.org/obo/CDAO_$1
keyword: phylogenetics
has URI prefix: http://purl.obolibrary.org/obo/CDAO_
keyword: taxonomy
keyword: life science
keyword: obo
keyword: ontology
has prefix: cdao
is deprecated: false
git repository: cdao
has responsible: https://orcid.org/0000-0002-8688-6599
is part of: Bioregistry
keyword: molecular biology
keyword: bioinformatics
keyword: evolution
has download URL: cdao.owl
has resource example: CDAO_0000072

UniProt Variants
0000005: 068078
is deprecated: false
has URI prefix: http://purl.uniprot.org/annotation/VAR_
has local unique identifier pattern: ^\d+$
has alternative prefix: SP_VAR
description: The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species.
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has prefix: uniprot.var
has alternative prefix: UniProtKB_VAR
has responsible: Alex Bateman
has resource example: VAR_068078
has provider formatter: http://purl.uniprot.org/annotation/VAR_$1
has alternative prefix: UPVAR

SWEET Ontology Realm Geologic Continental
keyword: realm
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/realmGeolContinental/$1
type: Resource
has URI prefix: http://sweetontology.net/realmGeolContinental/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Continental
is deprecated: false
has resource example: ActiveContinent
0000005: ActiveContinent
has prefix: sweet.reagcont
has alternative prefix: soreagcont
is part of: Bioregistry
keyword: geologic continental
git repository: sweet
contributor: Charles Tapley Hoyt

SWEET Ontology State Fluid
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has alternative prefix: sostf
0000005: FluidEquilibriumState
type: Resource
has provider formatter: http://sweetontology.net/stateFluid/$1
has resource example: FluidEquilibriumState
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Fluid
has prefix: sweet.stf
keyword: state fluid
is part of: Bioregistry
has URI prefix: http://sweetontology.net/stateFluid/

Database of Arabidopsis Transcription Factors
has provider formatter: http://planttfdb.cbi.pku.edu.cn/tf.php
has local unique identifier pattern: ^AT[1-5]G\d{5}(\.\d+)?$
is deprecated: true
has resource example: http://planttfdb.cbi.pku.edu.cn/tf.php
description: DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.
has URI prefix: http://planttfdb.cbi.pku.edu.cn/tf.php
keyword: regulation
has prefix: datf
is part of: Bioregistry
type: Resource
0000005: AT1G01030.1

Iranian Registry of Clinical Trials
has local unique identifier pattern: ^IRCT\d+N\d+$
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: IRCT20080904001199N7
description: Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage) Note that the website uses a different identifier then the one reported in this semantic space.
type: Resource
has prefix: irct

Mouse pathology ontology
has responsible: Dr Paul Schofield
git repository: mpath
0000005: 728
type: Resource
has alternative prefix: MPATH
keyword: biomedical science
has URI prefix: http://purl.obolibrary.org/obo/MPATH_
has provider formatter: http://purl.obolibrary.org/obo/MPATH_$1
keyword: anatomy
keyword: mutation
has prefix: mpath
keyword: histological assay
description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes
keyword: obo
keyword: ontology
has download URL: mpath.owl
is deprecated: false
has local unique identifier pattern: ^\d+$
keyword: strain
keyword: mouse
is part of: Bioregistry
keyword: disease
has resource example: MPATH 728
keyword: phenotype

SWEET Ontology Representation Scientific Units
has alternative prefix: sorepsu
has URI prefix: http://sweetontology.net/reprSciUnits/
type: Resource
0000005: BaseUnit
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Units
has resource example: BaseUnit
is deprecated: false
has prefix: sweet.repsu
keyword: representation scientific units
is part of: Bioregistry
git repository: sweet
has provider formatter: http://sweetontology.net/reprSciUnits/$1
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt

Publons Researcher
is deprecated: false
has resource example: https://publons.com/researcher/1981638
has provider formatter: https://publons.com/researcher/$1
has URI prefix: https://publons.com/researcher/
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
has prefix: publons.researcher
contributor: Charles Tapley Hoyt
0000005: 1981638
description: Database of researchers to track publications, citation metrics, peer reviews, and journal editing work.

Ambystoma Genetic Stock Center
keyword: larvae
has prefix: agsc
is part of: Bioregistry
type: Resource
keyword: k-12 teacher
has resource example: RRID:AGSC 100E
has provider formatter: https://scicrunch.org/resolver/RRID:AGSC_$1
0000005: 100E
keyword: adult
keyword: embryo
description: The Ambystoma Genetic Stock Center (AGSC) maintains a breeding colony of Mexican axolotls (Ambystoma mexicanum) and distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. [from homepage]
has responsible: https://orcid.org/0000-0002-8332-3176
is deprecated: false
keyword: salamander
keyword: ambystoma
has URI prefix: https://scicrunch.org/resolver/RRID:AGSC_

SWEET Ontology Realm Land Protected
keyword: protectedland
git repository: sweet
type: Resource
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sorealp
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/realmLandProtected/$1
has resource example: CityPark
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Protected
is deprecated: false
has URI prefix: http://sweetontology.net/realmLandProtected/
has prefix: sweet.realp
0000005: CityPark
is part of: Bioregistry

Antimicrobial Peptide Database
has resource example: http://aps.unmc.edu/AP/database/query_output.php
is deprecated: true
has URI prefix: http://aps.unmc.edu/AP/database/query_output.php
has provider formatter: http://aps.unmc.edu/AP/database/query_output.php
keyword: protein
description: The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.
has prefix: apd
has local unique identifier pattern: ^\d{5}$
is part of: Bioregistry
has responsible: Guangshun Wang
type: Resource
keyword: biology
0000005: 01001

SWEET Ontology Realm Ocean Feature
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Ocean Feature
has provider formatter: http://sweetontology.net/realmOceanFeature/$1
type: Resource
has resource example: EarthEasternBoundaryCurrent
keyword: realm
0000005: EarthEasternBoundaryCurrent
has alternative prefix: soreaofe
has URI prefix: http://sweetontology.net/realmOceanFeature/
keyword: ocean feature
has prefix: sweet.reaofe
is deprecated: false
is part of: Bioregistry

Metabolomics Workbench Study
is deprecated: false
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^ST[0-9]{6}$
has URI prefix: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php
has resource example: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php
description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).
has prefix: mw.study
0000005: ST000900
has provider formatter: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php

Data Model Language Controlled Vocabulary
0000005: 000001
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: mola
has provider formatter: http://cor.esipfed.org/ont/earthcube/MOLA_$1
has responsible: Ruth Duerr
description: The Data Model Language Controlled Vocabulary was created for NSF's EarthCube Program's Resource Registry. At this point it merely lists a few of the languages used by data model resources in the registry.
type: Resource
has URI prefix: http://cor.esipfed.org/ont/earthcube/MOLA_
keyword: metamodel
has prefix: earthcube.mola
has resource example: MOLA_000001

RepeatsDB Structure
has prefix: repeatsdb.structure
description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database.
has resource example: 2gc4E
0000005: 2gc4E
is deprecated: false
has URI prefix: https://repeatsdb.org/structure/
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$
has provider formatter: https://repeatsdb.org/structure/$1

Ontological Interpretations for Web Property Graphs
has responsible: https://orcid.org/0000-0002-6601-2165
has local unique identifier pattern: ^\w+$
description: This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]
has URI prefix: http://w3id.org/owlstar/
is deprecated: false
is part of: Bioregistry
0000005: AllSomeInterpretation
has prefix: owlstar
git repository: owlstar
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: http://w3id.org/owlstar/$1
has resource example: AllSomeInterpretation

TOKU-E Cell-culture Database
is part of: Bioregistry
has provider formatter: http://cell-lines.toku-e.com/Cell-Lines_$1.html
type: Resource
has prefix: tokue
is deprecated: true
has URI prefix: https://bioregistry.io/tokue:
description: Cell line databases/resources

LinkML
has URI prefix: https://w3id.org/linkml/
has resource example: SchemaDefinition
keyword: ontology and terminology
has prefix: linkml
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
keyword: data integration
git repository: linkml
has provider formatter: https://w3id.org/linkml/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks.
type: Resource
0000005: SchemaDefinition

PharmacoDB Cells
description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line.
contributor: Charles Tapley Hoyt
has resource example: 22RV1 12 2019
has prefix: pharmacodb.cell
0000005: 22RV1_12_2019
type: Resource
has provider formatter: https://pharmacodb.ca/cell_lines/$1
is deprecated: false
has URI prefix: https://pharmacodb.ca/cell_lines/
is part of: Bioregistry

SAREF4GRID: an extension of SAREF for the Smart Grid domain
has resource example: ActionOperation
has alternative prefix: s4grid
has URI prefix: https://saref.etsi.org/saref4grid/
is deprecated: false
is part of: Bioregistry
has provider formatter: https://saref.etsi.org/saref4grid/$1
keyword: engineering
0000005: ActionOperation
has prefix: saref.grid
keyword: nfdi4energy
description: This ontology extends the SAREF ontology for the smart grid domain.
type: Resource

Astrophysics Source Code Library
has URI prefix: http://ascl.net/
has local unique identifier pattern: ^[0-9\.]+$
has responsible: Alice Allen
keyword: astrophysics and astronomy
has prefix: ascl
has resource example: http://ascl.net/1801.012
has provider formatter: http://ascl.net/$1
type: Resource
0000005: 1801.012
contributor: https://orcid.org/0000-0002-1216-4761
description: The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001).
is deprecated: false
is part of: Bioregistry

has download URL
domain: Resource
description: A download link for the given resource
type: Property
range: string

SMS-Ontology
keyword: nfdi4energy
type: Resource
has prefix: udsaes.sms
description: Ontology for representing systems, models and simulations in RDF.
has URI prefix: https://purl.org/sms-ontology#
0000005: CanBeApproximated
git repository: sms-ontology
is deprecated: false
has provider formatter: https://purl.org/sms-ontology#$1
has resource example: CanBeApproximated
is part of: Bioregistry
keyword: mechanical engineering, energy technology

NeuroMorpho
type: Resource
has prefix: neuromorpho
has resource example: http://neuromorpho.org/neuron_info.jsp
0000005: Rosa2
is deprecated: false
has local unique identifier pattern: ^\w+$
has responsible: Giorgio Ascoli
has URI prefix: http://neuromorpho.org/neuron_info.jsp
has provider formatter: http://neuromorpho.org/neuron_info.jsp
is part of: Bioregistry
description: NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons.
keyword: structure
keyword: anatomy

Dublin Core Metadata Initiative Terms
0000005: title
keyword: ess
keyword: metadata standardization
has alternative prefix: dc.terms
has provider formatter: http://purl.org/dc/terms/$1
has alternative prefix: dct
keyword: ontology
has prefix: dcterms
description: This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.
is deprecated: false
keyword: digital planning and construction
keyword: resource metadata
keyword: fid baudigital
is part of: Bioregistry
type: Resource
has resource example: title
contributor: Charles Tapley Hoyt
has responsible: Michelle Futornick
has alternative prefix: terms
has download URL: dcterms.owl
has URI prefix: http://purl.org/dc/terms/
keyword: nfdi4ing
keyword: metadata
keyword: subject agnostic

VFDB Genus
has prefix: vfdb.genus
description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.
is part of: Bioregistry
has URI prefix: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi
type: Resource
has resource example: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi
is deprecated: false
has provider formatter: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi
0000005: Chlamydia
has local unique identifier pattern: ^\w+$

Electrocardiogram Ontology
0000005: 000000159
has responsible: https://orcid.org/0000-0003-1719-1651
type: Resource
has prefix: ecg
has resource example: ECG_000000159
keyword: biomedical science
keyword: heart
has provider formatter: http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1
has URI prefix: http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_
keyword: electrocardiography
is deprecated: false
description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.
keyword: ontology
has alternative prefix: ECGOntology
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has download URL: ecg.owl

Allen Institute Ontologies
description: This collection contains various brain atlases from the Allen Institute.
has part: Human Brain Atlas
has part: Mouse Brain Atlas
has part: Developing Mouse Brain Atlas
creator: Charles Tapley Hoyt
type: Collection
has part: Primate Brain Atlas
has part: Developing Human Brain Atlas

Omar S. Harb
label: Omar Harb
label: Jessica Kissinger

NONCODE v4 Gene
0000005: NONHSAG00001
has prefix: noncodev4.gene
has provider formatter: http://www.bioinfo.org/NONCODEv4/show_gene.php
is part of: Bioregistry
has URI prefix: http://www.bioinfo.org/NONCODEv4/show_gene.php
has local unique identifier pattern: ^NONHSAG\d{5}$
type: Resource
description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.
is deprecated: true
has resource example: http://www.bioinfo.org/NONCODEv4/show_gene.php

NIH Human Embryonic Stem Cell Registry
has provider formatter: https://grants.nih.gov/stem_cells/registry/current.htm
description: The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage)
has resource example: https://grants.nih.gov/stem_cells/registry/current.htm
is deprecated: false
has URI prefix: https://grants.nih.gov/stem_cells/registry/current.htm
0000005: NIHhESC-10-0083
has prefix: nihhesc
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt

Sickle Cell Disease Ontology
keyword: biomedical science
depends on: VEuPathDB ontology
depends on: Apollo Structured Vocabulary
depends on: Chemical Methods Ontology
depends on: Mammalian Phenotype Ontology
depends on: Human Disease Ontology
depends on: Vaccine Ontology
description: An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease.
depends on: NCI Thesaurus
depends on: Antibiotic Resistance Ontology
depends on: Clinical measurement ontology
has provider formatter: http://purl.obolibrary.org/obo/SCDO_$1
depends on: Malaria Ontology
has responsible: https://orcid.org/0000-0002-2193-0704
depends on: The Statistical Methods Ontology
keyword: obo
depends on: Infectious Disease Ontology
keyword: ontology
depends on: Environment Ontology
depends on: The Drug Ontology
has download URL: scdo.owl
depends on: Exposure ontology
depends on: Gender, Sex, and Sexual Orientation Ontology
depends on: Data Use Ontology
depends on: Vertebrate trait ontology
is deprecated: false
depends on: Ontology of Precision Medicine and Investigation
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/SCDO_
depends on: Neuro Behavior Ontology
depends on: Units of measurement ontology
depends on: Gazetteer
0000005: 0000728
depends on: Systems Biology Ontology
depends on: Ontology for General Medical Science
depends on: Ontology for Biomedical Investigations
depends on: Human Phenotype Ontology
has prefix: scdo
depends on: Chemical Entities of Biological Interest
keyword: sickle cell disease
has resource example: SCDO_0000728
depends on: Protein Ontology
keyword: genetic disorder
has local unique identifier pattern: ^\d{7}$
depends on: Human Developmental Stages
depends on: Symptom Ontology
depends on: Informed Consent Ontology
type: Resource
git repository: scdo-ontology

Image Data Resource
has resource example: https://idr.openmicroscopy.org/search/
keyword: life science
is deprecated: false
has prefix: idr
has local unique identifier pattern: ^[0-9]{4}$
is part of: Bioregistry
has URI prefix: https://idr.openmicroscopy.org/search/
keyword: botany
description: Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools.
type: Resource
has responsible: 0000-0003-4028-811X
keyword: biomedical science
0000005: 0001
has provider formatter: https://idr.openmicroscopy.org/search/

Chinese Biological Abstracts
type: Resource
0000005: 375364
description: CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.
has prefix: cba
keyword: bibliography
is deprecated: false
has resource example: https://europepmc.org/article/CBA/375364
has URI prefix: https://europepmc.org/article/CBA/
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://europepmc.org/article/CBA/$1

CATH Protein Structural Domain Superfamily
has URI prefix: http://www.cathdb.info/cathnode/
has local unique identifier pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$
has resource example: http://www.cathdb.info/cathnode/1.10.8.10
is deprecated: false
keyword: protein
has part: CATH superfamily
has prefix: cath
is part of: Bioregistry
keyword: evolutionary biology
type: Resource
has responsible: https://orcid.org/0000-0002-7141-8936
keyword: structure
0000005: 1.10.8.10
keyword: biology
has provider formatter: http://www.cathdb.info/cathnode/$1
keyword: classification
description: CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence.

Compositional Dietary Nutrition Ontology
depends on: Environment Ontology
depends on: Relation Ontology
is part of: Bioregistry
depends on: Phenotype And Trait Ontology
has responsible: Liliana Andres Hernandez
has resource example: CDNO_0000013
has provider formatter: http://purl.obolibrary.org/obo/CDNO_$1
has prefix: cdno
has local unique identifier pattern: ^\d{7}$
depends on: Chemical Entities of Biological Interest
has download URL: cdno.owl
type: Resource
keyword: obo
has URI prefix: http://purl.obolibrary.org/obo/CDNO_
depends on: Basic Formal Ontology
keyword: ontology
0000005: 0000013
git repository: cdno
is deprecated: false
description: The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. Whilst recognising that dietary nutrients within food substrates may be present as complex and dynamic physical and chemical structures or mixtures, CDNO focuses on components typically quantified in an analytical chemistry laboratory. The primary CDNO class ‘dietary nutritional component’ contains hierarchical sets of terms organised to reflect commonly used classifications of chemical food composition. This class does not represent an exhaustive classification of chemical components, but focuses on structuring terms according to widely accepted categories. This class is independent of, but may be used in conjunction with, classes that describe ‘analytical methods’ for quantification, ‘physical properties’ or ‘dietary function’. Quantification data may be used and reported in research literature, to inform food composition tables and labelling, or for supply chain quality assurance and control. More specifically, terms within the ‘nutritional component concentration’ class may be used to represent quantification of components described in the ‘dietary nutritional component’ class. Concentration data are intended to be described in conjunction with post-composed metadata concepts, such as represented by the Food Ontology (FoodOn) ‘Food product by organism’, which derives from some food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon) entity. The common vocabulary and relation…

OrthoDB
has responsible: Evgeny M Zdobnov
has prefix: orthodb
is deprecated: false
keyword: dna
keyword: protein
has local unique identifier pattern: ^\w+$
description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups
0000011: UniProt Protein
is part of: Bioregistry
type: Resource
has resource example: http://cegg.unige.ch/orthodb/results
0000005: Q9P0K8
has provider formatter: http://cegg.unige.ch/orthodb/results
keyword: life science
has URI prefix: http://cegg.unige.ch/orthodb/results
keyword: eukaryotic

Human Developmental Stages
keyword: anatomy
has alternative prefix: HsapDv
has download URL: hsapdv.owl
has provider formatter: http://purl.obolibrary.org/obo/HsapDv_$1
keyword: obo
appears in: Sickle Cell Disease Ontology
keyword: ontology
has prefix: hsapdv
keyword: life cycle stage
is deprecated: false
keyword: developmental biology
has URI prefix: http://purl.obolibrary.org/obo/HsapDv_
has responsible: Frédéric Bastian
has resource example: HsapDv_0000194
description: Life cycle stages for Human
is part of: Bioregistry
type: Resource
git repository: developmental-stage-ontologies
0000005: 0000194
has local unique identifier pattern: ^\d{7}$

Protein Interaction Network Analysis
has responsible: 0000-0002-8876-128X
has resource example: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do
0000011: UniProt Protein
has URI prefix: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do
is part of: Bioregistry
has provider formatter: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do
type: Resource
has local unique identifier pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$
0000005: Q13485
keyword: life science
description: Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.
keyword: data visualization
is deprecated: false
has prefix: pina

SWEET Ontology Material Elemental Molecule
has alternative prefix: somaem
is deprecated: false
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
keyword: elemental molecule
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/matrElementalMolecule/$1
has URI prefix: http://sweetontology.net/matrElementalMolecule/
has prefix: sweet.maem
type: Resource
keyword: materials
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Elemental Molecule
0000005: Allotrope
has resource example: Allotrope

Cellular Phenotypes
is deprecated: true
appears in: Cell Ontology
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has prefix: cp

ScerTF
type: Resource
has resource example: RSC3
has URI prefix: http://stormo.wustl.edu/ScerTF/details/
is deprecated: true
has prefix: scretf
0000005: RSC3
has provider formatter: http://stormo.wustl.edu/ScerTF/details/$1
has local unique identifier pattern: ^\w+$
is part of: Bioregistry
description: ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.

Environment Ontology
0000005: 09200010
appears in: Ontology for Nutritional Studies
keyword: epidemiology
has local unique identifier pattern: ^\d{7,8}$
appears in: Radiation Biology Ontology
depends on: NCBI Taxonomy
has download URL: envo.owl
has prefix: envo
depends on: Plant Ontology
depends on: Population and Community Ontology
description: The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations.
appears in: An ontology of core ecological entities
appears in: Sickle Cell Disease Ontology
keyword: environmental science
appears in: Agronomy Ontology
appears in: Population and Community Ontology
keyword: life science
keyword: ess
keyword: nutritional science
depends on: The Food Ontology
is deprecated: false
keyword: fair data spaces
has responsible: Pier Luigi Buttigieg
git repository: envo
has provider formatter: http://purl.obolibrary.org/obo/ENVO_$1
keyword: obo
keyword: ontology
appears in: Compositional Dietary Nutrition Ontology
appears in: The Food Ontology
depends on: Relation Ontology
has URI prefix: http://purl.obolibrary.org/obo/ENVO_
keyword: marine metagenome
has resource example: ENVO_09200010
is part of: Bioregistry
keyword: dataplant
keyword: ecology
keyword: nfdi4cat
appears in: Environmental conditions, treatments and exposures ontology
keyword: microbiome
keyword: nfdi4chem
keyword: environmental material
depends on: Uber Anatomy Ontology
keyword: earth sciences
keyword: life sciences, biology
depends on: Chemical Entities of Biological Interest
depends on: Gene Ontology
appears in: Uber Anatomy Ontology
type: Resource

Rat Genome Database strain
0000005: 5688061
is deprecated: false
has provider formatter: http://rgd.mcw.edu/rgdweb/report/strain/main.html
has prefix: rgd.strain
has resource example: http://rgd.mcw.edu/rgdweb/report/strain/main.html
description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology.
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has URI prefix: http://rgd.mcw.edu/rgdweb/report/strain/main.html
type: Resource

NanoParticle Ontology
has download URL: npo.owl
keyword: ontology
description: An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
git repository: npo
contributor: Charles Tapley Hoyt
keyword: molecular entity
keyword: nanoparticle
has prefix: npo
has URI prefix: http://purl.bioontology.org/ontology/npo#NPO_
has responsible: https://orcid.org/0000-0002-5892-6506
has provider formatter: http://purl.bioontology.org/ontology/npo#NPO_$1
has resource example: NPO 1731
type: Resource
keyword: structure
0000005: 1731
keyword: life science
is deprecated: false

Addiction Ontology
has prefix: addicto
has provider formatter: http://addictovocab.org/ADDICTO_$1
description: The Addiction Ontology (AddictO) is an ontology being developed all aspects of addiction research.
keyword: ontology
has resource example: ADDICTO_0000447
has responsible: https://orcid.org/0000-0001-6398-0921
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has download URL: addicto.owl
type: Resource
0000005: 0000447
git repository: addiction-ontology
has URI prefix: http://addictovocab.org/ADDICTO_

tricdb
is deprecated: false
has URI prefix: http://biomeddb.org/Disease/Details
has provider formatter: http://biomeddb.org/Disease/Details
has prefix: tricdb
has local unique identifier pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
is part of: Bioregistry
type: Resource
description: Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of Tri©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine.
has resource example: http://biomeddb.org/Disease/Details

Provisional Cell Ontology
type: Resource
has resource example: PCL_0011124
depends on: Phenotype And Trait Ontology
keyword: annotation
depends on: Uber Anatomy Ontology
has prefix: pcl
keyword: sequencing assay
depends on: Gene Ontology
keyword: cell
has local unique identifier pattern: ^\d{7}$
depends on: Sequence types and features ontology
depends on: Chemical Entities of Biological Interest
keyword: anatomy
depends on: Protein Ontology
has provider formatter: http://purl.obolibrary.org/obo/PCL_$1
keyword: life science
has responsible: David Osumi-Sutherland
keyword: obo
depends on: NCBI Taxonomy
keyword: cell biology
depends on: Basic Formal Ontology
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/PCL_
keyword: single-cell multimodal omics
is deprecated: false
git repository: provisional cell ontology
has download URL: pcl.owl
keyword: omics
depends on: Cell Ontology
depends on: Relation Ontology
0000005: 0011124
is part of: Bioregistry
keyword: phenomics
description: Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties.
depends on: OBO Metadata Ontology
depends on: Neuro Behavior Ontology
keyword: transcriptomics

A vocabulary for the catalysis disciplines
has reviewer: Charles Tapley Hoyt
has responsible: https://orcid.org/0000-0002-6242-2167
has URI prefix: https://w3id.org/nfdi4cat/voc4cat_
has resource example: voc4cat_0000123
description: Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science.
git repository: voc4cat
0000005: 0000123
is deprecated: false
is part of: Bioregistry
keyword: chemistry
keyword: nfdi4cat
contributor: https://orcid.org/0000-0002-5898-1820
keyword: nfdi4chem
keyword: fairmat
type: Resource
has local unique identifier pattern: ^\d{7,}$
has provider formatter: https://w3id.org/nfdi4cat/voc4cat_$1
has prefix: voc4cat

SWEET Ontology Realm Atmospheric
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Atmospheric
has alternative prefix: soreaa
keyword: realm
has resource example: AtmosphereLayer
0000005: AtmosphereLayer
has prefix: sweet.reaa
is deprecated: false
has URI prefix: http://sweetontology.net/realmAtmo/
keyword: atmospheric
is part of: Bioregistry
has provider formatter: http://sweetontology.net/realmAtmo/$1
contributor: Charles Tapley Hoyt

Transcriptional Regulatory Element Database
type: Resource
has prefix: tred
description: Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present.
has reviewer: Charles Tapley Hoyt
has resource example: http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi
is deprecated: true
has provider formatter: http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi
keyword: dna
keyword: regulation
is part of: Bioregistry
0000005: 21552
has URI prefix: http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi

SWEET Ontology Property Space Height
has provider formatter: http://sweetontology.net/propSpaceHeight/$1
is part of: Bioregistry
has URI prefix: http://sweetontology.net/propSpaceHeight/
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
has alternative prefix: sopropsh
has prefix: sweet.propsh
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: Altitude
keyword: space height
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Height
0000005: Altitude
is deprecated: false

CohesinDB - cohesin site
keyword: binding site
has reviewer: Charles Tapley Hoyt
contributor: https://orcid.org/0009-0000-6974-6386
has resource example: CDBP00415501
has responsible: Ryuichiro Nakato
has provider formatter: https://cohesindb.iqb.u-tokyo.ac.jp/browsepeak/eachpeak/$1
has URI prefix: https://cohesindb.iqb.u-tokyo.ac.jp/browsepeak/eachpeak/
is deprecated: false
keyword: protein
description: Contains identifiers of cohesin binding sites in human cells from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information.
has local unique identifier pattern: ^CDBP00\d{6}$
has prefix: cohesindb.binding
keyword: cohesin
is part of: Bioregistry
type: Resource
0000005: CDBP00415501

OpenEduHub Education Level
is deprecated: false
keyword: education level
0000005: 1
has prefix: oeh.educationlevel
keyword: open educational resources
has resource example: http://w3id.org/openeduhub/vocabs/educationalLevel/1
is part of: Bioregistry
has provider formatter: http://w3id.org/openeduhub/vocabs/educationalLevel/$1
type: Resource
contributor: Charles Tapley Hoyt
git repository: oeh-metadata-vocabs
description: A list of values for class levels. Created in the context of the OpenEduHub
has URI prefix: http://w3id.org/openeduhub/vocabs/educationalLevel/

DALIA Community
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has prefix: dalia.community
has URI prefix: https://search.dalia.education/communities/
description: A UUID for a community indexed in the Data Liteacy Alliance (DALIA) web application
has provider formatter: https://search.dalia.education/communities/$1
has local unique identifier pattern: ^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$
is deprecated: false

The Amphioxus Development and Anatomy Ontology
git repository: amphx ontology
contributor: https://orcid.org/0000-0002-1216-4761
has resource example: AMPHX_1000160
has provider formatter: http://purl.obolibrary.org/obo/AMPHX_$1
keyword: obo
has prefix: amphx
has URI prefix: http://purl.obolibrary.org/obo/AMPHX_
has responsible: Hector Escriva
keyword: ontology
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).
depends on: Uber Anatomy Ontology
0000005: 1000160
type: Resource
has download URL: amphx.owl

HomoloGene
has provider formatter: https://www.ncbi.nlm.nih.gov/homologene/$1
has URI prefix: https://www.ncbi.nlm.nih.gov/homologene/
keyword: genome
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has resource example: https://www.ncbi.nlm.nih.gov/homologene/1000
has responsible: Eric W. Sayers
type: Resource
0000005: 1000
keyword: gene
has prefix: homologene
description: HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.
keyword: life science
is deprecated: false

Clytia hemisphaerica Development and Anatomy Ontology
has prefix: clyh
depends on: Uber Anatomy Ontology
has URI prefix: http://purl.obolibrary.org/obo/CLYH_
git repository: clyh ontology
has download URL: clyh.owl
has resource example: CLYH_1000100
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/CLYH_$1
has responsible: https://orcid.org/0000-0002-7440-0467
description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.
keyword: obo
keyword: ontology
depends on: Relation Ontology
is deprecated: false
is part of: Bioregistry
depends on: Information Artifact Ontology
has local unique identifier pattern: ^\d+$
0000005: 1000100

TubercuList knowledge base
has prefix: myco.tuber
has alternative prefix: TubercuList
has local unique identifier pattern: ^Rv\d{4}(A|B|c)?$
has URI prefix: https://mycobrowser.epfl.ch/genes/
type: Resource
description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.
has provider formatter: https://mycobrowser.epfl.ch/genes/$1
is part of: MycoBrowser
has responsible: Stewart Thomas Cole
0000005: Rv1908c
has resource example: Rv1908c
is deprecated: false
keyword: dna
is part of: Bioregistry
keyword: protein
keyword: genome

Health Canada Drug Identification Number
0000005: 02069237
has local unique identifier pattern: ^\d{8}$
has prefix: hc.din
description: A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada.
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

Eschmeyer's Catalog of Fishes
contributor: Charles Tapley Hoyt
has reviewer: Charles Tapley Hoyt
has provider formatter: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp
type: Resource
is deprecated: true
has URI prefix: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp
has alternative prefix: CASGEN
has resource example: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp
contributor: https://orcid.org/0000-0001-9439-5346
0000005: 5359
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has prefix: casspc

Dynamic Ecological Information Management System - Site and dataset registry
description: DEIMS-SDR (Dynamic Ecological Information Management System - Site and dataset registry) is an information management system powered by eLTER. It allows you to discover long-term ecosystem research sites around the globe, along with the data gathered at those sites and the people and networks associated with them. DEIMS-SDR describes a wide range of sites, providing a wealth of information, including each site’s location, ecosystems, facilities, parameters measured and research themes. It is also possible to access a growing number of datasets and data products associated with the sites.
has responsible: Christoph Wohner
is part of: Bioregistry
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
has alternative prefix: deims.id
has reviewer: Charles Tapley Hoyt
has prefix: deims.site
has URI prefix: https://deims.org/
has provider formatter: https://deims.org/$1
has local unique identifier pattern: ^[0-9a-f\-]+$
is deprecated: false

ICD 11 Codes
0000005: NA06.8D
contributor: Charles Tapley Hoyt
has prefix: icd11.code
type: Resource
is deprecated: false
description: An ICD-11 code is a standardized alphanumeric identifier used to classify and document diseases, conditions, and health-related issues for global healthcare and statistical purposes.
has local unique identifier pattern: ^[0-9A-Z]+(\.[0-9A-Z]+)?$
is part of: Bioregistry

Competence Ontology
has provider formatter: http://purl.org/nemo/competence#$1
has prefix: nemo.competence
keyword: skills
is part of: Bioregistry
has URI prefix: http://purl.org/nemo/competence#
git repository: competence-ontology
contributor: Charles Tapley Hoyt
has resource example: CognitiveCompetence
type: Resource
keyword: competence
keyword: ontology
0000005: CognitiveCompetence
is deprecated: false
description: A small ontology expressing skills and competencies.

miRNEST
description: miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.
has provider formatter: http://rhesus.amu.edu.pl/mirnest/copy/details.php
0000005: MNEST029358
is part of: Bioregistry
has resource example: http://rhesus.amu.edu.pl/mirnest/copy/details.php
type: Resource
has local unique identifier pattern: ^MNEST\d+$
keyword: expression
has responsible: Michael Szcześniak
keyword: life science
has URI prefix: http://rhesus.amu.edu.pl/mirnest/copy/details.php
has prefix: mirnest
is deprecated: false
keyword: genomics
keyword: prediction

CorrDB
has local unique identifier pattern: ^[0-9]+$
has prefix: corrdb
keyword: genetics
is deprecated: false
has responsible: Zhiliang Hu
is part of: Bioregistry
has URI prefix: https://www.animalgenome.org/CorrDB/q/
has provider formatter: https://www.animalgenome.org/CorrDB/q/
description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.
keyword: animal genetics
keyword: systems biology
type: Resource
0000005: 37232
keyword: life science
has resource example: https://www.animalgenome.org/CorrDB/q/

AmphibiaWeb Species ID
has prefix: amphibiaweb.species
0000005: 149
has local unique identifier pattern: ^[1-9]\d*$
has provider formatter: https://amphibiaweb.org/species/$1
is deprecated: false
is part of: Bioregistry
description: identifier for a species, in the AmphibiaWeb database
has resource example: https://amphibiaweb.org/species/149
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: https://amphibiaweb.org/species/

Information Resource Registry
has prefix: infores
git repository: information-resource-registry
has provider formatter: https://w3id.org/information-resource-registry/$1
has reviewer: Charles Tapley Hoyt
type: Resource
description: The information resource registry is a listing of data sources present in the NCATS Data Translator system. Each information resource has an identifier, a short description, and a URL to more information about that resource.
has URI prefix: https://w3id.org/information-resource-registry/
is deprecated: false
0000005: agrkb
has local unique identifier pattern: ^[a-z0-9-_.]+$
has responsible: Sierra Moxon
has resource example: agrkb
contributor: https://orcid.org/0000-0002-7356-1779
is part of: Bioregistry

SWEET Ontology State Data Processing
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Data Processing
keyword: state data processing
has prefix: sweet.stdp
is deprecated: false
has resource example: Archived
0000005: Archived
has URI prefix: http://sweetontology.net/stateDataProcessing/
has alternative prefix: sostdp
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/stateDataProcessing/$1
is part of: Semantic Web for Earth and Environment Technology Ontology

Cell Line Ontology
keyword: cell line
keyword: obo
depends on: NCBI Taxonomy
0000005: 0000091
depends on: Human Disease Ontology
has download URL: clo.owl
keyword: cell biology
keyword: ontology
has alternative prefix: CLO
has resource example: CLO_0000091
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/CLO_
has provider formatter: http://purl.obolibrary.org/obo/CLO_$1
depends on: Cell Ontology
is part of: Bioregistry
type: Resource
appears in: Microbial Conditions Ontology
has prefix: clo
depends on: Uber Anatomy Ontology
keyword: cell
has local unique identifier pattern: ^\d{7}$
git repository: CLO
has responsible: Jie Zheng
keyword: morphology
keyword: life science
description: The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.

CharProt
description: CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.
is deprecated: true
has resource example: CH_001923
is part of: Bioregistry
has provider formatter: http://www.jcvi.org/charprotdb/index.cgi/view/$1
has prefix: charprot
type: Resource
has local unique identifier pattern: ^CH_\d+$
0000005: CH_001923
has URI prefix: http://www.jcvi.org/charprotdb/index.cgi/view/

GOLD genome
has URI prefix: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi
description: - DEPRECATION NOTE - Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.
is part of: Bioregistry
0000005: Gi07796
type: Resource
0000011: Genomes Online Database
has prefix: gold.genome
has resource example: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi
is deprecated: true
has local unique identifier pattern: ^(Gi|Gc)\d+$
has provider formatter: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi

Standards Ontology
keyword: engineering
0000005: AiiClassification
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
description: An ontology to describe standards related to Industry 4.0 and Smart Manufacturing
has URI prefix: https://w3id.org/i40/sto#
has prefix: tib.sto
has resource example: AiiClassification
has provider formatter: https://w3id.org/i40/sto#$1
is deprecated: false

SIDER Side Effect
has resource example: http://sideeffects.embl.de/se/C0017565
type: Resource
0000011: Unified Medical Language System Concept Unique Identifier
has prefix: sider.effect
has URI prefix: http://sideeffects.embl.de/se/
description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.
has provider formatter: http://sideeffects.embl.de/se/$1
0000005: C0017565
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^C\d+$

Physical Medicine and Rehabilitation
keyword: life science
has local unique identifier pattern: ^[a-z0-9]{32,32}$
is deprecated: false
keyword: systems biology
description: Resource for the community to store, retrieve, search, reference, and reuse CellML models.
keyword: ontology
has prefix: pmr.exposure
keyword: physiology
has provider formatter: https://models.physiomeproject.org/exposure/$1
keyword: mathematics
is part of: Bioregistry
has alternative prefix: pmr
has URI prefix: https://models.physiomeproject.org/exposure/
has responsible: Laia Subirats
has download URL: pmr.owl
type: Resource
keyword: biomedical science

Rodent Unidentified Gene-Encoded Large Proteins
is part of: Bioregistry
0000005: mKIAA4200
has provider formatter: https://www.kazusa.or.jp/rouge/gfpage/$1
description: The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.
has resource example: mKIAA4200
has prefix: rouge
has URI prefix: https://www.kazusa.or.jp/rouge/gfpage/
type: Resource
keyword: life science
has local unique identifier pattern: ^m\w+$
is deprecated: false
keyword: dna
keyword: protein
has responsible: https://orcid.org/0000-0002-3328-9571

UniPathway Reaction
description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions.
has provider formatter: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr
is part of: Bioregistry
has prefix: unipathway.reaction
has resource example: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr
type: Resource
has URI prefix: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr
0000005: UCR00226
has local unique identifier pattern: ^UCR\d{5}$
is deprecated: false

Pathway ontology
keyword: molecular entity
has URI prefix: http://purl.obolibrary.org/obo/PW_
has local unique identifier pattern: ^\d{7}$
description: The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.
type: Resource
keyword: enzymatic reaction
has prefix: pw
has provider formatter: http://purl.obolibrary.org/obo/PW_$1
keyword: drug metabolism
has responsible: G. Thomas Hayman
has download URL: pw.owl
keyword: life science
is deprecated: false
0000005: 0000423
keyword: drug
keyword: obo
git repository: PW-Pathway-Ontology
keyword: biological regulation
keyword: human
keyword: ontology
keyword: pathway
has resource example: PW_0000423
keyword: signaling
keyword: disease
is part of: Bioregistry

PesticideInfo chemical ID
0000005: PRI10
has URI prefix: https://www.pesticideinfo.org/chemical/
has prefix: pesticideinfo
has provider formatter: https://www.pesticideinfo.org/chemical/$1
is deprecated: false
description: chemical in the database supplied by Pesticide Action Network North America
has resource example: PRI10
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^PRI\d*$

SWEET Ontology Realm Land Volcanic
0000005: Caldera
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Volcanic
is part of: Bioregistry
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has alternative prefix: sorealv
has URI prefix: http://sweetontology.net/realmLandVolcanic/
has provider formatter: http://sweetontology.net/realmLandVolcanic/$1
has prefix: sweet.realv
has resource example: Caldera
is deprecated: false
keyword: volcanicland

Semantically-Interlinked Online Communities Access Ontology
description: Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining basic information on permissions and access rights.
has prefix: sioc.access
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: http://rdfs.org/sioc/access#
has resource example: Permission
has provider formatter: http://rdfs.org/sioc/access#$1
type: Resource
0000005: Permission
is deprecated: false

Publisher Item Identifier
0000005: S0960-9822(11)01319-4
description: A combination of an ISBN and local unique identifier for articles and other published works. Please see the [Wikipedia page](https://en.wikipedia.org/wiki/Publisher_Item_Identifier) for a detailed explanation. Some PIIs are used as the local identifiers in DOIs, such as https://doi.org/10.1136/S0003-4967(24)38620-0.
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has local unique identifier pattern: ^((S\d{4}-\d{4}\(\d{2}\)\d{5})|(B\d-\d{3}-\d{5}-\d/\d{5}))-[\d|X]$
is deprecated: false
appears in: PubMed
has prefix: pii

Hazardous Substances Data Bank
has prefix: hsdb
is deprecated: false
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/5621
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/
description: The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas.
0000005: 5621

OBOE Standard
type: Resource
has prefix: oboe.standard
is deprecated: false
keyword: units
0000005: Acre
has provider formatter: http://ecoinformatics.org/oboe/oboe.1.2/oboe-standards.owl$1
keyword: ontology
is part of: Bioregistry
has URI prefix: http://ecoinformatics.org/oboe/oboe.1.2/oboe-standards.owl
contributor: Charles Tapley Hoyt
has resource example: oboe-standards.owlAcre
description: Units in OBOE
keyword: unit

SWEET Ontology Process Chemical
type: Resource
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: soprocc
has provider formatter: http://sweetontology.net/procChemical/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process Chemical
0000005: Absorption
has resource example: Absorption
has URI prefix: http://sweetontology.net/procChemical/
is deprecated: false
has prefix: sweet.procc
keyword: chemical
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt

FAIRsharing Organization
type: Resource
contributor: Charles Tapley Hoyt
has resource example: https://fairsharing.org/organisations/3851
has URI prefix: https://fairsharing.org/organisations/
has provider formatter: https://fairsharing.org/organisations/$1
has responsible: https://orcid.org/0000-0002-7702-4495
has prefix: fairsharing.organization
0000005: 3851
is deprecated: false
description: An organization in FAIRsharing, including universities, labs, etc.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry

eagle-i resource ontology
keyword: life science
description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.
keyword: study design
has download URL: ero.owl
is deprecated: true
keyword: obo
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/ERO_
keyword: biospecimen
has responsible: https://orcid.org/0000-0002-3734-1859
has prefix: ero
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/ERO_$1
keyword: reagent
keyword: biomedical science
has resource example: ERO_0001655
0000005: 0001655

Plant Gall Ontology
depends on: Ontology for Biomedical Investigations
depends on: Phenotype And Trait Ontology
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
has responsible: https://orcid.org/0000-0002-2119-4663
depends on: Flora Phenotype Ontology
depends on: NCBI Taxonomy
depends on: Plant Ontology
keyword: obo
has URI prefix: http://purl.obolibrary.org/obo/GALLONT_
keyword: ontology
description: Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.
depends on: Common Anatomy Reference Ontology
is deprecated: false
has provider formatter: http://purl.obolibrary.org/obo/GALLONT_$1
git repository: gallont
has prefix: gallont
depends on: Relation Ontology
is part of: Bioregistry
type: Resource
depends on: Porifera Ontology
has download URL: gallont.owl

LINCS Cell
has prefix: lincs.cell
is deprecated: false
has URI prefix: http://lincsportal.ccs.miami.edu/cells/#/view/
is part of: Bioregistry
type: Resource
description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.
has local unique identifier pattern: ^(LCL|LDC|ES|LSC|LPC)-\d+$
has provider formatter: http://lincsportal.ccs.miami.edu/cells/#/view/$1
has alternative prefix: LINCS_LDP
0000005: LCL-2085
has resource example: view/LCL-2085

Orthology Ontology
has responsible: https://orcid.org/0000-0002-7558-2880
git repository: OrthologyOntology
keyword: comparative genomics
has download URL: orthOntology RC v2 A.owl
keyword: orthologous
keyword: region
is deprecated: false
0000005: HomologyRelation
description: The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.
has URI prefix: http://purl.org/net/orth#
keyword: ontology
keyword: homologous
is part of: Bioregistry
keyword: protein
has prefix: orth
keyword: paralogous
has resource example: HomologyRelation
has provider formatter: http://purl.org/net/orth#$1
type: Resource
keyword: gene

Open Digital Rights Language Ontology
keyword: metadata
has URI prefix: http://www.w3.org/ns/odrl/2/
0000005: assetConcepts
is deprecated: false
has provider formatter: http://www.w3.org/ns/odrl/2/$1
description: The ODRL Vocabulary and Expression defines a set of concepts and terms (the vocabulary) and encoding mechanism (the expression) for permissions and obligations statements describing digital content usage based on the ODRL Information Model.
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has prefix: odrl
has resource example: assetConcepts

Archival Resource Key
git repository: arks-org
description: Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that don’t return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations — libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver.
0000005: /53355/cl010066723
type: Resource
keyword: data retrieval
has resource example: cl010066723
keyword: subject agnostic
contributor: https://orcid.org/0000-0001-7604-8041
contributor: https://orcid.org/0000-0002-1216-4761
has local unique identifier pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$
has URI prefix: http://n2t.net/ark:
has provider formatter: http://n2t.net/ark:$1
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: ark
has responsible: https://orcid.org/0000-0001-7604-8041

Unified Medical Language System Atomic Unique Identifier
has alternative prefix: UMLS_ICD9CM_2005_AUI
has local unique identifier pattern: ^A\d+$
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
description: An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus.
has prefix: umls.aui
0000005: A0118748

European Genome-phenome Archive
has provider formatter: https://ega-archive.org/identifiers/$1
0000005: EGAD00001008392
is deprecated: false
is part of: Bioregistry
description: The European Genome-phenome Archive (EGA) is a global network for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems. Jointly managed by the European Bioinformatics Institute (EMBL-EBI) in Cambridge (UK) and the Centre for Genomic Regulation (CRG) in Barcelona.
type: Resource
has prefix: ega
has local unique identifier pattern: ^EGA[SCPNRXZDBF][0-9]{11}$
has resource example: EGAD00001008392
has URI prefix: https://ega-archive.org/identifiers/

Vaccine administered code set
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: vaccine
type: Resource
has download URL: cvx.owl
has resource example: https://biopragmatics.github.io/providers/cvx/54
has URI prefix: https://biopragmatics.github.io/providers/cvx/
keyword: ontology
has prefix: cvx
has provider formatter: https://biopragmatics.github.io/providers/cvx/$1
is deprecated: false
has responsible: IIS Helpdesk
0000005: 54
description: The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records.
has local unique identifier pattern: ^\d+$

RepeatsDB Protein
has local unique identifier pattern: ^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$
is deprecated: false
description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database.
has prefix: repeatsdb.protein
has provider formatter: https://repeatsdb.org/protein/$1
0000011: UniProt Protein
is part of: Bioregistry
has URI prefix: https://repeatsdb.org/protein/
type: Resource
0000005: P29894
has resource example: P29894

Eukaryotic Promoter Database
keyword: biology
contributor: 0000-0003-3947-488X
has prefix: epd
has responsible: https://orcid.org/0000-0002-0816-7775
0000005: TA_H3
has URI prefix: https://epd.expasy.org/cgi-bin/epd/query_result.pl
is deprecated: false
is part of: Bioregistry
has resource example: https://epd.expasy.org/cgi-bin/epd/query_result.pl
keyword: bioinformatics
description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.
has local unique identifier pattern: ^[A-Z-_0-9]+$
has provider formatter: https://epd.expasy.org/cgi-bin/epd/query_result.pl
type: Resource

Gene Location
has URI prefix: http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl
has resource example: http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl
0000005: 17503
is part of: Bioregistry
type: Resource
has reviewer: Charles Tapley Hoyt
has provider formatter: http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl
has prefix: genecards.geneloc
description: GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources
is deprecated: false
keyword: genome

GitHub Pull Request
keyword: software engineering
0000005: biopragmatics/bioregistry/416
is deprecated: false
keyword: version control
has URI prefix: https://bioregistry.io/resolve/github/pull/
keyword: knowledge and information systems
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has resource example: https://bioregistry.io/resolve/github/pull/biopragmatics/bioregistry/416
description: A pull request in any public repository on GitHub.
has prefix: github.pull
keyword: project management
has provider formatter: https://bioregistry.io/resolve/github/pull/$1

MolMeDB
git repository: MolMeDB
type: Resource
has prefix: molmedb
0000005: MM00040
keyword: biochemistry
has local unique identifier pattern: ^[Mm]{2}[0-9]{5,}(\.[0-9]+)?$
has responsible: https://orcid.org/0000-0001-9472-2589
keyword: molecular dynamics
keyword: molecular physical chemistry
keyword: computational chemistry
has URI prefix: https://molmedb.upol.cz/mol/
has provider formatter: https://molmedb.upol.cz/mol/$1
is deprecated: false
keyword: cheminformatics
keyword: molecular biology
keyword: chemistry
description: MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations.
contributor: Dominik Martinat
has resource example: MM00040
keyword: molecular chemistry
is part of: Bioregistry

Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens
has responsible: https://orcid.org/0000-0001-6583-9067
keyword: comparative genomics
has resource example: ISCW007415
0000005: ISCW007415
has provider formatter: https://vectorbase.org/gene/$1
keyword: population genetics
has URI prefix: https://vectorbase.org/gene/
keyword: genome
is deprecated: false
keyword: protein
keyword: genomics
description: VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host.
keyword: population dynamics
has prefix: vectorbase
keyword: functional genomics
is part of: Bioregistry
has local unique identifier pattern: ^\D{4}\d{6}(\-\D{2})?$
type: Resource
keyword: gene

NIF Gross Anatomy
has provider formatter: http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1
has prefix: nif.grossanatomy
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_
type: Resource
is deprecated: true
has responsible: Fahim Imam
keyword: obo
keyword: ontology

Database for Prokaryotic Operons
description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes.
has provider formatter: http://csbl.bmb.uga.edu/DOOR/operon.php
has URI prefix: http://csbl.bmb.uga.edu/DOOR/operon.php
type: Resource
has resource example: http://csbl.bmb.uga.edu/DOOR/operon.php
0000005: 1398574
is deprecated: true
has prefix: door
is part of: Bioregistry
keyword: dna
has local unique identifier pattern: ^\d+$

NONCODE v4 Transcript
has local unique identifier pattern: ^NONHSAT\d{6}$
is deprecated: true
0000005: NONHSAT000001
has provider formatter: http://www.bioinfo.org/NONCODEv4/show_rna.php
is part of: Bioregistry
description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.
type: Resource
has prefix: noncodev4.rna
has resource example: http://www.bioinfo.org/NONCODEv4/show_rna.php
has URI prefix: http://www.bioinfo.org/NONCODEv4/show_rna.php

Datanator Reaction
is deprecated: false
has URI prefix: https://datanator.info/reaction/
description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.
has local unique identifier pattern: ^.*?--%3E.*?$
is part of: Bioregistry
type: Resource
has resource example: XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N-->NBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N
has provider formatter: https://datanator.info/reaction/$1
has prefix: datanator.reaction

C. elegans phenotype
keyword: phenomics
has local unique identifier pattern: ^\d{7}$
has download URL: wbphenotype.owl
type: Resource
0000005: 0000983
has provider formatter: http://purl.obolibrary.org/obo/WBPhenotype_$1
git repository: c-elegans-phenotype-ontology
has URI prefix: http://purl.obolibrary.org/obo/WBPhenotype_
keyword: anatomy
keyword: life science
has responsible: https://orcid.org/0000-0001-9076-6015
keyword: obo
keyword: ontology
has prefix: wbphenotype
description: Ontology about C. elegans and other nematode phenotypes
keyword: worm
has alternative prefix: WBPhenotype
is deprecated: false
is part of: Bioregistry
keyword: phenotype
keyword: omics
has resource example: WBPhenotype_0000983

Sweet Potato Ontology
has responsible: https://orcid.org/0000-0003-0595-5271
has URI prefix: https://cropontology.org/rdf/CO_331:
has provider formatter: https://cropontology.org/rdf/CO_331:$1
keyword: life science
keyword: food
keyword: ontology
is deprecated: false
description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Sweet Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
has prefix: co_331
is part of: Bioregistry
git repository: Crop-Ontology
keyword: botany
keyword: agriculture
has download URL: CO 331.owl
has resource example: CO 331:0000088
has local unique identifier pattern: ^\d{7}$
type: Resource
0000005: 0000088

FAIR* Reviews Ontology
is deprecated: false
0000005: ReviewVersion
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has responsible: Silvio Peroni
keyword: subject agnostic
git repository: fr
has prefix: fr
description: An ontology that enables the description of reviews of scientific articles and other scholarly resources.

Fungal Growth Database
description: Identifiers represent experimental growth profiles documenting fungal species' ability to utilize specific carbon sources (plant biomass components, polysaccharides, and monosaccharides) in the FUNG-GROWTH database, which provides phenotypic data to support functional genome annotation and comparative analysis of carbohydrate metabolism across fungal species.
is part of: Bioregistry
type: Resource
has responsible: Vincent Robert
keyword: growth profiles
keyword: plant biomass
has provider formatter: https://www.fung-growth.org/page/Display%20page%20FG/$1
0000005: 86
keyword: monosaccharides
has prefix: funggrowth
has resource example: https://www.fung-growth.org/page/Display%20page%20FG/86
keyword: polysaccharides
is deprecated: false
keyword: fungi
contributor: Kangho Ji
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.fung-growth.org/page/Display%20page%20FG/
has local unique identifier pattern: ^\d+$

Machine-readable Cataloging (MARC) List for Languages
has URI prefix: https://id.loc.gov/vocabulary/languages/
is deprecated: false
has prefix: marc21
has resource example: amh
is part of: Bioregistry
has provider formatter: https://id.loc.gov/vocabulary/languages/$1
contributor: Charles Tapley Hoyt
description: MARC List for Languages provides three-character lowercase alphabetic strings that serve as the identifiers of languages and language groups. The codes are usually based on the first three letters of the English form or, in some cases, vernacular form of the corresponding language name. The codes are varied where necessary to resolve conflicts and are not intended to be abbreviations of a language name. When the name of a language is changed in the list, the original code is generally retained. The codes in this list are equivalent to those of ISO 639-2 (Bibliographic) codes and some codes from ISO 639-5, although the language name labels may differ. They are linked to the equivalent codes in ISO 639-2 and ISO 639-5 and the corresponding two-character codes in ISO 639-1. The list contains over 480 discrete codes. It is also searchable at: MARC Code List for Languages.
type: Resource
0000005: amh

Homeostasis imbalance process ontology
keyword: ontology
0000005: 0040379
is deprecated: false
is part of: Bioregistry
git repository: hoip
has resource example: HOIP_0040379
description: An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes.
has local unique identifier pattern: ^\d{7}$
type: Resource
has URI prefix: http://purl.bioontology.org/ontology/HOIP/HOIP_
contributor: Harry Caufield
has reviewer: Charles Tapley Hoyt
has prefix: hoip
has provider formatter: http://purl.bioontology.org/ontology/HOIP/HOIP_$1
has download URL: hoip 0308.owl
has responsible: Yuki Yamagata

SWEET Ontology State Role Chemical
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/stateRoleChemical/$1
has resource example: ChemicalRole
has alternative prefix: sostrc
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Chemical
0000005: ChemicalRole
keyword: state role chemical
has URI prefix: http://sweetontology.net/stateRoleChemical/
is deprecated: false
has prefix: sweet.strc

Chemical Entities of Biological Interest
keyword: natural product
has responsible: https://orcid.org/0000-0001-8123-5351
appears in: An ontology of core ecological entities
appears in: Sickle Cell Disease Ontology
keyword: ontology
appears in: Process Chemistry Ontology
is deprecated: false
keyword: small molecule
keyword: dataplant
has provider formatter: http://purl.obolibrary.org/obo/CHEBI_$1
keyword: chemistry
keyword: taxonomic classification
keyword: nfdi4cat
keyword: metabolomics
appears in: Compositional Dietary Nutrition Ontology
appears in: The Food Ontology
keyword: nfdi4chem
description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.
keyword: proteomics
appears in: ChEBI Integrated Role Ontology
keyword: molecular entity
keyword: chemical
has download URL: chebi.owl
appears in: Xenopus Phenotype Ontology
keyword: earth sciences
appears in: Environment Ontology
has local unique identifier pattern: ^\d+$
git repository: ChEBI
is part of: Bioregistry
appears in: Environmental conditions, treatments and exposures ontology
keyword: lipidomics
has alternative prefix: ChEBI
has prefix: chebi
appears in: Microbial Conditions Ontology
contributor: https://orcid.org/0009-0005-4625-8212
keyword: structure
appears in: Uber Anatomy Ontology
0000005: 138488
keyword: biochemistry
has alternative prefix: CHEBIID
type: Resource
appears in: Genomic Epidemiology Ontology
keyword: ess
appears in: Food-Biomarker Ontology
appears in: Provisional Cell Ontology
appears in: Ontology for Nutritional Studies
has alternative prefix: CHEBI
keyword: obo
has resource example: CHEBI_138488
appears in: Medical Action Ontology
has URI prefix: http://purl.obolibrary.org/obo/CHEBI_

Golm Metabolome Database
has prefix: gmd
has responsible: Joachim Kopka
is deprecated: false
is part of: Bioregistry
keyword: metabolomics
description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.
has provider formatter: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx
type: Resource
has URI prefix: https://bioregistry.io/gmd:
has local unique identifier pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
keyword: life science

Cell Cycle Ontology
keyword: obo
keyword: ontology
has responsible: Martin Kuiper
is deprecated: false
keyword: genomics
has local unique identifier pattern: ^\w+$
keyword: proteomics
keyword: molecular_function
keyword: functional genomics
is part of: Bioregistry
0000005: 0000003
has provider formatter: https://www.ebi.ac.uk/ols4/ontologies/cco/terms
type: Resource
keyword: cell cycle
has prefix: cco
description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.
has URI prefix: https://www.ebi.ac.uk/ols4/ontologies/cco/terms
keyword: cell
has resource example: https://www.ebi.ac.uk/ols4/ontologies/cco/terms
has download URL: cco.owl
keyword: life science

CIViC Therapy
has local unique identifier pattern: ^[0-9]+$
has prefix: civic.tid
has resource example: https://civicdb.org/links/drugs/14
has provider formatter: https://civicdb.org/links/drugs/$1
is deprecated: false
is part of: Bioregistry
has URI prefix: https://civicdb.org/links/drugs/
has responsible: Malachi Griffith
has alternative prefix: civic.therapy
description: Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.
0000005: 14
type: Resource

Kerafast cell lines
0000005: EJH014
has prefix: kerafast
has provider formatter: https://www.kerafast.com/Search
is deprecated: false
description: Cell line collections (Providers)
is part of: Bioregistry
has resource example: https://www.kerafast.com/Search
type: Resource
has URI prefix: https://bioregistry.io/kerafast:

Vibrational Spectroscopy Ontology
has resource example: VIBSO_0000008
keyword: chemistry
git repository: VibrationalSpectroscopyOntology
keyword: nfdi4chem
has prefix: vibso
has responsible: https://orcid.org/0000-0002-1595-3213
has local unique identifier pattern: ^\d{7}$
type: Resource
description: The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR.
has reviewer: Charles Tapley Hoyt
has URI prefix: http://purl.obolibrary.org/obo/VIBSO_
contributor: https://orcid.org/0000-0002-1595-3213
is deprecated: false
0000005: 0000008
has provider formatter: http://purl.obolibrary.org/obo/VIBSO_$1
is part of: Bioregistry

Signaling Network Open Resource
has provider formatter: https://signor.uniroma2.it/relation_result.php
keyword: ontology
0000005: SIGNOR-C41
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^SIGNOR\-[A-Z]+\d+$
has prefix: signor
type: Resource
has URI prefix: https://signor.uniroma2.it/relation_result.php
keyword: biology
has alternative prefix: SIGNOR
has resource example: https://signor.uniroma2.it/relation_result.php
description: SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature.
has responsible: Gianni Cesareni
has download URL: signor.owl

DAPHNE4NFDI Resources
has part: Electron Microscopy Glossary
type: Collection
description: Prefixes for ontologies relevant for DAPHNE4NFDI.
creator: Charles Tapley Hoyt

SWEET Ontology Representation Data Servcie Analysis
contributor: Charles Tapley Hoyt
has prefix: sweet.repdsa
has resource example: Animate
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sorepdsa
type: Resource
0000005: Animate
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Servcie Analysis
has URI prefix: http://sweetontology.net/reprDataServiceAnalysis/
is deprecated: false
keyword: representation data servcie analysis
has provider formatter: http://sweetontology.net/reprDataServiceAnalysis/$1
is part of: Bioregistry

Yeast Deletion and the Mitochondrial Proteomics Project
has local unique identifier pattern: ^Y[A-Z]{2}\d+[CW]$
type: Resource
has URI prefix: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi
is deprecated: true
has provider formatter: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi
keyword: protein
0000005: YAL001C
description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.
has prefix: ydpm
is part of: Bioregistry
has resource example: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi

PharmGKB Disease
description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.
type: Resource
has provider formatter: http://www.pharmgkb.org/disease/$1
has URI prefix: http://www.pharmgkb.org/disease/
0000005: PA447218
has download URL: pharmgkb.disease.owl
is deprecated: false
keyword: ontology
has local unique identifier pattern: ^PA\d+$
keyword: pharmacogenomics
is part of: Bioregistry
has resource example: PA447218
has responsible: Teri E Klein
has prefix: pharmgkb.disease

International Classification of Diseases, 10th Revision, Procedure Coding System
keyword: ontology
keyword: morbidity
has resource example: https://www.findacode.com/code.php
is deprecated: false
keyword: disease
keyword: electronic health record
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: diagnosis
keyword: epidemiology
type: Resource
has provider formatter: https://www.findacode.com/code.php
has URI prefix: https://www.findacode.com/code.php
keyword: biomedical science
keyword: hospital
keyword: health science
has prefix: icd10pcs
0000005: 01N50ZZ
description: ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis. ICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records.
keyword: classification

SWEET Ontology State System
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State System
has resource example: Coherent
has URI prefix: http://sweetontology.net/stateSystem/
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/stateSystem/$1
has prefix: sweet.stsy
is deprecated: false
0000005: Coherent
has alternative prefix: sostsy
keyword: state system

ChEMBL Compound
keyword: ontology
is deprecated: false
keyword: small molecule
description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.
0000005: CHEMBL465070
keyword: chemical
is part of: Bioregistry
has resource example: CHEMBL465070
has local unique identifier pattern: ^CHEMBL\d+$
has URI prefix: https://www.ebi.ac.uk/chembl/compound/inspect/
has download URL: chembl.compound.owl
has responsible: David Mendez Lopez
has prefix: chembl.compound
has provider formatter: https://www.ebi.ac.uk/chembl/compound/inspect/$1
type: Resource
keyword: compound

Melanoma Molecular Map Project Biomaps
has URI prefix: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp
is deprecated: false
has provider formatter: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
has alternative prefix: mmmp:biomaps
has resource example: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp
keyword: interaction
description: A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.
keyword: molecule
0000005: 37
has prefix: mmmp.biomaps
keyword: pathway

Subcellular Anatomy Ontology
description: SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.
has provider formatter: http://uri.neuinfo.org/nif/nifstd/sao$1
0000005: 5277619
keyword: owl
has download URL: sao.owl
type: Resource
has URI prefix: http://uri.neuinfo.org/nif/nifstd/sao
keyword: biochemistry
is deprecated: true
keyword: obo
keyword: ontology
has prefix: sao
has resource example: sao5277619
is part of: Bioregistry
has local unique identifier pattern: ^\d+$

SCancerRNA
is deprecated: false
is part of: Bioregistry
0000005: 9530
has local unique identifier pattern: ^\d+$
description: SCancerRNA provides identifiers for non-coding RNA biomarkers, including long ncRNA, microRNA, PIWI-interacting RNA, small nucleolar RNA, and circular RNA, with data on their differential expression at the cellular level in cancer.
has reviewer: https://orcid.org/0000-0001-9439-5346
has resource example: http://www.scancerrna.com/toDetail
type: Resource
has provider formatter: http://www.scancerrna.com/toDetail
contributor: Mufaddal Naguthanawala
has prefix: scancerrna
has responsible: https://orcid.org/0000-0001-7352-2959
has URI prefix: http://www.scancerrna.com/toDetail

Integrated Resource for Domestic Dog
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses.
has responsible: https://orcid.org/0000-0002-9922-9723
has prefix: idog
0000005: 4
has resource example: https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action
has provider formatter: https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action
has URI prefix: https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action

Dynamic Ecological Information Management System - Site and Dataset Registry - Taxonomy
has responsible: Christoph Wohner
has URI prefix: https://deims.org/taxonomy/term/
description: Taxonomy in DEIMS SDR
has prefix: deims.taxonomy
has resource example: https://deims.org/taxonomy/term/21157
is deprecated: false
0000005: 21157
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: https://deims.org/taxonomy/term/$1

C. elegans ORFeome cloning project
has prefix: worfdb
0000005: T01B6.1
has provider formatter: http://worfdb.dfci.harvard.edu/html/index.php
has local unique identifier pattern: ^\w+(\.\d+)?$
description: WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends).
is deprecated: false
keyword: dna
is part of: Bioregistry
has URI prefix: http://worfdb.dfci.harvard.edu/html/index.php
type: Resource
has resource example: http://worfdb.dfci.harvard.edu/html/index.php

biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology
keyword: gene
keyword: interaction
has reviewer: Charles Tapley Hoyt
description: bioPIXIE is a novel system for biological data integration and visualization. It allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate.
0000005: 12
is deprecated: true
has URI prefix: http://avis.princeton.edu/pixie/viewgraph.php
has prefix: biopixie
has provider formatter: http://avis.princeton.edu/pixie/viewgraph.php
has resource example: http://avis.princeton.edu/pixie/viewgraph.php
is part of: Bioregistry
type: Resource

Oral Health and Disease Ontology
description: The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.
is part of: Bioregistry
has download URL: ohd.owl
has local unique identifier pattern: ^\d{7}$
has resource example: OHD_0000006
type: Resource
keyword: dentistry
has provider formatter: http://purl.obolibrary.org/obo/OHD_$1
has responsible: https://orcid.org/0000-0001-9625-1899
has prefix: ohd
keyword: medicine
0000005: 0000006
is deprecated: false
keyword: obo
keyword: oral surgery
keyword: ontology
git repository: ohd-ontology
has URI prefix: http://purl.obolibrary.org/obo/OHD_

ChemPro Target
is part of: Bioregistry
has local unique identifier pattern: ^LDTP\d+$
has URI prefix: https://chemprosquare.idrblab.net/data/target/details/
has reviewer: https://orcid.org/0000-0001-9439-5346
has resource example: LDTP03903
type: Resource
description: ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for human proteins that interact with chemoproteomic probes.
contributor: Mufaddal Naguthanawala
has prefix: chempro.target
0000005: LDTP03903
has provider formatter: https://chemprosquare.idrblab.net/data/target/details/$1
has responsible: https://orcid.org/0000-0001-8069-0053
is deprecated: false

Animal Trait Ontology for Livestock
0000005: 0002233
keyword: phenotype
keyword: agriculture
is part of: Bioregistry
has prefix: atol
has provider formatter: http://opendata.inra.fr/ATOL/ATOL_$1
type: Resource
has URI prefix: http://opendata.inra.fr/ATOL/ATOL_
description: ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment. ATOL aims to: provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; represent traits as generic as possible for livestock vertebrates; make the ATOL ontology as operational as possible and closely related to measurement techniques; and structure the ontology in relation to animal production.
has local unique identifier pattern: ^\d{7}$
has resource example: ATOL_0002233
keyword: life science
keyword: livestock
has download URL: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php
keyword: animal husbandry
keyword: ontology
is deprecated: false
has responsible: Pierre-Yves LeBail

BCRC Strain Collection Catalog
keyword: cell lines
description: Cell line collections (Providers)
is deprecated: false
has local unique identifier pattern: ^\d+$
has provider formatter: https://catalog.bcrc.firdi.org.tw/BcrcContent
is part of: Bioregistry
has prefix: bcrc
contributor: Charles Tapley Hoyt
has resource example: https://catalog.bcrc.firdi.org.tw/BcrcContent
has URI prefix: https://catalog.bcrc.firdi.org.tw/BcrcContent
0000005: 60316
type: Resource

Packagist
has URI prefix: https://packagist.org/packages/
has provider formatter: https://packagist.org/packages/$1
type: Resource
contributor: Charles Tapley Hoyt
description: A repository of software packages written in PHP.
has resource example: swap
0000005: florianv/swap
has prefix: packagist
is deprecated: false
is part of: Bioregistry

miRBase mature miRNA
keyword: ontology
keyword: sequence
is deprecated: false
description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.
has resource example: http://mirbase.org/cgi-bin/mature.pl
is part of: Bioregistry
keyword: nucleotide
0000005: MIMAT0046872
has alternative prefix: MIRBASEM
has URI prefix: http://mirbase.org/cgi-bin/mature.pl
has prefix: mirbase.mature
has provider formatter: http://mirbase.org/cgi-bin/mature.pl
has download URL: mirbase.mature.owl
type: Resource
has local unique identifier pattern: ^MIMAT\d{7}$
has responsible: Sam Griffiths-Jones

ProtClustDB
is deprecated: false
has local unique identifier pattern: ^\w+$
0000005: O80725
description: ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.
keyword: genetics
keyword: genomics
is part of: Bioregistry
keyword: protein
has prefix: protclustdb
has URI prefix: https://www.ncbi.nlm.nih.gov/sites/entrez
has resource example: https://www.ncbi.nlm.nih.gov/sites/entrez
type: Resource
keyword: structure
has provider formatter: https://www.ncbi.nlm.nih.gov/sites/entrez
keyword: life science

ConfIDent Event
has provider formatter: https://www.confident-conference.org/index.php/Event:$1
has responsible: https://orcid.org/0000-0002-1595-3213
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has prefix: confident.event
keyword: meetings
has local unique identifier pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
description: Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.
keyword: conferences
keyword: metascience
has URI prefix: https://www.confident-conference.org/index.php/Event:
is deprecated: false

European Collection of Authenticated Cell Culture
type: Resource
description: The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs).
is deprecated: false
has resource example: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp
0000005: 90062901
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has URI prefix: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp
contributor: Charles Tapley Hoyt
has provider formatter: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp
has prefix: ecacc

Galaxy Training Network
keyword: learning resources
contributor: 0009-0005-0673-021X
is part of: Bioregistry
description: Identifiers in the GTN correspond to training materials in various formats (markdown, slides, video). The users can apply learned concepts directly within the framework via galaxy workflows.
keyword: training materials
0000005: T00148
has local unique identifier pattern: ^[A-Z]\d+$
type: Resource
has prefix: gtn
has reviewer: Charles Tapley Hoyt
has URI prefix: https://gxy.io/GTN:
contributor: Dilfuza Djamalova
keyword: galaxy
keyword: learning materials
has provider formatter: https://gxy.io/GTN:$1
has responsible: 0000-0003-3803-468X
git repository: training-material
is deprecated: false
has resource example: GTN:T00148

SARGON (SmArt eneRGy dOmain oNtology)
description: SARGON (SmArt eneRGy dOmain oNtology) is an open-source effort to define semantic descriptions of the smart assets in building automation and smart grid and the relationships between them. SARGON consists of an extensible dictionary of terms and concepts in and around building and smart grid, a set of relationships for linking and composing concepts together, and a flexible data model permitting seamless integration of SARGON with existing tools and databases. Through the use of powerful Semantic Web technology, SARGON can describe the broad set of Devices and custom features, assets and subsystems found across the building stock in a consistent matter.
keyword: nfdi4energy
type: Resource
0000005: AC-DC
has URI prefix: https://sargon-n5geh.netlify.app/ontology/1.0/object_properties/
has provider formatter: https://sargon-n5geh.netlify.app/ontology/1.0/object_properties/$1
has prefix: sargon
has resource example: AC-DC
is deprecated: false
keyword: engineering
is part of: Bioregistry

Intelligence Task Ontology
description: The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks.
has prefix: ito
git repository: ITO
type: Resource
keyword: artificial intelligence
keyword: natural language processing
has URI prefix: https://bioportal.bioontology.org/ontologies/ITO/
has provider formatter: https://bioportal.bioontology.org/ontologies/ITO/
0000005: 01625
has responsible: Matthias Samwald
keyword: ontology
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: https://bioportal.bioontology.org/ontologies/ITO/
keyword: machine learning
has download URL: ito.owl

Environment Ontology for Livestock
keyword: ontology
0000005: 0001927
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has download URL: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php
keyword: agriculture
has local unique identifier pattern: ^\d{7}$
description: The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems.
type: Resource
has provider formatter: http://purl.org/obo/owlEOL_$1
has URI prefix: http://purl.org/obo/owlEOL_
has prefix: eol
has resource example: owlEOL_0001927
keyword: environmental science
is deprecated: false
keyword: species-environment interaction
has responsible: Pierre-Yves LeBail
keyword: livestock
keyword: animal husbandry

National Xenopus Resource
is part of: Bioregistry
keyword: laevis
description: National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID]
type: Resource
keyword: xenopus
keyword: tropicalis
has resource example: RRID:NXR 0024
has URI prefix: https://scicrunch.org/resolver/RRID:NXR_
0000005: 0024
has prefix: nxr
has local unique identifier pattern: ^\d+$
has provider formatter: https://scicrunch.org/resolver/RRID:NXR_$1
is deprecated: false

Database of Interacting Proteins
has responsible: https://orcid.org/0000-0003-2432-5419
type: Resource
keyword: interaction
has local unique identifier pattern: ^DIP(\:)?\-\d{1,}[ENXS]$
keyword: biology
has resource example: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi
has provider formatter: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi
is deprecated: false
is part of: Bioregistry
keyword: protein
has prefix: dip
description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions
0000005: DIP-743N
has URI prefix: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi

GenBase
has prefix: genbase
has URI prefix: https://ngdc.cncb.ac.cn/genbase/search/gb/
description: GenBase is a genetic sequence database that accepts user submissions (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids, phages from any organism) and integrates data from INSDC.
contributor: Tanay Shah
is deprecated: false
has responsible: https://orcid.org/0000-0002-3019-8615
has reviewer: https://orcid.org/0000-0001-9439-5346
has resource example: C AA001108.1
is part of: Bioregistry
type: Resource
has provider formatter: https://ngdc.cncb.ac.cn/genbase/search/gb/$1
0000005: C_AA001108.1

The Ontology of Genes and Genomes
keyword: gene
keyword: biology
has resource example: OGG_3000887619
keyword: life science
has prefix: ogg
description: OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.
keyword: obo
keyword: ontology
is deprecated: false
has download URL: ogg.owl
keyword: genome
0000005: 3000887619
git repository: ogg
has URI prefix: http://purl.obolibrary.org/obo/OGG_
has provider formatter: http://purl.obolibrary.org/obo/OGG_$1
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has responsible: Yongqun Oliver He
keyword: gene name

TrichDB
0000005: TVAG_386080
has local unique identifier pattern: ^\w+$
is part of: Bioregistry
has prefix: trichdb
has URI prefix: http://trichdb.org/trichdb/showRecord.do
has resource example: http://trichdb.org/trichdb/showRecord.do
type: Resource
has provider formatter: http://trichdb.org/trichdb/showRecord.do
description: TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
has responsible: Omar S. Harb
keyword: genomics
is deprecated: false

Biofactoid
is deprecated: false
keyword: relationships
contributor: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
git repository: factoid
has prefix: biofactoid
type: Resource
has URI prefix: https://biofactoid.org/document/
has reviewer: Charles Tapley Hoyt
has responsible: https://orcid.org/0000-0002-8912-5699
keyword: database
description: Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications.
has local unique identifier pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
keyword: biocuration
has provider formatter: https://biofactoid.org/document/$1

SWEET Ontology Representation Mathematics Function
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has prefix: sweet.repmf
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Function
0000005: Affine
has URI prefix: http://sweetontology.net/reprMathFunction/
type: Resource
has resource example: Affine
is deprecated: false
has provider formatter: http://sweetontology.net/reprMathFunction/$1
keyword: representation mathematics function
is part of: Bioregistry
has alternative prefix: sorepmf

Open Graph protocol
contributor: Charles Tapley Hoyt
is part of: Bioregistry
has resource example: title
0000005: title
type: Resource
has prefix: og
keyword: data schema
has provider formatter: https://ogp.me/ns#$1
keyword: linked open data
keyword: semantic web
is deprecated: false
has URI prefix: https://ogp.me/ns#
keyword: api
description: A vocabulary for embedding provenance metadata into webpages via RDFa

Medical Subject Headings Vocabulary
has prefix: mesh.vocab
description: Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump
has provider formatter: http://id.nlm.nih.gov/mesh/vocab#$1
is deprecated: false
is part of: Bioregistry
has resource example: term
git repository: meshrdf
contributor: Charles Tapley Hoyt
has URI prefix: http://id.nlm.nih.gov/mesh/vocab#
type: Resource
0000005: term

Contributor Role Ontology
has prefix: cro
0000005: 0000038
has URI prefix: http://purl.obolibrary.org/obo/CRO_
has download URL: cro.owl
has responsible: Marijane White
is deprecated: false
keyword: obo
keyword: attribution
has provider formatter: http://purl.obolibrary.org/obo/CRO_$1
keyword: ontology
is part of: Bioregistry
description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability.
keyword: contributor roles
has local unique identifier pattern: ^\d{7}$
git repository: contributor-role-ontology
has resource example: CRO_0000038
type: Resource

BioSample
has alternative prefix: biosamples
keyword: rna
has resource example: SAMEA2397676
has provider formatter: https://www.ebi.ac.uk/biosamples/sample/$1
keyword: dna
is part of: Bioregistry
keyword: gold standard
keyword: stem cell
has prefix: biosample
has local unique identifier pattern: ^SAM[NED](\w)?\d+$
type: Resource
description: The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.
has URI prefix: https://www.ebi.ac.uk/biosamples/sample/
has responsible: Ilene Karsch-Mizrachi
keyword: biology
keyword: cell
0000005: SAMEA2397676
keyword: biomaterial
is deprecated: false
keyword: cell line

Ontology for vector surveillance and management
is part of: Bioregistry
has prefix: vsmo
has download URL: vsmo.owl
has URI prefix: http://purl.obolibrary.org/obo/VSMO_
contributor: Charles Tapley Hoyt
type: Resource
has responsible: Lars Eisen
has provider formatter: http://purl.obolibrary.org/obo/VSMO_$1
has resource example: VSMO_0000000
0000005: 0000000
keyword: ontology
is deprecated: false
description: an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems.

Human developmental anatomy, timed version
type: Resource
has resource example: EHDA 1
keyword: development
keyword: anatomy
has download URL: ehda.obo
has prefix: ehda
is deprecated: true
keyword: obo
keyword: ontology
keyword: human
has local unique identifier pattern: ^\d+$
description: A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.
is part of: Bioregistry
0000005: 1
has provider formatter: http://purl.obolibrary.org/obo/EHDA_$1
has URI prefix: http://purl.obolibrary.org/obo/EHDA_

Colorectal Cancer Atlas
0000005: ALA
has prefix: colonatlas
has resource example: http://www.coloncanceratlas.org/search_cell_line
is deprecated: false
description: Cell line databases/resources
has provider formatter: http://www.coloncanceratlas.org/search_cell_line
is part of: Bioregistry
has URI prefix: http://www.coloncanceratlas.org/search_cell_line
type: Resource

dbSNP Reference SNP number
keyword: life science
has resource example: rs121909098
has URI prefix: https://www.ncbi.nlm.nih.gov/snp/
git repository: tutorials
0000005: rs121909098
has responsible: https://orcid.org/0000-0001-7950-1374
is deprecated: false
is part of: Bioregistry
keyword: genome
has prefix: dbsnp
has provider formatter: https://www.ncbi.nlm.nih.gov/snp/$1
has local unique identifier pattern: ^rs\d+$
description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.
type: Resource

MimoDB
type: Resource
keyword: interaction
has resource example: http://immunet.cn/bdb/index.php/mimoset/1
keyword: life science
has responsible: https://orcid.org/0000-0003-2314-7104
is deprecated: false
description: MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.
0000005: 1
has prefix: mimodb
has URI prefix: http://immunet.cn/bdb/index.php/mimoset/
has provider formatter: http://immunet.cn/bdb/index.php/mimoset/$1
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: protein

Comprehensive Resource of Mammalian protein complexes
is deprecated: false
has provider formatter: https://mips.helmholtz-muenchen.de/corum/
description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.
has local unique identifier pattern: ^\d+$
has URI prefix: https://mips.helmholtz-muenchen.de/corum/
is part of: Bioregistry
keyword: protein
keyword: bioinformatics
has resource example: https://mips.helmholtz-muenchen.de/corum/
has responsible: Andreas Ruepp
has prefix: corum
type: Resource
0000005: 100
keyword: biology

FuTRES Ontology of Vertebrate Traits
depends on: Basic Formal Ontology
has URI prefix: http://purl.obolibrary.org/obo/FOVT_
has resource example: FOVT_0000009
0000005: 0000009
depends on: Biological Collections Ontology
keyword: obo
has prefix: fovt
keyword: ontology
description: These are the terms that are improted for FOVT to describe vertebrate traits.
depends on: Relation Ontology
is deprecated: false
is part of: Bioregistry
depends on: Information Artifact Ontology
has responsible: https://orcid.org/0000-0003-2699-3066
has provider formatter: http://purl.obolibrary.org/obo/FOVT_$1
depends on: Phenotype And Trait Ontology
depends on: Uber Anatomy Ontology
git repository: fovt
has local unique identifier pattern: ^\d{7}$
type: Resource
depends on: Ontology of Biological Attributes
depends on: Biological Spatial Ontology
has download URL: fovt.owl

CTD Disease
has local unique identifier pattern: ^D\d+$
is deprecated: false
has prefix: ctd.disease
has URI prefix: http://ctdbase.org/detail.go
is part of: Bioregistry
0000005: D053716
has provider formatter: http://ctdbase.org/detail.go
has resource example: http://ctdbase.org/detail.go
type: Resource
description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.
0000011: Medical Subject Headings

Oat Ontology
has resource example: CO 350:0000215
has URI prefix: https://cropontology.org/rdf/CO_350:
keyword: botany
keyword: agriculture
has provider formatter: https://cropontology.org/rdf/CO_350:$1
has prefix: co_350
has local unique identifier pattern: ^\d{7}$
has download URL: CO 350.owl
type: Resource
description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Oat Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. The Oat Trait Dictionary was commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/).
has responsible: Jean-Luc Jannink
keyword: life science
is deprecated: false
keyword: ontology
is part of: Bioregistry
0000005: 0000215
keyword: plant phenotypes and traits
git repository: Crop-Ontology
keyword: phenotype

DFG Classification of Subject Areas Ontology - 2020-2024
has provider formatter: https://w3id.org/dfgfo/2020/$1
is deprecated: false
keyword: digital planning and construction
keyword: fid baudigital
keyword: fid move
keyword: educational resources
keyword: open educational resources
is part of: Bioregistry
keyword: open educational resource
git repository: DFG-Fachsystematik-Ontology
type: Resource
keyword: nfdi4ing
has URI prefix: https://w3id.org/dfgfo/2020/
has resource example: https://w3id.org/dfgfo/2020/101-01
0000005: 101-01
keyword: educational science
keyword: ess
description: DFG Fachsystematik Ontology / DFG Classification of Subject Areas Ontology (DFGFO) encodes the DFG Classification of Subject Areas into an ontology, where each subject number are is enconded into a Class with subclass statements following the DFG Classification of Subject Areas hierarchy. Labels are provide German and English.
has prefix: dfg.fo

Assembling the Fungal Tree of Life - Category
has provider formatter: https://aftol.umn.edu/glossary
has resource example: https://aftol.umn.edu/glossary
is deprecated: false
0000005: 229
description: Categories in the AFTOL database
is part of: Bioregistry
has prefix: aftol.category
has URI prefix: https://aftol.umn.edu/glossary
contributor: Charles Tapley Hoyt
type: Resource

UniProt journal
is part of: Bioregistry
has local unique identifier pattern: ^\d{4}$
keyword: journal
contributor: Charles Tapley Hoyt
has resource example: https://www.uniprot.org/journals/3546
has URI prefix: https://www.uniprot.org/journals/
type: Resource
description: identifier for a scientific journal, in the UniProt database
has responsible: Alex Bateman
0000005: 3546
has provider formatter: https://www.uniprot.org/journals/$1
is deprecated: false
has prefix: uniprot.journal
keyword: publication

NOAA Fisheries Species Directory
is deprecated: false
has alternative prefix: noaa
description: Identifier for a species on the noaa fisheries website
is part of: Bioregistry
has prefix: noaa.species
has provider formatter: https://www.fisheries.noaa.gov/species/$1
has reviewer: Charles Tapley Hoyt
has URI prefix: https://www.fisheries.noaa.gov/species/
type: Resource
0000005: long-finned-pilot-whale
has resource example: long-finned-pilot-whale
contributor: https://orcid.org/0000-0003-2699-3066
has local unique identifier pattern: ^[a-z]+(\-[a-z]+)*$

Oryzabase Strain
is deprecated: false
0000005: 1
description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information.
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has provider formatter: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1
has URI prefix: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/
has resource example: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/1
has prefix: oryzabase.strain
type: Resource

Event (INOH pathway ontology)
keyword: obo
has URI prefix: http://purl.obolibrary.org/obo/IEV_
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/IEV_$1
keyword: pathway
is part of: Bioregistry
description: The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.
has resource example: IEV_0000000
has local unique identifier pattern: ^\d{7}$
type: Resource
0000005: 0000000
keyword: structure
has prefix: iev
is deprecated: true

SCOP(e) concise classification string
has resource example: http://scop.berkeley.edu/sccs=a.39.1.1
has prefix: scop.sccs
is deprecated: false
has provider formatter: http://scop.berkeley.edu/sccs=$1
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-5153-9079
type: Resource
0000005: a.39.1.1
contributor: Charles Tapley Hoyt
description: This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents the superfamily, and the last '1' represents the family.
has URI prefix: http://scop.berkeley.edu/sccs=

DrugBank
keyword: biomedical science
has URI prefix: https://go.drugbank.com/drugs/
keyword: life science
0000005: DB14938
has resource example: DB14938
is deprecated: false
keyword: drug
description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.
has local unique identifier pattern: ^DB\d{5}$
has alternative prefix: DrugBank
is part of: Bioregistry
keyword: protein
has alternative prefix: DRUGBANK_ID
has prefix: drugbank
has provider formatter: https://go.drugbank.com/drugs/$1
has responsible: David Wishart
type: Resource

UK Universities and Colleges Admissions Service
is part of: Bioregistry
keyword: bibliometrics
type: Resource
contributor: Charles Tapley Hoyt
description: An identifier for institutions in the United Kingdom, used in GRID and ROR.
has prefix: ucas
keyword: institution
0000005: N21
has local unique identifier pattern: ^\w\d+$
is deprecated: false

GLIDA GPCR
has provider formatter: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php
is deprecated: true
has URI prefix: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php
has resource example: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php
description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors.
has local unique identifier pattern: ^[A-Z-_0-9]+$
0000005: ACM1_HUMAN
is part of: Bioregistry
type: Resource
has prefix: glida.gpcr

International Genome Sample Resource
description: The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.
0000005: NA06985
is deprecated: false
is part of: Bioregistry
keyword: genomics
has URI prefix: https://www.internationalgenome.org/data-portal/sample/
has prefix: igsr
has provider formatter: https://www.internationalgenome.org/data-portal/sample/$1
type: Resource
keyword: comparative genomics
has resource example: NA06985
has responsible: Paul Flicek

Aquatic Sciences and Fisheries Information System
has URI prefix: https://www.fao.org/fishery/en/species/
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: fao.asfis
type: Resource
has alternative prefix: asfis
0000005: 20560
has reviewer: Charles Tapley Hoyt
has resource example: https://www.fao.org/fishery/en/species/20560
description: The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. ASFIS list of species includes 13,417 species items selected according to their interest or relation to fisheries and aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic and 3-alpha) and taxonomic information (scientific name, author(s), family, and higher taxonomic classification) are provided. An English name is available for most of the records, and about one third of them have also a French and Spanish name. Information is also provided about the availability of fishery production statistics on the species item in the FAO databases. (from homepage)
has provider formatter: https://www.fao.org/fishery/en/species/$1
is deprecated: false
contributor: Damion Dooley

Consortium of European Social Science Data Archives Vocabulary
has prefix: cessda
description: A vocabulary service for the social sciences, covering the Data Documentation Initiative (DDI) is an international standard for describing data produced by surveys and other observational methods in the social, behavioural, economic, and health sciences.
keyword: registry
is deprecated: false
has resource example: TopicClassification
is part of: Bioregistry
0000005: TopicClassification
type: Resource
has provider formatter: https://vocabularies.cessda.eu/vocabulary/$1
contributor: Charles Tapley Hoyt
has URI prefix: https://vocabularies.cessda.eu/vocabulary/

FooDB Food
description: Foods in FooDB
is part of: Bioregistry
has prefix: foodb.food
has URI prefix: https://foodb.ca/foods/
has local unique identifier pattern: ^FOOD\d+$
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: https://foodb.ca/foods/$1
has resource example: FOOD00020
is deprecated: false
0000005: FOOD00020

The S/MAR transaction DataBase
has resource example: http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi
has provider formatter: http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi
is part of: Bioregistry
keyword: protein
has prefix: s_mart_db
description: S/MARt DB collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix.
type: Resource
has reviewer: Charles Tapley Hoyt
0000005: SM0000020
is deprecated: false
has URI prefix: http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi

Sequence-Structural Templates of Single-member Superfamilies
has URI prefix: http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi
is part of: Bioregistry
keyword: protein
description: SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies.
0000005: 01.01.005
type: Resource
has resource example: http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi
keyword: structure
has prefix: sstoss
has reviewer: Charles Tapley Hoyt
is deprecated: true
has provider formatter: http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi

Arctic Data Center Academic Disciplines Ontology
0000005: 00000
has local unique identifier pattern: ^\d{5}$
is part of: Bioregistry
has provider formatter: https://purl.dataone.org/odo/ADCAD_$1
type: Resource
has resource example: ADCAD_00000
has download URL: ADCAD.ttl
has URI prefix: https://purl.dataone.org/odo/ADCAD_
has reviewer: Charles Tapley Hoyt
has prefix: adcad
description: An ontology to support disciplinary annotation of Arctic Data Center datasets.
git repository: adc-disciplines
contributor: Harry Caufield
keyword: ontology
is deprecated: false
has responsible: Bryce Mecum

Scopus Work
has alternative prefix: scopus.eid
0000005: 2-s2.0-0030770923
is deprecated: false
has local unique identifier pattern: ^2-s2\.0-\d+$
description: unique academic work identifier assigned in Scopus bibliographic database
has provider formatter: http://www.scopus.com/record/display.url
is part of: Bioregistry
has resource example: http://www.scopus.com/record/display.url
has prefix: scopus.work
has URI prefix: http://www.scopus.com/record/display.url
type: Resource

Selventa Chemicals
has URI prefix: https://biopragmatics.github.io/providers/schem/
has provider formatter: https://biopragmatics.github.io/providers/schem/$1
0000005: A0001
has resource example: A0001
has prefix: schem
is deprecated: false
is part of: Bioregistry
keyword: selventa
keyword: chemistry
description: Selventa legacy chemical namespace used with the Biological Expression Language
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^A\d{4}$
has responsible: Natalie L Catlett
type: Resource
keyword: bel

EAWAG Biocatalysis/Biodegradation Database enzyme
is deprecated: false
0000005: e0333
description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.
is part of: Bioregistry
has alternative prefix: UM-BBD_enzymeID
has URI prefix: http://eawag-bbd.ethz.ch/servlets/pageservlet
has local unique identifier pattern: ^e\d+$
type: Resource
has resource example: http://eawag-bbd.ethz.ch/servlets/pageservlet
has provider formatter: http://eawag-bbd.ethz.ch/servlets/pageservlet
has prefix: umbbd.enzyme

Sciflection
is part of: Bioregistry
type: Resource
description: Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions
has provider formatter: https://sciflection.com/$1
has URI prefix: https://sciflection.com/
is deprecated: false
has prefix: sciflection
has local unique identifier pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$

Human BioMolecular Atlas Program Donor
is part of: Bioregistry
has reviewer: https://orcid.org/0000-0001-9439-5346
has local unique identifier pattern: ^[a-f0-9]{32}$
type: Resource
has URI prefix: https://portal.hubmapconsortium.org/browse/donor/
has responsible: Katy Börner
has provider formatter: https://portal.hubmapconsortium.org/browse/donor/$1
has prefix: hubmap.donor
is deprecated: false
contributor: 0009-0008-8406-631X
description: The HuBMAP donors dataset contains demographic and clinical metadata for individuals who donated tissue samples. Each donor has a unique identifier used to link them to their associated tissue samples and derived experimental data.

Human Oral Microbiome Database
keyword: microbial
keyword: taxonomy
has provider formatter: http://www.homd.org/modules.php
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
0000005: 811
has URI prefix: http://www.homd.org/modules.php
has resource example: http://www.homd.org/modules.php
description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.
has responsible: 0000-0001-6689-317X
type: Resource
has prefix: homd.taxon

German Clinical Trials Register
has resource example: DRKS00031815
has prefix: drks
has provider formatter: https://drks.de/search/en/trial/$1
0000005: DRKS00031815
is part of: Bioregistry
has URI prefix: https://drks.de/search/en/trial/
description: The German Clinical Trials Register (DRKS) is the German WHO primary registry. It is competent for the registration of all patient-oriented clinical trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently, around 2,000 studies are added annually. (from website)
contributor: Charles Tapley Hoyt
type: Resource
has local unique identifier pattern: ^DRKS\d+$
is deprecated: false

Synapse Data Repository
is part of: Bioregistry
0000005: 41455251.1
has alternative prefix: syn
type: Resource
has responsible: Kevin Boske
description: Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate.
has provider formatter: https://www.synapse.org/Synapse:syn$1
has URI prefix: https://www.synapse.org/Synapse:syn
has resource example: Synapse:syn41455251.1
is deprecated: false
has local unique identifier pattern: ^[0-9]*\.*[0-9]*$
has prefix: synapse

SWEET Ontology Property Conductivity
has resource example: Conductance
is deprecated: false
has prefix: sweet.propcon
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Conductivity
has URI prefix: http://sweetontology.net/propConductivity/
is part of: Bioregistry
has alternative prefix: sopropcon
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
0000005: Conductance
has provider formatter: http://sweetontology.net/propConductivity/$1
keyword: conductivity

AOPWiki (Key Event Relationship)
has resource example: https://aopwiki.org/relationships/5
is deprecated: false
has prefix: aop.relationships
0000005: 5
description: International repository of Adverse Outcome Pathways.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: https://aopwiki.org/relationships/$1
has URI prefix: https://aopwiki.org/relationships/
type: Resource

SAREF extension for building devices
0000005: Actuator
has prefix: saref.building
has provider formatter: https://saref.etsi.org/saref4bldg/$1
is deprecated: false
description: This ontology extends the SAREF ontology for the building domain by defining building devices and how they are located in a building. This extension is based on the ISO 16739:2013 Industry Foundation Classes (IFC) standard for data sharing in the construction and facility management industries. The descriptions of the classes and properties extracted from IFC have been taken from the IFC documentation.
keyword: digital planning and construction
has resource example: Actuator
is part of: Bioregistry
keyword: engineering
keyword: fid baudigital
has alternative prefix: s4bldg
has URI prefix: https://saref.etsi.org/saref4bldg/
keyword: iot
type: Resource
keyword: nfdi4ing

An ontology of core ecological entities
has resource example: ECOCORE_00000001
has prefix: ecocore
description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.
has responsible: Pier Luigi Buttigieg
has download URL: ecocore.owl
keyword: obo
depends on: Environment Ontology
depends on: Relation Ontology
keyword: ontology
depends on: Information Artifact Ontology
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/ECOCORE_$1
depends on: Phenotype And Trait Ontology
depends on: Uber Anatomy Ontology
depends on: Chemical Entities of Biological Interest
git repository: ecocore
depends on: Gene Ontology
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/ECOCORE_
depends on: Plant Ontology
depends on: Population and Community Ontology
depends on: Basic Formal Ontology
0000005: 00000001

Mosquito gross anatomy ontology
has resource example: TGMA_0000984
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/TGMA_
keyword: mosquito
is part of: Bioregistry
0000005: 0000984
has provider formatter: http://purl.obolibrary.org/obo/TGMA_$1
has local unique identifier pattern: ^\d{7}$
type: Resource
git repository: TGMA
has prefix: tgma
has download URL: tgma.owl
is deprecated: true
description: A structured controlled vocabulary of the anatomy of mosquitoes.
has responsible: Pantelis Topalis
keyword: anatomy
keyword: life science
keyword: obo

DailyMed
has URI prefix: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm
description: DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.
is deprecated: false
has local unique identifier pattern: ^[A-Za-z0-9-]+$
has resource example: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm
is part of: Bioregistry
has provider formatter: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm
type: Resource
has prefix: dailymed

Secondary Metabolism Collaboratory - taxon
has URI prefix: https://smc.jgi.doe.gov/sources/
type: Resource
contributor: Mufaddal Naguthanawala
description: The secondary metabolism collaboratory is a database for secondary metabolite biosynthetic gene clusters. This prefix represents identifiers for bacteria and archaea sources linked to their associated set of biosynthetic gene clusters (BGCs).
has responsible: Daniel W Udwary
is deprecated: false
0000005: 1
has provider formatter: https://smc.jgi.doe.gov/sources/$1
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: smc.source
has local unique identifier pattern: ^\d+$
has resource example: https://smc.jgi.doe.gov/sources/1
is part of: Bioregistry

nextProt
has responsible: Monique Zahn
0000005: NX_O00165
type: Resource
has provider formatter: https://www.nextprot.org/db/entry/$1
has prefix: nextprot
keyword: life science
has alternative prefix: NXP
has local unique identifier pattern: ^NX_\w+$
description: neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases.
is deprecated: false
has URI prefix: https://www.nextprot.org/db/entry/
is part of: Bioregistry
has resource example: NX O00165
keyword: proteomics

SEED Reactions
type: Resource
description: ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.
has local unique identifier pattern: ^rxn\d+$
is deprecated: false
has prefix: seed.reaction
is part of: Bioregistry
has URI prefix: http://modelseed.org/biochem/reactions/
has provider formatter: http://modelseed.org/biochem/reactions/$1
0000005: rxn00001
has resource example: rxn00001

Cell Biolabs cell line products
has URI prefix: https://www.cellbiolabs.com/search
description: Cell line collections (Providers)
is part of: Bioregistry
has provider formatter: https://www.cellbiolabs.com/search
type: Resource
has resource example: https://www.cellbiolabs.com/search
has prefix: cell_biolabs
is deprecated: false
0000005: AKR-270

Ontology of Host Pathogen Interactions
has responsible: 0000-0002-5159-414X
is deprecated: false
keyword: obo
0000005: 9001411
has URI prefix: http://purl.obolibrary.org/obo/OHPI_
keyword: ontology
description: OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).
has download URL: ohpi.owl
keyword: infection process
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
keyword: bioinformatics
has prefix: ohpi
type: Resource
keyword: biomedical science
has resource example: OHPI_9001411
has provider formatter: http://purl.obolibrary.org/obo/OHPI_$1
keyword: host
keyword: pathogen
git repository: ohpi

OBO in OWL
0000005: hasDbXref
type: Resource
has alternative prefix: oboformat
has local unique identifier pattern: ^[\w-]+$
has URI prefix: http://www.geneontology.org/formats/oboInOwl#
has alternative prefix: oio
description: This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties
keyword: life science
is deprecated: false
has download URL: oboInOwl.owl
has responsible: https://orcid.org/0000-0002-6601-2165
git repository: go-ontology
keyword: ontology
has prefix: oboinowl
has provider formatter: http://www.geneontology.org/formats/oboInOwl#$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: hasDbXref

OpenADR ontology
keyword: nfdi4energy
0000005: BidEnergySetpointSignal
type: Resource
has URI prefix: https://w3id.org/def/openadr#
description: This ontology describes the openADR protocol based on the documentation provided by the openADR Profile B
has provider formatter: https://w3id.org/def/openadr#$1
is deprecated: false
is part of: Bioregistry
keyword: engineering
has resource example: BidEnergySetpointSignal
has prefix: openadr

SWEET Ontology Phenomena Geologic Fault
has provider formatter: http://sweetontology.net/phenGeolFault/$1
is deprecated: false
has prefix: sweet.phgf
keyword: geologic fault
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Fault
has resource example: Detachment
is part of: Bioregistry
0000005: Detachment
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
keyword: phenomena
has alternative prefix: sophgf
has URI prefix: http://sweetontology.net/phenGeolFault/
type: Resource

Ensembl Bacteria
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes.
has provider formatter: https://bacteria.ensembl.org/id/$1
keyword: comparative genomics
has local unique identifier pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$
has resource example: MU9 3181
has responsible: Paul Flicek
is deprecated: false
0000005: MU9_3181
is part of: Bioregistry
keyword: genome
keyword: genomics
has URI prefix: https://bacteria.ensembl.org/id/
has prefix: ensembl.bacteria
type: Resource

Transport Systems Tracker
has resource example: TR0000001
is part of: Bioregistry
description: The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes.
has URI prefix: https://transyt.bio.di.uminho.pt/reactions/
0000005: TR0000001
type: Resource
has local unique identifier pattern: ^T[A-Z]\d{7}$
is deprecated: false
has provider formatter: https://transyt.bio.di.uminho.pt/reactions/$1
has prefix: transyt

FDA Application
has local unique identifier pattern: ^\d{6}$
type: Resource
has reviewer: https://orcid.org/0000-0003-2473-2313
is deprecated: false
has resource example: https://fda.report/applications/070886
has prefix: fda.application
contributor: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://fda.report/applications/
description: This prefix is for FDA application identifiers. There are multiple types of FDA applications (https://www.fda.gov/drugs/how-drugs-are-developed-and-approved/types-applications), including New Drug Application (NDA). FDA.report provides access to all FDA databases, including applications, in a single portal, and can resolve FDA application identifiers.
0000005: 070886
is part of: Bioregistry
has provider formatter: https://fda.report/applications/$1

Audience Types Controlled Vocabulary
has provider formatter: http://cor.esipfed.org/ont/earthcube/AUT_$1
is deprecated: false
has prefix: earthcube.aut
keyword: audience type
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has responsible: Ruth Duerr
keyword: person
git repository: AUT
has local unique identifier pattern: ^\d{7}$
0000005: 0000001
type: Resource
has resource example: AUT_0000001
description: The Audience Types Controlled Vocabulary was created for NSF's EarthCube program's Resource Registry. The vocabulary defines the types of audience each resource in the program is targeted to. At this point the vocabulary is very bare - no term definitions even; however, the intention is to extend the vocabulary over time. If you would like to assist with this or in extending any of the other controlled vocabularies/ontologies developed as part of the Resource Registry project, please see https://github.com/earthcubearchitecture-ecresourcereg.
has URI prefix: http://cor.esipfed.org/ont/earthcube/AUT_
keyword: role

TUBES system ontology
is deprecated: false
has URI prefix: https://w3id.org/tso#
has provider formatter: https://w3id.org/tso#$1
description: The scope of the TUBES ontology is to explicitly define the topology of interconnected building service system and their relationship to the spatial structure. It has a strong alignment to other ontologies within the W3C community and aims to provide the means to link information at data level within the AEC industry.
is part of: Bioregistry
keyword: engineering
has resource example: AutomationSystem
0000005: AutomationSystem
type: Resource
keyword: nfdi4ing
has prefix: tib.tso

DALIA Open Educational Resource
description: A UUID for an open educational resource indexed in the Data Liteacy Alliance (DALIA) web application
is deprecated: false
has provider formatter: https://search.dalia.education/items/$1
is part of: Bioregistry
has URI prefix: https://search.dalia.education/items/
type: Resource
contributor: Charles Tapley Hoyt
has prefix: dalia.oer
has local unique identifier pattern: ^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$

SWEET Ontology Representation Data Service Reduction
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: representation data service reduction
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Service Reduction
0000005: Binning
has provider formatter: http://sweetontology.net/reprDataServiceReduction/$1
has resource example: Binning
is deprecated: false
has prefix: sweet.repdsr
has alternative prefix: sorepdsr
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: http://sweetontology.net/reprDataServiceReduction/

International Standard for Intelligent Information Request and Delivery Machinery Ontology
is part of: Bioregistry
git repository: models
has URI prefix: http://iirds.tekom.de/iirds/domain/machinery#
type: Resource
keyword: nfdi4ing
description: An ontology encoding machinery based on the Intelligent Information Request and Delivery (iiRDS) standard
has provider formatter: http://iirds.tekom.de/iirds/domain/machinery#$1
0000005: ConsumableSupply
keyword: computer science
is deprecated: false
has prefix: iirds.mch
has resource example: ConsumableSupply

CIViC Disease
has alternative prefix: civic.disease
is deprecated: false
has resource example: https://civicdb.org/links/diseases/46
has URI prefix: https://civicdb.org/links/diseases/
is part of: Bioregistry
description: Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.
has responsible: Malachi Griffith
0000005: 46
has prefix: civic.did
type: Resource
has local unique identifier pattern: ^[0-9]+$
has provider formatter: https://civicdb.org/links/diseases/$1

Data Commons
has prefix: datacommons
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has alternative prefix: dcid
git repository: website
has provider formatter: https://datacommons.org/browser/$1
has URI prefix: https://datacommons.org/browser/
has resource example: Gene
description: A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces.
is deprecated: false
0000005: Gene

JRBC Cell Bank
has resource example: https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi
has prefix: jcrb
is deprecated: false
description: Cell line collections (Providers)
has URI prefix: https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi
has local unique identifier pattern: ^JCRB\d+$
0000005: JCRB1355

ConfIDent Event Series
type: Resource
0000005: AAC
has URI prefix: https://www.confident-conference.org/index.php/Event_Series:
keyword: grouping
keyword: meetings
has prefix: confident.series
description: Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.
keyword: conferences
keyword: metascience
has resource example: Event Series:AAC
is deprecated: false
is part of: Bioregistry
has provider formatter: https://www.confident-conference.org/index.php/Event_Series:$1
contributor: Charles Tapley Hoyt
has responsible: https://orcid.org/0000-0002-1595-3213

Lifecycle Event Type
type: Resource
0000005: StudyProposal
has provider formatter: https://vocabularies.cessda.eu/vocabulary/LifecycleEventType#code_$1
has identifier space owner: 015em2733
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/LifecycleEventType#code_
has resource example: code StudyProposal
has prefix: ddi.lifecycleeventtype
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: Specifies the event happening over the data life cycle that is considered significant enough to document.

Vertebrate Breed Ontology
depends on: NCBI Taxonomy
has provider formatter: http://purl.obolibrary.org/obo/VBO_$1
0000005: 0000038
keyword: obo
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/VBO_
is deprecated: false
has download URL: vbo.owl
git repository: vertebrate-breed-ontology
has resource example: VBO_0000038
has responsible: https://orcid.org/0000-0002-4142-7153
description: Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.
is part of: Bioregistry
has prefix: vbo
type: Resource
has local unique identifier pattern: ^\d{7}$

SWEET Ontology Phenomena Planetary Climate
keyword: phenomena
0000005: Climate
has URI prefix: http://sweetontology.net/phenPlanetClimate/
is deprecated: false
has resource example: Climate
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Planetary Climate
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sophpc
type: Resource
has provider formatter: http://sweetontology.net/phenPlanetClimate/$1
has prefix: sweet.phpc
keyword: planetary climate

Protein Ensemble Database
has local unique identifier pattern: ^PED\d{5}$
has responsible: https://orcid.org/0000-0001-6603-5060
description: The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins.
has provider formatter: https://proteinensemble.org/$1
is deprecated: false
has part: Protein Ensemble Database ensemble
has URI prefix: https://proteinensemble.org/
has resource example: PED00037
is part of: Bioregistry
type: Resource
has prefix: ped
0000005: PED00037

Immune Epitope Database Receptors
is deprecated: false
keyword: immunology
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: bioinformatics
has prefix: iedb.receptor
has resource example: https://www.iedb.org/receptor/47
has reviewer: https://orcid.org/0000-0001-9439-5346
0000005: 47
type: Resource
has responsible: https://orcid.org/0000-0001-8957-7612
description: Identifiers for immune receptors, representing receptor complexes or groups studied for their interactions with antigens or epitopes.
contributor: Mufaddal Naguthanawala
has provider formatter: https://www.iedb.org/receptor/$1
has URI prefix: https://www.iedb.org/receptor/
keyword: life science

SWEET Ontology Material Industrial
is deprecated: false
has prefix: sweet.maind
0000005: Alloy
keyword: industrial
is part of: Bioregistry
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has URI prefix: http://sweetontology.net/matrIndustrial/
keyword: materials
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Industrial
has resource example: Alloy
has alternative prefix: somaind
has provider formatter: http://sweetontology.net/matrIndustrial/$1

Psychology Ontology
has download URL: apaonto.owl
description: An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege.
type: Resource
has provider formatter: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1
has prefix: apaonto
keyword: ontology
contributor: https://orcid.org/0000-0002-1216-4761
has resource example: Abdomen
is deprecated: false
0000005: Abdomen
has responsible: https://orcid.org/0000-0003-1082-8760
keyword: behavior
is part of: Bioregistry
keyword: psychology
has URI prefix: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#
contributor: Charles Tapley Hoyt

F-SNP
type: Resource
has prefix: fsnp
has provider formatter: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi
has local unique identifier pattern: ^rs\d+$
0000005: rs17852708
is deprecated: true
has resource example: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi
has URI prefix: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi
keyword: dna
keyword: protein
description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.
is part of: Bioregistry

European Joint Programme for Rare Disease Ontology
has prefix: ejprd
git repository: EJP-Ontology
has download URL: ejp-rd.owl
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
0000005: alternative_term
description: This ontology is designed to support data search, retrieval and information identification in the EJP-RD catalogs which covers the registries and biobanks for rare diseases. (from repository)
has provider formatter: http://purl.org/ejp-rd/vocabulary/$1
has URI prefix: http://purl.org/ejp-rd/vocabulary/
has resource example: alternative term
keyword: ontology
is deprecated: false

Chemical Entity Materials and Reactions Ontological Framework
description: A data model for managing information about chemical entities, ranging from atoms through molecules to complex mixtures.
has prefix: chemrof
git repository: chemrof
has responsible: https://orcid.org/0000-0002-6601-2165
has URI prefix: https://chemkg.github.io/chemrof/
keyword: ontology
has resource example: FullySpecifiedAtom
has provider formatter: https://chemkg.github.io/chemrof/$1
is deprecated: false
is part of: Bioregistry
keyword: chemistry
contributor: Charles Tapley Hoyt
keyword: nfdi4chem
0000005: FullySpecifiedAtom
has download URL: chemrof.owl.ttl
type: Resource

KEGG Drug Group
has alternative prefix: KEGG_DRUG_GROUP
is deprecated: false
0000005: DG00301
has prefix: kegg.dgroup
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
is part of: Kyoto Encyclopedia of Genes and Genomes
has local unique identifier pattern: ^DG\d+$
description: KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups. Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc. Structure - grouped as similar chemical structures having the same skeleton, etc. Target - grouped by drug targets Class - drug classes often representing similar mechanisms of action Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters Chemical groups are often used for identifying essentially the same active ingredients of drugs in different countries.
has alternative prefix: KEGG_DGROUP

Structural Classification of Protein - Stable Domain Identifier
description: A 7-character sid consists of "d" followed by the 4-character PDB ID of the file of origin, the PDB chain ID ('_' if none, '.' if multiple as is the case in genetic domains), and a single character (usually an integer) if needed to specify the domain uniquely ('_' if not). Sids are currently all lower case, even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_, and d1cph.1.
has provider formatter: http://scop.berkeley.edu/sid=$1
0000005: d4akea1
has resource example: http://scop.berkeley.edu/sid=d4akea1
is deprecated: false
has responsible: https://orcid.org/0000-0002-5153-9079
is part of: Bioregistry
has URI prefix: http://scop.berkeley.edu/sid=
type: Resource
contributor: Charles Tapley Hoyt
has prefix: scop.sid

InformAll Allergenic Food Database
has resource example: http://research.bmh.manchester.ac.uk/informall/allergenic-food/
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: The InformAll database was developed to provide a credible source of information on allergenic food materials of both plant and animal origin.
has prefix: informall
has URI prefix: http://research.bmh.manchester.ac.uk/informall/allergenic-food/
has provider formatter: http://research.bmh.manchester.ac.uk/informall/allergenic-food/
appears in: Human Disease Ontology
0000005: 410
is deprecated: false

KESTREL Ontology
type: Resource
is deprecated: false
has resource example: kestrelo_0000001
has prefix: kestrelo
has provider formatter: http://purl.obolibrary.org/obo/kestrelo_$1
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-8741-7823
contributor: Charles Tapley Hoyt
has URI prefix: http://purl.obolibrary.org/obo/kestrelo_
description: An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains
0000005: 0000001
has local unique identifier pattern: ^\d{7}$

Pathway Commons
has prefix: pathwaycommons
has URI prefix: http://www.pathwaycommons.org/pc/record2.do
has resource example: http://www.pathwaycommons.org/pc/record2.do
description: Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.
is deprecated: false
keyword: pathway
0000005: 485991
is part of: Bioregistry
has provider formatter: http://www.pathwaycommons.org/pc/record2.do
has local unique identifier pattern: ^\d+$
type: Resource
has responsible: https://orcid.org/0000-0001-6059-6270

UniChem compound
description: identifier of a compound in the UniChem database
type: Resource
0000005: 161671
has provider formatter: https://www.ebi.ac.uk/unichem/compoundsources
is deprecated: false
is part of: Bioregistry
has prefix: unichem
has local unique identifier pattern: ^\d+$
has resource example: https://www.ebi.ac.uk/unichem/compoundsources
has URI prefix: https://www.ebi.ac.uk/unichem/compoundsources

EndlessForms Studio Library
has provider formatter: https://graphics.endlessforms.info/library
is part of: Bioregistry
0000005: HUMAN0000001
contributor: Charles Tapley Hoyt
type: Resource
has responsible: Melissa D Clarkson
description: A collection of graphics that relate to a theme
has resource example: https://graphics.endlessforms.info/library
has URI prefix: https://graphics.endlessforms.info/library
is deprecated: false
has prefix: endlessforms.library

MobiDB
has resource example: P10636
description: MobiDB is a database of protein disorder and mobility annotations.
type: Resource
has URI prefix: https://mobidb.org/
0000005: P10636
keyword: biomedical science
has responsible: Silvio Tosatto
keyword: biology
has prefix: mobidb
has provider formatter: https://mobidb.org/$1
0000011: UniProt Protein
is deprecated: false
has local unique identifier pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$
is part of: Bioregistry

SWEET Ontology Relationships Space
has prefix: sweet.relsp
has provider formatter: http://sweetontology.net/relaSpace/$1
type: Resource
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Space
has alternative prefix: sorelsp
0000005: adjacentTo
is deprecated: false
is part of: Bioregistry
has URI prefix: http://sweetontology.net/relaSpace/
keyword: space
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: adjacentTo

HL7 External Code Systems
has part: https://oid-base.com/get/2.16.840.1.113883.6.163
has part: https://oid-base.com/get/2.16.840.1.113883.6.1
has part: https://oid-base.com/get/2.16.840.1.113883.6.174
has part: https://oid-base.com/get/2.16.840.1.113883.6.2
has part: https://oid-base.com/get/2.16.840.1.113883.6.42
has part: https://oid-base.com/get/2.16.840.1.113883.6.206
has part: https://oid-base.com/get/2.16.840.1.113883.6.229
has part: https://oid-base.com/get/2.16.840.1.113883.6.347
has part: https://oid-base.com/get/2.16.840.1.113883.6.208
type: Registry
has part: https://oid-base.com/get/2.16.840.1.113883.6.69
has part: https://oid-base.com/get/2.16.840.1.113883.6.43
description: HL7 External Code Systems are stored within the greater OID system
has part: https://oid-base.com/get/2.16.840.1.113883.6.119
has part: https://oid-base.com/get/2.16.840.1.113883.6.173
has part: https://oid-base.com/get/2.16.840.1.113883.6.281
has part: https://oid-base.com/get/2.16.840.1.113883.6.344
has part: https://oid-base.com/get/2.16.840.1.113883.6.256
has part: https://oid-base.com/get/2.16.840.1.113883.6.319
has part: https://oid-base.com/get/1.0.639.3
has part: https://oid-base.com/get/2.16.840.1.113883.6.189
has part: https://oid-base.com/get/2.16.840.1.113883.6.209
has part: https://oid-base.com/get/2.16.840.1.113883.6.88
has responsible: HL7 Support
has part: https://oid-base.com/get/2.16.840.1.113883.6.283
has part: https://oid-base.com/get/2.16.840.1.113883.6.339
has part: https://oid-base.com/get/2.16.840.1.113883.6.59
0000005: 2.16.840.1.113883.6.88
has part: https://oid-base.com/get/2.16.840.1.113883.5.1107
has part: https://oid-base.com/get/2.16.840.1.113883.6.8
has part: https://oid-base.com/get/2.16.840.1.113883.6.205
has part: https://oid-base.com/get/2.16.840.1.113883.6.61
has part: https://oid-base.com/get/1.2.840.10008.2.16.4
has part: https://oid-base.com/get/2.16.840.1.113883.6.254
has part: https://oid-base.com/get/2.16.840.1.113883.6.73
has part: https://oid-base.com/get/2.16.840.1.113883.6.3
has part: https://oid-base.com/get/2.16.840.1.113883.6.126
has part: https://oid-base.com/get/2.16.840.1.113883.6.175
has part: https://oid-base.com/get/2.16.840.1.113883.6.90
has part: https://oid-base.com/get/2.16.840.1.113883.6.340
has part: https://oid-base.com/get/2.16.840.1.113883.6.280
has part: https://oid-base.com/get/2.16.840.1.113883.6.77
has part: https://oid-base.com/get/2.16.840.1.113883.6.284
has part: https://oid-base.com/get/2.16.840.1.113883.6.177
has part: https://oid-base.com/get/2.16.840.1.113883.6.96
has part: https://oid-base.com/get/2.16.840.1.113883.6.4
has part: https://oid-base.com/get/2.16.840.1.113883.6.86
has part: https://oid-base.com/get/2.16.840.1.113883.6.120
has part: https://oid-base.com/get/2.16.840.1.113883.5.1105
has provider formatter: https://oid-base.com/get/$1
has part: https://oid-base.com/get/2.16.840.1.113883.6.60
has part: https://oid-base.com/get/2.16.840.1.113883.6.116
has part: https://oid-base.com/get/2.16.840.1.113883.6.128
has part: https://oid-base.com/get/2.16.840.1.113883.6.282

VIAF cluster ID
0000005: 75121530
keyword: subject agnostic
description: The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.
has URI prefix: http://viaf.org/viaf/
is deprecated: false
keyword: centrally registered identifier
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has resource example: http://viaf.org/viaf/75121530
has prefix: viaf
has provider formatter: http://viaf.org/viaf/$1
type: Resource

Sharkipedia Trend
has resource example: https://www.sharkipedia.org/trends/3447
type: Resource
description: Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone.
has reviewer: Charles Tapley Hoyt
has URI prefix: https://www.sharkipedia.org/trends/
contributor: https://orcid.org/0000-0001-9439-5346
0000005: 3447
is deprecated: false
has prefix: sharkipedia.trend
has provider formatter: https://www.sharkipedia.org/trends/$1
has responsible: Christopher Mull
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
git repository: sharkipedia

Database of Macromolecular Movements
type: Resource
description: The Molecular Movements Database lists motions in proteins and other macromolecules. It is arranged around a multi-level classification scheme and includes motions of loops, domains, and subunits.
keyword: classification
has URI prefix: http://www.molmovdb.org/cgi-bin/morph.cgi
is deprecated: false
keyword: small molecule
keyword: protein
0000005: f665230-5267
is part of: Bioregistry
has provider formatter: http://www.molmovdb.org/cgi-bin/morph.cgi
keyword: structure
has prefix: molmovdb
has reviewer: Charles Tapley Hoyt
has resource example: http://www.molmovdb.org/cgi-bin/morph.cgi

Biological Expression Language
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
keyword: biology
has responsible: Charles Tapley Hoyt
is deprecated: false
0000005: 9-1-1 Complex
has prefix: bel
description: The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents.

Publication Provenance Prefixes
has part: Digital Object Identifier
creator: Charles Tapley Hoyt
has part: PubMed
description: Prefixes useful in annotating documentation provenance.
has part: PubMed Central
has part: arXiv
type: Collection

DAML Periodic Table of the Elements
contributor: Charles Tapley Hoyt
has prefix: daml.pt
type: Resource
has resource example: Be
has URI prefix: http://www.daml.org/2003/01/periodictable/PeriodicTable#
has download URL: PeriodicTable.owl
keyword: ontology
is deprecated: false
0000005: Be
description: A representation of the periodic table of the elements in OWL, with both elements and a hierarchical classification. This is from the DARPA Agent Markup Language (DAML) project, which has been inactive since the mid 2000's.
is part of: Bioregistry
has provider formatter: http://www.daml.org/2003/01/periodictable/PeriodicTable#$1

MeSH 2012
0000011: Medical Subject Headings
description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012.
0000005: 17186
has provider formatter: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi
is deprecated: false
is part of: Bioregistry
has resource example: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi
has URI prefix: https://bioregistry.io/mesh.2012:
has local unique identifier pattern: ^[A-Za-z0-9]+$
type: Resource
has prefix: mesh.2012

Drosophila RNAi Screening Center
is part of: Bioregistry
has local unique identifier pattern: ^DRSC\d+$
0000005: DRSC05221
description: The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.
has URI prefix: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl
type: Resource
has provider formatter: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl
has resource example: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl
is deprecated: false
has prefix: drsc

DECIPHER CNV Syndromes
is part of: Bioregistry
has prefix: decipher
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
description: CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms
type: Resource
has provider formatter: https://www.deciphergenomics.org/syndrome/$1
has URI prefix: https://www.deciphergenomics.org/syndrome/
keyword: biomedical science
keyword: life science
is deprecated: false
0000005: 1
has resource example: https://www.deciphergenomics.org/syndrome/1
has responsible: https://orcid.org/0000-0002-0215-4084

MedlinePlus Health Topics
description: MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language.
type: Resource
has URI prefix: https://bioregistry.io/medlineplus:
keyword: biomedical science
keyword: health science
keyword: medicine
0000005: 002804
has resource example: 002804.htm
keyword: ontology
has provider formatter: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm
is deprecated: false
keyword: disease
has prefix: medlineplus
is part of: Bioregistry
has local unique identifier pattern: ^\d+$

International Standard for Intelligent Information Request and Delivery Software Ontology
is deprecated: false
has provider formatter: http://iirds.tekom.de/iirds/domain/software#$1
description: An ontology encoding software based on the Intelligent Information Request and Delivery (iiRDS) standard
is part of: Bioregistry
has resource example: iirdsSoftwareDomainEntity
has prefix: iirds.sft
git repository: models
has URI prefix: http://iirds.tekom.de/iirds/domain/software#
0000005: iirdsSoftwareDomainEntity
type: Resource
keyword: nfdi4ing
keyword: computer science

PRIDE Project
is deprecated: false
0000005: PXD000440
description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects.
has local unique identifier pattern: ^P(X|R|A)D\d{6}$
is part of: Bioregistry
has resource example: PXD000440
has provider formatter: https://www.ebi.ac.uk/pride/archive/projects/$1
has prefix: pride.project
has URI prefix: https://www.ebi.ac.uk/pride/archive/projects/
type: Resource

Panorama Public
keyword: metabolomics
keyword: proteomics
has prefix: panorama
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: https://bioregistry.io/panorama:
keyword: life science
0000005: FxnI151FMs
description: Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible.
has responsible: Brendan MacLean
is deprecated: false
has resource example: FxnI151FMs.url
has provider formatter: https://panoramaweb.org/$1.url

SWEET Ontology Realm Geologic Constituent
0000005: ArmoredRelictInclusion
type: Resource
keyword: geologic constituent
has alternative prefix: soreagcons
keyword: realm
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Constituent
has prefix: sweet.reagcons
has resource example: ArmoredRelictInclusion
has URI prefix: http://sweetontology.net/realmGeolConstituent/
has provider formatter: http://sweetontology.net/realmGeolConstituent/$1
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology

SWEET Ontology Realm Astrophysical
has alternative prefix: soreaas
keyword: astrophysical
has URI prefix: http://sweetontology.net/realmAstroStar/
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Astrophysical
0000005: ActiveRegion
has provider formatter: http://sweetontology.net/realmAstroStar/$1
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.reaas
type: Resource
keyword: realm
has resource example: ActiveRegion
is deprecated: false

MLCommons Association
description: MLCommons Association artifacts, including benchmark results, datasets, and saved models.
is deprecated: false
has URI prefix: https://www.mlcommons.org/mlc-id/
has prefix: mlc
is part of: Bioregistry
type: Resource
0000005: 0.7-123
has local unique identifier pattern: ^[0-9a-zA-Z\.\-\_]+$
has resource example: https://www.mlcommons.org/mlc-id/0.7-123
has provider formatter: https://www.mlcommons.org/mlc-id/$1

Sequence types and features ontology
git repository: SO-Ontologies
keyword: rna
keyword: genome
keyword: dna
has provider formatter: http://purl.obolibrary.org/obo/SO_$1
is part of: Bioregistry
0000005: 0001157
keyword: genomics
keyword: bioinformatics
has responsible: https://orcid.org/0000-0002-0831-6427
has download URL: so.owl
description: The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.
keyword: sequence annotation
keyword: deoxyribonucleic acid
has prefix: so
keyword: transcriptomics
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: gene
keyword: structure
keyword: biology
keyword: sequence feature
keyword: life science
has resource example: SO_0001157
keyword: region
keyword: ribonucleic acid
is deprecated: false
appears in: Provisional Cell Ontology
has URI prefix: http://purl.obolibrary.org/obo/SO_
keyword: obo
keyword: ontology

NFDI4Culture Resources
has part: Iconclass Classification
has part: NFDI4Culture Ontology
type: Collection
has part: GESAH Graphic Arts Ontology
has part: Building Topology Ontology
has part: PREMIS 3 Ontology
creator: https://orcid.org/0000-0002-0006-7542
creator: Charles Tapley Hoyt
has part: CIDOC Conceptual Reference Model
description: Prefixes for ontologies relevant for NFDI4Culture.

Web of Things Hypermedia Controls Ontology
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: https://www.w3.org/2019/wot/hypermedia#
0000005: AdditionalExpectedResponse
type: Resource
description: an ontology for links and forms, the main hypermedia controls in use on the Web. This ontology offers, among others, a means to reify RDF statements interpreted as links between Web resources. It also provides a versatile exchange format for links and forms in RESTful Web applications. [from homepage]
has provider formatter: https://www.w3.org/2019/wot/hypermedia#$1
has prefix: wot.hypermedia
has resource example: AdditionalExpectedResponse
is deprecated: false

MultiCellDS Digital Cell Line
0000005: MCDS_L_0000000001
has provider formatter: http://multicellds.org/MultiCellDB/$1
has local unique identifier pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$
has URI prefix: http://multicellds.org/MultiCellDB/
is part of: MultiCellDS
is deprecated: false
has resource example: MCDS L 0000000001
description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.
has prefix: multicellds.cell_line
is part of: Bioregistry
type: Resource

A Database of Human Hemoglobin Variants and Thalassemias
keyword: protein
has prefix: hbvar
has URI prefix: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3
type: Resource
0000005: 2526
has reviewer: Charles Tapley Hoyt
description: This is a relational database of information about hemoglobin variants and mutations that cause thalassemia.
has resource example: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3
is deprecated: false
has provider formatter: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3
is part of: Bioregistry

Industrial Ontology Foundry (IOF) Core Ontology
description: The IOF Core Ontology contains notions found to be common across multiple manufacturing domains. This file is an RDF implementation of these notions. The ontology utilizes the Basic Formal Ontology or BFO as a top-level ontology but also borrows terms from various domain-independent or mid-level ontologies. The purpose of the ontology is to serve as a foundation for ensuring consistency and interoperability across various domain-specific reference ontologies the IOF publishes.
has resource example: hasSpecifiedOutput
git repository: ontology
0000005: hasSpecifiedOutput
type: Resource
keyword: nfdi4ing
is deprecated: false
has provider formatter: https://spec.industrialontologies.org/ontology/core/Core/$1
has URI prefix: https://spec.industrialontologies.org/ontology/core/Core/
keyword: ontology
has prefix: iofcore
keyword: engineering
is part of: Bioregistry
has download URL: Core.rdf

SWEET Ontology Relationships Time
has URI prefix: http://sweetontology.net/relaTime/
keyword: time
has provider formatter: http://sweetontology.net/relaTime/$1
is deprecated: false
has prefix: sweet.relt
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: dayOfYear
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: dayOfYear
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Time
type: Resource
git repository: sweet
has alternative prefix: sorelt

Metabolic Atlas Metabolite
description: A subspace of Metabolic Atlas for compartment-specific records for metabolites.
contributor: Mihail Anton
keyword: chemistry
has local unique identifier pattern: ^MAM\d{5}\w$
is part of: Bioregistry
has prefix: metatlas.metabolite
has resource example: MAM01234c
is part of: Metabolic Atlas
has reviewer: Charles Tapley Hoyt
type: Resource
has responsible: Mihail Anton
0000005: MAM01234c
has URI prefix: https://metabolicatlas.org/identifier/MetabolicAtlas/
is deprecated: false
keyword: metabolites
has provider formatter: https://metabolicatlas.org/identifier/MetabolicAtlas/$1

WikiPathways
keyword: epidemiology
keyword: molecular interaction
has download URL: wikipathways.owl
keyword: drug interaction
keyword: reaction data
has resource example: WP732
has local unique identifier pattern: ^WP\d{1,5}(\_r\d+)?$
keyword: protein interactions
description: WikiPathways is a database of biological pathways maintained by and for the scientific community.
type: Resource
has responsible: Tim Vandermeersch
keyword: genetic interaction (sensu unexpected)
has provider formatter: http://www.wikipathways.org/instance/$1
has URI prefix: http://www.wikipathways.org/instance/
keyword: biological regulation
keyword: ontology
keyword: pathway
keyword: signaling
is deprecated: false
0000005: WP732
keyword: virology
contributor: Tim Vandermeersch
has prefix: wikipathways
is part of: Bioregistry

CoyPu Ontology
description: Ontology to describe companies and their supply network, employees, products, production materials, industries, events and relations.
has provider formatter: https://schema.coypu.org/global#$1
is deprecated: false
keyword: economics
0000005: AbductionOrForcedDisappearance
has prefix: coypu
is part of: Bioregistry
has URI prefix: https://schema.coypu.org/global#
type: Resource
has resource example: AbductionOrForcedDisappearance
keyword: coypu

BIND accession number
is deprecated: true
keyword: pathway
keyword: small molecule
is part of: Bioregistry
0000005: 98346
has provider formatter: http://www.bind.ca/Action
type: Resource
keyword: interaction
description: Accession number of an entry from the BIND database.
has URI prefix: http://www.bind.ca/Action
has resource example: http://www.bind.ca/Action
has prefix: bind

terms4FAIRskills
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: skills
0000005: 0000127
has local unique identifier pattern: ^\d{7}$
description: A terminology for the skills necessary to make data FAIR and to keep it FAIR.
type: Resource
keyword: nfdi4ing
keyword: fair
has prefix: t4fs
has resource example: T4FS_0000127
has responsible: https://orcid.org/0000-0002-7702-4495
keyword: subject agnostic
keyword: ess
git repository: FAIRterminology
has provider formatter: http://purl.obolibrary.org/obo/T4FS_$1
keyword: competence
keyword: obo
keyword: ontology
has download URL: t4fs.owl
keyword: curated information
has URI prefix: http://purl.obolibrary.org/obo/T4FS_
is deprecated: false
keyword: digital curation

ChemIDplus
has prefix: chemidplus
is part of: Bioregistry
has URI prefix: https://chem.nlm.nih.gov/chemidplus/rn/
type: Resource
keyword: structure
keyword: biomedical science
has alternative prefix: ChemIDplus
has local unique identifier pattern: ^\d+\-\d+\-\d+$
has provider formatter: https://chem.nlm.nih.gov/chemidplus/rn/$1
keyword: molecules
description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.
is deprecated: false
has resource example: https://chem.nlm.nih.gov/chemidplus/rn/57-27-2
keyword: chemistry
0000005: 57-27-2

Catalytic Site Atlas
keyword: enzyme
has resource example: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php
0000005: 1a05
description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.
is part of: Bioregistry
type: Resource
has provider formatter: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php
has URI prefix: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php
keyword: structure
has local unique identifier pattern: ^[0-9][A-Za-z0-9]{3}$
has prefix: csa
has responsible: Nicholas Furnham
keyword: life science
is deprecated: true

Category Scheme Election Studies
has URI prefix: https://vocabularies.cessda.eu/vocabulary/KategorienschemaWahlstudien#code_
has prefix: gesis.kategorienschemawahlstudien
is deprecated: false
0000005: 01
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has identifier space owner: 018afyw53
has provider formatter: https://vocabularies.cessda.eu/vocabulary/KategorienschemaWahlstudien#code_$1
type: Resource
has resource example: code_01
description: The Category Scheme Election Studies provides the ability to categorize election studies at the question and/or variable level.

APID Interactomes
type: Resource
0000005: P01116
has local unique identifier pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
has prefix: apid.interactions
contributor: https://orcid.org/0000-0002-1216-4761
has provider formatter: http://cicblade.dep.usal.es:8080/APID/Interactions.action
is deprecated: false
0000011: UniProt Protein
description: APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.
is part of: Bioregistry
has resource example: http://cicblade.dep.usal.es:8080/APID/Interactions.action
has URI prefix: http://cicblade.dep.usal.es:8080/APID/Interactions.action

Description of a Project
git repository: doap
has prefix: doap
keyword: society
keyword: metadata
keyword: semantic web
has resource example: Project
is deprecated: false
description: DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects.
has responsible: Edd Wilder-James
keyword: rdf
0000005: Project
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: http://usefulinc.com/ns/doap#
type: Resource
has provider formatter: http://usefulinc.com/ns/doap#$1

NIH HIV Reagent Program
is deprecated: false
has URI prefix: https://bioregistry.io/hivreagentprogram:
description: Cell line collections (Providers)
has provider formatter: https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx
has resource example: ARP-1513.aspx
is part of: Bioregistry
has prefix: hivreagentprogram
type: Resource
0000005: ARP-1513

SWEET Ontology Representation Mathematics Function Orthogonal
keyword: representation mathematics function orthogonal
is deprecated: false
has URI prefix: http://sweetontology.net/reprMathFunctionOrthogonal/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Function Orthogonal
0000005: Coefficient
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sorepmfo
has provider formatter: http://sweetontology.net/reprMathFunctionOrthogonal/$1
has resource example: Coefficient
has prefix: sweet.repmfo

ClinGen Allele Registry
has alternative prefix: CAID
has provider formatter: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid
description: ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides and maintains identifiers for alleles.
has local unique identifier pattern: ^CA\d+$
keyword: mutations
is part of: Bioregistry
contributor: Charles Tapley Hoyt
contributor: Sierra Moxon
has prefix: clingen.allele
has URI prefix: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid
type: Resource
keyword: alleles
has resource example: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid
0000005: CA981206459
has alternative prefix: clingene
keyword: genetics
is deprecated: false

SWEET Ontology Realm Biologic Biome
has prefix: sweet.reabb
has alternative prefix: soreabb
is deprecated: false
0000005: Anthromes
is part of: Bioregistry
has resource example: Anthromes
has URI prefix: http://sweetontology.net/realmBiolBiome/
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/realmBiolBiome/$1
type: Resource
keyword: realm
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Biologic Biome
keyword: biologic biome

Neuro Behavior Ontology
keyword: systemic neuroscience
has prefix: nbo
0000005: 0000564
has local unique identifier pattern: ^\d{7}$
appears in: Uber Anatomy Ontology
description: An ontology of human and animal behaviours and behavioural phenotypes
keyword: social and behavioural science
type: Resource
git repository: behavior-ontology
appears in: Provisional Cell Ontology
keyword: obo
appears in: Medical Action Ontology
has provider formatter: http://purl.obolibrary.org/obo/NBO_$1
has resource example: NBO_0000564
appears in: Sickle Cell Disease Ontology
keyword: ontology
is deprecated: false
has download URL: nbo.owl
keyword: phenotype
keyword: behavior
is part of: Bioregistry
appears in: Environmental conditions, treatments and exposures ontology
has URI prefix: http://purl.obolibrary.org/obo/NBO_
has responsible: George Gkoutos

SWEET Ontology Material Facility
has prefix: sweet.maf
keyword: materials
keyword: facility
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Facility
has URI prefix: http://sweetontology.net/matrFacility/
is deprecated: false
is part of: Bioregistry
has provider formatter: http://sweetontology.net/matrFacility/$1
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: AgriculturalProductionFacility
contributor: Charles Tapley Hoyt
0000005: AgriculturalProductionFacility
type: Resource
has alternative prefix: somaf
git repository: sweet

NIH RePORTER
is part of: Bioregistry
type: Resource
has reviewer: Charles Tapley Hoyt
has provider formatter: https://reporter.nih.gov/project-details/$1
has URI prefix: https://reporter.nih.gov/project-details/
has download URL: nihreporter.project.owl.gz
description: RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding.
keyword: ontology
has resource example: https://reporter.nih.gov/project-details/10343835
is deprecated: false
has responsible: NIH Reporter Helpdesk
contributor: https://orcid.org/0000-0001-9439-5346
has local unique identifier pattern: ^\d+$
0000005: 10343835
has prefix: nihreporter.project
keyword: bibliometrics
keyword: project

TogoID Ontology
is part of: Bioregistry
0000005: AffyProbeset
contributor: Charles Tapley Hoyt
git repository: togoid-config
has responsible: https://orcid.org/0000-0003-2391-0384
type: Resource
description: TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)
has provider formatter: https://togoid.dbcls.jp/#$1
has resource example: AffyProbeset
keyword: ontology
is deprecated: false
has URI prefix: https://togoid.dbcls.jp/#
has download URL: togoid-ontology.ttl
has prefix: togoid

Topology Data Bank of Transmembrane Proteins
is part of: Bioregistry
type: Resource
description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases.
has prefix: topdb
0000005: AP00378
has provider formatter: http://topdb.enzim.hu/
has local unique identifier pattern: ^[A-Z0-9]+$
has resource example: http://topdb.enzim.hu/
is deprecated: false
keyword: protein
has URI prefix: http://topdb.enzim.hu/

Symptom Ontology
keyword: diagnosis
keyword: pain medicine
has responsible: https://orcid.org/0000-0001-8910-9851
has download URL: symp.owl
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: biomedical science
0000005: 0019171
has resource example: SYMP_0019171
has provider formatter: http://purl.obolibrary.org/obo/SYMP_$1
has prefix: symp
keyword: life science
git repository: SymptomOntology
keyword: patient care
keyword: obo
has alternative prefix: SYMP
keyword: ontology
description: The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases.
appears in: Sickle Cell Disease Ontology
is deprecated: false
keyword: disease
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/SYMP_

A vocabulary for annotating vocabulary descriptions
is part of: Bioregistry
description: This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes.
contributor: Charles Tapley Hoyt
has URI prefix: https://vocab.org/vann/#
has provider formatter: https://vocab.org/vann/#$1
type: Resource
has resource example: usageNote
keyword: computer science
keyword: metadata
0000005: usageNote
is deprecated: false
has prefix: vann
keyword: miscellaneous

Selventa Diseases
keyword: bel
keyword: diseases
0000005: D0001
has prefix: sdis
description: Selventa legacy disease namespace used with the Biological Expression Language
is deprecated: false
has resource example: D0001
has local unique identifier pattern: ^D\d{4}$
keyword: selventa
has URI prefix: https://biopragmatics.github.io/providers/sdis/
has provider formatter: https://biopragmatics.github.io/providers/sdis/$1
is part of: Bioregistry
has responsible: Natalie L Catlett
contributor: Charles Tapley Hoyt
type: Resource

Food Interactions with Drugs Evidence Ontology
git repository: fideo
description: Food-Drug interactions automatically extracted from scientific literature
has download URL: fideo.owl
has URI prefix: http://purl.obolibrary.org/obo/FIDEO_
has provider formatter: http://purl.obolibrary.org/obo/FIDEO_$1
type: Resource
has responsible: Georgeta Bordea
has resource example: FIDEO_00000021
has prefix: fideo
keyword: obo
keyword: ontology
is deprecated: false
has local unique identifier pattern: ^\d+$
0000005: 00000021
is part of: Bioregistry

SWEET Ontology Realm Land Glacial
has resource example: Arete
is part of: Bioregistry
has prefix: sweet.realg
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
keyword: glacialland
has provider formatter: http://sweetontology.net/realmLandGlacial/$1
has alternative prefix: sorealg
0000005: Arete
has URI prefix: http://sweetontology.net/realmLandGlacial/
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Glacial

SeaDataNet device categories
keyword: earth sciences
has resource example: http://vocab.nerc.ac.uk/collection/L05/current/101
type: Resource
0000005: 101
keyword: ess
is deprecated: false
description: Terms used to classify groups of sensors, instruments, sources of algorithmically computed data (numerical models) or samplers (collectors of water, SPM, sediment, rock, air or biota samples).
has provider formatter: http://vocab.nerc.ac.uk/collection/L05/current/$1
has prefix: bodc.sdn
is part of: Bioregistry
has URI prefix: http://vocab.nerc.ac.uk/collection/L05/current/

SWEET Ontology Realm Atmospheric Boundary Layer
has provider formatter: http://sweetontology.net/realmAtmoBoundaryLayer/$1
has alternative prefix: soreaabl
keyword: atmospheric boundary layer
0000005: AtmosphericBoundaryLayer
has URI prefix: http://sweetontology.net/realmAtmoBoundaryLayer/
is deprecated: false
has resource example: AtmosphericBoundaryLayer
has prefix: sweet.reaabl
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Atmospheric Boundary Layer
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: realm

SPIKE Map
type: Resource
0000005: spike00001
description: SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.
has provider formatter: http://www.cs.tau.ac.il/~spike/maps/$1.html
keyword: pathway
is deprecated: false
keyword: dna
has URI prefix: https://bioregistry.io/spike.map:
has prefix: spike.map
has local unique identifier pattern: ^spike\d{5}$
has responsible: Yosef Shiloh
has resource example: spike00001.html
keyword: gene expression
is part of: Bioregistry

UniGene
has URI prefix: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi
is deprecated: true
keyword: dna
is part of: Bioregistry
keyword: protein
has resource example: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi
has local unique identifier pattern: ^\d+$
has provider formatter: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi
0000005: 4900
keyword: gene expression
has prefix: unigene
type: Resource
keyword: gene
description: A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
keyword: life science

DBPedia Ontology
has prefix: dbo
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has resource example: careerPrizeMoney
keyword: dbpedia
has provider formatter: https://dbpedia.org/ontology/$1
description: This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki.
keyword: ontology
is deprecated: false
has URI prefix: https://dbpedia.org/ontology/
0000005: careerPrizeMoney

FamPlex
has alternative prefix: famplex
keyword: ontology
0000005: GPIb_IX_V
is deprecated: false
has provider formatter: https://sorgerlab.github.io/famplex/$1
description: FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.
has URI prefix: https://sorgerlab.github.io/famplex/
is part of: Bioregistry
has local unique identifier pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$
type: Resource
has resource example: GPIb IX V
has responsible: https://orcid.org/0000-0001-9439-5346
has prefix: fplx

Modern Science Ontology
keyword: academy
is part of: Bioregistry
has provider formatter: https://w3id.org/skgo/modsci#$1
type: Resource
keyword: nfdi4ing
keyword: society
has URI prefix: https://w3id.org/skgo/modsci#
description: Modern Science Ontology (ModSci), for modeling relationships between modern science branches and related entities, such as scientific discoveries, phenomena, renowned scientists, instruments, etc. ModSci is an upper ontology that provides a unifying framework for the various domain ontologies that make up the Science Knowledge Graph Ontology Suite. The Systematic Approach for Building Ontologies (SABiO) has been followed in the development of ModSci. ModSci is a poly-hierarchical ontology that can be utilized in semantic web applications. ModSci powers two projects for semantically representing scholarly information: Open Research Knowledge Graph (for the categorization of research papers) and OpenResearch.org (for the categorization of the information about scientific events, research projects, scientific papers, publishers, and journals).
0000005: AcidbaseChemistry
has download URL: modsci.owl
has responsible: SaidFathalla
has resource example: AcidbaseChemistry
keyword: ontology
is deprecated: false
has prefix: modsci

ViralZone
has alternative prefix: vz
is deprecated: false
keyword: molecular biology
keyword: virology
has provider formatter: https://viralzone.expasy.org/$1
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has responsible: Philippe Le Mercier
keyword: epidemiology
has URI prefix: https://viralzone.expasy.org/
has prefix: viralzone
has resource example: https://viralzone.expasy.org/992
0000005: 992
keyword: virus
description: ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.
keyword: life science

Mouse adult gross anatomy
has prefix: ma
keyword: organ
keyword: ontology
git repository: adult-mouse-anatomy-ontology
has responsible: https://orcid.org/0000-0002-0956-8634
has local unique identifier pattern: ^\d+$
keyword: mouse
is deprecated: false
description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus)
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/MA_
0000005: 0002502
type: Resource
has resource example: MA_0002502
keyword: tissue
has download URL: ma.owl
keyword: anatomy
has provider formatter: http://purl.obolibrary.org/obo/MA_$1
keyword: obo

SWEET Ontology Phenomena System Complexity
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: Cascade
keyword: phenomena
keyword: system complexity
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena System Complexity
0000005: Cascade
is deprecated: false
has URI prefix: http://sweetontology.net/phenSystemComplexity/
has alternative prefix: sophsyc
has prefix: sweet.phsyc
has provider formatter: http://sweetontology.net/phenSystemComplexity/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt

GlyTouCan
has provider formatter: https://glytoucan.org/Structures/Glycans/$1
keyword: glycomics
is deprecated: false
has prefix: glytoucan
0000005: G00054MO
is part of: Bioregistry
has alternative prefix: glygen
has responsible: 0000-0003-3147-448X
has local unique identifier pattern: ^G[0-9]{5}[A-Z]{2}$
description: GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.
type: Resource
has URI prefix: https://glytoucan.org/Structures/Glycans/
has resource example: G00054MO
keyword: structural biology

SupraBank Interaction
has responsible: https://orcid.org/0000-0002-9676-9839
has prefix: suprabank.interaction
0000005: 2329
is deprecated: false
has local unique identifier pattern: ^\d+$
keyword: chemical
keyword: relationship
has resource example: https://suprabank.org/interactions/2329
has URI prefix: https://suprabank.org/interactions/
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
keyword: interaction
description: Interactions are SupraBank's way to collect information about experiments that describe the binding interaction between molecules. The form for creating an interaction enables you to list all experimental conditions. An interaction is similar to an entry in a table in your scientific publication, but providing machine readable comprehensive information. (from homepage)
has provider formatter: https://suprabank.org/interactions/$1

GrainGenes reference
is part of: Bioregistry
has URI prefix: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi
has resource example: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi
description: A database for Triticeae and Avena references.
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi
has prefix: graingenes.reference
0000005: WGS-95-1333
is deprecated: false

International Classification of Diseases, 10th Revision, Clinical Modification
has prefix: icd10cm
has provider formatter: https://www.icd10data.com/search
description: ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS).
keyword: ontology
keyword: morbidity
has alternative prefix: ICD10CM
keyword: disease
keyword: electronic health record
has URI prefix: https://www.icd10data.com/search
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: F45.21
keyword: diagnosis
has resource example: https://www.icd10data.com/search
type: Resource
has responsible: Patricia Brooks
keyword: biomedical science
keyword: health science
has local unique identifier pattern: ^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$
is deprecated: false
keyword: medicine

GeoNames
description: The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.
has prefix: geonames
keyword: geographic location
has provider formatter: https://www.geonames.org/$1
0000005: 3532759
type: Resource
has alternative prefix: Geomames
keyword: ontology
has resource example: https://www.geonames.org/3532759
is deprecated: false
has URI prefix: https://www.geonames.org/
keyword: geography
has download URL: geonames.owl
keyword: geoinformatics
has responsible: Marc Wick
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
is part of: Bioregistry
has alternative prefix: Geonamaes

Smart Applications Reference ontology
has prefix: saref
is part of: Bioregistry
type: Resource
keyword: iot
keyword: nfdi4ing
0000005: Actuation
description: The Smart Applications REFerence ontology (SAREF) is intended to enable interoperability between solutions from different providers and among various activity sectors in the Internet of Things (IoT), thus contributing to the development of the global digital market.
has resource example: Actuation
has provider formatter: https://saref.etsi.org/core/$1
keyword: industry
has URI prefix: https://saref.etsi.org/core/
keyword: services
is deprecated: false
keyword: engineering
keyword: digital planning and construction
keyword: fid baudigital

GRIN URL
type: Resource
description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.
has resource example: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail
0000005: 19333
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail
has prefix: grin.taxonomy
has URI prefix: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail

TAIR Protein
has URI prefix: https://www.arabidopsis.org/protein
description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept
0000005: 1009107926
has provider formatter: https://www.arabidopsis.org/protein
has responsible: 0000-0003-3871-858X
has resource example: https://www.arabidopsis.org/protein
has local unique identifier pattern: ^\d{10}$
has prefix: tair.protein
is deprecated: false
keyword: protein
contributor: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
type: Resource

GenInfo Identifier
has alternative prefix: NCBI_gi
has identifier space owner: 02meqm098
description: A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number.
has canonical: GenBank
has alternative prefix: ncbi.gi
is deprecated: false
has resource example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
has URI prefix: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
has prefix: ncbigi
is part of: Bioregistry
has provider formatter: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
has local unique identifier pattern: ^\d+$
0000005: 568815597
type: Resource
contributor: Charles Tapley Hoyt

ICEberg integrative and conjugative element
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php
has URI prefix: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php
type: Resource
0000005: 100
has alternative prefix: iceberg.ice
has prefix: iceberg.element
has resource example: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php
description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.

CTD Gene
description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.
has prefix: ctd.gene
has responsible: https://orcid.org/0000-0002-5741-7128
0000011: NCBI Gene
0000005: 101
has resource example: http://ctdbase.org/detail.go
is deprecated: false
has URI prefix: http://ctdbase.org/detail.go
has provider formatter: http://ctdbase.org/detail.go
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource

Cube db
has resource example: AKR
0000005: AKR
is deprecated: true
description: Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.
has URI prefix: https://bioregistry.io/cubedb:
has prefix: cubedb
has provider formatter: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^[A-Za-z_0-9]+$

EDAM Topic
git repository: edamontology
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: http://edamontology.org/topic_
has provider formatter: http://edamontology.org/topic_$1
has prefix: edam.topic
has resource example: topic_0003
keyword: ontology
is deprecated: false
has local unique identifier pattern: ^\d+$
has responsible: https://orcid.org/0000-0002-1509-4981
0000005: 0003
has download URL: EDAM.obo
description: A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.

Geographical Entity Ontology
is part of: Bioregistry
keyword: physical geography
has resource example: GEO_000000021
has URI prefix: http://purl.obolibrary.org/obo/GEO_
type: Resource
git repository: geographical-entity-ontology
has provider formatter: http://purl.obolibrary.org/obo/GEO_$1
keyword: human geography
has local unique identifier pattern: ^\d{9}$
keyword: geographic location
has responsible: William Hogan
description: An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in "The US declared war on Germany" vs. the US in "The plane entered US airspace".
has download URL: geo.owl
0000005: 000000021
is deprecated: false
keyword: obo
keyword: ontology
has prefix: geogeo

SWEET Ontology Property Pressure
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
keyword: pressure
has alternative prefix: sopropp
type: Resource
has prefix: sweet.propp
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Pressure
has provider formatter: http://sweetontology.net/propPressure/$1
0000005: AirPressure
is deprecated: false
has URI prefix: http://sweetontology.net/propPressure/
is part of: Bioregistry
has resource example: AirPressure

Node Package Manager
has URI prefix: https://www.npmjs.com/package/
has prefix: npm
has resource example: curies
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: A repository of software packages written in Javascript, TypeScript, and related.
0000005: @biopragmatics/curies
has provider formatter: https://www.npmjs.com/package/$1
type: Resource

VIPERdb
has URI prefix: https://viperdb.org/Info_Page.php
keyword: structure
has provider formatter: https://viperdb.org/Info_Page.php
is deprecated: false
has prefix: viperdb
0000011: PDB Structure
description: VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration.
0000005: 2c6s
keyword: small molecule
is part of: Bioregistry
has resource example: https://viperdb.org/Info_Page.php
type: Resource

European Commission Participant Identification Code (PIC)
has local unique identifier pattern: ^\d{9}$
is deprecated: false
has provider formatter: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/org-details/$1
is part of: Bioregistry
description: An identifier for an organization
has prefix: europe.pic
contributor: Charles Tapley Hoyt
has resource example: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/org-details/881104060
0000005: 881104060
type: Resource
has URI prefix: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/org-details/

Ontology of Organizational Structures of Trauma centers and Trauma systems
has download URL: oostt.owl
is part of: Bioregistry
description: The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2).
git repository: OOSTT
type: Resource
has resource example: OOSTT_00000099
is deprecated: false
has provider formatter: http://purl.obolibrary.org/obo/OOSTT_$1
has URI prefix: http://purl.obolibrary.org/obo/OOSTT_
keyword: obo
keyword: traumatology
has local unique identifier pattern: ^\d{8}$
keyword: ontology
has prefix: oostt
0000005: 00000099
has responsible: https://orcid.org/0000-0003-1834-3856

SWEET Ontology Property Space Multidimensional
0000005: AngularExtent
has alternative prefix: sopropsm
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Multidimensional
is deprecated: false
is part of: Bioregistry
has prefix: sweet.propsm
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: space multidimensional
has URI prefix: http://sweetontology.net/propSpaceMultidimensional/
has resource example: AngularExtent
has provider formatter: http://sweetontology.net/propSpaceMultidimensional/$1

SWEET Ontology Phenomena Wave
has URI prefix: http://sweetontology.net/phenWave/
has prefix: sweet.phw
keyword: wave
0000005: Acoustic
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Wave
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: Acoustic
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: phenomena
has provider formatter: http://sweetontology.net/phenWave/$1
has alternative prefix: sophw

Human Metabolome Database
has prefix: hmdb
0000005: HMDB00001
has responsible: David Wishart
keyword: biochemistry
keyword: life science
keyword: human
is deprecated: false
keyword: molecular biology
keyword: metabolomics
keyword: bioinformatics
has URI prefix: http://www.hmdb.ca/metabolites/
has alternative prefix: HMDB
keyword: omics
keyword: proteomics
description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.
has local unique identifier pattern: ^HMDB\d+$
keyword: chemical
has resource example: HMDB00001
is part of: Bioregistry
has provider formatter: http://www.hmdb.ca/metabolites/$1
keyword: phenomics
keyword: metabolite
type: Resource

MIMIC III Database
keyword: health sciences
keyword: clinical data
has prefix: cohd
git repository: mimic-omop
keyword: health
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: clinical trials
description: MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012
type: Resource

Selventa Families
keyword: bel
has provider formatter: https://biopragmatics.github.io/providers/sfam/$1
0000005: F0001
type: Resource
has prefix: sfam
keyword: protein families
description: Selventa legacy protein family namespace used with the Biological Expression Language
is deprecated: false
keyword: selventa
has resource example: F0001
is part of: Bioregistry
has local unique identifier pattern: ^F\d{4}$
contributor: Charles Tapley Hoyt
has URI prefix: https://biopragmatics.github.io/providers/sfam/

Simple Standard for Sharing Ontological Mappings
has reviewer: Charles Tapley Hoyt
0000005: mapping_justification
git repository: sssom
has prefix: sssom
has URI prefix: https://w3id.org/sssom/
has responsible: https://orcid.org/0000-0002-7356-1779
is deprecated: false
contributor: https://orcid.org/0000-0002-7356-1779
is part of: Bioregistry
description: SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as "sssom:mapping_justification" are defined in the sssom namespace.
type: Resource
has local unique identifier pattern: ^[A-Za-z_]+$
has provider formatter: https://w3id.org/sssom/$1
has resource example: mapping justification

Store DB
has prefix: storedb
has provider formatter: https://www.storedb.org/
keyword: preclinical studies
keyword: epidemiology
type: Resource
keyword: biomedical science
description: STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.
0000005: STUDY1040
has local unique identifier pattern: ^(STUDY|FILE|DATASET)\d+$
keyword: life science
has resource example: https://www.storedb.org/
is deprecated: false
is part of: Bioregistry
keyword: ecology
has URI prefix: https://www.storedb.org/
has responsible: Dr Paul Schofield

Natural Product Activity and Species Source Database
contributor: Charles Tapley Hoyt
keyword: chemical
has provider formatter: https://bidd.group/NPASS/compound.php
has responsible: https://orcid.org/0000-0002-5473-8022
type: Resource
description: Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.
0000005: NPC139585
has local unique identifier pattern: ^NPC\d+$
keyword: compound
keyword: natural product
keyword: ontology
has resource example: https://bidd.group/NPASS/compound.php
is deprecated: false
has download URL: npass.owl
keyword: small molecule
is part of: Bioregistry
has prefix: npass
has URI prefix: https://bidd.group/NPASS/compound.php

BRENDA Ligand Group
has local unique identifier pattern: ^\d+$
0000005: 18030
keyword: chemistry
contributor: Charles Tapley Hoyt
has resource example: https://www.brenda-enzymes.de/ligand.php
has provider formatter: https://www.brenda-enzymes.de/ligand.php
type: Resource
keyword: grouping
keyword: structrual bioinformatics
description: Information for ligand groups (chemical classes).
has prefix: brenda.ligandgroup
is deprecated: false
has URI prefix: https://www.brenda-enzymes.de/ligand.php
is part of: Bioregistry

Space Life Sciences Ontology
has provider formatter: http://purl.obolibrary.org/obo/SLSO_$1
keyword: obo
description: The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data.
keyword: ontology
is deprecated: false
git repository: LSDAO
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/SLSO_
type: Resource
has prefix: slso
has download URL: slso.owl
0000005: 0000000
has responsible: Daniel C. Berrios

FAIRsharing
keyword: biomedical science
has prefix: fairsharing
keyword: life science
keyword: environmental science
keyword: natural science
has URI prefix: https://fairsharing.org/
has responsible: https://orcid.org/0000-0002-7702-4495
keyword: ontology and terminology
git repository: FAIRsharing
description: The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.
has resource example: bsg-000052
0000005: bsg-000052
is deprecated: false
keyword: policy
keyword: agriculture
has local unique identifier pattern: ^(bsg-[dscp]?\d{6})|(FAIRsharing\.\w+)$
keyword: data governance
keyword: database management
keyword: humanities
is part of: Bioregistry
has provider formatter: https://fairsharing.org/$1
type: Resource
keyword: earth science

Mastodon
has prefix: mastodon
has resource example: https://fedirect.toolforge.org/
is deprecated: false
has provider formatter: https://fedirect.toolforge.org/
description: address on the Mastodon decentralized social network (the form is 'user@server.domain' without a leading '@')
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: https://fedirect.toolforge.org/
type: Resource
has local unique identifier pattern: ^[A-Za-z0-9_]+([A-Za-z0-9_\.]+[A-Za-z0-9_]+)?@[\d\w\.\-]+[0-9a-z]+$

Kaggle
type: Resource
has provider formatter: https://www.kaggle.com/$1
description: Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.
has URI prefix: https://www.kaggle.com/
has resource example: kepler-exoplanet-search-results
has local unique identifier pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$
is deprecated: false
has prefix: kaggle
is part of: Bioregistry
0000005: nasa/kepler-exoplanet-search-results

Sharkipedia Trait
has reviewer: Charles Tapley Hoyt
has resource example: https://www.sharkipedia.org/traits/13
has URI prefix: https://www.sharkipedia.org/traits/
0000005: 13
has provider formatter: https://www.sharkipedia.org/traits/$1
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has prefix: sharkipedia.trait
has responsible: Christopher Mull
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
description: Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone.
git repository: sharkipedia

G protein-coupled receptor database
0000005: RL3R1_HUMAN
description: The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.
keyword: life science
has prefix: gpcrdb
has URI prefix: https://gpcrdb.org/protein/
has provider formatter: https://gpcrdb.org/protein/$1
is deprecated: false
keyword: small molecule
keyword: protein
has responsible: https://orcid.org/0000-0002-4299-7561
keyword: molecular biology
has local unique identifier pattern: ^\w+$
has resource example: RL3R1 HUMAN
is part of: Bioregistry
type: Resource

Animal Genome QTL
has part: Animal Genome Chicken QTL
has prefix: qtldb
is deprecated: false
has URI prefix: https://www.animalgenome.org/QTLdb/q
has part: Animal Genome Sheep QTL
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: https://www.animalgenome.org/QTLdb/q
has resource example: https://www.animalgenome.org/QTLdb/q
has part: Animal Genome Pig QTL
type: Resource
description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent.
0000005: 4685
has part: Animal Genome Cattle QTL

VCell Published Models
type: Resource
is deprecated: false
has provider formatter: https://vcell.org/biomodel-$1
has prefix: vcell
has URI prefix: https://vcell.org/biomodel-
has local unique identifier pattern: ^\d{5,}$
0000005: 201022999
is part of: Bioregistry
description: Models developed with the Virtual Cell (VCell) software prorgam.
has resource example: biomodel-201022999

Encyclopedia of Life Schema
type: Resource
contributor: Charles Tapley Hoyt
0000005: body_symmetry
has resource example: body symmetry
has prefix: eol.schema
is deprecated: false
has provider formatter: http://eol.org/schema/terms/$1
is part of: Bioregistry
description: Predicates in the Encyclopedia of Life data schema for describing animals, plants, and other organisms
has URI prefix: http://eol.org/schema/terms/

RISM Online
description: RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project.
is deprecated: false
has provider formatter: https://rism.online/$1
is part of: Bioregistry
has resource example: https://rism.online/people/11035
has URI prefix: https://rism.online/
0000005: people/11035
type: Resource
has prefix: rism
has local unique identifier pattern: ^[a-z]+/[0-9]+$

DockerHub User
has provider formatter: https://hub.docker.com/u/$1
contributor: Charles Tapley Hoyt
description: A user in DockerHub
has URI prefix: https://hub.docker.com/u/
type: Resource
has resource example: cthoyt
is deprecated: false
has prefix: dockerhub.user
0000005: cthoyt
is part of: Bioregistry

Proteomics data and process provenance
has download URL: propreo.owl
keyword: proteomics
keyword: owl
has responsible: Satya S. Sahoo
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/PROPREO_
has resource example: PROPREO protein
description: A comprehensive proteomics data and process provenance ontology.
is deprecated: true
keyword: obo
has prefix: propreo
has provider formatter: http://purl.obolibrary.org/obo/PROPREO_$1
keyword: ontology
0000005: protein
is part of: Bioregistry

Gramene Growth Stage Ontology
has provider formatter: http://www.gramene.org/db/ontology/search
has prefix: gramene.growthstage
has resource example: http://www.gramene.org/db/ontology/search
0000005: 0007133
description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.
has alternative prefix: cpga
has alternative prefix: gro-cpga
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^\d{7}$
keyword: anatomy
is deprecated: true
keyword: obo
has URI prefix: http://www.gramene.org/db/ontology/search
keyword: ontology

COI Catalogue
has prefix: coi
contributor: Tanay Shah
has resource example: https://coicatalogue.uc.pt/index.php
has responsible: COI Catalogue
is deprecated: false
is part of: Bioregistry
description: COI Catalogue is a herbarium with c. 800.000 specimens, organised in separate collections due to the research priorities over the years.
has provider formatter: https://coicatalogue.uc.pt/index.php
has URI prefix: https://coicatalogue.uc.pt/index.php
has reviewer: https://orcid.org/0000-0001-9439-5346
0000005: 63812
type: Resource

EndlessForms Studio Image Collections
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: https://images.endlessforms.info/collection/
has responsible: Melissa D Clarkson
has resource example: https://images.endlessforms.info/collection/2
type: Resource
0000005: 2
has provider formatter: https://images.endlessforms.info/collection/$1
description: Collections of images, based on topics, such as the human skull collection
is deprecated: false
has prefix: endlessforms.collection

Apollo Structured Vocabulary
has resource example: APOLLO SV 00000443
type: Resource
keyword: epidemiology
keyword: biomedical science
keyword: pathogen
git repository: apollo-sv
has responsible: William Hogan
appears in: Sickle Cell Disease Ontology
has URI prefix: http://purl.obolibrary.org/obo/APOLLO_SV_
0000005: 00000443
description: An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.
is deprecated: false
has download URL: apollo sv.owl
keyword: obo
keyword: ontology
keyword: population genetics
has local unique identifier pattern: ^\d{8}$
keyword: infection process
has prefix: apollosv
has provider formatter: http://purl.obolibrary.org/obo/APOLLO_SV_$1
is part of: Bioregistry
keyword: ecology

MMsINC
type: Resource
keyword: structure
has resource example: http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php
has reviewer: Charles Tapley Hoyt
has URI prefix: http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php
is deprecated: false
0000005: MMs00000001
description: MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats.
has prefix: mmsinc
keyword: small molecule
is part of: Bioregistry
has provider formatter: http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php

Epilepsy Ontology
depends on: Basic Formal Ontology
keyword: ontology
is deprecated: false
description: A application driven Epilepsy Ontology with official terms from the ILAE.
has prefix: epio
has responsible: Alpha Tom Kodamullil
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/EPIO_
has provider formatter: http://purl.obolibrary.org/obo/EPIO_$1
has download URL: epio.owl
has local unique identifier pattern: ^\d{7}$
has resource example: EPIO_0000011
type: Resource
0000005: 0000011
git repository: EpilepsyOntology
keyword: obo

PANTHER Family
has prefix: panther.family
keyword: ontology
description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families.
keyword: pathway
is deprecated: false
is part of: Bioregistry
keyword: protein
has URI prefix: http://www.pantherdb.org/panther/family.do
has responsible: https://orcid.org/0000-0002-9074-3507
has local unique identifier pattern: ^PTHR\d{5}(\:SF\d{1,3})?$
has resource example: http://www.pantherdb.org/panther/family.do
has provider formatter: http://www.pantherdb.org/panther/family.do
0000005: PTHR12345
type: Resource
keyword: gene
keyword: classification

Tribolium Genome Database -- Insertion
has responsible: https://orcid.org/0000-0002-7984-0445
type: Resource
has prefix: beetlebase
description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.
keyword: life science
has resource example: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/
is deprecated: true
has local unique identifier pattern: ^TC\d+$
has provider formatter: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/
has URI prefix: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/
keyword: genome
0000005: TC010103
keyword: computational biology
is part of: Bioregistry

TIGR protein families
type: Resource
0000005: TIGR00010
has resource example: https://www.ncbi.nlm.nih.gov/cdd
contributor: https://orcid.org/0000-0002-6601-2165
has URI prefix: https://www.ncbi.nlm.nih.gov/cdd
description: TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins.
has provider formatter: https://www.ncbi.nlm.nih.gov/cdd
is deprecated: false
keyword: protein
has prefix: tigrfam
is part of: Bioregistry
has local unique identifier pattern: ^TIGR\d+$

biosimulations
description: BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools.
has provider formatter: https://biosimulations.org/projects/$1
type: Resource
0000005: Yeast-cell-cycle-Irons-J-Theor-Biol-2009
has URI prefix: https://biosimulations.org/projects/
has prefix: biosimulations
is deprecated: false
has resource example: Yeast-cell-cycle-Irons-J-Theor-Biol-2009
has local unique identifier pattern: ^[a-zA-Z0-9_-]{3,}$
is part of: Bioregistry

CESSDA Data Catalogue Collections
is part of: Bioregistry
has resource example: code BY-COVID
type: Resource
contributor: Charles Tapley Hoyt
0000005: BY-COVID
has identifier space owner: 02wg9xc72
is deprecated: false
has prefix: cessda.cessdadatacataloguecollections
description: This vocabulary holds the definitions and descriptions of the collections included in the CESSDA Data Catalogue.
has provider formatter: https://vocabularies.cessda.eu/vocabulary/CESSDADataCatalogueCollections#code_$1
has URI prefix: https://vocabularies.cessda.eu/vocabulary/CESSDADataCatalogueCollections#code_

Ontology of Genetic Susceptibility Factor
keyword: ontology
keyword: adverse reaction
has provider formatter: http://purl.obolibrary.org/obo/OGSF_$1
description: An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.
keyword: genetics
has download URL: ogsf.owl
keyword: disease
has URI prefix: http://purl.obolibrary.org/obo/OGSF_
has responsible: https://orcid.org/0000-0002-5379-5359
is part of: Bioregistry
keyword: genetic disorder
has prefix: ogsf
type: Resource
git repository: OGSF
keyword: epidemiology
keyword: biomedical science
0000005: 0000025
has resource example: OGSF_0000025
has local unique identifier pattern: ^\d{7}$
is deprecated: true
keyword: obo

Yeast Searching for Transcriptional Regulators and Consensus Tracking
description: YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.
is deprecated: false
keyword: dna
keyword: small molecule
keyword: regulation
has provider formatter: http://www.yeastract.com/view.php
is part of: Bioregistry
has URI prefix: http://www.yeastract.com/view.php
0000005: YBR125c
type: Resource
keyword: gene
has reviewer: Charles Tapley Hoyt
has resource example: http://www.yeastract.com/view.php
keyword: life science
has prefix: yeastract
has responsible: Isabel Sá-Correia

Catalogue of Life in Taiwan
has prefix: col.taiwan
description: Identifier (name code) for a taxon in the catalogue of life in taiwan
has local unique identifier pattern: ^[1-9]\d{5}$
is part of: Bioregistry
type: Resource
has provider formatter: https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php
has reviewer: Charles Tapley Hoyt
0000005: 431472
contributor: https://orcid.org/0000-0003-2699-3066
has resource example: https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php
has URI prefix: https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php
is deprecated: false

mirEX
has local unique identifier pattern: ^\d+(\w+)?$
is part of: Bioregistry
has provider formatter: http://comgen.pl/mirex1/
has prefix: mirex
has URI prefix: https://bioregistry.io/mirex:
type: Resource
keyword: life science
description: mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.
has resource example: http://comgen.pl/mirex1/
has responsible: Wojciech M. Karlowski
0000005: 165a
is deprecated: false

Molbase
has resource example: http://www.molbase.com/en/index.php
has URI prefix: http://www.molbase.com/en/index.php
has provider formatter: http://www.molbase.com/en/index.php
type: Resource
has local unique identifier pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$
0000005: 128796-39-4
description: Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier.
has prefix: molbase
is deprecated: false
is part of: Bioregistry

EDAM Data
has prefix: edam.data
type: Resource
has provider formatter: http://edamontology.org/data_$1
is deprecated: false
has resource example: data 1664
has URI prefix: http://edamontology.org/data_
keyword: ontology
description: Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.
has local unique identifier pattern: ^\d+$
git repository: edamontology
is part of: Bioregistry
0000005: 1664
has responsible: https://orcid.org/0000-0002-1509-4981
contributor: Charles Tapley Hoyt
has download URL: EDAM.obo

Austrian Library Network
has provider formatter: https://permalink.obvsg.at/$1
0000005: AC00963334
has resource example: https://permalink.obvsg.at/AC00963334
has URI prefix: https://permalink.obvsg.at/
has prefix: obv
is deprecated: false
has local unique identifier pattern: ^AC[0-9]{8}$
is part of: Bioregistry
description: The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections.
type: Resource

BioTools
has URI prefix: https://bio.tools/
type: Resource
has prefix: biotools
keyword: biomedical science
keyword: biology
has provider formatter: https://bio.tools/$1
has local unique identifier pattern: ^[-A-Za-z0-9\_]*$
has responsible: Hans Ienasescu
has resource example: bioregistry
git repository: biotoolsregistry
is deprecated: false
is part of: Bioregistry
0000005: bioregistry
keyword: bioinformatics
description: BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.

ExAC Gene
has provider formatter: http://exac.broadinstitute.org/gene/$1
type: Resource
0000005: ENSG00000169174
is deprecated: false
has URI prefix: http://exac.broadinstitute.org/gene/
is part of: Bioregistry
has resource example: ENSG00000169174
has prefix: exac.gene
has local unique identifier pattern: ^ENSG\d{11}$
description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.

DBPedia Resource
description: A semi-automatically generated knowledgebase
is part of: Bioregistry
has provider formatter: http://dbpedia.org/resource/$1
contributor: Charles Tapley Hoyt
has alternative prefix: dbr
has URI prefix: http://dbpedia.org/resource/
has resource example: Grenada
0000005: Grenada
type: Resource
has alternative prefix: dbpedia
has prefix: dbpedia.resource
is deprecated: false

Vertebrate Genome Annotation Database
description: A repository for high-quality gene models produced by the manual annotation of vertebrate genomes.
contributor: Charles Tapley Hoyt
is part of: Bioregistry
has responsible: https://orcid.org/0000-0003-0338-3070
type: Resource
has resource example: vega:OTTHUMG00000169812
0000005: OTTHUMG00000169812
has provider formatter: https://bioregistry.io/vega:$1
keyword: life science
has alternative prefix: VEGA
is deprecated: true
keyword: genome
has URI prefix: https://bioregistry.io/vega:
has prefix: vega

NFDI4Culture Ontology
0000005: 0001003
keyword: other subjects
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
type: Resource
contributor: Charles Tapley Hoyt
has URI prefix: https://nfdi4culture.de/ontology/CTO_
keyword: architecture
keyword: nfdi4culture
has provider formatter: https://nfdi4culture.de/ontology/CTO_$1
has resource example: CTO_0001003
description: The NFDI4Culture Ontology (CTO) is a domain-specific ontology module developed within the Task Area 5 of the NFDI4Culture initiative. (from homepage)
has prefix: nfdi4culture.cto
git repository: nfdi4culture
keyword: ontology
has download URL: cto.owl
is deprecated: false

PDBsum; at-a-glance overview of macromolecular structures
has provider formatter: https://www.ebi.ac.uk/pdbsum/$1
0000005: 1kfv
description: PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
is deprecated: false
keyword: protein
has resource example: 1kfv
0000011: PDB Structure
is part of: Bioregistry
has prefix: pdbsum
type: Resource
keyword: structure
keyword: interaction
has URI prefix: https://www.ebi.ac.uk/pdbsum/
keyword: structural biology
has responsible: Roman Laskowski
has reviewer: Charles Tapley Hoyt

FlowRepository
has resource example: FR-FCM-ZYGW
keyword: biology
has provider formatter: http://flowrepository.org/id/$1
keyword: life science
has URI prefix: http://flowrepository.org/id/
has local unique identifier pattern: ^FR\-FCM\-\w{4}$
keyword: cell biology
has prefix: flowrepository
is deprecated: false
description: FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field.
0000005: FR-FCM-ZYGW
has responsible: https://orcid.org/0000-0002-9765-2990
is part of: Bioregistry
type: Resource

Dynamic Ecological Information Management System - Site and Dataset Registry - Dataset
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: https://deims.org/dataset/
description: Datasets in DEIMS SDR
type: Resource
has provider formatter: https://deims.org/dataset/$1
has responsible: Christoph Wohner
has prefix: deims.dataset
is deprecated: false
has local unique identifier pattern: ^[0-9a-f\-]+$

RSNA Informatics RadLex
has resource example: RID1
is deprecated: false
has URI prefix: https://radlex.org/RID/
keyword: ontology
keyword: medical informatics
0000005: RID1
keyword: medical imaging
has prefix: radlex
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^RID\d+$
has provider formatter: https://radlex.org/RID/$1
keyword: diagnosis
type: Resource
keyword: radiology
keyword: clinical studies
has responsible: Radiological Society of North America
keyword: biomedical science
has download URL: radlex.owl
keyword: anatomy
description: A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research. RadLex provides the foundation for vital data resources used in radiology: - The LOINC/RSNA Radiology Playbook - RadElement Common Data Elements -RadReport Radiology Reporting Templates The development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.

Minimum PDDI Information Ontology
git repository: MPIO
has resource example: MPIO_0000004
description: An ontology of minimum information regarding potential drug-drug interaction information.
has local unique identifier pattern: ^\d{7}$
has URI prefix: http://purl.obolibrary.org/obo/MPIO_
type: Resource
has prefix: mpio
0000005: 0000004
has provider formatter: http://purl.obolibrary.org/obo/MPIO_$1
keyword: obo
keyword: ontology
has responsible: https://orcid.org/0000-0003-1834-3856
is deprecated: false
is part of: Bioregistry
has download URL: mpio.owl

Metabolic Encyclopedia for Pathway/Genome Databases
is deprecated: false
has provider formatter: https://metacyc.org/META/NEW-IMAGE
has URI prefix: https://metacyc.org/META/NEW-IMAGE
0000005: 12DICHLORETHDEG-PWY
description: MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data. MetaCyc is [curated](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation) from the scientific experimental literature according to an [extensive process](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)]. The majority of pathways occurring in it are from microorganisms and plants. MetaCyc stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number
has resource example: https://metacyc.org/META/NEW-IMAGE
is part of: Bioregistry
has reviewer: Charles Tapley Hoyt
contributor: 0000-0002-2411-565X
has responsible: https://orcid.org/0000-0002-5876-6418
type: Resource
has prefix: metacyc.pathway

Ontology of Arthropod Circulatory Systems
has local unique identifier pattern: ^\d{7}$
has provider formatter: http://purl.obolibrary.org/obo/OARCS_$1
type: Resource
has download URL: oarcs.owl
has prefix: oarcs
has responsible: Matt Yoder
keyword: angiology
has URI prefix: http://purl.obolibrary.org/obo/OARCS_
description: OArCS is an ontology describing the Arthropod ciruclatory system.
has resource example: OARCS_0000029
keyword: anatomy
is deprecated: false
keyword: obo
keyword: ontology
is part of: Bioregistry
0000005: 0000029
git repository: oarcs

Sol Genomics Network
keyword: comparative genomics
has resource example: http://solgenomics.net/phenome/locus_display.pl
has provider formatter: http://solgenomics.net/phenome/locus_display.pl
has URI prefix: http://solgenomics.net/phenome/locus_display.pl
has prefix: sgn
keyword: pathway
is deprecated: false
has local unique identifier pattern: ^\d+$
keyword: small molecule
is part of: Bioregistry
keyword: genome
keyword: genomics
keyword: botany
keyword: agriculture
keyword: plant
type: Resource
description: The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.
has responsible: Lukas A. Mueller
0000005: 0001

Contributor Roles Taxonomy
keyword: contributor roles
type: Resource
contributor: Charles Tapley Hoyt
keyword: nfdi4ing
0000005: software
description: CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output.
has resource example: software
has responsible: https://orcid.org/0000-0002-9298-3168
keyword: subject agnostic
has local unique identifier pattern: ^(conceptualization|data-curation|formal-analysis|funding-acquisition|investigation|methodology|project-administration|resources|software|supervision|validation|visualization|writing-original-draft|writing-review-editing)$
has download URL: credit.owl
has URI prefix: https://credit.niso.org/contributor-roles/
keyword: classification
keyword: attribution
keyword: ontology
keyword: resource metadata
is deprecated: false
keyword: digital planning and construction
keyword: data quality
keyword: fid baudigital
has prefix: credit
keyword: omics
has provider formatter: https://credit.niso.org/contributor-roles/$1
is part of: Bioregistry
keyword: fid move

Hepatitis C Virus Database Project
has URI prefix: https://euhcvdb.lyon.inserm.fr/euHCVdb/do/displayHCVEntry
description: the European Hepatitis C Virus Database (euHCVdb, euhcvdb.lyon.inserm.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.
has provider formatter: https://euhcvdb.lyon.inserm.fr/euHCVdb/do/displayHCVEntry
has prefix: hcvdb
is deprecated: false
has local unique identifier pattern: ^M\d{5}$
has resource example: https://euhcvdb.lyon.inserm.fr/euHCVdb/do/displayHCVEntry
is part of: Bioregistry
0000005: M58335
type: Resource
keyword: gene

Blue Brain Project Knowledge Graph
has prefix: bbkg
type: Resource
has URI prefix: https://bbp.epfl.ch/nexus/web/studios/public/
is deprecated: true
has provider formatter: https://bbp.epfl.ch/nexus/web/studios/public/$1
has local unique identifier pattern: ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$
is part of: Bioregistry
description: Blue Brain Project's published data as knowledge graphs and Web Studios.

Cell Lines Service
has URI prefix: https://www.cytion.com/
is deprecated: false
0000005: 300108/p3934_A-172
description: Cell line collections (Providers)
is part of: Bioregistry
has resource example: p3934 A-172
has provider formatter: https://www.cytion.com/$1
has prefix: cls
type: Resource

Ascomycete phenotype ontology
has responsible: Stacia R Engel
contributor: https://orcid.org/0000-0002-1216-4761
keyword: mutation
keyword: morphology
keyword: life science
keyword: study design
has prefix: apo
keyword: obo
keyword: cell biology
keyword: ontology
has resource example: APO_0000184
has download URL: apo.owl
is deprecated: false
keyword: life cycle stage
is part of: Bioregistry
keyword: genomics
keyword: phenotype
has provider formatter: http://purl.obolibrary.org/obo/APO_$1
description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi.
keyword: phenomics
has local unique identifier pattern: ^\d{7}$
type: Resource
0000005: 0000184
git repository: ascomycete-phenotype-ontology
has URI prefix: http://purl.obolibrary.org/obo/APO_

Gramene Reference
has prefix: gramene.reference
0000005: 6200
has resource example: http://www.gramene.org/db/literature/pub_search
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: http://www.gramene.org/db/literature/pub_search
contributor: Charles Tapley Hoyt
type: Resource
description: Literature references in Gramene
has provider formatter: http://www.gramene.org/db/literature/pub_search
has alternative prefix: gramene.ref
is deprecated: false

SWEET Ontology Process Physical
has URI prefix: http://sweetontology.net/procPhysical/
type: Resource
has provider formatter: http://sweetontology.net/procPhysical/$1
0000005: Abrasion
has prefix: sweet.procp
is deprecated: false
has resource example: Abrasion
keyword: physical
has alternative prefix: soprocp
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process Physical
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology

Global Trade Alerts Ontology
is deprecated: false
keyword: economics
is part of: Bioregistry
has resource example: AffectedCommercialFlow
description: An ontology for modeling global trade alerts, mainly inspired by the Global Trade Alerts repository.
has provider formatter: https://schema.coypu.org/gta#$1
has prefix: coypu.gta
type: Resource
keyword: coypu
0000005: AffectedCommercialFlow
has URI prefix: https://schema.coypu.org/gta#

Structural Database of Allergenic Proteins
has reviewer: Charles Tapley Hoyt
has prefix: sdap
0000005: 610
has provider formatter: http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02
is deprecated: false
keyword: protein
has resource example: http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02
is part of: Bioregistry
type: Resource
has URI prefix: http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02
keyword: structure
description: SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes.

Gene Ontology Issue Tracker
has provider formatter: https://github.com/geneontology/go-ontology/issues/$1
is deprecated: false
0000005: 23000
has prefix: go.issue
has resource example: https://github.com/geneontology/go-ontology/issues/23000
has URI prefix: https://github.com/geneontology/go-ontology/issues/
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
contributor: Charles Tapley Hoyt
description: An issue on the Gene Ontology GitHub issue tracker

Networked Knowledge Organization Systems/Services/Structures
is deprecated: false
has prefix: nkos
has provider formatter: http://w3id.org/nkos/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
description: NKOS is devoted to the discussion of the functional and data model for enabling knowledge organization systems/services (KOS), such as classification systems, thesauri, gazetteers, and ontologies, as networked interactive information services to support the description and retrieval of diverse information resources through the Internet. Knowledge Organization Systems/Services (KOS) model the underlying semantic structure of a domain. Embodied as Web-based services, they can facilitate resource discovery and retrieval. They act as semantic road maps and make possible a common orientation by indexers and future users (whether human or machine). -- Douglas Tudhope, Traugott Koch (2004).
has URI prefix: http://w3id.org/nkos/
has resource example: alignedWith
0000005: alignedWith

Health Canada Natural Product Number
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has resource example: http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do
type: Resource
has prefix: hc.npn
has provider formatter: http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do
description: The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada.
is deprecated: false
has URI prefix: http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do
0000005: 18125

Functional Requirements for Bibliographic Records
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has responsible: Silvio Peroni
git repository: frbr
has URI prefix: http://purl.org/vocab/frbr/core#
type: Resource
has prefix: frbr
keyword: subject agnostic
description: The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO.
has resource example: Expression
0000005: Expression
keyword: frbr
has provider formatter: http://purl.org/vocab/frbr/core#$1

Modular Ontology Modeling for Food Supply Chains
0000005: Agent
has provider formatter: http://dase.cs.ksu.edu/ontology/food-traceability#$1
description: Modular Ontology Modeling for Food Supply Chains.
has resource example: Agent
has prefix: tib.fto
is deprecated: false
keyword: economics
is part of: Bioregistry
has URI prefix: http://dase.cs.ksu.edu/ontology/food-traceability#
type: Resource
keyword: coypu

PiroplasmaDB
is deprecated: false
is part of: Bioregistry
0000005: TA14985
has provider formatter: http://piroplasmadb.org/piro/showRecord.do
has resource example: http://piroplasmadb.org/piro/showRecord.do
has local unique identifier pattern: ^TA\d+$
type: Resource
description: PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
has URI prefix: http://piroplasmadb.org/piro/showRecord.do
has prefix: piroplasma

Ontology for Modeling and Representation of Social Entities
keyword: health science
description: The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.
type: Resource
keyword: patient care
keyword: obo
has responsible: William Hogan
appears in: clinical LABoratory Ontology
keyword: ontology
is deprecated: false
keyword: social science
has resource example: OMRSE_00000022
has download URL: omrse.owl
has local unique identifier pattern: ^\d{8}$
git repository: OMRSE
keyword: demographics
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/OMRSE_$1
has prefix: omrse
keyword: biomedical science
keyword: hospital
0000005: 00000022
has URI prefix: http://purl.obolibrary.org/obo/OMRSE_

Basic Access Control ontology
is deprecated: false
description: The Basic Access Control ontology describes how access rights (access control) are defined on the web.
has provider formatter: http://www.w3.org/ns/auth/acl#$1
0000005: Access
has URI prefix: http://www.w3.org/ns/auth/acl#
is part of: Bioregistry
type: Resource
has prefix: acl
has resource example: Access
keyword: api

PROV Namespace
has provider formatter: http://www.w3.org/ns/prov#$1
keyword: ontology
description: The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web.
0000005: Activity
is part of: Bioregistry
has URI prefix: http://www.w3.org/ns/prov#
keyword: w3c rec
contributor: Charles Tapley Hoyt
has resource example: Activity
keyword: nfdi4chem
type: Resource
has download URL: prov.owl
keyword: nfdi4ing
has prefix: prov
keyword: ess
is deprecated: false

Chromosome Ontology
0000005: 10090-chr10qC
contributor: Harry Caufield
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
has download URL: chr.owl
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/CHR_
has provider formatter: http://purl.obolibrary.org/obo/CHR_$1
has prefix: chr
is part of: Bioregistry
git repository: monochrom
has resource example: CHR 10090-chr10qC
has reviewer: Charles Tapley Hoyt
description: The Chromosome Ontology is an automatically derived ontology of chromosomes and chromosome parts.
type: Resource

Registry
description: A type for entries in the Bioregistry's metaregistry.
type: Class

Merriam Webster Dictionary
has prefix: merriamwebster
has alternative prefix: merriam_webster
0000005: buccal_gland
has resource example: buccal gland
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: Online Dictionary
type: Resource
has provider formatter: https://www.merriam-webster.com/dictionary/$1
has URI prefix: https://www.merriam-webster.com/dictionary/

Fission Yeast Phenotype Ontology
0000005: 0001707
keyword: life science
is deprecated: false
keyword: obo
has download URL: fypo.owl
has resource example: FYPO_0001707
has provider formatter: http://purl.obolibrary.org/obo/FYPO_$1
keyword: ontology
keyword: genetics
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/FYPO_
keyword: phenotype
git repository: fypo
has responsible: Valerie Wood
keyword: go-term enrichment data
description: A formal ontology of phenotypes observed in fission yeast.
has local unique identifier pattern: ^\d{7}$
has prefix: fypo
type: Resource
keyword: phylogenetics

NCBI Taxonomy
appears in: Plant Gall Ontology
has alternative prefix: taxid
keyword: obo
keyword: ontology
appears in: Agronomy Ontology
appears in: Population and Community Ontology
appears in: Cell Line Ontology
is deprecated: false
keyword: dna
0000005: 2170610
is part of: Bioregistry
keyword: protein
keyword: genomics
has alternative prefix: uniprot.taxonomy
appears in: The Food Ontology
keyword: taxonomic classification
appears in: ChEBI Integrated Role Ontology
has alternative prefix: NCBI_taxid
keyword: omics
keyword: knowledge and information systems
keyword: proteomics
has alternative prefix: TaxonomyID
has alternative prefix: ncbiTaxUID
git repository: ncbitaxon
has provider formatter: http://purl.obolibrary.org/obo/NCBITaxon_$1
has alternative prefix: NCBITaxonomyID
has alternative prefix: NCBI Taxonomy
appears in: Environment Ontology
appears in: Cell Ontology
has download URL: ncbitaxon.owl
keyword: evolutionary biology
type: Resource
appears in: Environmental conditions, treatments and exposures ontology
appears in: Microbial Conditions Ontology
appears in: Vertebrate Breed Ontology
has URI prefix: http://purl.obolibrary.org/obo/NCBITaxon_
keyword: structure
appears in: Health Surveillance Ontology
has alternative prefix: TAX
keyword: biology
keyword: phylogenetics
has resource example: NCBITaxon_2170610
appears in: Uber Anatomy Ontology
keyword: taxonomy
has alternative prefix: NCBITaxon
appears in: Genomic Epidemiology Ontology
has alternative prefix: taxon
keyword: life science
has responsible: https://orcid.org/0000-0003-1839-5322
appears in: Ontology for Nutritional Studies
has identifier space owner: 02meqm098
has local unique identifier pattern: ^(\d+)|([a-zA-Z_]+)$
description: The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.
has prefix: ncbitaxon
has alternative prefix: taxonomy
has alternative prefix: NCBI_Taxon_ID
keyword: classification
appears in: Provisional Cell Ontology
appears in: Gene Ontology

Regulation of Transcription Ontology
keyword: life science
keyword: ontology
has prefix: reto
is deprecated: false
keyword: regulation of gene expression
is part of: Bioregistry
keyword: transcriptomics
keyword: transcript
type: Resource
description: Regulation of Transcription
has download URL: reto.owl

SHACL in SHACL
type: Resource
has prefix: shsh
is deprecated: false
is part of: Bioregistry
description: This shapes graph can be used to validate SHACL shapes graphs against a subset of the syntax rules.
0000005: ListShape

NIF Standard Ontology: External
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nifext_$1
contributor: Tom Gillespie
type: Resource
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nifext_
0000005: 7123
has alternative prefix: NIFEXT
has reviewer: Charles Tapley Hoyt
is deprecated: false
has resource example: nifext 7123
git repository: NIF-Ontology
has responsible: Tom Gillespie
has prefix: nif.ext
description: NIFEXT covers IRIs that were "external" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed.

The Bioinorganic Motif Database
has URI prefix: https://www.flymine.org/come/entry
has prefix: come
type: Resource
has provider formatter: https://www.flymine.org/come/entry
has resource example: https://www.flymine.org/come/entry
is deprecated: false
keyword: protein
description: COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif.
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: MOL000160
has alternative prefix: COMe

BERD@NFDI Collection
creator: Charles Tapley Hoyt
type: Collection
has part: Bioregistry
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for BERD@NFDI

PREFER Ontology
is part of: Bioregistry
type: Resource
has download URL: prefer.owl
description: An ontology for PREcision FERmentation.
has prefix: prefer
0000005: 0000020
keyword: ontology
is deprecated: false

Semantically-Interlinked Online Communities Services Ontology - SWAN Mapping
has provider formatter: http://rdfs.org/sioc/swan#$1
type: Resource
has URI prefix: http://rdfs.org/sioc/swan#
is deprecated: false
0000005: OnlineJournal
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: OnlineJournal
has prefix: sioc.swan
description: Mappings from SIOC to SWAN, with a small number of aux terms

A nomenclatural ontology for biological names
description: NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.
has local unique identifier pattern: ^\d{7}$
has resource example: NOMEN_0000295
is part of: Bioregistry
type: Resource
0000005: 0000295
has responsible: Matt Yoder
has prefix: nomen
keyword: obo
git repository: nomen
keyword: ontology
has download URL: nomen.owl
has provider formatter: http://purl.obolibrary.org/obo/NOMEN_$1
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/NOMEN_

TogoVar
has provider formatter: https://grch38.togovar.org/variant/$1
has resource example: tgv139393198
type: Resource
description: TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them.
has local unique identifier pattern: ^tgv[0-9]+$
0000005: tgv139393198
has URI prefix: https://grch38.togovar.org/variant/
has prefix: togovar
is deprecated: false
is part of: Bioregistry

Experimental condition ontology
0000005: 0000780
keyword: biomedical science
keyword: experimental measurement
has responsible: https://orcid.org/0000-0002-6443-9376
keyword: life science
keyword: study design
has prefix: xco
keyword: experimentally determined
keyword: obo
keyword: measurement
keyword: ontology
appears in: Agronomy Ontology
has download URL: xco.owl
has URI prefix: http://purl.obolibrary.org/obo/XCO_
is deprecated: false
keyword: experimental condition
has provider formatter: http://purl.obolibrary.org/obo/XCO_$1
keyword: assay
is part of: Bioregistry
description: Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.
has local unique identifier pattern: ^\d{7}$
appears in: Environmental conditions, treatments and exposures ontology
has resource example: XCO_0000780
type: Resource
git repository: XCO-experimental-condition-ontology

EDDA Study Designs Taxonomy
keyword: medicine
has provider formatter: http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1
has download URL: edda.owl
has URI prefix: http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#
keyword: ontology
is deprecated: false
is part of: Bioregistry
description: Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries.
has responsible: Tanja Bekhuis
has resource example: health care quality assessment
0000005: health_care_quality_assessment
type: Resource
has prefix: edda

Health Procedure Ontology
description: HEPRO is an ontology of informational entities and processes related to health procedures and health activities.
is deprecated: false
has provider formatter: http://purl.obolibrary.org/obo/HEPRO_$1
has prefix: hepro
git repository: HEPRO
has resource example: HEPRO_0000001
is part of: Bioregistry
has responsible: Paul Fabry
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/HEPRO_
has reviewer: Charles Tapley Hoyt
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
has identifier space owner: 00kybxq39
contributor: Paul Fabry
has download URL: HEPRO.owl
keyword: ontology

European Commission Library Thesaurus
is deprecated: false
has prefix: eclas
is part of: Bioregistry
keyword: literature
keyword: educational resources
type: Resource
0000005: 004.11.00.0100
has URI prefix: http://data.europa.eu/bkc/notation_
description: Dating from 1978 when catalogues of the Central Library of the Commission of the European Communities (now the European Union) were computerised, ECLAS is a thesaurus created by the Central Library of the Commission of the European Communities for indexing the publications and documents acquired by the Central Library of the Commission. ECLAS was based on the Macrothesaurus of OECD and complemented by the ILO thesaurus. After creation of EUROVOC in 1984, convergence started in order to bring ECLAS in line with EUROVOC, but it was never complete. ECLAS contains nineteen areas of interest in a hierarchical tree structure consisting of four levels. ECLAS is fully available in English and in French. The OP COMM ECLAS is maintained by the Publications Office of the European Union on the EU Vocabularies website.
has resource example: notation 004.11.00.0100
has provider formatter: http://data.europa.eu/bkc/notation_$1

Bgee organ
has resource example: http://bgee.unil.ch/bgee/bgee
type: Resource
description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures.
has local unique identifier pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$
is deprecated: true
has URI prefix: http://bgee.unil.ch/bgee/bgee
has prefix: bgee.organ
0000005: EHDAA:2185
is part of: Bioregistry
has provider formatter: http://bgee.unil.ch/bgee/bgee
contributor: 0000-0003-3947-488X

BioCyc collection of metabolic pathway databases
has responsible: https://orcid.org/0000-0002-5876-6418
type: Resource
has provider formatter: http://biocyc.org/getid
has prefix: biocyc
has URI prefix: http://biocyc.org/getid
has resource example: http://biocyc.org/getid
is deprecated: false
keyword: pathway
keyword: sequence
is part of: Bioregistry
keyword: genome
description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.
has local unique identifier pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$
0000005: ECOLI:CYT-D-UBIOX-CPLX

Virus Infectious Disease Ontology
has prefix: vido
0000005: 0001114
has responsible: John Beverly
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/VIDO_
description: The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.
is deprecated: false
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/VIDO_$1
has local unique identifier pattern: ^\d{7}$
has resource example: VIDO_0001114
type: Resource
has download URL: vido.owl
git repository: ido-virus

NIF Dysfunction
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1
type: Resource
has prefix: nif.dysfunction
is deprecated: true
has responsible: Fahim Imam
keyword: obo
has URI prefix: http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_
keyword: ontology

SKOS Thesaurus Extension
0000005: CompoundEquivalence
is deprecated: false
has alternative prefix: skosthes
has resource example: CompoundEquivalence
has prefix: skos.thes
is part of: Bioregistry
has URI prefix: https://www.dublincore.org/specifications/skos-thes/ns/#
has alternative prefix: skos-thes
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: https://www.dublincore.org/specifications/skos-thes/ns/#$1
description: SKOS-Thes: An extension to SKOS based on the ISO 25964 data model. The ISO 25964 standard, published in 2011, covers all aspects of developing thesauri and setting up mappings across vocabularies to encourage high quality information retrieval across networked resources. [from https://www.dublincore.org/specifications/skos-thes/]

FungiDB
has provider formatter: https://fungidb.org/fungidb/app/record/gene/$1
has local unique identifier pattern: ^[A-Za-z_0-9]+$
has prefix: fungidb
type: Resource
description: FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.
has responsible: https://orcid.org/0000-0002-7591-0020
has URI prefix: https://fungidb.org/fungidb/app/record/gene/
0000005: CNBG_0001
has resource example: CNBG_0001
is deprecated: false
is part of: Bioregistry
keyword: genomics

Reaxys eMolecules
is part of: Bioregistry
keyword: reagents
keyword: chemistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
keyword: vendor
has prefix: emolecules
description: Catalog of purchasable reagents and building blocks
type: Resource
has URI prefix: https://reaxys.emolecules.com/cgi-bin/more
has provider formatter: https://reaxys.emolecules.com/cgi-bin/more
0000005: 491187
has resource example: https://reaxys.emolecules.com/cgi-bin/more
is deprecated: false

Human BioMolecular Atlas Program Dataset
is part of: Bioregistry
type: Resource
description: The HuBMAP dataset collection provides high resolution molecular data from human tissues, with unique identifiers that enable tracking, citation, and integration of datasets across diverse assay types and donor samples for biomedical research.
has local unique identifier pattern: ^[a-f0-9]{32}$
has prefix: hubmap.dataset
has URI prefix: https://portal.hubmapconsortium.org/browse/dataset/
has responsible: Katy Börner
has provider formatter: https://portal.hubmapconsortium.org/browse/dataset/$1
is deprecated: false
has reviewer: https://orcid.org/0000-0001-9439-5346
contributor: 0009-0008-8406-631X

Type of Instrument
has URI prefix: https://vocabularies.cessda.eu/vocabulary/TypeOfInstrument#code_
0000005: Questionnaire
description: Includes a typology of data collection instruments.
type: Resource
has prefix: ddi.typeofinstrument
has provider formatter: https://vocabularies.cessda.eu/vocabulary/TypeOfInstrument#code_$1
has identifier space owner: 015em2733
is deprecated: false
has resource example: code Questionnaire
is part of: Bioregistry
contributor: Charles Tapley Hoyt

Decentralized Identifier
type: Resource
0000005: sov:WRfXPg8dantKVubE3HX8pw
has URI prefix: https://uniresolver.io/#did:
is deprecated: false
has prefix: did
has provider formatter: https://uniresolver.io/#did:$1
has resource example: did:sov:WRfXPg8dantKVubE3HX8pw
description: DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary.
has local unique identifier pattern: ^[a-z0-9]+:[A-Za-z0-9.\-:]+$
is part of: Bioregistry

SUPERFAMILY
has provider formatter: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi
0000005: SSF57615
keyword: classification
has local unique identifier pattern: ^\w+$
has responsible: Arun Prasad Pandurangan
is deprecated: false
keyword: genome
keyword: protein
is part of: Bioregistry
type: Resource
keyword: structure
has prefix: supfam
has resource example: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi
has URI prefix: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi
description: SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt.

Insect Cell Line Database
description: We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated from crop pest insects. Cell line information has been primarily obtained from previous compilations of insect cell lines. (from homepage)
has responsible: Surjeet Kumar Arya
is deprecated: false
has prefix: icldb
has provider formatter: https://entomology.ca.uky.edu/content/$1
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has URI prefix: https://entomology.ca.uky.edu/content/
0000005: 64ba
has resource example: 64ba

WiCell Research Institute Cell Collection
has resource example: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/ai10e-kctd13b.cmsx
is deprecated: false
has URI prefix: https://bioregistry.io/wicell:
description: Cell line collections (Providers)
has provider formatter: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx
is part of: Bioregistry
0000005: ai10e-kctd13b
has prefix: wicell
type: Resource

MEROPS Entry
keyword: enzyme
description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors.
has provider formatter: https://www.ebi.ac.uk/merops/cgi-bin/pepsum
has prefix: merops.entry
is deprecated: false
keyword: protein
has alternative prefix: merops.inhibitor
has URI prefix: https://www.ebi.ac.uk/merops/cgi-bin/pepsum
has resource example: https://www.ebi.ac.uk/merops/cgi-bin/pepsum
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^[SCTAGMNUIX]{1,2}\d{2}\.([AB]\d{2}|\d{3})$
keyword: structure
keyword: biomedical science
has responsible: Neil D Rawlings
0000005: I31.952
keyword: life science

LIPID MAPS
has resource example: http://www.lipidmaps.org/data/LMSDRecord.php
has local unique identifier pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$
type: Resource
keyword: structure
keyword: lipid
keyword: biomedical science
has alternative prefix: LIPID_MAPS_instance
keyword: systems biology
keyword: taxonomy
keyword: life science
is deprecated: false
has responsible: https://orcid.org/0000-0003-3738-3140
keyword: endocrinology
has alternative prefix: LIPID MAPS
is part of: Bioregistry
has prefix: lipidmaps
has alternative prefix: LIPID_MAPS_class
has provider formatter: http://www.lipidmaps.org/data/LMSDRecord.php
description: The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.
0000005: LMPR0102010012
has URI prefix: http://www.lipidmaps.org/data/LMSDRecord.php

The Ageing Gene Database
has URI prefix: http://genomics.senescence.info/genes/details.php
keyword: longevity
type: Resource
description: GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group.
0000005: 0001
has reviewer: Charles Tapley Hoyt
has provider formatter: http://genomics.senescence.info/genes/details.php
has responsible: https://orcid.org/0000-0002-6363-2465
is deprecated: false
has resource example: http://genomics.senescence.info/genes/details.php
is part of: Bioregistry
has prefix: hagr.genage
keyword: genes
keyword: aging

SitEx
0000005: 1000
has provider formatter: http://www-bionet.sscc.ru/sitex/index.php
keyword: structure
description: SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.
is deprecated: true
has responsible: Irina Medvedeva
keyword: life science
keyword: domain
keyword: eukaryotic
has prefix: sitex
keyword: sequence
has resource example: http://www-bionet.sscc.ru/sitex/index.php
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has URI prefix: http://www-bionet.sscc.ru/sitex/index.php
type: Resource

GlycomeDB
type: Resource
keyword: life science
has resource example: G77500AY
has prefix: glycomedb
keyword: molecules
has canonical: GlyTouCan
has provider formatter: https://glytoucan.org/Structures/Glycans/$1
description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.
is deprecated: false
has local unique identifier pattern: ^\w+$
0000005: G77500AY
is part of: Bioregistry
has responsible: 0000-0003-3147-448X
has URI prefix: https://glytoucan.org/Structures/Glycans/
keyword: structure
keyword: small molecules

SWEET Ontology Realm Astrophysical Heliosphere
has URI prefix: http://sweetontology.net/realmAstroHelio/
has prefix: sweet.reaah
type: Resource
is deprecated: false
has alternative prefix: soreaah
keyword: astrophysical heliosphere
0000005: DLayer
is part of: Bioregistry
has provider formatter: http://sweetontology.net/realmAstroHelio/$1
contributor: Charles Tapley Hoyt
git repository: sweet
has resource example: DLayer
keyword: realm
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Astrophysical Heliosphere

Agronomy Ontology
has provider formatter: http://purl.obolibrary.org/obo/AGRO_$1
keyword: farming systems research
depends on: Phenotype And Trait Ontology
depends on: Ontology for Biomedical Investigations
description: AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities
keyword: agriculture
has responsible: Marie-Angélique Laporte
depends on: Gene Ontology
keyword: agronomy
0000005: 00020007
type: Resource
depends on: Experimental condition ontology
has download URL: agro.owl
depends on: Plant Ontology
depends on: NCBI Taxonomy
keyword: plant breeding
depends on: Basic Formal Ontology
keyword: cropping systems
depends on: Plant Trait Ontology
contributor: https://orcid.org/0000-0002-1216-4761
depends on: The Food Ontology
has resource example: AGRO_00020007
keyword: obo
depends on: Plant Experimental Conditions Ontology
git repository: agro
has local unique identifier pattern: ^\d{8}$
has URI prefix: http://purl.obolibrary.org/obo/AGRO_
depends on: Environment Ontology
depends on: Relation Ontology
keyword: ontology
has prefix: agro
is deprecated: false
is part of: Bioregistry
depends on: Information Artifact Ontology
keyword: dataplant
depends on: Units of measurement ontology

BioPortal
has responsible: John Graybeal
type: Resource
is deprecated: true
description: BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.
has local unique identifier pattern: ^(\d+)|(\w+)$
keyword: life science
git repository: ncbo
keyword: ontology and terminology
keyword: ontology
has prefix: bioportal
is part of: Bioregistry
has URI prefix: http://bioportal.bioontology.org/ontologies/
has provider formatter: http://bioportal.bioontology.org/ontologies/$1
0000005: 1046
has resource example: http://bioportal.bioontology.org/ontologies/1046

NCBI Genetic Code
description: Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
contributor: Charles Tapley Hoyt
has alternative prefix: gc
has alternative prefix: gc_id
has URI prefix: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi#SG
has responsible: Andrzej Elzanowski
has provider formatter: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi#SG$1
has download URL: ncbi.gc.owl
0000005: 11
keyword: ontology
keyword: genome
keyword: genetic code
is deprecated: false
has resource example: SG11
has prefix: ncbi.gc

BiGG Model
keyword: ontology
has resource example: iECABU c1320
has URI prefix: http://bigg.ucsd.edu/models/
keyword: pathway
has prefix: bigg.model
is deprecated: false
0000005: iECABU_c1320
keyword: metabolic model
is part of: Bioregistry
description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.
has responsible: https://orcid.org/0000-0003-1238-1499
type: Resource
has local unique identifier pattern: ^[a-z_A-Z0-9]+$
has download URL: bigg.model.owl
has provider formatter: http://bigg.ucsd.edu/models/$1

Endogenous Regulatory OligoPeptide knowledgebase-Moscow
description: EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.).
is deprecated: false
keyword: protein
has prefix: eropmoscow
has provider formatter: http://erop.inbi.ras.ru/result2.php
has resource example: http://erop.inbi.ras.ru/result2.php
is part of: Bioregistry
type: Resource
has reviewer: Charles Tapley Hoyt
has URI prefix: http://erop.inbi.ras.ru/result2.php
0000005: E00002

PhenX Toolkit
has resource example: https://www.phenxtoolkit.org/protocols/view/130502
keyword: environmental science
is deprecated: false
keyword: life science
has prefix: phenx
0000005: 130502
keyword: ontology
is part of: Bioregistry
has alternative prefix: phenxtoolkit
keyword: disease
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
keyword: phenotype
has responsible: PhenX Admin
has download URL: phenx.owl
has URI prefix: https://www.phenxtoolkit.org/protocols/view/
description: A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants.
has provider formatter: https://www.phenxtoolkit.org/protocols/view/$1
type: Resource
keyword: biomedical science
keyword: exposure

ISO 15926-14
contributor: Charles Tapley Hoyt
has URI prefix: http://standards.iso.org/iso/15926/part14/
type: Resource
has provider formatter: http://standards.iso.org/iso/15926/part14/$1
has resource example: activityBoundOf
0000005: activityBoundOf
description: The primary purpose of ISO 15926 is to provide a foundation ontology to support the integration and sharing of data related to the lifecycle of a process plant in such a way that it is consistent, unambiguous, and minimizing the number of ways something could be expressed. Further purpose of ISO 15926-14 is to meet needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient reasoning and that capture lifecycle information. A specific purpose is to demonstrate lifecycle modelling through a representation of the lifecycle model of ISO/IEC 81346-1. Another specific purpose is to exemplify how this standard can be used to develop industrial ontologies through various real-world use cases from industry. (from https://nfdi4cat.org/services/ontologie-sammlung/)
has prefix: iso15926
is deprecated: false
is part of: Bioregistry

UniProt Resource
has resource example: DB-0174
has responsible: Alex Bateman
has local unique identifier pattern: ^DB-\d{4}$
0000005: DB-0174
has alternative prefix: uniprot.database
is deprecated: false
has provider formatter: https://www.uniprot.org/database/$1
is part of: Bioregistry
description: The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources.
has alternative prefix: uniprot.db
has URI prefix: https://www.uniprot.org/database/
has prefix: uniprot.resource
contributor: Charles Tapley Hoyt
type: Resource

SWEET Ontology Property Fraction
has prefix: sweet.propfr
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Fraction
is part of: Bioregistry
git repository: sweet
has alternative prefix: sopropfr
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: fraction
has resource example: Absorptance
type: Resource
0000005: Absorptance
has provider formatter: http://sweetontology.net/propFraction/$1
has URI prefix: http://sweetontology.net/propFraction/
is deprecated: false

Ontology of Adverse Events
type: Resource
has responsible: Yongqun Oliver He
keyword: biomedical science
has resource example: OAE_0002959
git repository: OAE
0000005: 0002959
has local unique identifier pattern: ^\d{7}$
keyword: drug
has prefix: oae
has provider formatter: http://purl.obolibrary.org/obo/OAE_$1
keyword: obo
keyword: adverse reaction
keyword: ontology
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/OAE_
description: The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.
is part of: Bioregistry
has download URL: oae.owl
keyword: vaccine

Type of Frequency
is part of: Bioregistry
description: Indicates the frequency of data collection events.
contributor: Charles Tapley Hoyt
0000005: Continuous
has resource example: code Continuous
type: Resource
has identifier space owner: 015em2733
is deprecated: false
has prefix: ddi.typeoffrequency
has provider formatter: https://vocabularies.cessda.eu/vocabulary/TypeOfFrequency#code_$1
has URI prefix: https://vocabularies.cessda.eu/vocabulary/TypeOfFrequency#code_

SWEET Ontology Material Rock
has resource example: Breccia
is deprecated: false
has provider formatter: http://sweetontology.net/matrRock/$1
has alternative prefix: somarock
has URI prefix: http://sweetontology.net/matrRock/
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: materials
keyword: rock
0000005: Breccia
has prefix: sweet.marock
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Rock

SED-ML data format
has local unique identifier pattern: ^[a-z]+(\..*?)?$
has resource example: format:csv
description: Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).
is deprecated: false
has prefix: sedml.format
has provider formatter: https://sed-ml.org/urns.html#format:$1
is part of: Bioregistry
has URI prefix: https://sed-ml.org/urns.html#format:
0000005: csv
type: Resource

BacDive
has resource example: https://bacdive.dsmz.de/strain/131392
has URI prefix: https://bacdive.dsmz.de/strain/
type: Resource
keyword: microbiology
has local unique identifier pattern: ^[0-9]+$
has responsible: Lorenz Reimer
0000005: 131392
keyword: life science
is deprecated: false
description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.
keyword: biodiversity
has prefix: bacdive
is part of: Bioregistry
has provider formatter: https://bacdive.dsmz.de/strain/$1

SWEET Ontology Property Space Thickness
has provider formatter: http://sweetontology.net/propSpaceThickness/$1
is deprecated: false
has URI prefix: http://sweetontology.net/propSpaceThickness/
has prefix: sweet.propst
has alternative prefix: sopropst
is part of: Bioregistry
has resource example: AverageAnnualPrecipitation
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Thickness
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: space thickness
0000005: AverageAnnualPrecipitation

NFDI4Chem Collection
has part: Physico-chemical process
has part: SupraBank Additive
has part: Experimental Factor Ontology
has part: eNanoMapper ontology
has part: EDAM Ontology
has part: FAIR Vocabulary
has part: NCI Thesaurus
has part: Chemical Information Ontology
creator: https://orcid.org/0000-0002-1595-3213
has part: Semanticscience Integrated Ontology
has part: ChEBI Integrated Role Ontology
has part: Time Ontology in OWL
has part: Physico-chemical methods and properties
has part: Sensor, Observation, Sample, and Actuator Ontology
has part: Software ontology
has part: Gainesville Core Ontology
has part: Environment Ontology
has part: REPRODUCE-ME Ontology
has part: Relation Ontology
has part: Data Use Ontology
has part: Computational Chemistry Ontology
has part: OntoRXN
has part: SupraBank Solvent
has part: Allotrope Merged Ontology Suite
has part: Information Artifact Ontology
has part: SupraBank Interaction
has part: OntoSpecies - Chemical Species Ontology for Data Integration and Knowledge Discovery
has part: Semantic Sensor Network Ontology
has part: Scientific Evidence and Provenance Information Ontology
has part: Units of measurement ontology
has part: Name Reaction Ontology
type: Collection
has part: Ontology for Biomedical Investigations
has part: Mass spectrometry ontology
has part: Molecular Process Ontology
has part: Phenotype And Trait Ontology
has part: BRENDA Tissue Ontology
has part: The Extensible Observation Ontology
has part: Ontology for Chemical Kinetic Reaction Mechanisms
has part: Vibrational Spectroscopy Ontology
has part: Ontology of units of Measure
has part: Chemical Entities of Biological Interest
has part: NMR-instrument specific component of metabolomics investigations
has part: PROV Namespace
has part: SupraBank Buffer
has part: Protein modification
has part: System capabilities, operating ranges, and survival ranges ontology
has part: Process Chemistry Ontology
has part: Chemical Entity Materials and Reactions Ontological Framework
has part: Chemical Methods Ontology
has part: A vocabulary for the catalysis disciplines
has part: Basic Formal Ontology
description: A collection of ontologies relevant within the [NFDI4Chem project](https://www.nfdi4chem.de/) that is mostly based on the overview paper [Ontologies4Chem: the landscape of ontologies in chemistry](https://doi.org/10.1515/pac-2021-2007). NFDI4Chem deploys a [custom instance](https://terminology.nfdi4chem.de/ts/) of the Ontology Lookup Service (OLS), called NFDI4Chem Terminology Services (TS), that provides the ontologies in this list. This list contains ontologies that cover various domains of chemistry (e.g. ChEBI, CHMO, and RXNO), those that are dependencies of these chemistry specific ontologies (e.g. BFO, RO, IAO, and OBI) as well as those ontologies, which where indexed in the NFDI4Chem TS for interoperability research purposes (e.g. PROV-O, SOSA, and OBOE).
has part: SupraBank Molecule

The Audio Commons Ontology
type: Resource
has provider formatter: https://w3id.org/ac-ontology/aco#$1
description: The Audio Commons Ontology has been created in the context of the European project [Audio Commons](https://www.audiocommons.org/), which were aimed at favouring sharing and reuse of audio content (both of musical and non-musical nature), specially using [Creative Commons](https://creativecommons.org/) licenses. It is designed specifically to integrate access to multiple heterogeneously structured audio content providers. In particular the following ones have been considered in the project: - [Freesound](https://freesound.org/), a collaborative database of Creative Commons Licensed sounds; - [Jamendo](https://www.jamendo.com/), a music website for independent artists; - [Europeana Sounds](https://www.eusounds.eu/), a European project collecting and sharing data from several archives of sounds and sound-related media; - [Internet Archive](https://archive.org/), a non-profit library of millions of freely accessible media contents. ### The base model ![A diagram showing the entities Work, Expression, Manifestation, Item](./img/FRBR-Group-1-entities-and-basic-relations.svg.png) The Audio Commons ontology is based on [Functional Requirements for Bibliographic Records (FRBR)](https://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records), a bibliographic model designed for user tasks of retrieval and access in online library catalogues and bibliographic databases. FRBR distinguish the products of intellectual or artistic endeavor in four main classes: work, expression, manifestation, item. It is available as RDF vocabulary at https://vocab.org/frbr/core. For further information on FRBR, check the [standard](https://repository.ifla.org/handle/123456789/811). Another important model related to audio is the [Music Ontology](http://musicontology.com/), which is also based on the FRBR model. Our ontology is more generic than the Music Ontology but is interoperable with it to support the specificities of music-related audio content. The Audio Commons ontology w…
has prefix: tib.n0
keyword: nfdi4ing
0000005: AnalogSignal
has resource example: AnalogSignal
is deprecated: false
is part of: Bioregistry
keyword: engineering
has URI prefix: https://w3id.org/ac-ontology/aco#

SWEET Ontology Phenomena
0000005: AirSeaExchange
keyword: phenomena
is deprecated: false
has provider formatter: http://sweetontology.net/phen/$1
is part of: Bioregistry
has prefix: sweet.ph
has URI prefix: http://sweetontology.net/phen/
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has alternative prefix: soph
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena
type: Resource
has resource example: AirSeaExchange

Glycosciences.DB
has responsible: Thomas Lütteke
type: Resource
has alternative prefix: glycosciences.db
has prefix: glycosciencesdb
has resource example: http://www.glycosciences.de/database/start.php
has provider formatter: http://www.glycosciences.de/database/start.php
has reviewer: Charles Tapley Hoyt
has URI prefix: http://www.glycosciences.de/database/start.php
0000005: 1
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates.
contributor: https://orcid.org/0000-0002-6601-2165

NMR-instrument specific component of metabolomics investigations
is deprecated: true
keyword: nmr
has resource example: https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms
git repository: nmrCV
keyword: obo
description: nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi.
keyword: ontology
keyword: chemical and environmental engineering
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: chemistry
has alternative prefix: nmrcv
has prefix: nmr
keyword: nfdi4chem
has download URL: nmrCV.owl
keyword: owl
0000005: 1000003
has provider formatter: https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms
has URI prefix: https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms
type: Resource
has responsible: https://orcid.org/0000-0001-8014-6648

SWEET Ontology State Solid
has URI prefix: http://sweetontology.net/stateSolid/
is deprecated: false
has prefix: sweet.stso
0000005: SolidState
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has alternative prefix: sostso
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Solid
has resource example: SolidState
keyword: state solid
has provider formatter: http://sweetontology.net/stateSolid/$1

Curriculum Course Syllabus Ontology
keyword: curriculum
is part of: Bioregistry
keyword: open educational resources
contributor: Charles Tapley Hoyt
has URI prefix: https://w3id.org/ccso/ccso#
type: Resource
0000005: AcademicStaff
description: CCSO is an educational ontology acting as a data model for concepts and entities within an academic setting, enabling also the annotation of potentially available resources. The ontology aims to conceptualize educational entities within Curriculum and Syllabus with appropriate coverage and quality, in order to support rich services on top for improving curriculum management and automatically enabling syllabus semantic processes. (from homepage)
has provider formatter: https://w3id.org/ccso/ccso#$1
keyword: education
has download URL: CCSO 071owl.owl
git repository: CCSO
keyword: oer
keyword: curricula
keyword: ontology
has resource example: AcademicStaff
is deprecated: false
has prefix: ccso
keyword: oers

SWEET Ontology Material Plant
has resource example: Branch
has prefix: sweet.mapl
is part of: Bioregistry
keyword: plant
has provider formatter: http://sweetontology.net/matrPlant/$1
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
keyword: materials
0000005: Branch
is deprecated: false
has URI prefix: http://sweetontology.net/matrPlant/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Plant
has alternative prefix: somapl

Bio-Pesticides DataBase
keyword: pesticides
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has resource example: 2404.htm
contributor: Charles Tapley Hoyt
has prefix: bpdb
keyword: biology
has provider formatter: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm
keyword: biopesticides
has URI prefix: https://bioregistry.io/bpdb:
is deprecated: false
0000005: 2404
description: Database of biopesticides maintained by the University of Hertfordshire

EDCC Taxonomy
has resource example: c 00098e55
is deprecated: false
has URI prefix: http://data.europa.eu/ett/kos/c_
keyword: educational resources
description: EDCC Taxonomy contains the terms that are used to classify citizens' requests to the Europe Direct Contact Centre (EDCC). EDCC Taxonomy is maintained by the Directorate-General for Communication of the European Commission and published by the Publications Office of the European Union on the EU Vocabularies website.
is part of: Bioregistry
has provider formatter: http://data.europa.eu/ett/kos/c_$1
has prefix: edcc
type: Resource
0000005: 00098e55

FAIR Vocabulary
keyword: computer science
description: This is the formal vocabulary (ontology) describing the FAIR principles.
is deprecated: false
has prefix: fair
keyword: digital planning and construction
is part of: Bioregistry
has resource example: FAIR
keyword: fid baudigital
keyword: nfdi4chem
keyword: fid move
has URI prefix: https://w3id.org/fair/principles/terms/
has provider formatter: https://w3id.org/fair/principles/terms/$1
type: Resource
keyword: nfdi4ing
0000005: FAIR

Continuous Automated Model Evaluation
keyword: life science
has prefix: cameo
0000005: 2019-08-03_00000089_1
is deprecated: false
is part of: Bioregistry
description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB.
has responsible: 0000-0003-2715-335X
has resource example: 2019-08-03 00000089 1
type: Resource
has URI prefix: https://www.cameo3d.org/sp/targets/target/
has local unique identifier pattern: ^[0-9\-_]+$
has provider formatter: https://www.cameo3d.org/sp/targets/target/$1

SpBase
has prefix: spbase
is deprecated: true
keyword: rna
description: SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases.
keyword: genome
keyword: dna
is part of: Bioregistry
type: Resource
has URI prefix: http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php
has resource example: http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php
0000005: SPU_000001
has reviewer: Charles Tapley Hoyt
has provider formatter: http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php

SWEET Ontology Representation
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation
has provider formatter: http://sweetontology.net/repr/$1
0000005: CardinalScale
has prefix: sweet.rep
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: CardinalScale
has alternative prefix: sorep
keyword: representation
is deprecated: false
has URI prefix: http://sweetontology.net/repr/

Tribology Ontology for Artificial Intelligence
git repository: tribAIn
keyword: nfdi4ing
has prefix: tribain
0000005: 100Cr6
type: Resource
is deprecated: false
has provider formatter: http://ktmfk.de/ontology/tribAIn/$1
description: The tribAIn1 ontology aims to formalize knowledge gained from tribological experiments for reuse, comparison and documentation. Therefore, the tribAin ontology provides concepts for the specification of methodological background knowledge of experimental design, the documentation of the experimental setup and the representation of different kinds of results (e.g. measurements series, analysis, interpretation in natural-language). Using the EXPO2 (ontology of scientific experiments) as basis, gives tribAIn a generic background about scientific experimental design, methodology and results representation.
keyword: engineering
has resource example: 100Cr6
has URI prefix: http://ktmfk.de/ontology/tribAIn/
is part of: Bioregistry

Ontology for simulation, modelling, and optimization
is deprecated: true
description: OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/)
has resource example: application case
0000005: application_case
keyword: nfdi4cat
has prefix: nfdi4chem.osmo
is part of: Bioregistry
type: Resource
keyword: material science
contributor: Charles Tapley Hoyt
has provider formatter: https://purl.org/vimmp/osmo#$1
has URI prefix: https://purl.org/vimmp/osmo#
keyword: computer science

WikiPathways Types
is part of: Bioregistry
has URI prefix: http://vocabularies.wikipathways.org/wpTypes#
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: http://vocabularies.wikipathways.org/wpTypes#$1
has download URL: wpTypes.owl
description: Types used in WikiPathways RDF
has responsible: Tim Vandermeersch
git repository: WpVocabularies
keyword: ontology
has alternative prefix: wptypes
has prefix: wikipathways.type
is deprecated: false
has alternative prefix: wikipathways.types
has resource example: Arrow
0000005: Arrow

Gleaning Resource Descriptions from Dialects of Languages
0000005: transformation
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
description: GRDDL is a mechanism for Gleaning Resource Descriptions from Dialects of Languages. It is a technique for obtaining RDF data from XML documents and in particular XHTML pages. Authors may explicitly associate documents with transformation algorithms, typically represented in XSLT, using a link element in the head of the document. Alternatively, the information needed to obtain the transformation may be held in an associated metadata profile document or namespace document. Clients reading the document can follow links across the Web using techniques described in the GRDDL specification to discover the appropriate transformations. This document uses a number of examples from the GRDDL Use Cases document to illustrate, in detail, the techniques GRDDL provides for associating documents with appropriate instructions for extracting any embedded data. (from homepage)
has provider formatter: http://www.w3.org/2003/g/data-view#$1
keyword: vocabularies
has resource example: transformation
has prefix: grddl
is deprecated: false
has URI prefix: http://www.w3.org/2003/g/data-view#

NCBI Protein
0000005: CAA71118.1
is part of: Bioregistry
has local unique identifier pattern: ^\w+_?\d+(.\d+)?$
keyword: protein
has URI prefix: https://www.ncbi.nlm.nih.gov/protein/
has provider formatter: https://www.ncbi.nlm.nih.gov/protein/$1
has prefix: ncbiprotein
description: The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
type: Resource
has resource example: CAA71118.1
is deprecated: false
has identifier space owner: 02meqm098

3D Metabolites
0000005: B00162
has resource example: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php
has URI prefix: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php
description: 3DMET is a database collecting three-dimensional structures of natural metabolites.
keyword: metabolomics
keyword: chemical
is part of: Bioregistry
keyword: metabolite
type: Resource
keyword: structure
has alternative prefix: 3dmet
has local unique identifier pattern: ^B\d{5}$
keyword: life science
has prefix: _3dmet
is deprecated: true
has provider formatter: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php

Dublin Core Types
has download URL: dcmitype.owl
has resource example: Collection
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has alternative prefix: dcmitype
has URI prefix: http://purl.org/dc/dcmitype/
has responsible: Kim Durante
has alternative prefix: dcmitypes
0000005: Collection
has provider formatter: http://purl.org/dc/dcmitype/$1
keyword: ontology
description: This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.
is deprecated: false
has prefix: dctypes

KEGG Disease
is part of: Bioregistry
has prefix: kegg.disease
type: Resource
is part of: Kyoto Encyclopedia of Genes and Genomes
0000005: H00076
has provider formatter: http://www.kegg.jp/entry/$1
keyword: classification
has resource example: H00076
has URI prefix: http://www.kegg.jp/entry/
is deprecated: false
has local unique identifier pattern: ^H\d+$
description: The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.

International Classifications of Diseases
has part: International Classification of Diseases, 9th Revision
type: Collection
has part: International Classification of Diseases, 9th Revision, Clinical Modification
has part: International Classification of Diseases, 10th Revision, Procedure Coding System
creator: Charles Tapley Hoyt
has part: International Classification of Diseases, 10th Revision, Clinical Modification
description: This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions.
has part: International Classification of Diseases, 11th Revision (Foundation Component)
has part: International Classification of Diseases, 10th Revision
has part: International Classification of Diseases for Oncology
has part: ICD 11 Codes

G-Rich Sequences Database
has resource example: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php
description: GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.
is deprecated: true
keyword: rna
keyword: dna
has local unique identifier pattern: ^\d+$
has provider formatter: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php
is part of: Bioregistry
has URI prefix: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php
0000005: 10142
has prefix: grsdb
type: Resource

SWEET Ontology State Storm
has prefix: sweet.stst
keyword: state storm
is deprecated: false
has alternative prefix: sostst
has provider formatter: http://sweetontology.net/stateStorm/$1
0000005: BeaufortScale
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Storm
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has URI prefix: http://sweetontology.net/stateStorm/
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: BeaufortScale

The Software Description Ontology
0000005: CatalogIdentifier
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
has URI prefix: https://w3id.org/okn/o/sd#
has resource example: CatalogIdentifier
keyword: computer science
git repository: SoftwareDescriptionOntology
has provider formatter: https://w3id.org/okn/o/sd#$1
is deprecated: false
description: An ontology for describing software components, including their metadata (attribution, licensing, usage instructions, how to get support) and their inputs, outputs and variables. The ontology extends schema.org and codemeta vocabularies and is based on OntoSoft, which proposed a vocabulary for describing software by asking scientists questions.
has prefix: okn.sd
has responsible: https://orcid.org/0000-0003-0454-7145

Genetic Testing Registry
contributor: Charles Tapley Hoyt
has provider formatter: https://www.ncbi.nlm.nih.gov/gtr/conditions/$1
0000005: AN0097748
has prefix: gtr.condition
description: The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease
appears in: Mondo Disease Ontology
type: Resource
has URI prefix: https://www.ncbi.nlm.nih.gov/gtr/conditions/
has resource example: AN0097748
has alternative prefix: medgen.gtr
is deprecated: false
is part of: Bioregistry
has alternative prefix: gtr

Research Resource Identifiers
has part: VDRC
type: Registry
has part: IMSR EM
has part: RGD
has part: DGGR
has part: MGI
has part: SCR
has part: NSRRC
has part: CVCL
has part: BDSC
has part: RRRC
has part: Addgene
0000007: https://scicrunch.org/resolver/RRID:$1_$2
has part: SAMN
has part: FlyBase
has part: TSC
has part: IMSR RBRC
has part: MMRRC
0000005: AB
has part: AB
has responsible: https://orcid.org/0000-0002-5497-0243
has part: IMSR APB
has part: BCBC
has part: IMSR JAX
has part: ZIRC
has part: NXR
has part: AGSC
description: The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools
has part: IMSR TAC
has part: WB-STRAIN:WBStrain

Horizon Discovery cell line collection
has provider formatter: https://horizondiscovery.com/en/search
has prefix: horizon_discovery
0000005: HD+118-001
description: Cell line collections (Providers)
is part of: Bioregistry
has resource example: https://horizondiscovery.com/en/search
has URI prefix: https://horizondiscovery.com/en/search
type: Resource
is deprecated: false

Ontology for General Medical Science
has prefix: ogms
is part of: Bioregistry
keyword: disease
has download URL: ogms.owl
has resource example: OGMS_0000031
keyword: diagnosis
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: cancer
has responsible: https://orcid.org/0000-0003-1346-1327
keyword: biomedical science
appears in: clinical LABoratory Ontology
has URI prefix: http://purl.obolibrary.org/obo/OGMS_
keyword: disease phenotype
appears in: Sickle Cell Disease Ontology
description: The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.
has provider formatter: http://purl.obolibrary.org/obo/OGMS_$1
has alternative prefix: ogms/OMRE
keyword: medicine
is deprecated: false
keyword: obo
git repository: ogms
0000005: 0000031
keyword: ontology

Genomic Data Commons Data Portal
has provider formatter: https://portal.gdc.cancer.gov/cases/$1
has URI prefix: https://portal.gdc.cancer.gov/cases/
is deprecated: false
is part of: Bioregistry
description: The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.
has local unique identifier pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$
type: Resource
has prefix: gdc

DrugBank Metabolite
description: Metabolites in drugbank
0000005: DBMET02292
has prefix: drugbank.metabolite
has URI prefix: https://go.drugbank.com/metabolites/
is deprecated: false
is part of: Bioregistry
has resource example: DBMET02292
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^DBMET\d+$
type: Resource
has responsible: David Wishart
has provider formatter: https://go.drugbank.com/metabolites/$1

Genomics Cohorts Knowledge Ontology
has local unique identifier pattern: ^\d{7}$
has provider formatter: http://purl.obolibrary.org/obo/GECKO_$1
type: Resource
has responsible: https://orcid.org/0000-0003-4871-5569
0000005: 0000044
has prefix: gecko
keyword: experimental measurement
git repository: GECKO
keyword: life science
keyword: obo
has resource example: GECKO_0000044
keyword: ontology
keyword: biospecimen
description: An ontology to represent genomics cohort attributes.
is deprecated: false
keyword: statistics
is part of: Bioregistry
keyword: genomics
has URI prefix: http://purl.obolibrary.org/obo/GECKO_
has download URL: gecko.owl

Dynamic Ecological Information Management System - Site and Dataset Registry - Activity
type: Resource
has prefix: deims.activity
description: Activities in DEIMS SDR
has URI prefix: https://deims.org/activity/
is deprecated: false
has local unique identifier pattern: ^[0-9a-f\-]+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://deims.org/activity/$1
has responsible: Christoph Wohner

Beet Ontology
keyword: phenotype
description: This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution and breeding company within the project. Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Beet Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
keyword: botany
keyword: agriculture
has responsible: Elizabeth Arnaud
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: https://cropontology.org/rdf/CO_333:$1
has prefix: co_333
type: Resource
git repository: Crop-Ontology
has URI prefix: https://cropontology.org/rdf/CO_333:
0000005: 3000045
keyword: plant breeding
keyword: life science
keyword: food
keyword: ontology
is deprecated: false
keyword: plant phenotypes and traits
has resource example: CO 333:3000045
has download URL: CO 333.owl

Gender, Sex, and Sexual Orientation Ontology
keyword: obo
has resource example: GSSO_002368
appears in: Sickle Cell Disease Ontology
keyword: ontology
appears in: Ontology for Avida digital evolution platform
git repository: GSSO
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/GSSO_
has responsible: Clair Kronk
has provider formatter: http://purl.obolibrary.org/obo/GSSO_$1
has download URL: gsso.owl
is part of: Bioregistry
description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology.
0000005: 002368
has local unique identifier pattern: ^\d{6}$
has prefix: gsso
type: Resource

ClinVar Submission
has local unique identifier pattern: ^SCV\d+(\.\d+)?$
0000005: SCV000151292
is deprecated: false
is part of: Bioregistry
has resource example: http://www.ncbi.nlm.nih.gov/clinvar
has URI prefix: http://www.ncbi.nlm.nih.gov/clinvar
type: Resource
has provider formatter: http://www.ncbi.nlm.nih.gov/clinvar
has prefix: clinvar.submission
description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.

Fachsystematik LinSearch
is part of: Bioregistry
has resource example: arc
description: Fächer für die LinSearch-Fachzuordnung
has provider formatter: https://purl.org/linsearch/$1
type: Resource
keyword: computer science
has URI prefix: https://purl.org/linsearch/
git repository: annif automated indexing at tib
0000005: arc
keyword: miscellaneous
has prefix: tib.linsearch
is deprecated: false

Animal Genome Size Database
has URI prefix: http://www.genomesize.com/result_species.php
has reviewer: Charles Tapley Hoyt
0000005: 4779
keyword: life science
description: A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources.
has resource example: http://www.genomesize.com/result_species.php
has provider formatter: http://www.genomesize.com/result_species.php
contributor: https://orcid.org/0000-0002-1216-4761
is deprecated: false
keyword: dna
keyword: genome
has prefix: agsd
is part of: Bioregistry
type: Resource

Medical Dictionary for Regulatory Activities Terminology
has prefix: meddra
has resource example: https://bioportal.bioontology.org/ontologies/MEDDRA
has alternative prefix: Medical Dictionary for Regulatory Activities
has URI prefix: https://bioportal.bioontology.org/ontologies/MEDDRA
keyword: preclinical studies
type: Resource
keyword: biomedical science
has alternative prefix: MEDRA
has alternative prefix: MedDRA
keyword: medicine
description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).
is deprecated: false
has responsible: MedDRA MSSO
has alternative prefix: MeDRA
has provider formatter: https://bioportal.bioontology.org/ontologies/MEDDRA
keyword: ontology
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: disease
0000005: 10015919

EC number
has URI prefix: https://www.echa.europa.eu/information-on-chemicals/ec-inventory/-/dislist/details/
0000005: 200-003-9
has prefix: ecn
is deprecated: false
has resource example: https://www.echa.europa.eu/information-on-chemicals/ec-inventory/-/dislist/details/200-003-9
has provider formatter: https://www.echa.europa.eu/information-on-chemicals/ec-inventory/-/dislist/details/$1
description: identifier for a chemical compound per EINECS or ELINCS
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^\d{3}-\d{3}-\d$
type: Resource

Medical Action Ontology
depends on: Information Artifact Ontology
is deprecated: false
depends on: Neuro Behavior Ontology
is part of: Bioregistry
has resource example: MAXO_0000008
has URI prefix: http://purl.obolibrary.org/obo/MAXO_
depends on: Ontology for Biomedical Investigations
depends on: Human Phenotype Ontology
depends on: Uber Anatomy Ontology
has provider formatter: http://purl.obolibrary.org/obo/MAXO_$1
has local unique identifier pattern: ^\d{7}$
appears in: Environmental conditions, treatments and exposures ontology
depends on: Chemical Entities of Biological Interest
depends on: Gene Ontology
type: Resource
keyword: medicine
has prefix: maxo
has responsible: https://orcid.org/0000-0001-7941-2961
git repository: MAxO
depends on: The Food Ontology
description: An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations.
has download URL: maxo.owl
keyword: obo
keyword: rare disorder
keyword: ontology
depends on: Relation Ontology
0000005: 0000008

Dewey Decimal Classification
has provider formatter: http://dewey.info/class/$1/e23/
type: Resource
description: The Dewey Decimal Classification (DDC) system, devised by library pioneer Melvil Dewey in the 1870s and owned by OCLC since 1988, provides a dynamic structure for the organization of library collections. Now in its 23rd edition, and available in print and Web versions, the DDC is the world's most widely used library classification system.
has URI prefix: https://bioregistry.io/ddc:
0000005: 325.4
has resource example: e23
has local unique identifier pattern: ^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\.[0-9]+(-[0-9]{3}\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$
is deprecated: false
has prefix: ddc
is part of: Bioregistry
contributor: Charles Tapley Hoyt

Commonality Type
has resource example: code Identical
has prefix: ddi.commonalitytype
is part of: Bioregistry
description: Describes the degree of similarity between two items or schemes (collections of items).
has provider formatter: https://vocabularies.cessda.eu/vocabulary/CommonalityType#code_$1
contributor: Charles Tapley Hoyt
has URI prefix: https://vocabularies.cessda.eu/vocabulary/CommonalityType#code_
type: Resource
0000005: Identical
has identifier space owner: 015em2733
is deprecated: false

Retail Energy Market of Great Britain
git repository: GBEnergy
is deprecated: false
is part of: Bioregistry
has provider formatter: https://www.lidcast.co.uk/ontologies/RE#$1
has prefix: tib.re
has resource example: Advanced Meter
0000005: Advanced_Meter
keyword: nfdi4energy
type: Resource
has URI prefix: https://www.lidcast.co.uk/ontologies/RE#
description: An ontology of the Retail Energy Market of Great Britain created by Lidcast Data Limited.

Maggot
0000005: frim1
has prefix: maggot
is part of: Bioregistry
has local unique identifier pattern: ^[A-Za-z0-9]+$
has URI prefix: https://pmb-bordeaux.fr/maggot/metadata/
description: Sharing descriptive Metadata is the first essential step towards Open Scientific Data. With this in mind, Maggot was specifically designed to annotate datasets by creating a metadata file to attach to the storage space. Indeed, it allows users to easily add descriptive metadata to datasets produced within a collective of people (research unit, platform, multi-partner project, etc.). This approach fits perfectly into a data management plan as it addresses the issues of data organization and documentation, data storage and frictionless metadata sharing within this same collective and beyond.
type: Resource
has provider formatter: https://pmb-bordeaux.fr/maggot/metadata/$1
has resource example: frim1
is deprecated: false

SWEET Ontology Property Chemical
keyword: chemical
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Chemical
is part of: Bioregistry
has provider formatter: http://sweetontology.net/propChemical/$1
type: Resource
has URI prefix: http://sweetontology.net/propChemical/
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
0000005: Abundance
has resource example: Abundance
has prefix: sweet.propche
has alternative prefix: sopropche
is deprecated: false

FlyBase Controlled Vocabulary
has prefix: fbcv
keyword: obo
keyword: ontology
has download URL: fbcv.owl
has responsible: Clare Pilgrim
appears in: Ontology for Avida digital evolution platform
git repository: flybase-controlled-vocabulary
keyword: expression data
is deprecated: false
keyword: phenotype
has provider formatter: http://purl.obolibrary.org/obo/FBcv_$1
description: A structured controlled vocabulary used for various aspects of annotation by FlyBase.
has alternative prefix: FBcv
is part of: Bioregistry
has resource example: FBcv_0000586
has part: Drosophila Phenotype Ontology
keyword: descriptor
type: Resource
keyword: fly
has URI prefix: http://purl.obolibrary.org/obo/FBcv_
0000005: 0000586
has local unique identifier pattern: ^\d{7}$
keyword: life science

Standard-Thesaurus Wirtschaft
has prefix: zbw.stw
is deprecated: false
0000005: n
has resource example: http://zbw.eu/stw/thsys/n
description: Der Thesaurus enthält Vokabular zu allen ökonomischen Themenstellungen: über 6.000 Schlagwörter und über 28.000 zusätzliche Synonyme als Zugangshilfe, um individuelle Formulierungen bei der Suche aufzufangen. Auch Fachbegriffe aus benachbarten Bereichen wie z.B. Recht, Soziologie oder Politik sowie Geobegriffe sind dort zu finden. Wenn Sie Schlagwörter aus diesem Vokabular auswählen, können Sie sicher sein Treffer zu erhalten, die zu dem gewünschten Sachgebiet passen. [from homepage]
keyword: economics
is part of: Bioregistry
has provider formatter: http://zbw.eu/stw/thsys/$1
contributor: Charles Tapley Hoyt
keyword: educational resources
keyword: nfdi4energy
type: Resource
has URI prefix: http://zbw.eu/stw/thsys/

CTD Chemical
is deprecated: false
0000005: D001151
is part of: Bioregistry
has provider formatter: http://ctdbase.org/detail.go
has prefix: ctd.chemical
type: Resource
has URI prefix: http://ctdbase.org/detail.go
has local unique identifier pattern: ^[CD]\d+$
description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.
0000011: Medical Subject Headings
has resource example: http://ctdbase.org/detail.go

CRISPRdb
is part of: Bioregistry
description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data.
has provider formatter: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi
type: Resource
has prefix: crisprdb
has responsible: 0000-0002-8951-466X
has local unique identifier pattern: ^[0-9]+$
0000005: 551115
keyword: life science
has URI prefix: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi
has resource example: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi
is deprecated: false

ICEberg family
has provider formatter: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php
is deprecated: false
has resource example: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php
has URI prefix: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php
0000005: 1
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.
type: Resource
has prefix: iceberg.family
has responsible: Hong-Yu Ou

Computer Retrieval of Information on Science Projects Thesaurus
has alternative prefix: CRISP Thesaurus
has alternative prefix: CSP2005
is part of: Bioregistry
has prefix: csp
type: Resource
keyword: biomedical science
keyword: biology
keyword: anatomy
keyword: medicine
is deprecated: true
0000005: 2004-2820
description: CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains. Note that while still available and included in Unified Medical Language System (UMLS), it has not been updated since 2006.
keyword: food
has alternative prefix: CRISP Thesaurus, 2006
has alternative prefix: CRISP
has URI prefix: http://purl.bioontology.org/ontology/CSP/
keyword: ontology
has resource example: http://purl.bioontology.org/ontology/CSP/2004-2820
keyword: chemical biology
has provider formatter: http://purl.bioontology.org/ontology/CSP/$1
keyword: disease
keyword: social science

LncBook
is part of: Bioregistry
has provider formatter: https://ngdc.cncb.ac.cn/lncbook/gene
description: LncBook accommodates a high-quality collection of human lncRNA genes and transcripts, and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional signatures of lncRNAs in human diseases and different biological contexts.
type: Resource
0000005: HSALNG0006197
has URI prefix: https://ngdc.cncb.ac.cn/lncbook/gene
is deprecated: false
has resource example: https://ngdc.cncb.ac.cn/lncbook/gene
has local unique identifier pattern: ^HSALNG\d{7}$
has prefix: lncbook

SEED Subsystem
has alternative prefix: seed
has resource example: https://pubseed.theseed.org/SubsysEditor.cgi
type: Resource
is deprecated: true
description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.
has provider formatter: https://pubseed.theseed.org/SubsysEditor.cgi
has URI prefix: https://pubseed.theseed.org/SubsysEditor.cgi
0000005: Biotin_biosynthesis
contributor: https://orcid.org/0000-0002-7674-5194
contributor: https://orcid.org/0000-0003-1982-9065
has prefix: seed.subsystem
has local unique identifier pattern: ^\w+$
git repository: TheSEED
is part of: Bioregistry

Pathguide
has part: http://www.pathguide.org/fullrecord.php
type: Registry
description: Pathguide contains information about 702 biological pathway related resources and molecular interaction related resources. Click on a link to go to the resource home page or 'Details' for a description page. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated. (from homepage)
0000005: 235
has responsible: https://orcid.org/0000-0003-0185-8861
has provider formatter: http://www.pathguide.org/fullrecord.php

WormBase RNAi
is deprecated: false
has resource example: WBRNAi00086878
0000005: WBRNAi00086878
has prefix: wb.rnai
is part of: Bioregistry
type: Resource
has provider formatter: https://www.wormbase.org/species/c_elegans/rnai/$1
has local unique identifier pattern: ^WBRNAi\d{8}$
description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.
has URI prefix: https://www.wormbase.org/species/c_elegans/rnai/

GND ID
keyword: culture
has local unique identifier pattern: ^[0-9X\-]+$
is deprecated: false
has resource example: https://lobid.org/gnd/117145750
keyword: social science
keyword: knowledge and information systems
0000005: 117145750
is part of: Bioregistry
has provider formatter: https://lobid.org/gnd/$1
type: Resource
description: The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners.
has prefix: gnd
has URI prefix: https://lobid.org/gnd/

SubtiWiki
keyword: life science
has URI prefix: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/
is deprecated: false
has prefix: subtiwiki
has provider formatter: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1
has responsible: https://orcid.org/0000-0001-5881-5390
keyword: rna
description: SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon.
keyword: dna
is part of: Bioregistry
keyword: protein
has local unique identifier pattern: ^BSU\d{5}$
0000005: BSU29180
has resource example: BSU29180
type: Resource
keyword: gene

e-Rad researcher number
description: identifier for researchers in Japan used in government-based research funding (from 1980s)
keyword: person
keyword: researcher
type: Resource
has provider formatter: https://nrid.nii.ac.jp/ja/nrid/10000$1
has local unique identifier pattern: ^\d{8}$
is deprecated: false
has URI prefix: https://nrid.nii.ac.jp/ja/nrid/10000
0000005: 00011461
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: https://nrid.nii.ac.jp/ja/nrid/1000000011461
has prefix: kaken

NeuroLex Anatomy
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has resource example: nlx anat 090201
description: NLXANAT covers anatomy terms. Almost all terms are also in Uberon.
has reviewer: Charles Tapley Hoyt
keyword: anatomy
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1
0000005: 090201
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_anat_
has prefix: nlx.anat
has responsible: Tom Gillespie

The Ecosystem Ontology
has provider formatter: http://purl.dataone.org/odo/ECSO_$1
keyword: earth sciences
has prefix: ecso
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
git repository: sem-prov-ontologies
keyword: earth science
keyword: ecosystem science
has URI prefix: http://purl.dataone.org/odo/ECSO_
keyword: ess
keyword: fair data spaces
has download URL: d1-ECSO.owl
keyword: ontology
keyword: chemical and environmental engineering
is deprecated: false
has responsible: Bryce Mecum
keyword: ecosystem
0000005: 00000532
description: DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases
has resource example: ECSO_00000532

Multum MediSource Lexicon
0000005: 3355
is deprecated: false
is part of: Bioregistry
has alternative prefix: MMSL_CODE
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
description: The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included.
type: Resource
has prefix: mmsl

Mouse Developmental Anatomy Ontology
has resource example: EMAPA_26753
keyword: anatomy
description: An ontology for mouse anatomy covering embryonic development and postnatal stages.
has download URL: emapa.owl
keyword: obo
keyword: animal organ development
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/EMAPA_$1
has responsible: https://orcid.org/0000-0002-0956-8634
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: developmental biology
git repository: developmental-mouse-anatomy-ontology
keyword: bioinformatics
has alternative prefix: EMAPA_RETIRED
keyword: gene expression
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/EMAPA_
0000005: 26753
has prefix: emapa

NIF Standard Ontology: Digital Resources
is deprecated: false
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_res_
git repository: NIF-Ontology
has alternative prefix: NLXRES
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_res_$1
has resource example: nlx res 090924
0000005: 090924
has responsible: Tom Gillespie
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
keyword: software and information systems
has reviewer: Charles Tapley Hoyt
contributor: Tom Gillespie
has prefix: nlx.res
description: NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites

CCDC Number
has resource example: https://www.ccdc.cam.ac.uk/services/structures
has provider formatter: https://www.ccdc.cam.ac.uk/services/structures
description: The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC.
has prefix: ccdc
has local unique identifier pattern: ^\d{6,7}$
is deprecated: false
is part of: Bioregistry
0000005: 1829126
type: Resource
has URI prefix: https://bioregistry.io/ccdc:

GESAH Graphic Arts Ontology
has prefix: gesah
has URI prefix: http://ontology.tib.eu/gesah/
is deprecated: false
is part of: Bioregistry
description: The GESAH Graphic Arts Ontology is designed for the inventory, classification and structured description of works on paper.
has provider formatter: http://ontology.tib.eu/gesah/$1
type: Resource
0000005: applies_to
keyword: architecture
has resource example: applies to
keyword: nfdi4culture
keyword: history

Mobilome Ontology
0000005: 0000001
description: The Mobilome Ontology describes bacterial mobile genetic elements, their mechanisms, and associated epidemiology.
has download URL: mobio.owl
has prefix: mobio
keyword: ontology
is deprecated: false
has resource example: MOBIO_0000001
has provider formatter: http://purl.obolibrary.org/obo/MOBIO_$1
has URI prefix: http://purl.obolibrary.org/obo/MOBIO_
git repository: mobio
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

Silvio Tosatto
label: Silvio C.E. Tosatto

Theiler Stage
has URI prefix: https://www.emouseatlas.org/emap/ema/DAOAnatomyJSP/anatomy.html
0000005: 23
appears in: Mouse Developmental Anatomy Ontology with Theiler Stage
has reviewer: Charles Tapley Hoyt
appears in: Mouse Developmental Stages
description: Theiler stages (TS) define mouse development by a set of morphological criteria ([Theiler, 1989](https://doi.org/10.1007/978-3-642-88418-4)). This staging scheme is used because embryos at the same gestational age can have developed at different rates and therefore exhibit different morphological characteristics. Theiler stages may in some cases correspond to a single gestation age, but more often cover a range of ages. (from [https://www.informatics.jax.org/glossary/theiler](https://www.informatics.jax.org/glossary/theiler))
has resource example: https://www.emouseatlas.org/emap/ema/DAOAnatomyJSP/anatomy.html
has provider formatter: https://www.emouseatlas.org/emap/ema/DAOAnatomyJSP/anatomy.html
has alternative prefix: thielerstage
is deprecated: false
has local unique identifier pattern: ^\d+[a-d]?$
has responsible: https://orcid.org/0000-0002-0956-8634
has prefix: theiler
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

EDAM Format
0000005: 1915
has provider formatter: http://edamontology.org/format_$1
has resource example: format 1915
type: Resource
has prefix: edam.format
has URI prefix: http://edamontology.org/format_
keyword: ontology
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has responsible: https://orcid.org/0000-0002-1509-4981
contributor: Charles Tapley Hoyt
has download URL: EDAM.obo
description: A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.
git repository: edamontology

PhosphoSite Curation
has resource example: https://www.phosphosite.org/curatedInfoAction.action
has URI prefix: https://www.phosphosite.org/curatedInfoAction.action
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has reviewer: Charles Tapley Hoyt
has provider formatter: https://www.phosphosite.org/curatedInfoAction.action
description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to curation records that collect information extracted from specific publications.
0000005: 34665743
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has prefix: phosphosite.curation

SWEET Ontology Relationships Scientific
has provider formatter: http://sweetontology.net/relaSci/$1
is deprecated: false
0000005: causedBy
has prefix: sweet.relsc
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has URI prefix: http://sweetontology.net/relaSci/
has resource example: causedBy
has alternative prefix: sorelsc
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Scientific
type: Resource
keyword: scientific

VegBank
has URI prefix: http://vegbank.org/cite/
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^VB\.[A-Za-z][A-Za-z]\..*$
has prefix: vegbank
0000005: VB.Ob.3736.GRSM125
description: VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited.
type: Resource
has provider formatter: http://vegbank.org/cite/$1
has resource example: VB.Ob.3736.GRSM125

A Knowledge Resource for Innate Immunity Interactions and Pathways
is deprecated: false
keyword: protein
has resource example: http://www.innatedb.ca/getGeneCard.do
has URI prefix: http://www.innatedb.ca/getGeneCard.do
is part of: Bioregistry
0000005: 20021
type: Resource
keyword: gene
keyword: interaction
has provider formatter: http://www.innatedb.ca/getGeneCard.do
has reviewer: Charles Tapley Hoyt
keyword: life science
has responsible: David Lynn
description: InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation.
keyword: immunology
has prefix: innatedb
keyword: pathway

Drosophila gross anatomy
description: An ontology representing the gross anatomy of Drosophila melanogaster.
has resource example: FBbt_00007294
has responsible: Clare Pilgrim
has download URL: fbbt.owl
has alternative prefix: FBbt_root
keyword: anatomy
has URI prefix: http://purl.obolibrary.org/obo/FBbt_
keyword: life science
has provider formatter: http://purl.obolibrary.org/obo/FBbt_$1
keyword: obo
keyword: ontology
has local unique identifier pattern: ^\d{8}$
has prefix: fbbt
git repository: drosophila-anatomy-developmental-ontology
keyword: life cycle stage
is deprecated: false
is part of: Bioregistry
keyword: developmental biology
has alternative prefix: FBbt
0000005: 00007294
keyword: phenotype
keyword: gene expression
type: Resource
keyword: fly

MatrixDB
has provider formatter: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort
0000005: MULT_4_VAR1_bovine
description: MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
keyword: interaction
keyword: biology
has responsible: Sylvie Ricard-Blum
has URI prefix: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort
has prefix: matrixdb
appears in: Complex Portal
has resource example: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort
keyword: small molecule
is deprecated: false
contributor: https://orcid.org/0000-0001-7456-0594
keyword: protein

SWEET Ontology Property Dimensionless Ratio
is deprecated: false
has resource example: BowenRatio
0000005: BowenRatio
has URI prefix: http://sweetontology.net/propDimensionlessRatio/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Dimensionless Ratio
keyword: dimensionless ratio
has provider formatter: http://sweetontology.net/propDimensionlessRatio/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.propdr
has alternative prefix: sopropdr

Metabolomics Workbench Project
has local unique identifier pattern: ^PR[0-9]{6}$
0000005: PR000001
is deprecated: false
has resource example: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php
has prefix: mw.project
is part of: Bioregistry
type: Resource
has URI prefix: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php
description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).
has provider formatter: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php

EDAM Operation
description: A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.
git repository: edamontology
is part of: Bioregistry
has URI prefix: http://edamontology.org/operation_
contributor: Charles Tapley Hoyt
type: Resource
has resource example: operation_0004
has prefix: edam.operation
0000005: 0004
keyword: ontology
is deprecated: false
has local unique identifier pattern: ^\d+$
has responsible: https://orcid.org/0000-0002-1509-4981
has download URL: EDAM.obo
has provider formatter: http://edamontology.org/operation_$1

Informed Consent Ontology
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/ICO_$1
type: Resource
has responsible: Yongqun Oliver He
git repository: ICO
has URI prefix: http://purl.obolibrary.org/obo/ICO_
keyword: clinical studies
keyword: biomedical science
has local unique identifier pattern: ^\d{7}$
keyword: health science
has resource example: ICO_0000066
keyword: medicine
has prefix: ico
0000005: 0000066
keyword: obo
appears in: Sickle Cell Disease Ontology
keyword: ontology
has download URL: ico.owl
is deprecated: false
description: The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.

Amazon Standard Identification Number
description: Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue.
contributor: https://orcid.org/0000-0002-1216-4761
has prefix: asin
0000005: 0471491039
is deprecated: false
is part of: Bioregistry
has URI prefix: https://amzn.com/
has provider formatter: https://amzn.com/$1
has local unique identifier pattern: ^[0-9]{10}$
has resource example: https://amzn.com/0471491039
type: Resource

CESSDA Persistent Identifier Types
is part of: Bioregistry
0000005: ARK
contributor: Charles Tapley Hoyt
type: Resource
has identifier space owner: 02wg9xc72
has provider formatter: https://vocabularies.cessda.eu/vocabulary/CessdaPersistentIdentifierTypes#code_$1
has URI prefix: https://vocabularies.cessda.eu/vocabulary/CessdaPersistentIdentifierTypes#code_
has prefix: cessda.cessdapersistentidentifiertypes
description: Lists the types of persistent identifiers that CESSDA accepts as study level PIDs in its data catalogue.
is deprecated: false
has resource example: code ARK

Social Science Research Network Author
keyword: person
is part of: Bioregistry
keyword: researcher
has resource example: https://ssrn.com/author=112517
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^[1-9]\d{0,6}$
0000005: 112517
type: Resource
description: identifier for an author at the Social Science Research Network
has URI prefix: https://ssrn.com/author=
is deprecated: false
has provider formatter: https://ssrn.com/author=$1
has prefix: ssrn.author

Gene Ontology Registry
has provider formatter: https://bioregistry.io/metaregistry/go/$1
contributor: Charles Tapley Hoyt
description: A database-specific registry supporting curation in the Gene Ontology
type: Resource
has URI prefix: https://bioregistry.io/metaregistry/go/
has prefix: go.resource
is deprecated: false
has resource example: CHEBI
0000005: CHEBI
is part of: Bioregistry

Ontology for Nutritional Epidemiology
keyword: epidemiology
has download URL: one.owl
has responsible: https://orcid.org/0000-0001-9202-5309
keyword: nutritional science
has provider formatter: http://purl.obolibrary.org/obo/ONE_$1
depends on: The Food Ontology
is deprecated: false
has prefix: one
has URI prefix: http://purl.obolibrary.org/obo/ONE_
has resource example: ONE_0001021
keyword: obo
keyword: ontology
description: An ontology to standardize research output of nutritional epidemiologic studies.
is part of: Bioregistry
git repository: Nutritional-epidemiologic-ontologies
keyword: metabolomics
depends on: Ontology for Biomedical Investigations
0000005: 0001021
depends on: Ontology for Nutritional Studies
has local unique identifier pattern: ^\d{7}$
type: Resource

Genotype Ontology
has local unique identifier pattern: ^\d{7}$
has prefix: geno
type: Resource
has download URL: geno.owl
0000005: 0000632
has responsible: Matthew Brush
keyword: disease phenotype
has resource example: GENO_0000632
keyword: genotype
keyword: obo
git repository: GENO-ontology
keyword: ontology
is deprecated: false
is part of: Bioregistry
description: GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013
keyword: genomics
has provider formatter: http://purl.obolibrary.org/obo/GENO_$1
has URI prefix: http://purl.obolibrary.org/obo/GENO_

AntWeb
has provider formatter: http://www.antweb.org/specimen.do
keyword: anatomy
type: Resource
0000005: casent0106247
keyword: life science
has local unique identifier pattern: ^casent\d+(\-D\d+)?$
has prefix: antweb
keyword: classification
has URI prefix: http://www.antweb.org/specimen.do
is deprecated: false
has resource example: http://www.antweb.org/specimen.do
is part of: Bioregistry
description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.

Protocol for Web Description Resources (POWDER): POWDER-S Vocabulary
has resource example: structure
0000005: structure
has URI prefix: http://www.w3.org/2007/05/powder-s#
has provider formatter: http://www.w3.org/2007/05/powder-s#$1
description: The Protocol for Web Description Resources (POWDER) allows metadata to be associated with groups of resources such as those found on a Web site. Its main 'unit of information' is the Description Resource (DR), one or more of which are contained in a POWDER document. Processing such a document yields RDF triples describing the resources that are within the scope of the DRs. POWDER documents are written in XML and have relatively loose semantics, however, a GRDDL transform, associated with the root namespace, renders the data in RDF/OWL with more formal semantics. [from homepage]
keyword: api
is deprecated: false
has prefix: wdrs
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

Brachiaria Ontology
description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Brachiaria Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
keyword: life science
is deprecated: false
has download URL: CO 345.owl
keyword: ontology
has responsible: Elizabeth Arnaud
keyword: plant phenotypes and traits
is part of: Bioregistry
keyword: phenotype
git repository: Crop-Ontology
keyword: botany
0000005: 0000127
keyword: agriculture
has URI prefix: https://cropontology.org/rdf/CO_345:
has prefix: co_345
has local unique identifier pattern: ^\d{7}$
type: Resource
has resource example: CO 345:0000127
has provider formatter: https://cropontology.org/rdf/CO_345:$1

European Nucleotide Archive
has URI prefix: https://www.ebi.ac.uk/ena/browser/view/
has prefix: ena.embl
description: The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers.
is deprecated: false
keyword: biodiversity
keyword: genomics
keyword: dna
has canonical: International Nucleotide Sequence Database Collaboration (INSDC) Run
keyword: bioinformatics
has responsible: https://orcid.org/0000-0001-7954-7057
has resource example: BN000065
keyword: functional genomics
is part of: Bioregistry
keyword: transcriptomics
type: Resource
0000005: BN000065
has alternative prefix: ena
has provider formatter: https://www.ebi.ac.uk/ena/browser/view/$1
has local unique identifier pattern: ^[A-Z]+[0-9]+(\.\d+)?$
keyword: metagenomics
has identifier space owner: 02catss52
keyword: data management

Gene Ontology Annotation Database
0000011: UniProt Protein
is part of: Bioregistry
keyword: protein
has prefix: goa
has responsible: Rachael P. Huntley
has resource example: https://www.ebi.ac.uk/QuickGO/GProtein
has URI prefix: https://www.ebi.ac.uk/QuickGO/GProtein
type: Resource
keyword: gene
description: The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.
keyword: biology
0000005: P12345
keyword: life science
is deprecated: false
has provider formatter: https://www.ebi.ac.uk/QuickGO/GProtein
has local unique identifier pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$
keyword: ontology

Simple Knowledge Organization System
keyword: w3c rec
has prefix: skos
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
keyword: computer science
keyword: subject agnostic
has resource example: prefLabel
has download URL: skos.owl
description: SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web
keyword: miscellaneous
0000005: prefLabel
has responsible: https://orcid.org/0000-0001-9018-4680
has URI prefix: http://www.w3.org/2004/02/skos/core#
keyword: ontology
is deprecated: false
has provider formatter: http://www.w3.org/2004/02/skos/core#$1

Porifera Ontology
is part of: Bioregistry
keyword: phylogeny
type: Resource
depends on: Uber Anatomy Ontology
has download URL: poro.owl
has local unique identifier pattern: ^\d{7}$
keyword: anatomy
keyword: taxonomy
has provider formatter: http://purl.obolibrary.org/obo/PORO_$1
has URI prefix: http://purl.obolibrary.org/obo/PORO_
git repository: porifera-ontology
keyword: obo
appears in: Plant Gall Ontology
keyword: ontology
has prefix: poro
is deprecated: false
0000005: 0000550
has resource example: PORO_0000550
has responsible: https://orcid.org/0000-0002-9654-0073
keyword: taxonomic classification
description: An ontology describing the anatomical structures and characteristics of Porifera (sponges)
depends on: Relation Ontology

BitterDB Compound
0000005: 46
type: Resource
description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.
is deprecated: false
has resource example: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php
is part of: Bioregistry
has URI prefix: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php
has local unique identifier pattern: ^\d+$
has provider formatter: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php
has prefix: bitterdb.cpd

BioNumbers
has prefix: bionumbers
has URI prefix: https://bionumbers.hms.harvard.edu/bionumber.aspx
has provider formatter: https://bionumbers.hms.harvard.edu/bionumber.aspx
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has resource example: https://bionumbers.hms.harvard.edu/bionumber.aspx
type: Resource
0000005: 104674
description: BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data.
is deprecated: false

Animal Genome Sheep QTL
description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs.
has resource example: https://www.animalgenome.org/QTLdb/q
has URI prefix: https://www.animalgenome.org/QTLdb/q
is deprecated: false
0000005: 19803
is part of: Bioregistry
keyword: genome
keyword: dna
has local unique identifier pattern: ^\d+$
has prefix: sheepqtldb
type: Resource
has provider formatter: https://www.animalgenome.org/QTLdb/q
is part of: Animal Genome QTL

Suggested Ontology for Pharmacogenomics
description: SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.
has URI prefix: http://purl.obolibrary.org/obo/SOPHARM_
has responsible: Adrien Coulet
type: Resource
is deprecated: true
keyword: obo
has download URL: sopharm.owl
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/SOPHARM_$1
is part of: Bioregistry
has prefix: sopharm

Key Performance Indicator ontology
type: Resource
description: The Key Performance Indicator module aims to model the metrics defined at the beginning of building renovation activities to monitor the conformance with typical requirements related to energy efficient buildings.
keyword: nfdi4ing
has resource example: Goal
keyword: computer science
keyword: civil engineering
has prefix: kpio
is deprecated: false
keyword: digital planning and construction
has provider formatter: http://bimerr.iot.linkeddata.es/def/key-performance-indicator#$1
keyword: fid baudigital
has URI prefix: http://bimerr.iot.linkeddata.es/def/key-performance-indicator#
is part of: Bioregistry
0000005: Goal

The Cert Ontology
0000005: Certificate
is deprecated: false
keyword: quality
description: Ontology for Certificates and crypto stuff.
has prefix: cert
is part of: Bioregistry
type: Resource

MedGen Concept Unique ID
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has responsible: Megan S. Kane
has local unique identifier pattern: ^CN\d+$
has prefix: medgen.cid
is deprecated: false
0000005: CN970821
description: This vocabulary is used internally inside MedGen to assign temporary identifiers to terms that will later get put in UMLS. Mappings between MedGen, MedGen CIDs, and UMLS can be found [here](https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.gz).

OBO Metadata Ontology
description: An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).
git repository: ontology-metadata
has prefix: omo
appears in: Cell Ontology
has local unique identifier pattern: ^\d{7}$
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/OMO_$1
appears in: Uber Anatomy Ontology
has URI prefix: http://purl.obolibrary.org/obo/OMO_
appears in: Provisional Cell Ontology
has responsible: https://orcid.org/0000-0002-6601-2165
keyword: obo
keyword: ontology
has download URL: omo.owl
0000005: 0003003
is deprecated: false
has resource example: OMO_0003003
is part of: Bioregistry

ChemPro Probe
has provider formatter: https://chemprosquare.idrblab.net/data/probe/details/$1
has resource example: LDPC0032
contributor: Mufaddal Naguthanawala
has URI prefix: https://chemprosquare.idrblab.net/data/probe/details/
0000005: LDPC0032
has responsible: https://orcid.org/0000-0001-8069-0053
is deprecated: false
has local unique identifier pattern: ^LDPC\d+$
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: chempro.probe
is part of: Bioregistry
type: Resource
description: ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for chemoproteomic probes used to label human proteins in living cells.

NFDI MatWerk Ontology
is part of: Bioregistry
has prefix: mwo
has local unique identifier pattern: ^\d{7}$
type: Resource
contributor: Charles Tapley Hoyt
has resource example: mwo_0001109
has responsible: Hossein Beygi Nasrabadi
has URI prefix: http://purls.helmholtz-metadaten.de/mwo/mwo_
has download URL: mwo.owl
description: NFDI-MatWerk aims to establish a digital infrastructure for Materials Science and Engineering (MSE), fostering improved data sharing and collaboration. This repository provides comprehensive documentation for NFDI MatWerk Ontology (MWO) v3.0.0, a foundational framework designed to structure research data and enhance interoperability within the MSE community. To ensure compliance with top-level ontology standards, MWO v3.0.0 is aligned with the Basic Formal Ontology (BFO) and incorporates the modular approach of the NFDIcore mid-level ontology, enriching metadata through standardized classes and properties. The mwo addresses key aspects of MSE research data, including the NFDI-MatWerk community structure, covering task areas, infrastructure use cases, projects, researchers, and organizations. It also describes essential NFDI resources, such as software, workflows, ontologies, publications, datasets, metadata schemas, instruments, facilities, and educational materials. Additionally, mwo represents NFDI-MatWerk services, academic events, courses, and international collaborations. As the foundation for the MSE Knowledge Graph, mwo facilitates efficient data integration and retrieval, promoting collaboration and knowledge representation across MSE domains. This digital transformation enhances data discoverability, reusability, and accelerates scientific exchange, innovation, and discoveries by optimizing research data management and accessibility. (from repository)
has provider formatter: http://purls.helmholtz-metadaten.de/mwo/mwo_$1
keyword: ontology
git repository: mwo
0000005: 0001109
is deprecated: false

SWEET Ontology Material Mineral
is deprecated: false
has resource example: Calcite
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Mineral
keyword: mineral
has provider formatter: http://sweetontology.net/matrMineral/$1
0000005: Calcite
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: http://sweetontology.net/matrMineral/
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: somamin
keyword: materials
has prefix: sweet.mamin

Data Source Type
has identifier space owner: 015em2733
type: Resource
has resource example: code RegistersRecordsAccounts
has prefix: ddi.datasourcetype
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/DataSourceType#code_
has provider formatter: https://vocabularies.cessda.eu/vocabulary/DataSourceType#code_$1
description: Includes a typology of data sources.
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: RegistersRecordsAccounts

Livestock Product Trait Ontology
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/LPT_
has provider formatter: http://purl.obolibrary.org/obo/LPT_$1
description: The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.
has responsible: Carissa Park
0000005: 0000156
git repository: livestock-product-trait-ontology
is deprecated: false
has download URL: lpt.owl
keyword: animal husbandry
keyword: ontology
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: phenotype
has resource example: LPT_0000156
has prefix: lpt

C. elegans Gross Anatomy Ontology
keyword: ontology
has prefix: wbbt
keyword: worm
description: Ontology about the gross anatomy of the C. elegans
is part of: Bioregistry
0000005: 0001290
has URI prefix: http://purl.obolibrary.org/obo/WBbt_
has responsible: https://orcid.org/0000-0002-8151-7479
has resource example: WBbt_0001290
has local unique identifier pattern: ^\d{7}$
type: Resource
git repository: c-elegans-gross-anatomy-ontology
has download URL: wbbt.owl
keyword: anatomy
keyword: cell
has provider formatter: http://purl.obolibrary.org/obo/WBbt_$1
has alternative prefix: WBbt
keyword: life science
is deprecated: false
keyword: obo

Fly taxonomy
has local unique identifier pattern: ^\d{8}$
has provider formatter: http://purl.obolibrary.org/obo/FBSP_$1
has resource example: FBSP_00000000
is part of: Bioregistry
description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.
type: Resource
0000005: 00000000
has prefix: fbsp
is deprecated: true
keyword: obo
keyword: ontology
has responsible: Clare Pilgrim
has URI prefix: http://purl.obolibrary.org/obo/FBSP_
has download URL: fbsp.owl

Overview of Medical Research in the Netherlands
0000005: 53367
is deprecated: false
has reviewer: https://orcid.org/0000-0001-9439-5346
contributor: https://orcid.org/0009-0001-6787-3995
description: The new national clinical trials registry of the Netherlands
has local unique identifier pattern: ^\d{5}$
is part of: Bioregistry
has resource example: https://onderzoekmetmensen.nl/en/trial/53367
has prefix: omon
type: Resource
has provider formatter: https://onderzoekmetmensen.nl/en/trial/$1
has URI prefix: https://onderzoekmetmensen.nl/en/trial/

Platynereis Developmental Stages
has download URL: pdumdv.owl
description: Life cycle stages for Platynereis dumerilii
has resource example: PdumDv_0001410
has local unique identifier pattern: ^\d{7}$
has alternative prefix: PdumDv
keyword: life science
has URI prefix: http://purl.obolibrary.org/obo/PdumDv_
0000005: 0001410
keyword: obo
is deprecated: true
has responsible: Frédéric Bastian
keyword: ontology
keyword: life cycle stage
keyword: developmental biology
has provider formatter: http://purl.obolibrary.org/obo/PdumDv_$1
is part of: Bioregistry
has prefix: pdumdv
type: Resource
git repository: developmental-stage-ontologies

Data Documentation Initiative Vocabulary
has prefix: ddi
has URI prefix: http://rdf-vocabulary.ddialliance.org/lifecycle#
keyword: ontology
keyword: drug discovery
keyword: registry
is deprecated: false
has provider formatter: http://rdf-vocabulary.ddialliance.org/lifecycle#$1
is part of: Bioregistry
has responsible: https://orcid.org/0000-0001-6489-3029
contributor: Charles Tapley Hoyt
has resource example: Instrument
0000005: Instrument
type: Resource
keyword: biomedical science
description: A set of controlled vocabularies in the Data Documentation Initiative, each of which has its own code.
has download URL: ddi.owl

nmrXiv project
has resource example: P136
has URI prefix: https://nmrxiv.org/project/
is deprecated: false
description: A project in the nmrXiv
has responsible: https://orcid.org/0000-0002-2564-3243
has prefix: nmrxiv.project
keyword: project
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://nmrxiv.org/project/$1
keyword: datasets
has local unique identifier pattern: ^P\d+$
type: Resource
0000005: P136

format controlled vocabulary
description: Controlled vocabulary for the Dublin Core term format
keyword: life sciences, biology
0000005: e001
type: Resource
has prefix: tdwg.format
has provider formatter: http://rs.tdwg.org/format/$1
keyword: fair data spaces
has URI prefix: http://rs.tdwg.org/format/
has resource example: e001
is deprecated: false
is part of: Bioregistry

The cBioPortal for Cancer Genomics
description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.
has URI prefix: https://www.cbioportal.org/study/summary
has provider formatter: https://www.cbioportal.org/study/summary
has local unique identifier pattern: ^[a-z0-9\_]+$
git repository: cbioportal
has prefix: cbioportal
is deprecated: false
0000005: laml_tcga_pub
is part of: Bioregistry
keyword: genomics
keyword: proteomics
keyword: preclinical studies
has resource example: https://www.cbioportal.org/study/summary
has responsible: https://orcid.org/0000-0002-5739-1781
type: Resource
keyword: biomedical science

Generative Artificial Intelligence Delegation Taxonomy
keyword: attribution
keyword: ontology
has resource example: https://w3id.org/gaidet/0000001
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: The Generative Artificial Intelligence Delegation Taxonomy (GAIDeT) assigns identifiers to contributor roles as an extension to the Contributor Roles Taxonomy (CRediT) to support promoting transparency and accountability in academic publishing when AI contribtors are involved in research. It is operationalized in the [GAIDeT Declaration Generator](https://panbibliotekar.github.io/gaidet-declaration/), an interactive tool for researchers to disclose the delegation of tasks to generative AI (GAI) tools in accordance with the GAIDeT taxonomy.
has prefix: gaidet
has URI prefix: https://w3id.org/gaidet/
0000005: 0000001
keyword: contributor roles
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: artificial intelligence
has responsible: https://orcid.org/0000-0002-5067-4498
has provider formatter: https://w3id.org/gaidet/$1
has download URL: gaidet.owl
is deprecated: false
git repository: gaidet-declaration
keyword: delegation

Name Reaction Ontology
has local unique identifier pattern: ^\d{7}$
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/RXNO_
has responsible: Colin Batchelor
keyword: obo
keyword: ontology
0000005: 0000253
is deprecated: false
has provider formatter: http://purl.obolibrary.org/obo/RXNO_$1
keyword: chemistry
keyword: nfdi4cat
description: RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization.
keyword: nfdi4chem
keyword: molecular chemistry
is part of: Bioregistry
has download URL: rxno.owl
git repository: rxno
has prefix: rxno
keyword: reaction data
has resource example: RXNO_0000253

Biolink Model
keyword: ontology
keyword: medical informatics
has local unique identifier pattern: ^\S+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
git repository: biolink-model
0000005: Gene
keyword: translational medicine
description: A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations.
keyword: functional genomics
has URI prefix: https://biolink.github.io/biolink-model/
is part of: Bioregistry
keyword: medical biotechnology
type: Resource
keyword: biomedical science
has prefix: biolink
has download URL: biolink.owl
has resource example: Gene
has provider formatter: https://biolink.github.io/biolink-model/$1

NONCODE v3
keyword: expression
0000005: 377550
is deprecated: true
has URI prefix: http://www.noncode.org/NONCODERv3/ncrna.php
has local unique identifier pattern: ^\d+$
has responsible: https://orcid.org/0000-0001-6049-8347
has prefix: noncodev3
has provider formatter: http://www.noncode.org/NONCODERv3/ncrna.php
keyword: nucleotide
is part of: Bioregistry
has resource example: http://www.noncode.org/NONCODERv3/ncrna.php
type: Resource
description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.

Open Data Commons for Spinal Cord Injury
has responsible: Jeffrey Grethe
is part of: Bioregistry
description: The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data.
has URI prefix: https://odc-sci.org/data/
keyword: neuroscience
keyword: biomedical science
has provider formatter: https://odc-sci.org/data/$1
type: Resource
keyword: neurology
keyword: neurobiology
has local unique identifier pattern: ^[0-9]*$
is deprecated: false
has prefix: odc.sci
0000005: 602
has resource example: https://odc-sci.org/data/602

WoRMS-ID for taxa
0000005: 146421
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has prefix: worms
has responsible: https://orcid.org/0000-0002-8160-7941
has provider formatter: http://www.marinespecies.org/aphia.php
keyword: taxonomy
type: Resource
keyword: environmental science
has resource example: http://www.marinespecies.org/aphia.php
has URI prefix: http://www.marinespecies.org/aphia.php
contributor: https://orcid.org/0000-0003-2699-3066
description: The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts.
keyword: biodiversity
is deprecated: false

Disease Class
description: Legacy disease classes that later became MONDO
is deprecated: true
keyword: ontology
0000005: 0000598
has provider formatter: https://biopragmatics.github.io/providers/diseaseclass/$1
appears in: Experimental Factor Ontology
has download URL: missing-omc.obo
is part of: Bioregistry
type: Resource
has URI prefix: https://biopragmatics.github.io/providers/diseaseclass/
contributor: Charles Tapley Hoyt
has prefix: diseaseclass
has resource example: https://biopragmatics.github.io/providers/diseaseclass/0000598
has local unique identifier pattern: ^\d{7}$

BIOZIL
has resource example: ls-c35719-120
contributor: Charles Tapley Hoyt
keyword: vendor
type: Resource
description: Redistributor of bilogics and biomedical supplies
keyword: life sciences
0000005: ls-c35719-120
is deprecated: false
has URI prefix: https://www.biozol.de/en/product/
keyword: biologics
has provider formatter: https://www.biozol.de/en/product/$1
has prefix: biozil
is part of: Bioregistry

Extensible Markup Language
type: Resource
0000005: lang
keyword: subject agnostic
description: The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML.
has resource example: lang
is deprecated: false
has URI prefix: http://www.w3.org/XML/1998/namespace#
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: xml
has provider formatter: http://www.w3.org/XML/1998/namespace#$1

Genetic and Rare Diseases Information Center
is part of: Bioregistry
has responsible: https://orcid.org/0000-0001-7697-3026
type: Resource
contributor: Charles Tapley Hoyt
keyword: symptom
keyword: condition
has provider formatter: https://rarediseases.info.nih.gov/diseases/$1/index
has alternative prefix: Genetic and Rare Diseases Information Center
keyword: ontology
has download URL: gard.owl
is deprecated: false
keyword: disease
has resource example: index
0000005: 6038
has URI prefix: https://bioregistry.io/gard:
has prefix: gard
has alternative prefix: GARD
has local unique identifier pattern: ^\d+$
description: Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease.

SWEET Ontology Property Categorical
has URI prefix: http://sweetontology.net/propCategorical/
contributor: Charles Tapley Hoyt
has resource example: CategoricalProperty
type: Resource
git repository: sweet
0000005: CategoricalProperty
keyword: categorical
has provider formatter: http://sweetontology.net/propCategorical/$1
is deprecated: false
is part of: Bioregistry
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Categorical
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sopropcat
has prefix: sweet.propcat

PubChem Cell Line
has local unique identifier pattern: ^\d+$
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/cell/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: cell lines
has prefix: pubchem.cell
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/cell/$1
type: Resource
keyword: bioactivities
0000005: 31
is deprecated: false
keyword: chemistry
description: Cell Lines in PubChem
has resource example: https://pubchem.ncbi.nlm.nih.gov/cell/31

Tetrahymena Stock Center
keyword: eukaryota
type: Resource
keyword: molecular
keyword: tetrahymena thermophila
keyword: research
has local unique identifier pattern: ^SD\d+$
keyword: cellular
keyword: biology
keyword: culture
keyword: cell
description: Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID]
has prefix: tsc
has resource example: https://tetrahymena.vet.cornell.edu/display.php
keyword: genetics
keyword: model
is deprecated: false
0000005: SD00043
is part of: Bioregistry
has URI prefix: https://tetrahymena.vet.cornell.edu/display.php
has provider formatter: https://tetrahymena.vet.cornell.edu/display.php
keyword: protozoan
keyword: repository

Brick Ontology
keyword: architecture
keyword: building design
has resource example: Ablutions Room
description: Brick is an open-source effort to standardize semantic descriptions of the physical, logical and virtual assets in buildings and the relationships between them. Brick consists of an extensible dictionary of terms and concepts in and around buildings, a set of relationships for linking and composing concepts together, and a flexible data model permitting seamless integration of Brick with existing tools and databases. Through the use of powerful Semantic Web technology, Brick can describe the broad set of idiosyncratic and custom features, assets and subsystems found across the building stock in a consistent matter. Adopting Brick as the canonical description of a building enables the following: 1) Brick lowers the cost of deploying analytics, energy efficiency measures and intelligent controls across buildings, 2) Brick presents an integrated, cross-vendor representation of the multitude of subsystems in modern buildings: HVAC, lighting, fire, security and so on, 3) Brick simplifies the development of smart analytics and control applications, and 4) Brick reduces the reliance upon the non-standard, unstructured labels endemic to building management systems.
keyword: civil engineering
keyword: systems engineering
keyword: building informatics
keyword: power engineering
has provider formatter: https://brickschema.org/schema/Brick#$1
has URI prefix: https://brickschema.org/schema/Brick#
is deprecated: false
keyword: digital planning and construction
is part of: Bioregistry
keyword: engineering
has prefix: brick
keyword: fid baudigital
git repository: Brick
keyword: building information modeling
keyword: energy engineering
keyword: industrial engineering
keyword: nfdi4energy
type: Resource
0000005: Ablutions_Room
keyword: nfdi4ing

Digital Construction Energy (dices)
0000005: EnergyProperty
description: An ontology for energy systems and energy efficiency in the construction and renovation domain
has prefix: digitalconstruction.energy
keyword: civil engineering
has URI prefix: https://w3id.org/digitalconstruction/0.5/Energy#
has provider formatter: https://w3id.org/digitalconstruction/0.5/Energy#$1
is deprecated: false
keyword: digital planning and construction
keyword: fid baudigital
has resource example: EnergyProperty
is part of: Bioregistry
keyword: nfdi4energy
type: Resource
keyword: nfdi4ing

Lebanon Clinical Trials Registry
contributor: Charles Tapley Hoyt
type: Resource
has prefix: lbctr
has local unique identifier pattern: ^LBCTR\d+$
description: The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. It includes trials that target humans from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. (from homepage)
is deprecated: false
0000005: LBCTR2023015204
is part of: Bioregistry

BitterDB Receptor
description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has URI prefix: http://bitterdb.agri.huji.ac.il/Receptor.php
has prefix: bitterdb.rec
has resource example: http://bitterdb.agri.huji.ac.il/Receptor.php
is deprecated: false
0000005: 1
has provider formatter: http://bitterdb.agri.huji.ac.il/Receptor.php

Adverse Event Reporting Ontology
has download URL: aero.owl
has resource example: AERO_0000125
has URI prefix: http://purl.obolibrary.org/obo/AERO_
description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events
0000005: 0000125
keyword: preclinical studies
is part of: Bioregistry
has prefix: aero
type: Resource
keyword: biomedical science
has responsible: Melanie Courtot
has local unique identifier pattern: ^\d{7}$
keyword: health science
keyword: medicine
is deprecated: true
has provider formatter: http://purl.obolibrary.org/obo/AERO_$1
keyword: obo
keyword: ontology
keyword: adverse reaction
contributor: https://orcid.org/0000-0002-1216-4761
keyword: electronic health record

Genomics of Drug Sensitivity in Cancer
is deprecated: false
has prefix: gdsc
description: The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.
is part of: Bioregistry
has provider formatter: https://www.cancerrxgene.org/translation/Drug/$1
has URI prefix: https://www.cancerrxgene.org/translation/Drug/
has resource example: https://www.cancerrxgene.org/translation/Drug/1242
type: Resource
0000005: 1242
has local unique identifier pattern: ^[0-9]+$

ArrayMap
keyword: genomics
is part of: Bioregistry
has prefix: arraymap
keyword: bioinformatics
has responsible: Michael Baudis
has provider formatter: https://www.arraymap.org/pgx:$1
0000005: icdom:8500_3
type: Resource
keyword: biomedical science
description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome.
has local unique identifier pattern: ^[\w\-:,]{3,64}$
keyword: life science
is deprecated: false
has resource example: pgx:icdom:8500 3
has URI prefix: https://www.arraymap.org/pgx:

SWEET Ontology Representation Space Direction
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space Direction
type: Resource
has alternative prefix: sorepsd
has resource example: Counterclockwise
is deprecated: false
has prefix: sweet.repsd
keyword: representation space direction
0000005: Counterclockwise
has provider formatter: http://sweetontology.net/reprSpaceDirection/$1
has URI prefix: http://sweetontology.net/reprSpaceDirection/
is part of: Bioregistry

Human Protein Complex Map
has provider formatter: https://humap3.proteincomplexes.org/displayComplexes
is part of: Bioregistry
type: Resource
has alternative prefix: humap3
contributor: Charles Tapley Hoyt
has resource example: https://humap3.proteincomplexes.org/displayComplexes
has prefix: humap
has URI prefix: https://humap3.proteincomplexes.org/displayComplexes
has responsible: https://orcid.org/0000-0002-1260-4413
0000005: huMAP3_04143.1
description: The hu.MAP integrates several large scale protein interaction datasets to obtain a comprehensive view of protein complexes.
is deprecated: false

Bacterial Tyrosine Kinase Database
has local unique identifier pattern: ^[A-Z0-9]+$
keyword: microbial
keyword: life science
keyword: domain
has prefix: bykdb
keyword: sequence
0000011: UniProt Protein
is deprecated: false
description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information.
has responsible: Alain J. Cozzone
has URI prefix: https://bioregistry.io/bykdb:
has resource example: A0A009HB13.html
0000005: A0A009HB13
is part of: Bioregistry
type: Resource
has provider formatter: https://bykdb.lyon.inserm.fr/data/html/annotated/$1.html

SWEET Ontology Material Organic Compound
0000005: Alkane
has resource example: Alkane
keyword: organic compound
is deprecated: false
has URI prefix: http://sweetontology.net/matrOrganicCompound/
has prefix: sweet.maoc
is part of: Bioregistry
has alternative prefix: somaoc
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
keyword: materials
has provider formatter: http://sweetontology.net/matrOrganicCompound/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Organic Compound

CAPS-DB
has resource example: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster
is deprecated: false
has local unique identifier pattern: ^\d+$
0000005: 434
is part of: Bioregistry
description: CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.
has prefix: caps
has provider formatter: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster
type: Resource
has URI prefix: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster

KYinno cell lines
has URI prefix: https://www.kyinno.com/
type: Resource
has resource example: https://www.kyinno.com/
0000005: KC-0979
has prefix: kyinno
is deprecated: false
has provider formatter: https://www.kyinno.com/
description: Cell line collections (Providers)
is part of: Bioregistry

NASA Open Science Data Repository Study
type: Resource
0000005: OSD-678
has local unique identifier pattern: ^OSD-\d+$
description: Identifiers for space-related data from studies that investigate biological and health responses of terrestrial life to spaceflight
contributor: Mufaddal Naguthanawala
has resource example: OSD-678
is deprecated: false
has provider formatter: https://osdr.nasa.gov/bio/repo/data/studies/$1
has prefix: nasaosdr.study
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://osdr.nasa.gov/bio/repo/data/studies/
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-8542-2389

SWEET Ontology Phenomena Solid
is part of: Bioregistry
git repository: sweet
has provider formatter: http://sweetontology.net/phenSolid/$1
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
keyword: phenomena
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Solid
has resource example: Ablation
type: Resource
has alternative prefix: sophso
has URI prefix: http://sweetontology.net/phenSolid/
is deprecated: false
has prefix: sweet.phso
0000005: Ablation
keyword: solid

SWEET Ontology Materials
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.ma
has alternative prefix: soma
0000005: Air
has URI prefix: http://sweetontology.net/matr/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Materials
type: Resource
has resource example: Air
keyword: materials
has provider formatter: http://sweetontology.net/matr/$1
is deprecated: false
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt

Observational Medical Outcomes Partnership
has URI prefix: https://athena.ohdsi.org/search-terms/terms/
has resource example: https://athena.ohdsi.org/search-terms/terms/1
has prefix: omop
is deprecated: false
has alternative prefix: OMOP
has provider formatter: https://athena.ohdsi.org/search-terms/terms/$1
0000005: 1
description: The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format.
contributor: https://orcid.org/0000-0002-7356-1779
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

Orphanet Rare Disease Ontology
is deprecated: false
0000005: C023
keyword: rare disorder
keyword: ontology
keyword: disease
is part of: Bioregistry
has provider formatter: http://www.orpha.net/ORDO/Orphanet_$1
keyword: phenotype
description: The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).
keyword: diagnosis
has local unique identifier pattern: ^C?\d+$
has responsible: Marc Hanauer
has download URL: ordo orphanet.owl
type: Resource
keyword: gene
keyword: biomedical science
has resource example: Orphanet C023
has URI prefix: http://www.orpha.net/ORDO/Orphanet_
has canonical: Orphanet
has alternative prefix: ordo
has prefix: orphanet.ordo
keyword: health science

Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
keyword: evidence
has provider formatter: http://purl.obolibrary.org/obo/DIDEO_$1
has resource example: DIDEO_00000180
is part of: Bioregistry
type: Resource
keyword: drug interaction
git repository: DIDEO
keyword: biochemistry
description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology
keyword: obo
keyword: natural product
0000005: 00000180
keyword: ontology
has download URL: dideo.owl
has local unique identifier pattern: ^\d{8}$
has responsible: https://orcid.org/0000-0003-1834-3856
has prefix: dideo
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/DIDEO_

Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology
depends on: Uber Anatomy Ontology
has local unique identifier pattern: ^\d{7}$
0000005: 0000001
type: Resource
keyword: tissue
has responsible: https://orcid.org/0000-0002-3528-5267
keyword: anatomy
keyword: life science
keyword: organelle
keyword: obo
has prefix: plana
appears in: Planarian Phenotype Ontology
has URI prefix: http://purl.obolibrary.org/obo/PLANA_
keyword: organ
depends on: Relation Ontology
description: PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.
keyword: ontology
git repository: planaria-ontology
is deprecated: false
is part of: Bioregistry
keyword: developmental biology
has provider formatter: http://purl.obolibrary.org/obo/PLANA_$1
has resource example: PLANA_0000001
has download URL: plana.owl

Locus Reference Genomic
has resource example: 1.xml
has provider formatter: http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml
description: A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI.
has prefix: lrg
is deprecated: false
has local unique identifier pattern: ^\d+$
0000005: 1
is part of: Bioregistry
type: Resource
has URI prefix: https://bioregistry.io/lrg:

Library of Congress Relator
description: Relator terms and their associated codes designate the relationship between an agent and a bibliographic resource.
type: Resource
has provider formatter: https://id.loc.gov/vocabulary/relators/$1
has URI prefix: https://id.loc.gov/vocabulary/relators/
is deprecated: false
0000005: arc
has resource example: arc
is part of: Bioregistry
has prefix: loc.relator
contributor: Charles Tapley Hoyt

National Center for Advancing Translation Sciences BioPlanet
is deprecated: false
has responsible: https://orcid.org/0000-0001-8886-8311
has resource example: https://tripod.nih.gov/bioplanet/detail.jsp
has URI prefix: https://tripod.nih.gov/bioplanet/detail.jsp
has local unique identifier pattern: ^\d+$
0000005: 3
is part of: Bioregistry
description: The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays.
has provider formatter: https://tripod.nih.gov/bioplanet/detail.jsp
contributor: Sierra Moxon
type: Resource
has reviewer: Charles Tapley Hoyt
has prefix: ncats.bioplanet

AGROVOC
contributor: https://orcid.org/0000-0002-2404-1582
keyword: food
is deprecated: false
keyword: forest management
has URI prefix: http://aims.fao.org/aos/agrovoc/c_
has provider formatter: http://aims.fao.org/aos/agrovoc/c_$1
keyword: knowledge and information systems
description: AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages.
keyword: botany
keyword: agriculture
is part of: Bioregistry
keyword: climate
has prefix: agrovoc
keyword: agronomy
type: Resource
has resource example: c 2842
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^[a-z0-9]+$
has responsible: https://orcid.org/0000-0003-3541-3334
keyword: food security
keyword: aquaculture
keyword: water management
0000005: 2842
keyword: agricultural products
keyword: nutritional science
keyword: environmental science
keyword: fisheries science
keyword: data management

Signaling Pathways Project
is deprecated: false
has provider formatter: https://www.signalingpathways.org/datasets/dataset.jsf
has resource example: https://www.signalingpathways.org/datasets/dataset.jsf
keyword: omics
0000005: 10.1621/vwN2g2HaX3
is part of: Bioregistry
has local unique identifier pattern: ^10.\w{4}/\w{10}$
keyword: transcriptomics
type: Resource
description: The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways.
has prefix: spp
has responsible: Neil McKenna
has URI prefix: https://www.signalingpathways.org/datasets/dataset.jsf

Exercise Medicine Ontology
keyword: obo
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/EXMO_
is deprecated: false
description: A core reference ontology built upon BFO about exercise medicine. This ontology contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise.
0000005: 0000008
has responsible: https://orcid.org/0000-0002-9295-2767
git repository: EXMO
is part of: Bioregistry
type: Resource
has prefix: exmo
has provider formatter: http://purl.obolibrary.org/obo/EXMO_$1
has download URL: exmo.owl

Cathy H. Wu
label: Cathy Wu

LigandBook
has local unique identifier pattern: ^[0-9]+$
has provider formatter: https://ligandbook.org/package/$1
has resource example: https://ligandbook.org/package/785
is deprecated: false
0000005: 785
is part of: Bioregistry
type: Resource
has URI prefix: https://ligandbook.org/package/
has prefix: ligandbook
description: Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community.

InChIKey
has URI prefix: https://www.chemspider.com/search
is deprecated: false
0000005: RYYVLZVUVIJVGH-UHFFFAOYSA-N
description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.
has local unique identifier pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])?$
is part of: Bioregistry
has resource example: https://www.chemspider.com/search
has provider formatter: https://www.chemspider.com/search
has prefix: inchikey
type: Resource

Experimental Measurements Purposes and Treatments ontologY
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: EMPTY_00000085
contributor: Charles Tapley Hoyt
has URI prefix: http://purl.obolibrary.org/obo/EMPTY_
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/EMPTY_$1
has download URL: empty.owl
0000005: 00000085
has prefix: empty
is deprecated: false
description: The Experimental Measurements, Purposes, and Treatments ontologY (EMPTY) is a structured vocabulary designed to capture and standardize the scientific reasoning behind experimental measurements. It addresses a critical gap in existing metadata standards, which primarily focus on technical specifications rather than scientific intent. The ontology provides a common language to express why a measurement was taken and the conceptual conditions under which it should be interpreted. By focusing on experimental purposes and treatments, EMPTY is designed to significantly improve the findability, interoperability, and reusability of scientific data. This enables researchers to discover relevant datasets for meta-analyses and cross-disciplinary research based on shared scientific goals. (from https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2753)
keyword: ontology
git repository: empty-ontology

ChemBank
is part of: Bioregistry
keyword: chemical
keyword: metabolite
type: Resource
description: ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG).
has URI prefix: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm
is deprecated: true
has reviewer: Charles Tapley Hoyt
has resource example: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm
has provider formatter: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm
0000005: 1000000
has prefix: chembank

KEGG Glycan
has prefix: kegg.glycan
has resource example: G00123
is deprecated: false
keyword: small molecule
has URI prefix: https://www.kegg.jp/entry/
description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.
is part of: Bioregistry
type: Resource
is part of: Kyoto Encyclopedia of Genes and Genomes
has provider formatter: https://www.kegg.jp/entry/$1
has responsible: Minoru Kanehisa
has local unique identifier pattern: ^G\d+$
0000005: G00123

CNCB Genome Warehouse
has resource example: show
is deprecated: false
has provider formatter: https://ngdc.cncb.ac.cn/gwh/Genome/$1/show
contributor: 0009-0008-8406-631X
description: The China National Center for Bioinformation's (CNCB) Genome Warehouse (GWH) is a public repository holding genetic information for a wide range of species including humans, plants, animals, and microorganisms. Identifiers in this resource correspond to genomes of various species. The goal of the resource is to make genomic data accessible to researchers in areas like precision medicine and biotechnology.
is part of: Bioregistry
0000005: 167047
has responsible: https://orcid.org/0000-0002-9922-9723
has prefix: cncb.gwh
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://bioregistry.io/cncb.gwh:
has local unique identifier pattern: ^\d{6}$
type: Resource

Maize Ontology
keyword: phenotype
git repository: Crop-Ontology
keyword: botany
has provider formatter: https://cropontology.org/rdf/CO_322:$1
keyword: agriculture
has local unique identifier pattern: ^\d{7}$
0000005: 0000773
type: Resource
has URI prefix: https://cropontology.org/rdf/CO_322:
keyword: life science
has prefix: co_322
is deprecated: false
keyword: food
has download URL: CO 322.owl
keyword: ontology
has responsible: Elizabeth Arnaud
keyword: plant phenotypes and traits
description: The Maize Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
is part of: Bioregistry
has resource example: CO 322:0000773

SWEET Ontology Phenomena Wave Noise
has URI prefix: http://sweetontology.net/phenWaveNoise/
is deprecated: false
has prefix: sweet.phwn
has provider formatter: http://sweetontology.net/phenWaveNoise/$1
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: phenomena
has alternative prefix: sophwn
has resource example: AmbientNoise
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Wave Noise
keyword: wave noise
0000005: AmbientNoise

BindingDB
keyword: interaction
has URI prefix: http://www.bindingdb.org/rwd/entry/
has provider formatter: http://www.bindingdb.org/rwd/entry/$1
keyword: life science
has prefix: bindingdb
has responsible: https://orcid.org/0000-0002-3375-1738
has resource example: http://www.bindingdb.org/rwd/entry/999
keyword: drug discovery
keyword: computational chemistry
keyword: medicinal chemistry
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: protein
description: BindingDB is the first public database of protein-small molecule affinity data.
keyword: chemistry
0000005: 999
type: Resource

Software ontology
keyword: dataplant
keyword: bioinformatics
keyword: nfdi4chem
has URI prefix: http://purl.obolibrary.org/obo/SWO_
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
keyword: license
has prefix: swo
keyword: algorithm
keyword: computer science
appears in: Model Card Report Ontology
has provider formatter: http://purl.obolibrary.org/obo/SWO_$1
has local unique identifier pattern: ^\d{7,8}$
git repository: swo
keyword: obo
has resource example: SWO_0000144
keyword: ontology
has responsible: https://orcid.org/0000-0002-7702-4495
0000005: 0000144
description: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.
has download URL: swo.owl
is deprecated: false

Gene Expression Analysis Resource
has prefix: gear
is deprecated: false
has local unique identifier pattern: ^[dp]\.[a-z0-9]{8}$
is part of: Bioregistry
has responsible: Joshua Orvis
0000005: d.a59037e8
has provider formatter: https://umgear.org/p
has URI prefix: https://umgear.org/p
has reviewer: Charles Tapley Hoyt
has resource example: https://umgear.org/p
type: Resource
contributor: Joshua Orvis
description: The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains.
git repository: gEAR

Rfam database of RNA families
has responsible: https://orcid.org/0000-0001-7279-2682
keyword: genetics
is part of: Bioregistry
0000005: RF00230
has URI prefix: https://rfam.org/family/
has provider formatter: https://rfam.org/family/$1
has local unique identifier pattern: ^RF\d{5}$
type: Resource
description: The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.
has resource example: RF00230
has prefix: rfam
is deprecated: false

Zebrafish Information Network Gene
is part of: Bioregistry
has URI prefix: http://zfin.org/
keyword: fish
type: Resource
keyword: zebrafish line
keyword: gene
keyword: antibody
keyword: zebrafish
description: ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.
keyword: research
has download URL: zfin.owl.gz
keyword: expressed sequence tag
keyword: pathology
has prefix: zfin
keyword: cdna
keyword: adult
keyword: embryo
has resource example: ZDB-GENE-041118-11
0000005: ZDB-GENE-041118-11
has local unique identifier pattern: ^ZDB\-\w+\-\d+\-\d+$
has alternative prefix: ZFIN
keyword: ontology
keyword: animal physiology
keyword: genetics
is deprecated: false
keyword: genome
keyword: genomics
keyword: developmental biology
has provider formatter: http://zfin.org/$1
has responsible: https://orcid.org/0000-0001-5831-7439

Genome Taxonomy Database
has download URL: gtdb.owl
0000005: g__Prochlorococcus_A
has resource example: https://gtdb.ecogenomic.org/tree
type: Resource
has local unique identifier pattern: ^[cdfgops]__\w+\S+$
description: The Genome Taxonomy Database (GTDB) is an initiative to establish a standardized microbial taxonomy based on genome phylogeny.
has reviewer: Charles Tapley Hoyt
has URI prefix: https://gtdb.ecogenomic.org/tree
keyword: taxonomy
is deprecated: false
has provider formatter: https://gtdb.ecogenomic.org/tree
contributor: https://orcid.org/0000-0003-1982-9065
keyword: ontology
is part of: Bioregistry
has prefix: gtdb
has responsible: Donovan Parks

Livestock Breed Ontology
has local unique identifier pattern: ^\d{7}$
has download URL: lbo.owl
type: Resource
has URI prefix: https://bioportal.bioontology.org/ontologies/LBO/
has provider formatter: https://bioportal.bioontology.org/ontologies/LBO/
keyword: animal breeding
has responsible: Carissa Park
has resource example: https://bioportal.bioontology.org/ontologies/LBO/
keyword: animal husbandry
keyword: ontology
description: The Livestock Breed Ontology (LBO) is a controlled vocabulary for the unambiguous description of breeds. Its utility include proper identification of inherited variation sources in genetics/genomic studies.
git repository: livestock-breed-ontology
keyword: genetics
is deprecated: false
is part of: Bioregistry
keyword: genomics
0000005: 0000487
has prefix: lbo

Merck Index Reaction
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: https://www.rsc.org/Merck-Index/reaction/
appears in: Name Reaction Ontology
type: Resource
has local unique identifier pattern: ^r\d+$
is deprecated: true
has prefix: merckindex.reaction
0000005: r376
has resource example: r376
has provider formatter: https://www.rsc.org/Merck-Index/reaction/$1
description: Chemical reactions in the Merck Index. This website doesn't exist anymore

Allgemeines Metadatenprofil für Bildungsressourcen
keyword: schema
has local unique identifier pattern: ^[a-z]\w+$
keyword: open educational resources
is part of: Bioregistry
keyword: open educational resource
type: Resource
has reviewer: Charles Tapley Hoyt
has prefix: kim.amb
git repository: amb
contributor: Martin Voigt
keyword: learning materials
has URI prefix: https://dini-ag-kim.github.io/amb/20231019/#
has responsible: Adrian Pohl
is deprecated: false
0000005: conditionsofaccess
keyword: learning material
has provider formatter: https://dini-ag-kim.github.io/amb/20231019/#$1
description: A cross-sectoral metadata profile for describing teaching and learning resources, primarily based on [schema.org](https://schema.org) and the Learning Resource Metadata Initiative LRMI, and additionally utilizing elements of the Simple Knowledge Organization System SKOS. A JSON-LD11-compliant data structure is defined in the form of this HTML specification, including a JSON schema against which data can be automatically checked for conformity with the profile.
has resource example: conditionsofaccess

ChemFOnt Chemical
has local unique identifier pattern: ^CFc\d{9}$
has provider formatter: https://www.chemfont.ca/chemicals/$1
has reviewer: Charles Tapley Hoyt
description: The Chemical Functional Ontology (ChemFOnt) is a hierarchical, OWL-compatible ontology describing the functions and actions of biologically important chemicals including primary metabolites, secondary metabolites, natural products, food chemicals, synthetic food additives, drugs, herbicides, pesticides and environmental chemicals. The identifiers in this semantic space correspond to individual chemicals.
keyword: ontology
has resource example: https://www.chemfont.ca/chemicals/CFc000239295
is deprecated: false
has URI prefix: https://www.chemfont.ca/chemicals/
contributor: https://orcid.org/0000-0001-9439-5346
0000005: CFc000239295
has prefix: chemfont.chemical
keyword: chemical
has responsible: David Wishart
is part of: Bioregistry
type: Resource

PDB ligand
type: Resource
keyword: structure
keyword: interaction
is deprecated: false
has prefix: pdb.ligand
0000005: TRQ
has alternative prefix: PDB_CHEM_ID
keyword: small molecule
is part of: Bioregistry
keyword: protein
has resource example: TRQ
description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands.
has provider formatter: http://www.rcsb.org/ligand/$1
has local unique identifier pattern: ^[A-Za-z0-9]+$
has URI prefix: http://www.rcsb.org/ligand/

Mental Functioning Ontology
keyword: cognition
has prefix: mf
has download URL: mf.owl
keyword: cognitive neuroscience
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: biomedical science
0000005: 0000091
has resource example: MF_0000091
keyword: mental health
has URI prefix: http://purl.obolibrary.org/obo/MF_
keyword: obo
has responsible: https://orcid.org/0000-0002-3469-4923
has provider formatter: http://purl.obolibrary.org/obo/MF_$1
keyword: ontology
is deprecated: false
description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.
is part of: Bioregistry
git repository: mental-functioning-ontology

ArchDB
has reviewer: Charles Tapley Hoyt
has responsible: https://orcid.org/0000-0002-6421-1080
keyword: life science
keyword: classification
has resource example: http://sbi.imim.es/cgi-bin/archdb//loops.pl
0000005: 39421
has URI prefix: http://sbi.imim.es/cgi-bin/archdb//loops.pl
is deprecated: false
description: ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al.
keyword: protein
has prefix: archdb
is part of: Bioregistry
has provider formatter: http://sbi.imim.es/cgi-bin/archdb//loops.pl
type: Resource

Teleost Anatomy Ontology
type: Resource
has prefix: tao
has download URL: tao.owl
has alternative prefix: TAO_RETIRED
has responsible: https://orcid.org/0000-0003-3162-7490
has local unique identifier pattern: ^\d{7}$
keyword: anatomy
has resource example: TAO_0000086
keyword: classification
is deprecated: true
keyword: obo
keyword: ontology
0000005: 0000086
has URI prefix: http://purl.obolibrary.org/obo/TAO_
has provider formatter: http://purl.obolibrary.org/obo/TAO_$1
description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa
is part of: Bioregistry

SWEET Ontology Representation Mathematics Solution
has provider formatter: http://sweetontology.net/reprMathSolution/$1
is part of: Bioregistry
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Solution
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has alternative prefix: sorepmso
keyword: representation mathematics solution
has prefix: sweet.repmso
0000005: AlgebraicSolution
has resource example: AlgebraicSolution
has URI prefix: http://sweetontology.net/reprMathSolution/
is deprecated: false

SWEET Ontology Process Wave
has URI prefix: http://sweetontology.net/procWave/
has alternative prefix: soprocw
keyword: wave
is deprecated: false
has prefix: sweet.procw
is part of: Bioregistry
has resource example: Absorption
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/procWave/$1
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process Wave
type: Resource
0000005: Absorption

Protege Ontology
is deprecated: false
description: An ontology of metadata from protege
has provider formatter: http://protege.stanford.edu/plugins/owl/protege#$1
is part of: Bioregistry
has resource example: defaultLanguage
contributor: Charles Tapley Hoyt
type: Resource
0000005: defaultLanguage
has prefix: protege
has URI prefix: http://protege.stanford.edu/plugins/owl/protege#

Ontology for computer aided process engineering
has prefix: nfdi4chem.ontocape
is deprecated: true
description: OntoCAPE is a large-scale ontology for the domain of Computer Aided Process Engineering (CAPE). Represented in a formal, machine-interpretable ontology language, OntoCAPE captures consensual knowledge of the process engineering domain in a generic way such that it can be reused and shared by groups of people and across software systems. On the basis of OntoCAPE, novel software support for various engineering activities can be developed; possible applications include the systematic management and retrieval of simulation models and design documents, electronic procurement of plant equipment, mathematical modeling, as well as the integration of design data from distributed sources.
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

Lipid Ontology
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/LIPRO_$1
description: An ontology representation of the LIPIDMAPS nomenclature classification.
is deprecated: true
has prefix: lipro
keyword: obo
has URI prefix: http://purl.obolibrary.org/obo/LIPRO_
keyword: ontology
has download URL: lipro.owl
has responsible: Christopher Baker
is part of: Bioregistry

Web of Things Security Ontology
is deprecated: false
0000005: APIKeySecurityScheme
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: https://www.w3.org/2019/wot/security#$1
has URI prefix: https://www.w3.org/2019/wot/security#
has prefix: wot.security
description: an RDF vocabulary for the security metadata definitions
has resource example: APIKeySecurityScheme

MaizeGDB Locus
has responsible: Margaret R. Woodhouse
type: Resource
has URI prefix: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi
has prefix: maizegdb.locus
keyword: life science
has resource example: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi
0000005: 25011
has alternative prefix: MaizeGDB
keyword: genetics
is deprecated: false
description: MaizeGDB is the maize research community's central repository for genetics and genomics information.
is part of: Bioregistry
keyword: genome
keyword: genomics
keyword: dna
has local unique identifier pattern: ^\d+$
has provider formatter: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi

Web Ontology Language
contributor: Charles Tapley Hoyt
type: Resource
keyword: informatics
keyword: computer science
0000005: Ontology
keyword: subject agnostic
has provider formatter: http://www.w3.org/2002/07/owl#$1
has URI prefix: http://www.w3.org/2002/07/owl#
has download URL: download.trig.gz
has resource example: Ontology
has prefix: owl
keyword: ontology
keyword: ontology and terminology
is deprecated: false
is part of: Bioregistry
has responsible: https://orcid.org/0000-0001-5699-0515
keyword: w3c rec
description: Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages.

Protein and Associated NucleotideDomains with Inferred Trees
has URI prefix: http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi
description: PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.
is deprecated: false
keyword: dna
is part of: Bioregistry
keyword: protein
has provider formatter: http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi
0000011: Pfam protein family
0000005: PF00004
has resource example: http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi
has prefix: pandit
type: Resource
keyword: structure
has reviewer: Charles Tapley Hoyt

Genatlas
keyword: disorder
has provider formatter: http://genatlas.medecine.univ-paris5.fr/fiche.php
type: Resource
has URI prefix: http://genatlas.medecine.univ-paris5.fr/fiche.php
keyword: gene
0000005: HBB
keyword: life science
has resource example: http://genatlas.medecine.univ-paris5.fr/fiche.php
is deprecated: false
has prefix: genatlas
has local unique identifier pattern: ^\w+$
keyword: human
description: GenAtlas is a database containing information on human genes, markers and phenotypes.
is part of: Bioregistry

nmrXiv compound
contributor: Charles Tapley Hoyt
description: compounds appearing in nmrXiv that have associated spectra.
has resource example: https://nmrxiv.org/spectra
keyword: chemical
has provider formatter: https://nmrxiv.org/spectra
type: Resource
has URI prefix: https://nmrxiv.org/spectra
keyword: compound
has responsible: https://orcid.org/0000-0002-2564-3243
is deprecated: false
has prefix: nmrxiv.compound
is part of: Bioregistry
0000005: 188

WikiPathways GPML Vocabulary
has alternative prefix: wikipathways.gpml
type: Resource
has URI prefix: http://vocabularies.wikipathways.org/gpml#
has responsible: Tim Vandermeersch
has reviewer: Charles Tapley Hoyt
has resource example: DataNode
contributor: https://orcid.org/0000-0001-9439-5346
has prefix: gpml
0000005: DataNode
git repository: WpVocabularies
keyword: ontology
description: The WikiPatwhays Graphical Pathway Markup Language (GPML) vocabulary.
has local unique identifier pattern: ^[A-Za-z]+$
contributor: Javier Millán Acosta
is deprecated: false
is part of: Bioregistry
has download URL: gpml.owl
has provider formatter: http://vocabularies.wikipathways.org/gpml#$1

EcoPortal
has part: DSW
has part: WLMO
has part: ACSUBTYPE
has part: FOVT
has part: ECOCORE
has part: EUROVOC
has part: ECSO
has part: SIBO
has part: BCO
has part: PECO
has part: EUROSCIVOC
0000005: AGROVOC
type: Registry
has part: PORO
has part: CODATA-RDMT
has part: DWCEM
has part: DWCDOE
has part: ACVARIANT
has part: PCO
has part: DWCPW
has part: OBOE
description: The LifeWatch ERIC repository of semantic resources for the ecological domain.
has part: AGROVOC
has responsible: Xeni Kechagioglou
has part: FABIO
has part: CMECS
has part: ENVTHES
has provider formatter: http://ecoportal.lifewatch.eu/ontologies/$1
has part: STY

The COVID-19 epidemiology and monitoring ontology
git repository: covid19-epidemiology-ontology
type: Resource
has reviewer: Charles Tapley Hoyt
has download URL: cemo.owl
has responsible: Núria Queralt Rosinach
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://biopragmatics.github.io/providers/cemo/
has prefix: cemo
keyword: ontology
0000005: secondary_attack_rate
has resource example: secondary attack rate
is part of: Bioregistry
has local unique identifier pattern: ^[0-9a-z_-]+$
has provider formatter: https://biopragmatics.github.io/providers/cemo/$1
description: The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response.

SWEET Ontology Phenomena Biology
has alternative prefix: sophb
keyword: phenomena
keyword: biology
has URI prefix: http://sweetontology.net/phenBiol/
type: Resource
is deprecated: false
has resource example: Assimilation
0000005: Assimilation
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Biology
is part of: Bioregistry
has prefix: sweet.phb
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/phenBiol/$1

DBPedia Property
0000005: insertion
has prefix: dbpedia.property
is deprecated: false
appears in: FuTRES Ontology of Vertebrate Traits
has provider formatter: http://dbpedia.org/property/$1
description: Properties in DBPedia.
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has resource example: insertion
has URI prefix: http://dbpedia.org/property/

clinical LABoratory Ontology
keyword: obo
keyword: ontology
depends on: Ontology of Precision Medicine and Investigation
depends on: Information Artifact Ontology
is deprecated: false
has download URL: labo.owl
is part of: Bioregistry
has prefix: labo
description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.
depends on: Ontology for Modeling and Representation of Social Entities
has responsible: Paul Fabry
has provider formatter: http://purl.obolibrary.org/obo/LABO_$1
depends on: Ontology for General Medical Science
depends on: Ontology for Biomedical Investigations
has URI prefix: http://purl.obolibrary.org/obo/LABO_
has local unique identifier pattern: ^\d{7}$
type: Resource
git repository: LABO
depends on: Ontologized MIABIS
0000005: 0000124
has resource example: LABO_0000124

PseudoGene
keyword: ontology
has responsible: Mark Gerstein
has URI prefix: https://bioregistry.io/pseudogene:
has prefix: pseudogene
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has alternative prefix: pseudogene.org
0000005: PGOHUM00000289843
type: Resource
keyword: gene
is deprecated: true
description: This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.
has provider formatter: https://bioregistry.io/pseudogene:$1
has resource example: pseudogene:PGOHUM00000289843

System capabilities, operating ranges, and survival ranges ontology
keyword: nfdi4chem
has resource example: qualityOfObservation
is part of: Bioregistry
type: Resource
has responsible: https://orcid.org/0000-0002-3884-3420
keyword: nfdi4ing
0000005: qualityOfObservation
has provider formatter: http://www.w3.org/ns/ssn/systems/$1
has reviewer: Charles Tapley Hoyt
has URI prefix: http://www.w3.org/ns/ssn/systems/
is deprecated: false
contributor: https://orcid.org/0000-0002-1595-3213
keyword: engineering
description: This ontology describes system capabilities, operating ranges, and survival ranges. Please report any errors to the W3C Spatial Data on the Web Working Group via the SDW WG Public List public-sdw-wg@w3.org
has prefix: ssn.system

UniProt Post-Translational Modification
has local unique identifier pattern: ^PTM-\d{4}$
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has resource example: PTM-0450
0000005: PTM-0450
has provider formatter: https://biopragmatics.github.io/providers/uniprot.ptm/$1
is part of: Bioregistry
description: The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format
type: Resource
keyword: post-translational modification
contributor: Charles Tapley Hoyt
keyword: structural biology
has prefix: uniprot.ptm
keyword: biochemistry
has alternative prefix: PTM
has URI prefix: https://biopragmatics.github.io/providers/uniprot.ptm/
has responsible: Alex Bateman
keyword: ontology
has download URL: uniprot.ptm.owl

INSPIRE theme register
description: The INSPIRE theme register contains all spatial data themes, as defined in the Annexes of the INSPIRE Directive ( Directive 2007/2/EC of the European Parliament and of the Council of 14 March 2007 establishing an Infrastructure for Spatial Information in the European Community (INSPIRE)). The descriptions of the themes are based on version 3.0 of the "Definition of Annex Themes and Scope (D 2.3)" by the data specifications drafting team and subsequent updates by the INSPIRE Thematic Working Groups (TWGs). (from homepage)
has prefix: inspire.theme
type: Resource
0000005: mr
has URI prefix: https://inspire.ec.europa.eu/theme/
has provider formatter: https://inspire.ec.europa.eu/theme/$1
is deprecated: false
has resource example: mr
is part of: Bioregistry
contributor: Charles Tapley Hoyt

UniProt Chain
has provider formatter: http://purl.uniprot.org/annotation/$1
has responsible: Alex Bateman
has alternative prefix: UPPRO
has resource example: PRO_0000016681
has prefix: uniprot.chain
0000005: PRO_0000016681
is deprecated: false
description: This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein.
is part of: Bioregistry
has URI prefix: http://purl.uniprot.org/annotation/
has local unique identifier pattern: ^PRO_[0-9]{10}$
type: Resource

The Cell Cycle DB
keyword: pathway
is part of: Bioregistry
keyword: protein
description: Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle
has provider formatter: http://www.itb.cnr.it/cellcycle/gene_rep.php
type: Resource
has resource example: http://www.itb.cnr.it/cellcycle/gene_rep.php
keyword: gene
has prefix: tccd
has reviewer: Charles Tapley Hoyt
is deprecated: true
0000005: TP53
has URI prefix: http://www.itb.cnr.it/cellcycle/gene_rep.php

CryptoDB
0000005: cgd7_230
has provider formatter: https://cryptodb.org/cryptodb/app/record/gene/$1
has responsible: Omar S. Harb
has resource example: cgd7 230
is deprecated: false
description: CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
keyword: genome
keyword: genomics
keyword: parasitology
has local unique identifier pattern: ^\w+$
keyword: functional genomics
is part of: Bioregistry
type: Resource
has prefix: cryptodb
has URI prefix: https://cryptodb.org/cryptodb/app/record/gene/

Affymetrix Probeset
description: An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.
has prefix: affy.probeset
is deprecated: false
has URI prefix: http://bio2rdf.org/affymetrix:
has resource example: affymetrix:243002 at
0000005: 243002_at
has provider formatter: http://bio2rdf.org/affymetrix:$1
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^\d{4,}((_[asx])?_at)?$

Dictyostelium discoideum phenotype ontology
keyword: phenomics
git repository: dicty-phenotype-ontology
keyword: soil science
has local unique identifier pattern: ^\d{7}$
type: Resource
has responsible: https://orcid.org/0000-0002-4532-2703
keyword: microbe-host interaction phenotype
has prefix: ddpheno
keyword: anatomy
has resource example: DDPHENO_0001417
keyword: life science
keyword: microbial ecology
keyword: obo
keyword: ontology
0000005: 0001417
is deprecated: false
is part of: Bioregistry
has download URL: ddpheno.owl
keyword: developmental biology
keyword: phenotype
description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.
has URI prefix: http://purl.obolibrary.org/obo/DDPHENO_
has provider formatter: http://purl.obolibrary.org/obo/DDPHENO_$1

Linked Data Platform Vocabulary
0000005: Resource
description: A set of best practices and simple approach for a read-write Linked Data architecture, based on HTTP access to web resources that describe their state using the RDF data model.
keyword: api
has prefix: ldp
is deprecated: false
is part of: Bioregistry
type: Resource

PSI Extended File Format
has prefix: peff
has URI prefix: https://biopragmatics.github.io/providers/peff/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has download URL: psi-peff-OBSOLETE-DO NOT USE.obo
0000005: 0001011
has provider formatter: https://biopragmatics.github.io/providers/peff/$1
has resource example: https://biopragmatics.github.io/providers/peff/0001011
has local unique identifier pattern: ^\d{7}$
type: Resource
is deprecated: true
keyword: ontology

Time Ontology in OWL
keyword: resource metadata
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-3884-3420
contributor: Charles Tapley Hoyt
has prefix: time
0000005: DateTimeDescription
has provider formatter: http://www.w3.org/2006/time#$1
git repository: sdw
keyword: nfdi4chem
has download URL: time.owl
type: Resource
description: Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars.
keyword: data coordination
has URI prefix: http://www.w3.org/2006/time#
keyword: subject agnostic
keyword: ess
keyword: metadata standardization
has resource example: DateTimeDescription
is deprecated: false
keyword: fair data spaces
keyword: time
keyword: ontology

XHTML Vocabulary
contributor: Charles Tapley Hoyt
has resource example: alternate
type: Resource
has URI prefix: http://www.w3.org/1999/xhtml/vocab#
description: This is a vocabulary collection utilized by XHTML Family modules and document types using XHTML Modularization, including XHTML Role and XHTML + RDFa as defined in rdfa-syntax. The XHTML specifications are developed by the W3C XHTML 2 Working Group as part of the W3C HTML Activity. [from homepage]
0000005: alternate
is deprecated: false
keyword: api
has provider formatter: http://www.w3.org/1999/xhtml/vocab#$1
has prefix: xhv
is part of: Bioregistry

Functional Genome Annotations with Transcriptional Activities
has reviewer: https://orcid.org/0000-0001-9439-5346
has local unique identifier pattern: ^FC(HS|MM)_\d+$
has provider formatter: https://fanta.bio/cre/$1
type: Resource
0000005: FCHS_301358
contributor: Mufaddal Naguthanawala
has resource example: FCHS_301358
is deprecated: false
has URI prefix: https://fanta.bio/cre/
description: Functional annotations of genomes for studying gene regulation, with a primary focus on cis-regulatory elements (CREs) such as promoters and enhancers.
has prefix: fanta
is part of: Bioregistry

HGNC Gene Group
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.
keyword: gene family
has resource example: !/group/141
type: Resource
has responsible: Elspeth Bruford
keyword: gene
keyword: gene group
has URI prefix: https://www.genenames.org/data/genegroup/#!/group/
has provider formatter: https://www.genenames.org/data/genegroup/#!/group/$1
has download URL: hgnc.genegroup.owl
0000005: 141
has prefix: hgnc.genegroup
keyword: ontology

PyPI
is deprecated: false
has prefix: pypi
description: The Python Package Index (PyPI) is a repository for Python packages.
has URI prefix: https://pypi.org/project/
0000005: numpy
is part of: Bioregistry
has resource example: numpy
type: Resource
has provider formatter: https://pypi.org/project/$1
has local unique identifier pattern: ^[a-zA-Z_][a-zA-Z0-9\-_]+$

ListDB Ontology
has prefix: listdb.onto
git repository: listdb
keyword: traffic engineering
is deprecated: false
keyword: fid move
has provider formatter: https://w3id.org/listdb/onto#$1
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
has URI prefix: https://w3id.org/listdb/onto#
0000005: C0000000001
has resource example: https://w3id.org/listdb/onto#C0000000001
description: This is an ontology draft for the description of metadata of traffic observations, in particular video recordings of road traffic. The traffic observations are e.g. used to design test scenarios for the effectiveness assessment of automated driving systems. The ontology draft resulted from an exchange of the Chair of Automobile Engineering at TU Dresden (https://tu-dresden.de/bu/verkehr/iad/kft?set_language=en) with representatives of NFDI4Ing (Community Cluster 4.4, Archetype Golo, Base Services S3) and FID move in NFDI4Ing's Special Interest Group "Metadata and Ontologies". An essential part of that meeting was the presentation of the reseaerch data management approach at the Chair of Automobile Engineering, in particular its tooling, its metadata approach and its workflow. Traffic observations are managed with ListDB, a solution combined of a SharePoint instance and a virtual machine for data servicing . An accompanying Codebook defines relevant metadata that should be provided for each road traffic observation. ListDB is currently used internally within TU Dresden, but is intentended to be hosted publicly until spring 2023. The ontology draft is, in fact, based on the Codebook (v. 1.0.0.) and an attempt to make a machine-readable document out of it, applying standards from the Semantic Web Stack (RDF(S) and OWL). The draft is constantly being developed further in this context.

SWEET Ontology State Visibility
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has prefix: sweet.stv
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Visibility
keyword: state visibility
has alternative prefix: sostv
has resource example: Clear
is deprecated: false
has URI prefix: http://sweetontology.net/stateVisibility/
has provider formatter: http://sweetontology.net/stateVisibility/$1
0000005: Clear
is part of: Bioregistry

SWEET Ontology State Space
has prefix: sweet.stsp
is deprecated: false
keyword: state space
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Space
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
type: Resource
is part of: Semantic Web for Earth and Environment Technology Ontology
has URI prefix: http://sweetontology.net/stateSpace/
0000005: Big
has alternative prefix: sostsp
has provider formatter: http://sweetontology.net/stateSpace/$1
has resource example: Big

VirGen
keyword: genome
has prefix: virgen
0000005: AY321118
is part of: Bioregistry
type: Resource
description: VirGen a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences.
is deprecated: false

KEGG Compound
has provider formatter: https://www.kegg.jp/entry/$1
has alternative prefix: KEGG.COMPOUND
is deprecated: false
description: KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.
has alternative prefix: KEGG COMPOUND
has URI prefix: https://www.kegg.jp/entry/
keyword: small molecule
0000005: C12345
is part of: Bioregistry
has local unique identifier pattern: ^C\d+$
is part of: Kyoto Encyclopedia of Genes and Genomes
has resource example: C12345
has responsible: Minoru Kanehisa
type: Resource
has prefix: kegg.compound

MycoBrowser
0000005: ML0224
has provider formatter: https://mycobrowser.epfl.ch/genes/$1
has part: MycoBrowser leprae
has resource example: ML0224
is deprecated: false
has prefix: myco
has part: MycoBrowser smegmatis
description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.
has part: MycoBrowser marinum
has URI prefix: https://mycobrowser.epfl.ch/genes/
is part of: Bioregistry
has part: TubercuList knowledge base
contributor: Charles Tapley Hoyt
type: Resource

Network of Different Plant Genomic Research Projects
has local unique identifier pattern: ^\w+$
has resource example: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi
has provider formatter: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi
has prefix: gabi
is part of: Bioregistry
keyword: plant
type: Resource
keyword: gene
has URI prefix: https://bioregistry.io/gabi:
is deprecated: true
has responsible: Birgit Kersten
0000005: 2679240
keyword: genome
description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.

SWEET Ontology Property Charge
has alternative prefix: sopropcha
is deprecated: false
has provider formatter: http://sweetontology.net/propCharge/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Charge
is part of: Bioregistry
has URI prefix: http://sweetontology.net/propCharge/
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has prefix: sweet.propcha
keyword: charge
has resource example: Capacitance
0000005: Capacitance

Brazilian Registry of Clinical Trials
has provider formatter: https://ensaiosclinicos.gov.br/rg/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
0000005: RBR-6qvdftm
is deprecated: false
has resource example: RBR-6qvdftm
has URI prefix: https://ensaiosclinicos.gov.br/rg/
has prefix: rebec
description: Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant.
has local unique identifier pattern: ^RBR-\w+$

Type of Telephone
is deprecated: false
is part of: Bioregistry
description: Identifies the type of telephone entered as contact information for an individual or an organization.
contributor: Charles Tapley Hoyt
has resource example: code Fixed
type: Resource
has identifier space owner: 015em2733
0000005: Fixed
has URI prefix: https://vocabularies.cessda.eu/vocabulary/TypeOfTelephone#code_
has prefix: ddi.typeoftelephone
has provider formatter: https://vocabularies.cessda.eu/vocabulary/TypeOfTelephone#code_$1

Jackson Laboratories Mouse Strain
has alternative prefix: jaxMiceUID
has prefix: jaxmice
has alternative prefix: jax
has provider formatter: https://www.jax.org/strain/$1
keyword: repository
is part of: Bioregistry
type: Resource
keyword: genetic engineering
contributor: Charles Tapley Hoyt
keyword: gene
description: A catalogue of mouse strains supplied by The Jackson Laboratory. Each identifier corresponds to a mouse strain.
0000005: 004435
keyword: subject
keyword: research
has local unique identifier pattern: ^\d{6}$
keyword: knockout
keyword: life science
keyword: supply
has resource example: https://www.jax.org/strain/004435
keyword: model
is deprecated: false
keyword: strain
keyword: mouse
keyword: mice
has URI prefix: https://www.jax.org/strain/

Minimum Information about any (x) Sequence
has provider formatter: https://w3id.org/mixs/$1
type: Resource
contributor: https://orcid.org/0000-0001-9076-6066
contributor: https://orcid.org/0000-0002-6601-2165
has reviewer: Charles Tapley Hoyt
has local unique identifier pattern: ^\d{7}$
has download URL: mixs.owl.ttl
contributor: Chris Hunter
contributor: https://orcid.org/0000-0002-8741-7823
description: The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample.
has resource example: https://w3id.org/mixs/0001056
keyword: ontology
has URI prefix: https://w3id.org/mixs/
has responsible: https://orcid.org/0000-0001-9076-6066
is deprecated: false
0000005: 0001056
has prefix: mixs
is part of: Bioregistry

Building Topology Ontology
0000005: Building
has provider formatter: https://w3id.org/bot#$1
keyword: fid baudigital
has prefix: bot
git repository: bot
is part of: Bioregistry
has URI prefix: https://w3id.org/bot#
keyword: architecture
keyword: nfdi4ing
keyword: nfdi4culture
has resource example: Building
description: The Building Topology Ontology (BOT) is a minimal ontology for describing the core topological concepts of a building.
keyword: civil engineering
type: Resource
is deprecated: false
keyword: digital planning and construction

Semantically-Interlinked Online Communities Actions Ontology
is part of: Bioregistry
description: An ontology of predicates for actions in SIOC
contributor: Charles Tapley Hoyt
type: Resource
has resource example: DigitalArtifact
0000005: DigitalArtifact
is deprecated: false
has URI prefix: http://rdfs.org/sioc/actions#
has prefix: sioc.actions
has provider formatter: http://rdfs.org/sioc/actions#$1

ISTransbase
has resource example: IST028
contributor: Tanay Shah
is deprecated: false
has provider formatter: https://istransbase.scbdd.com/database/trans/$1
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
description: ISTransbase is a highly reliable and accessible database that focuses on inhibitors and substrates of drug transporters, offering a wealth of vital information encompassing experimental methods, transport parameters, and references.
type: Resource
has URI prefix: https://istransbase.scbdd.com/database/trans/
0000005: IST028
has prefix: istransbase

E-cyanobacterium entity
has URI prefix: https://www.e-cyanobacterium.org/bcs/entity/
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: ecyano.entity
0000005: 23
type: Resource
has resource example: https://www.e-cyanobacterium.org/bcs/entity/23
has provider formatter: https://www.e-cyanobacterium.org/bcs/entity/$1
is deprecated: false
description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.

Minimal Information About Anatomy ontology
has prefix: miaa
type: Resource
is deprecated: true
contributor: Charles Tapley Hoyt
is part of: Bioregistry

Data Science Ontology
keyword: data science
is deprecated: false
git repository: datascienceontology
is part of: Bioregistry
has responsible: 0000-0002-8600-949X
description: The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science.
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: https://www.datascienceontology.org/concept/
has provider formatter: https://www.datascienceontology.org/concept/$1
has prefix: dso
has resource example: classification-model
0000005: classification-model
keyword: ontology

Compluyeast-2D-DB
type: Resource
is deprecated: true
has provider formatter: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi
has URI prefix: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi
0000005: O08709
has resource example: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi
has prefix: compulyeast
description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record.
0000011: UniProt Protein
is part of: Bioregistry
keyword: protein
has local unique identifier pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$

Eukaryotic Genes
has reviewer: Charles Tapley Hoyt
keyword: life science
0000005: MGgn0008978
has prefix: eugenes
description: euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information.
has responsible: https://orcid.org/0000-0002-6646-7274
has resource example: http://eugenes.org:7072/.bin/fbidq.html
keyword: ontology
has URI prefix: http://eugenes.org:7072/.bin/fbidq.html
is deprecated: false
keyword: genome
is part of: Bioregistry
type: Resource
has provider formatter: http://eugenes.org:7072/.bin/fbidq.html

Collagen Mutation Database
has resource example: https://eds.gene.le.ac.uk/home.php
has prefix: collagenmutdb
0000005: COL3A1
has URI prefix: https://eds.gene.le.ac.uk/home.php
is deprecated: false
is part of: Bioregistry
has provider formatter: https://eds.gene.le.ac.uk/home.php
0000011: HGNC gene symbol
type: Resource
keyword: gene
description: This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes.
has reviewer: Charles Tapley Hoyt

Antibody Registry
is part of: Bioregistry
has resource example: AB_493771
has provider formatter: http://antibodyregistry.org/AB_$1
type: Resource
description: The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.
keyword: reagent
keyword: antibody
has local unique identifier pattern: ^\d{6}$
keyword: unique identifiers
0000005: 493771
contributor: https://orcid.org/0000-0002-1216-4761
has URI prefix: http://antibodyregistry.org/AB_
is deprecated: false
has responsible: https://orcid.org/0000-0002-5497-0243
has prefix: antibodyregistry

The Dietary Restriction Gene Database
has provider formatter: http://genomics.senescence.info/diet/details.php
has responsible: https://orcid.org/0000-0002-6363-2465
is deprecated: false
keyword: dietary restriction
keyword: genes
keyword: aging
keyword: longevity
is part of: Bioregistry
has prefix: hagr.gendr
has resource example: http://genomics.senescence.info/diet/details.php
type: Resource
description: GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals
has URI prefix: http://genomics.senescence.info/diet/details.php
has reviewer: Charles Tapley Hoyt
0000005: 2

uBio NameBank
0000005: 2555646
is deprecated: true
has resource example: http://www.ubio.org/browser/details.php
has URI prefix: http://www.ubio.org/browser/details.php
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: http://www.ubio.org/browser/details.php
has prefix: ubio.namebank
type: Resource
description: NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.

Scholarly Contributions and Roles Ontology
is part of: Bioregistry
keyword: academy
has resource example: IntellectualContribution
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: http://purl.org/spar/scoro/
keyword: subject agnostic
has prefix: scoro
description: An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator).
has provider formatter: http://purl.org/spar/scoro/$1
0000005: IntellectualContribution
is deprecated: false
git repository: scoro
has responsible: Silvio Peroni

SWISS-MODEL Repository
type: Resource
keyword: structure
0000005: P23298
has prefix: swiss-model
has provider formatter: https://swissmodel.expasy.org/repository/uniprot/$1
keyword: life science
has local unique identifier pattern: ^\w+$
has resource example: P23298
0000011: UniProt Protein
has URI prefix: https://swissmodel.expasy.org/repository/uniprot/
is deprecated: false
description: The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences.
is part of: Bioregistry
has responsible: 0000-0003-2715-335X
keyword: protein
keyword: proteomics

PaN Experimental technique
is deprecated: false
0000005: 00001
keyword: photon science
has prefix: panet
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
has URI prefix: http://purl.org/pan-science/PaNET/PaNET
keyword: experimental measurement
has resource example: PaNET00001
keyword: x-ray diffraction
has download URL: panet.owl
description: The ExPaNDS Photon and Neutron Experimental Techniques (PaNET) ontology provides a taxonomy and thesaurus of photon and neutron (PaN) experimental techniques. Based mainly on accelerator-based light sources and neutron facilities, the primary use of the ontology is to enhance the FAIRness of PaN data catalogues services. The ontology defines specific techniques in terms of more general technique classes and provides synonyms and references.
has provider formatter: http://purl.org/pan-science/PaNET/PaNET$1
keyword: physics
keyword: ontology
keyword: imaging
keyword: neutron science

Metabolic Network Exchange Database
keyword: interaction
has reviewer: Charles Tapley Hoyt
description: The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another.
has resource example: http://metnetonline.org/browse_pathway2.php
has prefix: metnetdb
has provider formatter: http://metnetonline.org/browse_pathway2.php
keyword: rna
keyword: pathway
is deprecated: false
keyword: dna
keyword: small molecule
keyword: regulation
is part of: Bioregistry
keyword: protein
0000005: 377369
has URI prefix: http://metnetonline.org/browse_pathway2.php
type: Resource

Open Data Commons for Traumatic Brain Injury
description: The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data.
type: Resource
has local unique identifier pattern: ^[0-9]*$
0000005: 408
is deprecated: false
has URI prefix: https://odc-tbi.org/data/
has prefix: odc.tbi
has provider formatter: https://odc-tbi.org/data/$1
has resource example: https://odc-tbi.org/data/408
is part of: Bioregistry

Health Surveillance Ontology
depends on: Ontology for Biomedical Investigations
depends on: Uber Anatomy Ontology
has provider formatter: http://purl.obolibrary.org/obo/HSO_$1
has URI prefix: http://purl.obolibrary.org/obo/HSO_
is part of: Bioregistry
type: Resource
depends on: NCBI Taxonomy
has download URL: hso.owl
depends on: Basic Formal Ontology
has resource example: HSO_0000062
has local unique identifier pattern: ^\d{7}$
git repository: HSO
keyword: obo
has responsible: Fernanda Dorea
depends on: Relation Ontology
keyword: ontology
is deprecated: false
description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.
0000005: 0000062
has prefix: hso

Decentralized Biomedical Ontology
contributor: Charles Tapley Hoyt
has alternative prefix: DeBiO
has resource example: https://biopragmatics.github.io/debio/0000001
description: A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON.
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
has prefix: debio
type: Resource
has download URL: debio.owl
has provider formatter: https://biopragmatics.github.io/debio/$1
has responsible: Charles Tapley Hoyt
is deprecated: false
keyword: ontology
has URI prefix: https://biopragmatics.github.io/debio/
is part of: Bioregistry

Austrian Fields of Science and Technology Classification
keyword: educational resources
has URI prefix: https://vocabs.acdh.oeaw.ac.at/oefosdisciplines/
is part of: Bioregistry
has provider formatter: https://vocabs.acdh.oeaw.ac.at/oefosdisciplines/$1
has prefix: oefos
type: Resource
keyword: educational science
description: The Austrian Fields of Science and Technology Classification (ÖFOS 2012) is the Austrian version of the revised international Fields of Science and Technology Classification of the OECD (FOS) published in the Frascati Manual 2015 as Fields of Research and Development (FORD). These fields are adjusted to national needs, whose application for international comparisons is binding, particularly within the European Statistical System. The six major Fields of Science: Natural Sciences; Technical Sciences; Human Medicine, Health Sciences; Agricultural Sciences, Veterinary Medicine; Social Sciences and Humanities remained unchanged in comparison to ÖFOS 2002. In order to ensure international comparability, the previous 2-digit levels from 2002, which are no longer applicable, were replaced by new 3-digit levels (groups) according to the international FOS respectively FORD. These 3-digit levels were provided with further sub-groups (4-digits) taking into account the comments of the international classification. It is therefore feasible that the new Austrian Fields of Science adapt to national peculiarities of the Austrian research activities. The research area with the corresponding 6-digits in alphabetical order serves as a description of the fields of activities and research projects and/or for the coverage of the main scientific activities of a statistical unit in the research and development surveys. (Current revision status: August 2017)
0000005: 509015
is deprecated: false
has resource example: https://vocabs.acdh.oeaw.ac.at/oefosdisciplines/509015

Human Dephosphorylation Database
is deprecated: false
has URI prefix: http://www.depod.bioss.uni-freiburg.de/showp.php
is part of: Bioregistry
has prefix: depod
has resource example: http://www.depod.bioss.uni-freiburg.de/showp.php
0000011: HGNC gene symbol
description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources.
has responsible: General Enquiries
type: Resource
keyword: life science
has provider formatter: http://www.depod.bioss.uni-freiburg.de/showp.php
has local unique identifier pattern: ^[A-Z0-9]+$
0000005: PTPN1

Anatomical Entity Ontology
keyword: obo
has prefix: aeo
0000005: 0001017
keyword: ontology
contributor: https://orcid.org/0000-0002-1216-4761
appears in: Human developmental anatomy, abstract
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
git repository: human-developmental-anatomy-ontology
type: Resource
has resource example: AEO_0001017
has download URL: aeo.owl
has provider formatter: http://purl.obolibrary.org/obo/AEO_$1
has alternative prefix: AEO_RETIRED
has URI prefix: http://purl.obolibrary.org/obo/AEO_
keyword: anatomy
is deprecated: true
description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology

Systems Biology Ontology
has responsible: https://orcid.org/0000-0003-0705-9809
description: The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.
keyword: earth sciences
is part of: Bioregistry
keyword: life sciences, biology
type: Resource
git repository: SBO
keyword: molecular interaction
has download URL: sbo.owl
has local unique identifier pattern: ^\d{7}$
keyword: systems biology
keyword: ess
has URI prefix: http://purl.obolibrary.org/obo/SBO_
has provider formatter: http://purl.obolibrary.org/obo/SBO_$1
keyword: obo
0000005: 0000485
keyword: ontology
has prefix: sbo
appears in: Sickle Cell Disease Ontology
appears in: Process Chemistry Ontology
has resource example: SBO_0000485
keyword: pathway
is deprecated: false
keyword: nfdi4cat

Handle
description: Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)
has provider formatter: http://hdl.handle.net/$1
keyword: subject agnostic
has URI prefix: http://hdl.handle.net/
has alternative prefix: handle
has resource example: http://hdl.handle.net/2381/12775
is deprecated: false
keyword: centrally registered identifier
0000005: 2381/12775
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has prefix: hdl
has local unique identifier pattern: ^\d+/.+$

International Molecular Exchange
type: Resource
has URI prefix: https://www.ebi.ac.uk/intact/imex/main.xhtml
keyword: interaction
keyword: molecule
has identifier space owner: 02catss52
has provider formatter: https://www.ebi.ac.uk/intact/imex/main.xhtml
has local unique identifier pattern: ^\d+(-\d+)?$
0000005: 19210-3
has responsible: Sandra Orchard
is deprecated: false
has prefix: imex
has resource example: https://www.ebi.ac.uk/intact/imex/main.xhtml
description: The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.
is part of: Bioregistry

Gainesville Core Ontology
has download URL: gc.owl
keyword: ontology
0000005: Aromatic
is part of: Bioregistry
keyword: chemistry
contributor: Charles Tapley Hoyt
keyword: nfdi4chem
has prefix: gainesville.core
has URI prefix: http://purl.org/gc/
type: Resource
description: Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations
has provider formatter: http://purl.org/gc/$1
has resource example: Aromatic
is deprecated: false

Vocabulary of Interlinked Datasets
type: Resource
contributor: Charles Tapley Hoyt
has prefix: void
has provider formatter: http://rdfs.org/ns/void#$1
keyword: metadata
has URI prefix: http://rdfs.org/ns/void#
has resource example: feature
is deprecated: false
description: The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary.
0000005: feature
is part of: Bioregistry

Scholia Registry
is deprecated: false
has provider formatter: https://bioregistry.io/metaregistry/scholia/$1
has URI prefix: https://bioregistry.io/metaregistry/scholia/
has resource example: doi
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: A frontend to Wikidata
has prefix: scholia.resource
0000005: doi
keyword: wikidata
keyword: registry

Cardiovascular Disease Ontology
has provider formatter: http://purl.obolibrary.org/obo/CVDO_$1
0000005: 0000546
keyword: cardiovascular disease
git repository: CVDO
keyword: obo
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/CVDO_
is deprecated: false
is part of: Bioregistry
has prefix: cvdo
has responsible: Paul Fabry
has resource example: CVDO_0000546
keyword: cardiology
has local unique identifier pattern: ^\d{7}$
type: Resource
has download URL: cvdo.owl
description: An ontology to describe entities related to cardiovascular diseases

Daniel C. Berrios
label: Dan Berrios

Plant Trait Ontology
has provider formatter: http://purl.obolibrary.org/obo/TO_$1
keyword: structure
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: ess
keyword: trait
has URI prefix: http://purl.obolibrary.org/obo/TO_
keyword: obo
has resource example: TO_0000630
description: A controlled vocabulary to describe phenotypic traits in plants.
keyword: ontology
appears in: Agronomy Ontology
is deprecated: false
has prefix: to
has responsible: Pankaj Jaiswal
keyword: dataplant
keyword: phenotype
has download URL: to.owl
0000005: 0000630
keyword: botany
keyword: earth sciences
git repository: plant-trait-ontology
keyword: plant
keyword: life cycle
is part of: Bioregistry

Plant Experimental Conditions Ontology
type: Resource
appears in: Microbial Conditions Ontology
has provider formatter: https://browser.planteome.org/amigo/term/PECO:$1
keyword: experimental measurement
0000005: 0007114
has download URL: peco.owl
has responsible: Pankaj Jaiswal
keyword: study design
keyword: experimentally determined
keyword: obo
keyword: ontology
appears in: Agronomy Ontology
has URI prefix: https://browser.planteome.org/amigo/term/PECO:
is deprecated: false
description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.
keyword: dataplant
keyword: experimental condition
git repository: plant-experimental-conditions-ontology
has resource example: PECO:0007114
has prefix: peco
keyword: botany
keyword: life sciences, biology
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$

Ontology of Microbial Phenotypes
keyword: microbial ecology
keyword: obo
has prefix: omp
keyword: ontology
has download URL: omp.owl
is deprecated: false
keyword: dataplant
keyword: chemical biology
description: An ontology of phenotypes covering microbes
keyword: phenotype
keyword: omics
has provider formatter: http://purl.obolibrary.org/obo/OMP_$1
keyword: life sciences, biology
has resource example: OMP_0005067
is part of: Bioregistry
keyword: phenomics
git repository: OMP-ontology
0000005: 0005067
keyword: microbiology
type: Resource
appears in: Microbial Conditions Ontology
keyword: data analysis
has URI prefix: http://purl.obolibrary.org/obo/OMP_
has responsible: James C. Hu
keyword: microbe-host interaction phenotype
has local unique identifier pattern: ^\d{7}$

Homologous Vertebrate Genes Database
type: Resource
keyword: gene
has provider formatter: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl
has URI prefix: https://bioregistry.io/hovergen:
keyword: life science
description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.
has responsible: https://orcid.org/0000-0003-2836-3463
is deprecated: true
has local unique identifier pattern: ^HBG\d+$
keyword: dna
keyword: protein
0000005: HBG004341
has resource example: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl
has prefix: hovergen
is part of: Bioregistry

Clinical measurement ontology
has URI prefix: http://purl.obolibrary.org/obo/CMO_
keyword: obo
has provider formatter: http://purl.obolibrary.org/obo/CMO_$1
keyword: ontology
appears in: Sickle Cell Disease Ontology
is deprecated: false
keyword: disease
keyword: electronic health record
is part of: Bioregistry
keyword: phenotype
git repository: CMO-Clinical-Measurement-Ontology
has local unique identifier pattern: ^\d{7}$
keyword: preclinical studies
type: Resource
has resource example: CMO_0001350
keyword: biomedical science
0000005: 0001350
description: Morphological and physiological measurement records generated from clinical and model organism research and health programs.
has prefix: cmo
has download URL: cmo.owl
keyword: life science
has responsible: https://orcid.org/0000-0002-6443-9376
keyword: model organisms

An SKOS extension for representing statistical classifications
description: An extension of SKOS for representaion of nomenclatures
keyword: vocabularies
type: Resource
has prefix: xkos
is deprecated: false
0000005: belongsTo
is part of: Bioregistry

SWEET Ontology Phenomena Geologic Geomorphology
is part of: Semantic Web for Earth and Environment Technology Ontology
has URI prefix: http://sweetontology.net/phenGeolGeomorphology/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Geomorphology
has resource example: Abrasion
type: Resource
keyword: phenomena
0000005: Abrasion
has prefix: sweet.phgg
has alternative prefix: sophgg
is deprecated: false
has provider formatter: http://sweetontology.net/phenGeolGeomorphology/$1
keyword: geologic geomorphology
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt

EndlessForms Studio Graphic
is deprecated: false
0000005: HUMAN0000789
is part of: Bioregistry
has resource example: HUMAN0000789
contributor: Charles Tapley Hoyt
has provider formatter: https://endlessforms.info/graphics/$1
has responsible: Melissa D Clarkson
description: A vector graphic for an anatomical entity useful for biological and biomedical informatics applications.
type: Resource
has URI prefix: https://endlessforms.info/graphics/
has prefix: endlessforms.graphic

Dialnet book ID
has URI prefix: https://dialnet.unirioja.es/servlet/libro
is part of: Bioregistry
description: identifier of a book in Dialnet
has provider formatter: https://dialnet.unirioja.es/servlet/libro
type: Resource
contributor: Charles Tapley Hoyt
has prefix: dialnet.book
has resource example: https://dialnet.unirioja.es/servlet/libro
0000005: 187021
is deprecated: false

Cancer cell LInes GEne fusions portAl
type: Resource
has prefix: ligea
0000005: CCLE_867
has provider formatter: http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1
is deprecated: false
description: Polymorphism and mutation databases
has URI prefix: http://hpc-bioinformatics.cineca.it/fusion/cell_line/
has resource example: CCLE 867
is part of: Bioregistry

Natural Product-Drug Interaction Research Data Repository
type: Resource
has prefix: napdi
has local unique identifier pattern: ^[0-9]+$
description: The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs).
0000005: 28
is deprecated: false
keyword: pharmacology
has resource example: https://repo.napdi.org/study/28
is part of: Bioregistry
has provider formatter: https://repo.napdi.org/study/$1
has URI prefix: https://repo.napdi.org/study/
keyword: biomedical science
has responsible: Richard Boyce

TreeFam
has resource example: TF101014
has provider formatter: http://www.treefam.org/family/$1
is deprecated: false
keyword: classification
has local unique identifier pattern: ^\w{1,2}\d+$
description: TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.
is part of: Bioregistry
0000005: TF101014
has prefix: treefam
has responsible: Fabian Schreiber
type: Resource
keyword: gene
has URI prefix: http://www.treefam.org/family/

Protein Ontology
keyword: rdf
appears in: Sickle Cell Disease Ontology
keyword: ontology
has prefix: pr
keyword: biocuration
has local unique identifier pattern: ^(?:\d{9}|[OPQ][0-9][A-Z0-9]{3}[0-9](?:-\d+)?|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2}(?:-\d+)?)$
description: The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies.
keyword: phosphorylation
is deprecated: false
keyword: metaproteomics
keyword: plant phenotypes and traits
has alternative prefix: PR
keyword: protein
has provider formatter: http://purl.obolibrary.org/obo/PR_$1
keyword: phenotype
has responsible: https://orcid.org/0000-0001-5809-9523
has alternative prefix: PRO
keyword: omics
keyword: proteomics
appears in: ChEBI Integrated Role Ontology
keyword: methylation
keyword: functional genomics
has URI prefix: http://purl.obolibrary.org/obo/PR_
keyword: qtl
is part of: Bioregistry
keyword: phenomics
git repository: PRoteinOntology
keyword: craniofacial phenotype
appears in: Cell Ontology
keyword: enhancer
0000005: 000000024
type: Resource
has download URL: pr.owl
keyword: phenology
keyword: data analysis
keyword: annotation
keyword: protein-containing complex
keyword: glycosylation
keyword: protein acetylation
keyword: biology
keyword: microbe-host interaction phenotype
contributor: https://orcid.org/0000-0001-5809-9523
keyword: post-translational modification site prediction
appears in: Uber Anatomy Ontology
keyword: disease phenotype
has resource example: PR_000000024
appears in: Provisional Cell Ontology
keyword: obo

Registry and database of bioparts for synthetic biology
has local unique identifier pattern: ^OENC\d+$
description: This database provides identifiers for catalytic bioparts which are fundamental to the design, construction, and optimization of biological systems for specific metabolic pathways. It provides basic information, function information (including catalytic functions, qualitative and quantitative parameters, and biopart expression), and sequence information (nucleotide sequence and amino acid sequence)
has resource example: OENC205
has provider formatter: https://www.biosino.org/rdbsb/bioparts_detail/$1
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
has prefix: rdbsb
has responsible: Guoqing Zhang
type: Resource
has URI prefix: https://www.biosino.org/rdbsb/bioparts_detail/
0000005: OENC205
contributor: Mufaddal Naguthanawala
is deprecated: false

bioRxiv
keyword: preprints
has local unique identifier pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$
description: The bioRxiv is a preprint server for biology
is deprecated: false
keyword: publishing
0000005: 2022.07.08.499378
has URI prefix: https://www.biorxiv.org/content/10.1101/
has resource example: https://www.biorxiv.org/content/10.1101/2022.07.08.499378
is part of: Bioregistry
has provider formatter: https://www.biorxiv.org/content/10.1101/$1
contributor: Charles Tapley Hoyt
type: Resource
has prefix: biorxiv

Cooperative Patent Classification
has local unique identifier pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$
type: Resource
has prefix: cpc
description: The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.
has resource example: https://worldwide.espacenet.com/classification
has URI prefix: https://worldwide.espacenet.com/classification
has provider formatter: https://worldwide.espacenet.com/classification
is deprecated: false
is part of: Bioregistry
0000005: A01M1/026

CEDS Learning Resource Type
keyword: educational resources
has prefix: ceds.learning_resource_type
has resource example: AlternateAssessment
keyword: open educational resources
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: AlternateAssessment
description: A vocabulary for learning resource types
type: Resource
has URI prefix: https://ceds.ed.gov/element/000928#
keyword: learning materials
is deprecated: false
has provider formatter: https://ceds.ed.gov/element/000928#$1

RIKEN Bioresource Center Cell Bank
keyword: experimental animal
keyword: sperm
keyword: seed
keyword: plant
keyword: bioresource
is part of: Bioregistry
has local unique identifier pattern: ^RCB\d+$
has URI prefix: https://cellbank.brc.riken.jp/cell_bank/CellInfo/
contributor: Charles Tapley Hoyt
has resource example: https://cellbank.brc.riken.jp/cell_bank/CellInfo/
type: Resource
keyword: recombinant host
keyword: tissue
has responsible: https://orcid.org/0000-0002-9450-5151
keyword: gene
has prefix: rcb
keyword: cell
keyword: virus
keyword: cultured cell
keyword: faseb list
keyword: cell line
keyword: embryo
keyword: genetic material
keyword: animal
keyword: organ
description: Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center.
has provider formatter: https://cellbank.brc.riken.jp/cell_bank/CellInfo/
is deprecated: false
keyword: experimental plant
keyword: dna
keyword: cultured cell line
0000005: RCB0002

NASA Open Science Data Repository Mission
has prefix: nasaosdr.mission
contributor: Mufaddal Naguthanawala
has provider formatter: https://osdr.nasa.gov/bio/repo/data/missions/$1
has resource example: ARCBedrest
is deprecated: false
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-8542-2389
has reviewer: https://orcid.org/0000-0001-9439-5346
0000005: ARCBedrest
has local unique identifier pattern: ^.+$
has URI prefix: https://osdr.nasa.gov/bio/repo/data/missions/
type: Resource
description: Identifiers for missions associated with experiments that investigate biological and health responses of terrestrial life to spaceflight

Addgene Plasmid Repository
keyword: life science
keyword: faseb list
is deprecated: false
has local unique identifier pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$
keyword: bio.tools
has provider formatter: http://addgene.org/$1
has resource example: http://addgene.org/50943
has prefix: addgene
0000005: 50943
description: Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world.
is part of: Bioregistry
keyword: molecular biology
keyword: repository
keyword: plasmid
type: Resource
keyword: sequence alignment
has URI prefix: http://addgene.org/
has responsible: Joanne Kamens

International Fungal Working Group Fungal Barcoding.
description: DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
0000005: 2224
has provider formatter: http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T
type: Resource
is deprecated: true
has URI prefix: https://bioregistry.io/fbol:
has prefix: fbol

SAREF4WEAR: an extension of SAREF for Wearables
keyword: iot
type: Resource
keyword: nfdi4ing
description: SAREF4WEAR is an extension of SAREF for Wearables
has alternative prefix: s4wear
has provider formatter: https://saref.etsi.org/saref4wear/$1
has URI prefix: https://saref.etsi.org/saref4wear/
is deprecated: false
has prefix: saref.wearable
0000005: BiometricProperty
has resource example: BiometricProperty
keyword: engineering
is part of: Bioregistry

DisProt region
has resource example: DP00086r013
has local unique identifier pattern: ^DP\d{5}r\d{3}$
is part of: Bioregistry
has URI prefix: https://www.disprot.org/
has provider formatter: https://www.disprot.org/$1
has prefix: disprot.region
0000005: DP00086r013
type: Resource
description: DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature.
is part of: DisProt
is deprecated: false

Lattes Platform number
description: number for the Lattes Platform entry on the person or group. Relationship between entry and subject must be supported by a source.
0000005: 0061106995455595
has prefix: lattes
is deprecated: false
has provider formatter: https://lattes.cnpq.br/$1
keyword: person
has URI prefix: https://lattes.cnpq.br/
has local unique identifier pattern: ^\d{16}$
is part of: Bioregistry
keyword: researcher
type: Resource
contributor: Charles Tapley Hoyt
has resource example: https://lattes.cnpq.br/0061106995455595

Barley Ontology
has download URL: CO 323.owl
keyword: botany
keyword: agriculture
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
type: Resource
has resource example: CO 323:0000252
git repository: Crop-Ontology
description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Its focus is on traits and variable used in field trials for breeding.
has provider formatter: https://cropontology.org/rdf/CO_323:$1
0000005: 0000252
has prefix: co_323
keyword: ontology
has URI prefix: https://cropontology.org/rdf/CO_323:
is deprecated: false
keyword: plant phenotypes and traits
keyword: phenotype

The Echinoderm Anatomy and Development Ontology
has local unique identifier pattern: ^\d{7}$
type: Resource
has download URL: ecao.owl
description: None
has prefix: ecao
has resource example: ECAO_0107180
is deprecated: false
0000005: 0107180
has provider formatter: http://purl.obolibrary.org/obo/ECAO_$1
keyword: obo
git repository: ecao ontology
keyword: ontology
depends on: Cell Ontology
depends on: Relation Ontology
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-3625-0955
has URI prefix: http://purl.obolibrary.org/obo/ECAO_
depends on: Uber Anatomy Ontology

Pathogen Transmission Ontology
0000005: 0000024
has resource example: TRANS_0000024
has responsible: https://orcid.org/0000-0001-8910-9851
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
has prefix: trans
type: Resource
keyword: biomedical science
keyword: host
keyword: pathogen
description: The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.
has URI prefix: http://purl.obolibrary.org/obo/TRANS_
keyword: obo
git repository: PathogenTransmissionOntology
keyword: ontology
has download URL: trans.owl
keyword: infection process
is deprecated: false
has provider formatter: http://purl.obolibrary.org/obo/TRANS_$1

KEGG BRITE
keyword: ontology
keyword: pathway
is deprecated: false
description: KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships.
has resource example: ko00002
is part of: Bioregistry
has prefix: kegg.brite
type: Resource
has provider formatter: https://www.kegg.jp/brite/$1
0000005: ko00002
has URI prefix: https://www.kegg.jp/brite/
keyword: classification

HOMD Sequence Metainformation
has provider formatter: https://v31.homd.org/genome/genome_description
description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.
has URI prefix: https://v31.homd.org/genome/genome_description
keyword: microbial
has local unique identifier pattern: ^SEQF\d+(?:\.\d+)?$
keyword: genome
is deprecated: false
has prefix: homd.seq
has resource example: https://v31.homd.org/genome/genome_description
0000005: SEQF1003.1
is part of: Bioregistry
type: Resource
has responsible: 0000-0001-6689-317X

Cryo Electron Microscopy
is deprecated: false
has provider formatter: http://scipion.i2pc.es/ontology/CRYOEM_$1
has download URL: cryoem.owl
keyword: electron microscopy
is part of: Bioregistry
type: Resource
keyword: structural biology
description: The CryoEM Ontology for describing objects and workflows in Single Particle Analysis by Cryo Electron Microscopy.
has resource example: CRYOEM_0000052
has local unique identifier pattern: ^\d{7}$
0000005: 0000052
git repository: cryoem
keyword: bioimaging
has URI prefix: http://scipion.i2pc.es/ontology/CRYOEM_
has prefix: cryoem
keyword: ontology
has responsible: Carlos Oscar S. Sorzano

Transporter Classification Database
has prefix: tcdb
has local unique identifier pattern: ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$
type: Resource
has alternative prefix: TC
keyword: structure
keyword: phylogenetics
has URI prefix: http://www.tcdb.org/search/result.php
keyword: life science
0000005: 5.A.1.1.1
is deprecated: false
has resource example: http://www.tcdb.org/search/result.php
description: The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally.
has responsible: https://orcid.org/0000-0001-5530-0017
keyword: cell biology
keyword: computational biology
is part of: Bioregistry
keyword: protein
keyword: knowledge and information systems
has provider formatter: http://www.tcdb.org/search/result.php

University hospital Medical Information Network Clinical Trial Registry
has prefix: uminctr
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^UMIN\d+$|^C\d+$
description: An additional Japanese clinical trial registry
contributor: Charles Tapley Hoyt
0000005: UMIN000049383
type: Resource

MarRef
has provider formatter: https://mmp.sfb.uit.no/databases/marref/#/records/$1
is deprecated: false
has resource example: records/MMP3312982.2
has URI prefix: https://mmp.sfb.uit.no/databases/marref/#/records/
has prefix: mmp.ref
is part of: Bioregistry
description: MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes.
type: Resource
0000005: MMP3312982.2
has local unique identifier pattern: ^MMP\d+.\d+$

Quinoa Ontology
has local unique identifier pattern: ^\d{7}$
has prefix: co_367
has download URL: CO 367.owl
0000005: 0000004
has resource example: CO 367:0000004
keyword: ontology
has URI prefix: https://cropontology.org/rdf/CO_367:
is deprecated: false
description: Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation Challenge Program (GCP) describe traits variables of Quinoa Germinate Database http://germinate.quinoadb.org. Quinoa Phenotyping Consortium Creation Date 23.05.2021
has responsible: Elizabeth Arnaud
is part of: Bioregistry
has provider formatter: https://cropontology.org/rdf/CO_367:$1
type: Resource
git repository: Crop-Ontology

Type of Concept Group
is deprecated: false
has resource example: code Administrative
0000005: Administrative
has URI prefix: https://vocabularies.cessda.eu/vocabulary/TypeOfConceptGroup#code_
has provider formatter: https://vocabularies.cessda.eu/vocabulary/TypeOfConceptGroup#code_$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: ddi.typeofconceptgroup
type: Resource
description: Specifies the rationale for creating a concept group.
has identifier space owner: 015em2733

BioMagResBank
has reviewer: Charles Tapley Hoyt
description: A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids.
has prefix: biomagresbank
is deprecated: false
is part of: Bioregistry
keyword: protein
has URI prefix: http://www.bmrb.wisc.edu/data_library/generate_summary.php
has provider formatter: http://www.bmrb.wisc.edu/data_library/generate_summary.php
type: Resource
has resource example: http://www.bmrb.wisc.edu/data_library/generate_summary.php
0000005: 10046

GALEN
description: A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.
is deprecated: true
has responsible: Julian Seidenberg
has download URL: galen.owl
has provider formatter: http://www.co-ode.org/ontologies/galen#$1
has URI prefix: http://www.co-ode.org/ontologies/galen#
has prefix: galen
keyword: ontology
has resource example: MagnitudeValueType
is part of: Bioregistry
0000005: MagnitudeValueType
type: Resource

Cell Ontology
has provider formatter: http://purl.obolibrary.org/obo/CL_$1
depends on: Gene Ontology
depends on: Protein Ontology
has local unique identifier pattern: ^\d{7}$
description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.
type: Resource
appears in: Microbial Conditions Ontology
has resource example: CL_0000062
contributor: https://orcid.org/0000-0002-6523-4866
keyword: annotation
depends on: NCBI Taxonomy
appears in: The Echinoderm Anatomy and Development Ontology
has responsible: David Osumi-Sutherland
has URI prefix: http://purl.obolibrary.org/obo/CL_
keyword: cell
appears in: Uber Anatomy Ontology
git repository: cell-ontology
keyword: anatomy
keyword: morphology
keyword: life science
has download URL: cl.owl
appears in: Provisional Cell Ontology
appears in: Gene Ontology
0000005: 0000062
keyword: obo
has prefix: cl
keyword: ontology
keyword: cell biology
depends on: Relation Ontology
keyword: immunology
appears in: Cell Line Ontology
is deprecated: false
depends on: OBO Metadata Ontology
is part of: Bioregistry
keyword: immunogenetics
appears in: Human developmental anatomy, abstract
keyword: omics
depends on: Uber Anatomy Ontology
depends on: Phenotype And Trait Ontology
appears in: Xenopus Phenotype Ontology

CohesinDB - cohesin-related chromatin loop
is part of: Bioregistry
has URI prefix: https://cohesindb.iqb.u-tokyo.ac.jp/browseloop/eachloop/
type: Resource
has provider formatter: https://cohesindb.iqb.u-tokyo.ac.jp/browseloop/eachloop/$1
keyword: interaction
description: Contains identifiers of cohesin-related chromatin loops from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each identifier represents a single cohesin-related chromatin loop. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information.
0000005: CDBL00540805
has reviewer: Charles Tapley Hoyt
contributor: https://orcid.org/0009-0000-6974-6386
keyword: chromatin loop
is deprecated: false
has local unique identifier pattern: ^CDBL00\d{6}$
keyword: protein
has prefix: cohesindb.loops
has responsible: Ryuichiro Nakato
has resource example: CDBL00540805
keyword: cohesin

GXA Expt
has local unique identifier pattern: ^[AEP]-\w{4}-\d+$
is deprecated: false
has resource example: E-MTAB-2037
description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.
is part of: Bioregistry
has URI prefix: https://www.ebi.ac.uk/gxa/experiments/
type: Resource
has provider formatter: https://www.ebi.ac.uk/gxa/experiments/$1
0000005: E-MTAB-2037
has identifier space owner: 02catss52
has prefix: gxa.expt

World Health Organization Verbal Autopsy Code
has prefix: who.va
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
0000005: VAs-09.01
keyword: cause of death
is part of: Bioregistry
type: Resource
keyword: verbal autopsy
has local unique identifier pattern: ^VAs-\d{2}(?:\.\d{2})?$
has reviewer: Charles Tapley Hoyt
description: Identifiers assigned by the World Health Organization for coding causes of death from verbal autopsy (VA) reports. These codes are produced as outputs in standard VA analysis software.

Agilent Probe
description: This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.
keyword: transcriptomics
type: Resource
has local unique identifier pattern: ^A_\d+_.+$
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: A_24_P98555
has prefix: agilent.probe

NucleaRDB
is deprecated: false
has alternative prefix: nuclearbd
has local unique identifier pattern: ^\w+\_\w+$
0000005: prgr_human
is part of: Bioregistry
type: Resource
description: NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.
has provider formatter: http://www.receptors.org/nucleardb/proteins/$1
has URI prefix: http://www.receptors.org/nucleardb/proteins/
has resource example: prgr human
has prefix: nucleardb
has responsible: https://orcid.org/0000-0002-1067-7053
keyword: classification

InterPro
is deprecated: false
keyword: protein
keyword: bioinformatics
has alternative prefix: IP
has download URL: interpro.owl
description: InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
has URI prefix: https://www.ebi.ac.uk/interpro/entry/InterPro/
is part of: Bioregistry
has local unique identifier pattern: ^IPR\d{6}$
has alternative prefix: IPR
keyword: biology
has provider formatter: https://www.ebi.ac.uk/interpro/entry/InterPro/$1
type: Resource
has resource example: IPR016380
has prefix: interpro
0000005: IPR016380
git repository: interpro-blog
has alternative prefix: InterPro
keyword: domain
keyword: obo
has responsible: Alex Bateman
keyword: ontology

Gramene protein
0000005: 78073
is deprecated: false
has prefix: gramene.protein
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
has provider formatter: http://www.gramene.org/db/protein/protein_search
description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.
has URI prefix: http://www.gramene.org/db/protein/protein_search
has alternative prefix: GR_PROTEIN
has resource example: http://www.gramene.org/db/protein/protein_search

CIViC Assertion
0000005: 3
is part of: Bioregistry
type: Resource
has responsible: Malachi Griffith
has prefix: civic.aid
has alternative prefix: civic.assertion
has provider formatter: https://civicdb.org/links/assertions/$1
description: A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.
has resource example: https://civicdb.org/links/assertions/3
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has URI prefix: https://civicdb.org/links/assertions/

Social Science Research Network Article
has provider formatter: https://ssrn.com/abstract=$1
0000005: 1667659
has URI prefix: https://ssrn.com/abstract=
has prefix: ssrn.article
description: identifier for an article/paper at the SSRN
is deprecated: false
has resource example: https://ssrn.com/abstract=1667659
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt

Bambara Groundnut Ontology
keyword: ontology
is deprecated: false
has responsible: Elizabeth Arnaud
is part of: Bioregistry
type: Resource
has URI prefix: https://cropontology.org/rdf/CO_366:
git repository: Crop-Ontology
description: This ontology is a part of the the Crop Ontology project , as an essential source of traits and variables to support the standardization of the breeding databases.
0000005: 0000072
has resource example: CO 366:0000072
has download URL: CO 366.owl
has local unique identifier pattern: ^\d{7}$
has provider formatter: https://cropontology.org/rdf/CO_366:$1
has prefix: co_366

Ontology for Immune Epitopes
contributor: Charles Tapley Hoyt
0000005: 0000001
description: The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes.
has local unique identifier pattern: ^\d{7}$
git repository: ONTIE
type: Resource
has responsible: Bjoern Peters
keyword: major histocompatibility complex
has provider formatter: https://ontology.iedb.org/ontology/ONTIE_$1
keyword: life science
is deprecated: false
has resource example: ONTIE_0000001
keyword: ontology
has URI prefix: https://ontology.iedb.org/ontology/ONTIE_
keyword: immunology
keyword: infection process
has download URL: ontie.owl
has prefix: ontie
is part of: Bioregistry

PharmGKB pathway
has URI prefix: http://www.pharmgkb.org/pathway/
type: Resource
has responsible: Teri E Klein
has prefix: pharmgkb.pathways
0000005: PA146123006
has provider formatter: http://www.pharmgkb.org/pathway/$1
description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.
keyword: ontology
has resource example: PA146123006
keyword: pathway
is deprecated: false
keyword: pharmacogenomics
has local unique identifier pattern: ^PA\d+$
has download URL: pharmgkb.pathways.owl
is part of: Bioregistry

World Wildlife Fund Ecoregion
has prefix: wwf.ecoregion
type: Resource
has URI prefix: https://www.worldwildlife.org/ecoregions/
has reviewer: Charles Tapley Hoyt
description: WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
has provider formatter: https://www.worldwildlife.org/ecoregions/$1
is deprecated: false
has resource example: AT1402
has local unique identifier pattern: ^AT\d+$
has alternative prefix: WWF
0000005: AT1402
is part of: Bioregistry
contributor: https://orcid.org/0000-0002-6601-2165

SWEET Ontology Property Space Location
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has prefix: sweet.propsl
keyword: space location
has provider formatter: http://sweetontology.net/propSpaceLocation/$1
type: Resource
has resource example: Center
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Location
is deprecated: false
0000005: Center
has alternative prefix: sopropsl
has URI prefix: http://sweetontology.net/propSpaceLocation/
is part of: Bioregistry

Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa.
has responsible: Paul Flicek
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes.
has provider formatter: https://metazoa.ensembl.org/id/$1
is part of: Bioregistry
has local unique identifier pattern: ^\w+(\.)?\d+$
0000005: FBtr0084214
has prefix: ensembl.metazoa
keyword: comparative genomics
type: Resource
has resource example: FBtr0084214
has URI prefix: https://metazoa.ensembl.org/id/
keyword: genome
keyword: genomics
is deprecated: false

Cambridge Structural Database
is part of: Bioregistry
keyword: chemistry
has resource example: https://www.ccdc.cam.ac.uk/services/structures
keyword: organic chemistry
type: Resource
0000005: PELNAW
has responsible: https://orcid.org/0000-0001-8921-9575
has local unique identifier pattern: ^[A-Z]{6}(\d{2})?$
keyword: biochemistry
is deprecated: false
has URI prefix: https://bioregistry.io/csd:
has provider formatter: https://www.ccdc.cam.ac.uk/services/structures
description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode.
keyword: organic molecular chemistry
has prefix: csd

SWEET Ontology Human Decision
has prefix: sweet.hud
has alternative prefix: sohud
has URI prefix: http://sweetontology.net/humanDecision/
is deprecated: false
has provider formatter: http://sweetontology.net/humanDecision/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Decision
0000005: Allocation
is part of: Bioregistry
has resource example: Allocation
keyword: decision
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt

Agricultural Online Access
has resource example: IND608186955
has local unique identifier pattern: ^(IND|GUA)\d+$
has responsible: 0000-0001-8522-334X
type: Resource
has alternative prefix: AGR
contributor: https://orcid.org/0000-0002-1216-4761
has alternative prefix: AGRICOLA_ID
appears in: Chemical Entities of Biological Interest
has provider formatter: https://europepmc.org/article/AGR/$1
description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.
has prefix: agricola
is deprecated: false
has URI prefix: https://europepmc.org/article/AGR/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
appears in: PubMed Central
contributor: https://orcid.org/0000-0002-6601-2165
0000005: IND608186955

eggNOG
description: eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).
has URI prefix: http://eggnog.embl.de/version_3.0/cgi/search.py
has resource example: http://eggnog.embl.de/version_3.0/cgi/search.py
has responsible: https://orcid.org/0000-0003-4195-5025
is part of: Bioregistry
type: Resource
keyword: gene
has provider formatter: http://eggnog.embl.de/version_3.0/cgi/search.py
keyword: life science
is deprecated: true
has prefix: eggnog
has local unique identifier pattern: ^\w+$
0000005: veNOG12876

Adverse Outcome Pathway Ontology
git repository: aop-ontology
has reviewer: Charles Tapley Hoyt
has prefix: aopo
has URI prefix: http://aopkb.org/aop_ontology#
description: The AOPO provides classes and relationships for the semantic representation of the Adverse Outcome Pathway framework.
has provider formatter: http://aopkb.org/aop_ontology#$1
keyword: adverse outcome pathway
keyword: ontology
is deprecated: false
contributor: Javier Millán Acosta
is part of: Bioregistry
type: Resource
has resource example: AdverseOutcomePathway
has local unique identifier pattern: ^[A-Za-z_]+$
0000005: AdverseOutcomePathway
has download URL: aopo.owl
has responsible: https://orcid.org/0000-0003-4977-5352

Cell Version Control Repository
is deprecated: false
has provider formatter: https://www.cellrepo.com/repositories/$1
0000005: 82
is part of: Bioregistry
type: Resource
description: The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines
has URI prefix: https://www.cellrepo.com/repositories/
has resource example: https://www.cellrepo.com/repositories/82
has local unique identifier pattern: ^[0-9]+$
has prefix: cellrepo

YeTFasCo
has URI prefix: http://yetfasco.ccbr.utoronto.ca/showPFM.php
has provider formatter: http://yetfasco.ccbr.utoronto.ca/showPFM.php
has prefix: yetfasco
is deprecated: false
description: The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.
has local unique identifier pattern: ^\w+\_\d+(\.\d+)?$
is part of: Bioregistry
has resource example: http://yetfasco.ccbr.utoronto.ca/showPFM.php
0000005: YOR172W_571.0
type: Resource

ESCO Occupation
has provider formatter: http://data.europa.eu/esco/occupation/$1
has prefix: esco.occupation
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
description: The ESCO occupations pillar is built on ISCO-08 which serves as its hierarchical structure. ISCO-08 provides the top four levels for the occupations pillar and ESCO occupations are located at level 5 and lower. In ESCO, each occupation is mapped to exactly one ISCO-08 code. [from homepage]
has URI prefix: http://data.europa.eu/esco/occupation/
is deprecated: false

Animal Genome Chicken QTL
has prefix: chickenqtldb
type: Resource
has resource example: https://www.animalgenome.org/QTLdb/q
has provider formatter: https://www.animalgenome.org/QTLdb/q
is part of: Animal Genome QTL
has URI prefix: https://www.animalgenome.org/QTLdb/q
0000005: 14362
keyword: genome
is deprecated: false
keyword: dna
has local unique identifier pattern: ^\d+$
description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs.
is part of: Bioregistry

Exif data description vocabulary
is part of: Bioregistry
type: Resource
has prefix: exif
description: Vocabulary to describe an Exif format picture data. All Exif 2.2 tags are defined as RDF properties, as well as several terms to help this schema.
keyword: image
0000005: orientation
is deprecated: false

National Drug Code
has provider formatter: http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1
description: The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily.
has prefix: ndc
type: Resource
has local unique identifier pattern: ^\d+\-\d+\-\d+$
has resource example: http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/0002-1975-61
0000005: 0002-1975-61
is deprecated: false
is part of: Bioregistry
has URI prefix: http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/

Genomic Distribution of structural Superfamilies
type: Resource
0000005: 46946
is deprecated: true
description: Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases.
has URI prefix: http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi
keyword: classification
is part of: Bioregistry
keyword: genome
has provider formatter: http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi
has prefix: gendis
has resource example: http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi
has reviewer: Charles Tapley Hoyt

BugBase Expt
type: Resource
has provider formatter: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php
has URI prefix: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php
is deprecated: true
has prefix: bugbase.expt
has resource example: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php
0000005: 288
description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments.
is part of: Bioregistry
has local unique identifier pattern: ^\d+$

Semantic Mapping Vocabulary
git repository: semantic-mapping-vocabulary
has resource example: LexicalMatching
has alternative prefix: semapv_voc
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: LexicalMatching
has download URL: semapv.owl
type: Resource
has alternative prefix: sempav_voc
has provider formatter: https://w3id.org/semapv/vocab/$1
has identifier space owner: Q115518213
description: The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata.
keyword: ontology
has responsible: https://orcid.org/0000-0002-7356-1779
has URI prefix: https://w3id.org/semapv/vocab/
is deprecated: false
has prefix: semapv

LINCS Protein
is deprecated: false
0000005: 200282
has URI prefix: https://lincs.hms.harvard.edu/db/proteins/
has prefix: lincs.protein
has resource example: https://lincs.hms.harvard.edu/db/proteins/200282
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
description: The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.
type: Resource
has provider formatter: https://lincs.hms.harvard.edu/db/proteins/$1

BiGG Compartment
description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments.
has provider formatter: http://bigg.ucsd.edu/compartments/$1
keyword: compartment
keyword: ontology
has prefix: bigg.compartment
is deprecated: false
is part of: Bioregistry
has URI prefix: http://bigg.ucsd.edu/compartments/
has resource example: http://bigg.ucsd.edu/compartments/c
has local unique identifier pattern: ^c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y$
has responsible: https://orcid.org/0000-0003-1238-1499
0000005: c
type: Resource
keyword: cellular component
keyword: subcellular compartment
has download URL: bigg.compartment.owl

BioCatalogue Service
has URI prefix: https://www.biocatalogue.org/services/
has provider formatter: https://www.biocatalogue.org/services/$1
has prefix: biocatalogue.service
has responsible: Carole Goble
keyword: registry
description: The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all.
is deprecated: false
0000005: 614
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
has resource example: https://www.biocatalogue.org/services/614

Semantic Resource Types Vocabulary
0000005: 000001
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: semantic resource
description: The Semantic Resource Types Vocabulary was created for NSF's EarthCube Program's Resource Repository. Includes entries for things like 'thesaurus', 'ontology', 'controlled vocabulary', 'taxonomy'.
has provider formatter: http://cor.esipfed.org/ont/earthcube/srt_$1
has responsible: Ruth Duerr
type: Resource
has resource example: srt_000001
git repository: srt
has prefix: earthcube.srt
has URI prefix: http://cor.esipfed.org/ont/earthcube/srt_

MobiVoc Open Mobility Vocabulary 1.1.4
keyword: fid move
0000005: AccessCondition
type: Resource
keyword: nfdi4ing
has resource example: AccessCondition
is deprecated: false
description: MobiVoc is an open vocabulary for future-oriented mobility solutions.
keyword: traffic engineering
has prefix: mobivoc
has provider formatter: http://schema.mobivoc.org/#$1
is part of: Bioregistry
has URI prefix: http://schema.mobivoc.org/#

Office of Scientific and Technical Information (OSTI)
has reviewer: Charles Tapley Hoyt
type: Resource
contributor: https://orcid.org/0000-0002-8741-7823
keyword: publication
has resource example: https://www.osti.gov/biblio/1668761
has prefix: osti.article
is deprecated: false
has URI prefix: https://www.osti.gov/biblio/
keyword: articles
has provider formatter: https://www.osti.gov/biblio/$1
keyword: article
keyword: publications
0000005: 1668761
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: The U.S. Department of Energy (DOE) Office of Scientific and Technical Information (OSTI) is the main metadata archive for permanent storage of registered [DOE DOI products](https://www.osti.gov/pids/doi-services/doe-data-id-service) (datasets, code, articles, patents, multimedia, etc.). When a DOI is minted a unique OSTI identifier for each record [{osti_id}](https://www.osti.gov/api/v1/docs#endpoints-singlerecord) is provided as the suffix in the DOI schema ([{site-specific-prefix}/{user-supplied-doi-infix}/{osti_id}](https://www.osti.gov/pids/doi-services)) and can be alternatively used as the main product identifier endpoint when [searching OSTI.GOV](https://www.osti.gov/search-tools) registry archive (see example below). OSTI.GOV is the primary registry and search tool for all Department of Energy (DOE) funded science, technology, and engineering research and development (R&D) results and the organizational hub for information about the DOE Office of Scientific and Technical Information (OSTI. **Data Product Type Example:** - https://www.osti.gov/biblio/1668761 - https://www.osti.gov/search/semantic:1668761 - https://www.osti.gov/dataexplorer/biblio/dataset/1668761 - https://www.osti.gov/api/v1/records/1668761 - https://doi.org/10.11578/1668761 **Other Core Product Registry Examples:** - Journal Articles: https://www.osti.gov/pages/biblio - Datasets: https://www.osti.gov/dataexplorer/biblio/dataset/ - Software: https://www.osti.gov/doecode/biblio/ - Patents: https://www.osti.gov/doepatents/biblio/ - Multimedia: https://www.osti.gov/sciencecinema/biblio/

NFDI4Energy Resources
has part: Energy Market Roles ontology
creator: Charles Tapley Hoyt
has part: Big Open Network of Sustainability Assessment Information Ontology
has part: Ontology Modeling for Intelligent Domotic Environments
has part: Functional Mock-up Interface Ontology
has part: Standard-Thesaurus Wirtschaft
has part: SARGON (SmArt eneRGy dOmain oNtology)
has part: Open Energy Ontology
has part: SAREF4EE: the EEbus/Energy@home extension of SAREF
has part: Brick Ontology
description: Prefixes for ontologies relevant for the NFDI4Energy
has part: Retail Energy Market of Great Britain
has part: Digital Construction Energy (dices)
type: Collection
has part: SAREF4GRID: an extension of SAREF for the Smart Grid domain
has part: OpenADR ontology
has part: SMS-Ontology
has part: Mid-level Energy Ontology

NFDI4Earth Collection
has part: Bioregistry
type: Collection
creator: Charles Tapley Hoyt
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Earth

EVORA Ontology
has URI prefix: https://w3id.org/evorao/
git repository: evora-ontology
keyword: ontology
is deprecated: false
has resource example: AlternateName
0000005: AlternateName
has download URL: evorao.owl
has prefix: evorao
is part of: Bioregistry
has provider formatter: https://w3id.org/evorao/$1
type: Resource
description: The EVORAO Ontology provides a structured and harmonized vocabulary for describing shareable pathogens as characterized biological materials, along with their derived products and associated services, organized into collections. Developed within the EVORA project, it supports consistent metadata annotation across research infrastructures, promoting findability, accessibility, interoperability, and reusability (FAIR). By aligning with relevant standards and ontologies, EVORAO facilitates cross-domain collaboration, integration, and sharing of pathogenic resources and services to enhance pandemic preparedness and response. While initially focused on virology, EVORAO is designed to be extensible and also supports metadata harmonization for other pathogens. [from repository]

HMS Library of Integrated Network-based Cellular Signatures Datasets
is part of: Bioregistry
has resource example: https://lincs.hms.harvard.edu/db/datasets/20003
contributor: Charles Tapley Hoyt
has prefix: hms.lincs.dataset
has URI prefix: https://lincs.hms.harvard.edu/db/datasets/
type: Resource
has provider formatter: https://lincs.hms.harvard.edu/db/datasets/$1
is deprecated: false
has local unique identifier pattern: ^2\d{4}$
0000005: 20003
description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.

COSMIC Cell Lines
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
0000005: 906801
contributor: Charles Tapley Hoyt
has prefix: cosmic.cell
has URI prefix: https://cancer.sanger.ac.uk/cell_lines/sample/overview
type: Resource
description: COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer
has provider formatter: https://cancer.sanger.ac.uk/cell_lines/sample/overview
has resource example: https://cancer.sanger.ac.uk/cell_lines/sample/overview

French National Center for Scientific Research - Research Group Identifier
has prefix: cnrs
has provider formatter: https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin
has URI prefix: https://bioregistry.io/cnrs:
is deprecated: false
description: identifier for an academic research group issued by the CNRS
is part of: Bioregistry
has resource example: https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin
contributor: Charles Tapley Hoyt
0000005: UMR7315
type: Resource
has local unique identifier pattern: ^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY|UPS)\d+$

Ribocentre
is part of: Bioregistry
has responsible: Lin Huang
has URI prefix: https://www.ribocentre.org/docs/
description: Ribocentre is designed to contain comprehensive information of all natural ribozymes.
has reviewer: Charles Tapley Hoyt
type: Resource
has alternative prefix: ribocenter
git repository: ribocentre.github.io
has local unique identifier pattern: ^[a-zA-Z0-9-]+$
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
0000005: hammer
has resource example: hammer
has prefix: ribocentre
has provider formatter: https://www.ribocentre.org/docs/$1

DepMap Cell Lines
has responsible: https://orcid.org/0000-0002-2857-4685
0000005: ACH-000001
keyword: cancer cell line
has prefix: depmap
description: Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells.
has resource example: ACH-000001
type: Resource
has URI prefix: https://depmap.org/portal/cell_line/
keyword: cell
is deprecated: false
keyword: cell line
has provider formatter: https://depmap.org/portal/cell_line/$1
keyword: ontology
has download URL: depmap.owl
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^ACH-\d+$

UniProt Diseases
has local unique identifier pattern: ^DI-\d{5}$
is part of: Bioregistry
has provider formatter: https://www.uniprot.org/diseases/$1
type: Resource
contributor: Charles Tapley Hoyt
has URI prefix: https://www.uniprot.org/diseases/
0000005: DI-04240
description: The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary.
has alternative prefix: SP_DI
has responsible: Alex Bateman
has prefix: uniprot.disease
keyword: ontology
has download URL: https://rest.uniprot.org/diseases/stream
has resource example: DI-04240
is deprecated: false
has alternative prefix: DI

Peruvian Clinical Trial Registry
contributor: Charles Tapley Hoyt
has URI prefix: https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp
has local unique identifier pattern: ^\d+-\d+(-[A-Z])?$
description: The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website)
type: Resource
0000005: 046-19
has prefix: repec
has resource example: https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp
has provider formatter: https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp
is deprecated: false
is part of: Bioregistry

FAIRsharing User
has resource example: https://fairsharing.org/users/5112
description: A user of FAIRsharing
has provider formatter: https://fairsharing.org/users/$1
type: Resource
has responsible: https://orcid.org/0000-0002-7702-4495
is deprecated: false
0000005: 5112
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: fairsharing.user
has URI prefix: https://fairsharing.org/users/

SWEET Ontology Relationships Chemical
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Chemical
has URI prefix: http://sweetontology.net/relaChemical/
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: atomicMass
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: chemical
has prefix: sweet.relch
has alternative prefix: sorelch
has provider formatter: http://sweetontology.net/relaChemical/$1
type: Resource
has resource example: atomicMass

Open Researcher and Contributor
keyword: subject agnostic
has provider formatter: https://orcid.org/$1
has responsible: Will Simpson
has URI prefix: https://orcid.org/
is deprecated: false
has alternative prefix: ORCID
has alternative prefix: ORCiD
keyword: person
0000005: 0000-0003-4423-4370
has local unique identifier pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$
description: ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities.
has prefix: orcid
git repository: ORCID
is part of: Bioregistry
type: Resource
has resource example: Charles Tapley Hoyt

Progenetix
is deprecated: false
keyword: genomics
has alternative prefix: Progenetix
has responsible: Michael Baudis
has provider formatter: https://progenetix.org/services/ids/$1
has local unique identifier pattern: ^\w{3,15}[-_]\w[\w.-]{3,128}$
description: The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt "neoplasm" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs.
is part of: Bioregistry
type: Resource
has resource example: pgxbs-kftva5zv
has prefix: pgx
keyword: biomedical science
0000005: pgxbs-kftva5zv
has URI prefix: https://progenetix.org/services/ids/

Gazetteer
git repository: gaz
appears in: Sickle Cell Disease Ontology
keyword: geographic location
keyword: environmental science
is deprecated: false
has download URL: gaz.owl
keyword: obo
keyword: ontology
has local unique identifier pattern: ^\d{8}$
has prefix: gaz
is part of: Bioregistry
description: A gazetteer constructed on ontological principles. The countries are actively maintained.
0000005: 00620027
has provider formatter: http://purl.obolibrary.org/obo/GAZ_$1
has responsible: https://orcid.org/0000-0001-8910-9851
type: Resource
has resource example: GAZ_00620027
has URI prefix: http://purl.obolibrary.org/obo/GAZ_

Orientations of Proteins in Membranes Database
has URI prefix: http://opm.phar.umich.edu/protein.php
is part of: Bioregistry
description: The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.
type: Resource
has local unique identifier pattern: ^[0-9][A-Za-z0-9]{3}$
has resource example: http://opm.phar.umich.edu/protein.php
has prefix: opm
has provider formatter: http://opm.phar.umich.edu/protein.php
is deprecated: false
0000005: 1h68

Information Artifact Ontology
git repository: IAO
keyword: nfdi4ing
keyword: reagent
keyword: biomedical science
keyword: experimental measurement
has provider formatter: http://purl.obolibrary.org/obo/IAO_$1
0000005: 0000030
has URI prefix: http://purl.obolibrary.org/obo/IAO_
keyword: subject agnostic
has responsible: Jie Zheng
has local unique identifier pattern: ^\d{7}$
keyword: data identity and mapping
keyword: data management
type: Resource
appears in: Model Card Report Ontology
keyword: fair data spaces
keyword: study design
description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.
keyword: obo
appears in: Medical Action Ontology
appears in: clinical LABoratory Ontology
appears in: An ontology of core ecological entities
keyword: ontology
appears in: Agronomy Ontology
appears in: Population and Community Ontology
has prefix: iao
is deprecated: false
appears in: Performance Summary Display Ontology
appears in: FuTRES Ontology of Vertebrate Traits
keyword: assay
appears in: Clytia hemisphaerica Development and Anatomy Ontology
keyword: nfdi4chem
has resource example: IAO_0000030
keyword: knowledge and information systems
keyword: drug report
has download URL: iao.owl
appears in: Xenopus Phenotype Ontology
is part of: Bioregistry
appears in: Data Use Ontology
appears in: Environmental conditions, treatments and exposures ontology

INSDC CDS
has provider formatter: http://getentry.ddbj.nig.ac.jp/getentry/dad/$1
0000005: AAA35559
type: Resource
has local unique identifier pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
description: The coding sequence or protein identifiers as maintained in INSDC.
is deprecated: false
has canonical: NCBI Protein
has resource example: http://getentry.ddbj.nig.ac.jp/getentry/dad/AAA35559
has URI prefix: http://getentry.ddbj.nig.ac.jp/getentry/dad/
is part of: Bioregistry
has prefix: insdc.cds

National Microbiome Data Collaborative
contributor: Donny Winston
has prefix: nmdc
type: Resource
has reviewer: Charles Tapley Hoyt
description: An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.
is deprecated: false
has URI prefix: https://w3id.org/nmdc/
has provider formatter: https://w3id.org/nmdc/$1
0000005: y3ax-8bq3-60
has resource example: y3ax-8bq3-60
has responsible: Donny Winston
has local unique identifier pattern: ^.{2,}$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: microbiome

Authorea author ID
is part of: Bioregistry
has resource example: https://www.authorea.com/users/229233
description: identifier for an author on the Authorea writing service
has prefix: authorea.author
type: Resource
0000005: 229233
is deprecated: false
has URI prefix: https://www.authorea.com/users/
has provider formatter: https://www.authorea.com/users/$1
has local unique identifier pattern: ^[1-9]\d*$

UniProt Subcellular Locations
has download URL: https://rest.uniprot.org/locations/stream
keyword: ontology
has alternative prefix: UniProtKB-SubCell
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms.
0000005: SL-0002
has URI prefix: https://www.uniprot.org/locations/
has provider formatter: https://www.uniprot.org/locations/$1
type: Resource
has resource example: SL-0002
has responsible: Alex Bateman
has prefix: uniprot.location
has alternative prefix: SP_SL
has alternative prefix: UPLOC
has local unique identifier pattern: ^SL-\d+$

FaBiO, the FRBR-aligned Bibliographic Ontology
description: The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references.
keyword: miscellaneous
has download URL: fabio.owl
has URI prefix: https://sparontologies.github.io/fabio/current/fabio.html#
keyword: ontology
is deprecated: false
has resource example: d4e2515
has provider formatter: https://sparontologies.github.io/fabio/current/fabio.html#$1
has responsible: Silvio Peroni
git repository: fabio
is part of: Bioregistry
keyword: literature
contributor: Charles Tapley Hoyt
type: Resource
keyword: spar
0000005: d4e2515
has prefix: fabio
keyword: subject agnostic

Transcription Factor Database
0000005: 0045310
has resource example: http://www.transcriptionfactor.org/index.cgi
has prefix: dbd
keyword: genome
is deprecated: false
keyword: regulation
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has provider formatter: http://www.transcriptionfactor.org/index.cgi
has URI prefix: https://bioregistry.io/dbd:
type: Resource
description: The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins.

Paleobiology Database
description: The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.
has URI prefix: http://fossilworks.org/
keyword: taxonomy
is deprecated: false
has resource example: http://fossilworks.org/
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has prefix: paleodb
type: Resource
has provider formatter: http://fossilworks.org/
0000005: 83088

Computational Chemistry Ontology
has URI prefix: http://theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#
is deprecated: false
keyword: chemistry
keyword: nfdi4cat
has download URL: ontocompchem.owl
keyword: nfdi4chem
description: Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)
is part of: Bioregistry
has prefix: worldavatar.compchem
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: http://theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#$1
keyword: ontology
keyword: chemical and environmental engineering

Japan Collection of Microorganisms
has resource example: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number
has URI prefix: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number
keyword: microbial
description: The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.
keyword: taxonomy
type: Resource
keyword: life science
has prefix: jcm
is deprecated: false
0000005: 17254
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has provider formatter: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number

Polytraits Trait Definitions
has URI prefix: http://polytraits.lifewatchgreece.eu/traitspublic_traitdefinitions.php#
is deprecated: false
has resource example: PRED
is part of: Bioregistry
has prefix: polytraits.trait
type: Resource
contributor: Charles Tapley Hoyt
0000005: PRED
description: Reproductive and behavioural traits of both adult and larval stages, as well as information on environmental preferences and a few morphological traits.
has provider formatter: http://polytraits.lifewatchgreece.eu/traitspublic_traitdefinitions.php#$1

Time Zone
has URI prefix: https://vocabularies.cessda.eu/vocabulary/TimeZone#code_
type: Resource
description: Time zone specification as an offset from UTC (Coordinated Universal Time) in terms of hours and minutes.
has prefix: ddi.timezone
has identifier space owner: 015em2733
has resource example: code -12:00
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://vocabularies.cessda.eu/vocabulary/TimeZone#code_$1
0000005: -12:00

An Educational and Career-Oriented Recommendation Ontology
has URI prefix: https://github.com/tibonto/educor#
type: Resource
has resource example: stri
has prefix: educor
git repository: educor
is deprecated: false
has provider formatter: https://github.com/tibonto/educor#$1
has responsible: Eleni Ilkou
is part of: Bioregistry
description: An educational ontology for personalised recommendation learning systems that is based on learning path and user profile. It represents the key components for a personalised learning system based on our requirement analysis.
contributor: Charles Tapley Hoyt
0000005: stri

SWEET Ontology Realm Land Tectonic
has prefix: sweet.realt
is deprecated: false
0000005: AseismicRidge
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Tectonic
keyword: tectonicland
is part of: Bioregistry
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/realmLandTectonic/$1
has alternative prefix: sorealt
type: Resource
has resource example: AseismicRidge
has URI prefix: http://sweetontology.net/realmLandTectonic/

Graphic Descriptor Ontology
has resource example: https://gdo.endlessforms.info/view/classes
has prefix: gdo
has download URL: gdoa.owl
git repository: GDO-GDOA
keyword: ontology
has provider formatter: https://gdo.endlessforms.info/view/classes
has URI prefix: https://gdo.endlessforms.info/view/classes
is deprecated: false
0000005: 0000016
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has responsible: Melissa D Clarkson
description: The Graphic Descriptor Ontology (GDO) is intended for use in describing graphics that represent the form of objects. It uses the language of visual communication, illustration, and technical drawing. The GDO is rooted in the Basic Formal Ontology (BFO) and uses several classes from the Information Entity Ontology of the Common Core Ontologies as a mid-level ontology. [from https://gdo.endlessforms.info/about]
type: Resource

RubyGems
contributor: Charles Tapley Hoyt
type: Resource
has prefix: rubygems
has resource example: bel
description: A repository of software packages written in Ruby.
is deprecated: false
has URI prefix: https://rubygems.org/gems/
has provider formatter: https://rubygems.org/gems/$1
0000005: bel
is part of: Bioregistry

Publishing Roles Ontology
has resource example: RoleInTime
is part of: Bioregistry
description: An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians.
has URI prefix: http://purl.org/spar/pro/
contributor: Charles Tapley Hoyt
has responsible: Silvio Peroni
keyword: subject agnostic
type: Resource
has provider formatter: http://purl.org/spar/pro/$1
git repository: pro
is deprecated: false
has prefix: puro
0000005: RoleInTime

Medical Data Models
keyword: translational medicine
has local unique identifier pattern: ^\d+$
has provider formatter: https://medical-data-models.org/forms/$1
is part of: Bioregistry
has resource example: https://medical-data-models.org/forms/4776
type: Resource
keyword: biomedical science
has URI prefix: https://medical-data-models.org/forms/
0000005: 4776
description: The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.
keyword: medicine
has prefix: mdm
is deprecated: false
has responsible: https://orcid.org/0000-0003-3062-8192

Development Data Object Service
has URI prefix: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/
has local unique identifier pattern: ^[a-zA-Z0-9\-:#\.]+$
has prefix: dev.ga4ghdos
is deprecated: false
is part of: Bioregistry
has resource example: 2017-03-24T18:43:16.886826-05:00
has provider formatter: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1
type: Resource
description: Assists in resolving data across cloud resources.

Golm Metabolome Database Profile
has local unique identifier pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
has resource example: http://gmd.mpimp-golm.mpg.de/profile/default.aspx
is deprecated: false
has prefix: gmd.profile
is part of: Bioregistry
description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.
has URI prefix: http://gmd.mpimp-golm.mpg.de/profile/default.aspx
type: Resource
has provider formatter: http://gmd.mpimp-golm.mpg.de/profile/default.aspx

NDFI4Cat Collection
has part: Chemical Methods Ontology
has part: A vocabulary for the catalysis disciplines
has part: Basic Formal Ontology
has part: Physico-chemical process
has part: EDAM Ontology
has part: Chemical Information Ontology
description: A collection of ontologies relevant for chemistry. The NFDI program deploys a [custom instance](https://terminology.tib.eu/ts/ontologies?collection=NFDI4CAT&and=false&page=1) of the Ontology Lookup Service (OLS) that provides the ontologies in this list. A further analysis of the metadata landscape of the ontologies in this list can be found [here](https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat). OntoCompChem and OntoKin appear on the NFDI4Cat list but have not yet been registered in the Bioregistry because the resources are missing/incomplete such that they do not meet minimum Bioregistry metadata standards. These might be added in the future if additional metadata can be found.
has part: Ontology for computer aided process engineering
has part: Descriptive Ontology for Linguistic and Cognitive Engineering
has part: Environment Ontology
has part: Chemical Analysis Ontology
has part: Allotrope Merged Ontology Suite
has part: Computational Chemistry Ontology
has part: BioAssay Ontology
has part: Elementary Multiperspective Material Ontology
has part: Ontology for simulation, modelling, and optimization
has part: Name Reaction Ontology
has part: Mass spectrometry ontology
has part: ISO 15926-14
has part: Molecular Process Ontology
creator: Charles Tapley Hoyt
type: Collection
has part: Systems Biology Ontology
has part: Ontology for Biomedical Investigations
has part: Ontology for Chemical Kinetic Reaction Mechanisms
has part: Crystallographic Information Framework
creator: Hendrik Borgelt
has part: Chemical Entities of Biological Interest
has part: Ontology of units of Measure
has part: Metadata4Ing

Phenotype And Trait Ontology
appears in: Uber Anatomy Ontology
keyword: ess
appears in: Lepidoptera Anatomy Ontology
appears in: Radiation Biology Ontology
appears in: Provisional Cell Ontology
appears in: Planarian Phenotype Ontology
has prefix: pato
appears in: Plant Gall Ontology
keyword: obo
has download URL: pato.owl
keyword: ontology
has resource example: PATO_0001998
appears in: An ontology of core ecological entities
appears in: Process Chemistry Ontology
description: PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.
appears in: Agronomy Ontology
appears in: Population and Community Ontology
0000005: 0001998
keyword: biodiversity
has URI prefix: http://purl.obolibrary.org/obo/PATO_
appears in: Coleoptera Anatomy Ontology
is deprecated: false
keyword: quality
keyword: dataplant
has responsible: George Gkoutos
appears in: FuTRES Ontology of Vertebrate Traits
keyword: phenotype
appears in: Compositional Dietary Nutrition Ontology
keyword: nfdi4chem
appears in: Xenopus Phenotype Ontology
keyword: earth sciences
appears in: Zebrafish Phenotype Ontology
keyword: life sciences, biology
appears in: Cell Ontology
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
appears in: Environmental conditions, treatments and exposures ontology
appears in: Ontology for the Anatomy of the Insect SkeletoMuscular system
type: Resource
appears in: Microbial Conditions Ontology
git repository: pato
has provider formatter: http://purl.obolibrary.org/obo/PATO_$1
appears in: Pathogen Host Interaction Phenotype Ontology
keyword: biology
appears in: Mass spectrometry ontology

SwissLipid
has alternative prefix: swisslipids
keyword: life science
is deprecated: false
has download URL: slm.owl.gz
has URI prefix: https://www.swisslipids.org/#/entity/SLM:
keyword: ontology
has prefix: slm
description: SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.
has alternative prefix: swisslipid
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has responsible: https://orcid.org/0000-0003-2148-9135
keyword: metabolomics
0000005: 000000341
has provider formatter: https://www.swisslipids.org/#/entity/SLM:$1
type: Resource
has resource example: entity/SLM:000000341

Protein Alignment organised as Structural Superfamily
0000005: 46977
is deprecated: true
keyword: classification
has prefix: pass2
has URI prefix: https://caps.ncbs.res.in/pass2.8/
is part of: Bioregistry
keyword: genome
keyword: dna
has local unique identifier pattern: ^\d+$
description: The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.
has resource example: https://caps.ncbs.res.in/pass2.8/
type: Resource
keyword: structure
has provider formatter: https://caps.ncbs.res.in/pass2.8/

Human Gene Mutation Database
has URI prefix: http://www.hgmd.cf.ac.uk/ac/gene.php
is deprecated: false
is part of: Bioregistry
has prefix: hgmd
type: Resource
has local unique identifier pattern: ^[A-Z_0-9]+$
0000005: CALM1
has provider formatter: http://www.hgmd.cf.ac.uk/ac/gene.php
has resource example: http://www.hgmd.cf.ac.uk/ac/gene.php
description: The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases.

Alzforum Mutations
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has alternative prefix: Alzforum_mut
keyword: alzheimer's disease
has provider formatter: https://www.alzforum.org/mutations/$1
keyword: variants
description: Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease.
contributor: https://orcid.org/0000-0002-1216-4761
has URI prefix: https://www.alzforum.org/mutations/
has prefix: alzforum.mutation
is deprecated: false
0000005: app-d678n-tottori
keyword: genes
has resource example: app-d678n-tottori

UniRule
has provider formatter: https://www.uniprot.org/unirule/$1
has prefix: unirule
is deprecated: false
is part of: Bioregistry
has URI prefix: https://www.uniprot.org/unirule/
type: Resource
has resource example: UR000124451
contributor: Charles Tapley Hoyt
0000005: UR000124451
description: Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites.
has responsible: Alex Bateman

Wikidata
keyword: genomics
keyword: chemistry
keyword: metabolomics
has responsible: Denny Vrandečić
has local unique identifier pattern: ^(Q|P|E|L)\d+$
has URI prefix: http://www.wikidata.org/entity/
keyword: proteomics
0000005: Q47475003
has alternative prefix: WD_Entity
has provider formatter: http://www.wikidata.org/entity/$1
type: Resource
has prefix: wikidata
has alternative prefix: wd
has part: Wikidata Property
keyword: subject agnostic
is deprecated: false
description: Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.
has resource example: Q47475003
has alternative prefix: wdeschema
has part: Wikidata Entity
is part of: Bioregistry

SWEET Ontology Phenomena Atmosphere Precipitation
has alternative prefix: sophatmopc
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: atmosphere precipitation
has prefix: sweet.phatmopc
has URI prefix: http://sweetontology.net/phenAtmoPrecipitation/
type: Resource
git repository: sweet
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Precipitation
keyword: phenomena
has provider formatter: http://sweetontology.net/phenAtmoPrecipitation/$1
0000005: AtmosphericPrecipitation
has resource example: AtmosphericPrecipitation

KEGG genome
description: KEGG Genome is a collection of organisms whose genomes have been completely sequenced.
is part of: Bioregistry
type: Resource
is part of: Kyoto Encyclopedia of Genes and Genomes
0000005: T06648
has alternative prefix: kegg_genomes
has alternative prefix: kegg_genome
has resource example: T06648
has provider formatter: http://www.kegg.jp/entry/$1
keyword: ontology
has download URL: kegg.genome.owl
has prefix: kegg.genome
has local unique identifier pattern: ^(T0\d+|\w{3,5})$
has URI prefix: http://www.kegg.jp/entry/
is deprecated: false
keyword: genome
has responsible: Minoru Kanehisa

Abcam
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
description: Vendor for assays, cells, and antibodies
has URI prefix: https://bioregistry.io/abcam:
has resource example: ab275461.html
has provider formatter: https://www.abcam.com/$1.html
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: abcam
0000005: ab275461

CIViC gene
has responsible: Malachi Griffith
has download URL: civic.gid.owl
has provider formatter: https://civicdb.org/links/gene/$1
has alternative prefix: civic.gene
type: Resource
has URI prefix: https://civicdb.org/links/gene/
keyword: gene
has local unique identifier pattern: ^[0-9]+$
description: A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis
has prefix: civic.gid
is deprecated: false
0000005: 272
keyword: ontology
has resource example: https://civicdb.org/links/gene/272
is part of: Bioregistry

Global Biodiversity Information Facility
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
git repository: gbif
type: Resource
description: Database of living organisms, taxonomic. The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.
keyword: metagenomics
has resource example: https://www.gbif.org/species/4238
keyword: taxonomy
keyword: natural science
has prefix: gbif
has responsible: https://orcid.org/0000-0001-6215-3617
keyword: natural history
keyword: marine biology
0000005: 4238
is deprecated: false
keyword: biodiversity
keyword: bioinformatics
has provider formatter: https://www.gbif.org/species/$1
has URI prefix: https://www.gbif.org/species/

Resources for modeling Open Educational Resources
has part: Educational Sectors Vocabulary
has part: International Standard Classification of Education, 1997 Edition
has part: OER Schema
has part: VIVO Ontology
has part: OpenEduHub Education Level
has part: International Standard Classification of Education, 2013 Edition
has part: KIM Education Level
has part: Allgemeines Metadatenprofil für Bildungsressourcen
has part: International Standard Classification of Education, 2011 Edition
has part: U.S. Education Level Vocabulary
has part: Higher Education Resource Types
has part: Conditions of Access
type: Collection
has part: LRMI Educational Use Vocabulary
has part: KIM School Subjects
has part: Curriculum Course Syllabus Ontology
has part: LRMI Interact Type Vocabulary
has part: LRMI Educational Audience Role Vocabulary
has part: terms4FAIRskills
has part: German University Subject Classification System
has part: Lehrplan Ontology
has part: Library of Congress Format Description Document
has part: Schema.org
creator: Charles Tapley Hoyt
has part: KIM German School Types
has part: Media Types
has part: UNESCO Thesaurus
has part: EDAM Ontology
has part: Arctic Data Center Academic Disciplines Ontology
has part: LRMI Alignment Type Vocabulary
has part: Learning Resource Metadata Innovation Terms
creator: Martin Voigt
has part: LRMI Learning Resource Type Concept Scheme
description: The prefixes appearing in this collection correspond resources whose entities could appear as values for target groups, media types, educational levels, and other fields in OER data models. It can also include parts that are used to construct schemas for OERs It was originally curated as part of the publication [_Teaching RDM in a smart advanced inorganic lab course and its provision in the DALIA platform_ (arxiv:2509.18902)](https://arxiv.org/pdf/2509.18902).
has part: Educational Context
has part: MoDALIA Ontology
has part: Gender, Sex, and Sexual Orientation Ontology
has part: CEDS Learning Resource Type

OMA Group
is deprecated: false
has local unique identifier pattern: ^[A-Z]+$
has URI prefix: https://omabrowser.org/cgi-bin/gateway.pl
0000005: LCSCCPN
is part of: Bioregistry
has prefix: oma.grp
has resource example: https://omabrowser.org/cgi-bin/gateway.pl
has provider formatter: https://omabrowser.org/cgi-bin/gateway.pl
type: Resource
description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.

Bilateria anatomy
description: This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource.
keyword: anatomy
0000005: 0000000
is deprecated: true
keyword: obo
keyword: ontology
has prefix: bila
has URI prefix: http://purl.obolibrary.org/obo/BILA_
keyword: gene expression
has resource example: BILA_0000000
has responsible: Thorsten Henrich
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/BILA_$1
type: Resource
has download URL: bila.owl
has local unique identifier pattern: ^\d{7}$

Next Generation Biobanking Ontology
keyword: obo
has provider formatter: http://purl.obolibrary.org/obo/NGBO_$1
keyword: ontology
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/NGBO_
has download URL: ngbo.owl
description: Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
has responsible: Dalia Alghamdi
type: Resource
0000005: 6000122
has resource example: NGBO_6000122
git repository: NGBO
has prefix: ngbo

SWEET Ontology Phenomena Cycle
has resource example: AnnualCycle
keyword: phenomena
has prefix: sweet.phcy
0000005: AnnualCycle
keyword: cycle
has URI prefix: http://sweetontology.net/phenCycle/
is deprecated: false
is part of: Bioregistry
has provider formatter: http://sweetontology.net/phenCycle/$1
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Cycle
has alternative prefix: sophcy
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt

TDWG Taxon Rank LSID Ontology
git repository: ontology
keyword: ontology
is deprecated: false
has URI prefix: http://rs.tdwg.org/ontology/voc/TaxonRank#
has provider formatter: http://rs.tdwg.org/ontology/voc/TaxonRank#$1
has prefix: tdwg.taxonrank
has responsible: https://orcid.org/0000-0003-4581-1379
description: Ontology describing a controlled vocabulary for taxon ranks.
is part of: Bioregistry
has resource example: InfragenericTaxon
type: Resource
contributor: Charles Tapley Hoyt
has download URL: TaxonRank.rdf
0000005: InfragenericTaxon

Tim Vandermeersch
label: Egon Willighagen

Pazar Transcription Factor
is part of: Bioregistry
keyword: dna
keyword: regulation
has local unique identifier pattern: ^TF\w+$
has responsible: https://orcid.org/0000-0001-6098-6412
has URI prefix: http://www.pazar.info/cgi-bin/tf_search.cgi
has prefix: pazar
type: Resource
has resource example: http://www.pazar.info/cgi-bin/tf_search.cgi
keyword: life science
is deprecated: true
description: The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.
has provider formatter: http://www.pazar.info/cgi-bin/tf_search.cgi
keyword: rna
0000005: TF0001053

Digital Object Identifier
has URI prefix: https://doi.org/
contributor: https://orcid.org/0000-0002-3012-7446
is part of: Bioregistry
contributor: https://orcid.org/0000-0002-6601-2165
has provider formatter: https://doi.org/$1
keyword: subject agnostic
has responsible: https://orcid.org/0000-0001-9551-9662
keyword: bibliography
0000005: 10.1038/s41597-022-01807-3
has prefix: doi
has resource example: s41597-022-01807-3
type: Resource
has local unique identifier pattern: ^10.\d{2,9}/.*$
is deprecated: false
keyword: centrally registered identifier
description: The Digital Object Identifier System is for identifying content objects in the digital environment.

OMIM Phenotypic Series
contributor: Charles Tapley Hoyt
keyword: phenotype
has download URL: omim.ps.owl
contributor: Sierra Moxon
type: Resource
0000005: 214100
has alternative prefix: mim.ps
has provider formatter: https://omim.org/MIM:PS$1
has URI prefix: https://omim.org/MIM:PS
has prefix: omim.ps
description: A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.
keyword: ontology
has alternative prefix: MIMPS
has responsible: https://orcid.org/0000-0002-1780-5230
has resource example: MIM:PS214100
has alternative prefix: PS
is deprecated: false
is part of: Bioregistry
keyword: disease
has local unique identifier pattern: ^\d+$
has alternative prefix: OMIMPS

Human Induced Pluripotent Stem Cells Initiative
type: Resource
is deprecated: false
description: Cell line databases/resources
has provider formatter: https://www.hipsci.org/#/lines/$1
has prefix: hipsci
is part of: Bioregistry
0000005: HPSI0114i-bezi_1
has resource example: lines/HPSI0114i-bezi 1
has URI prefix: https://www.hipsci.org/#/lines/
contributor: https://orcid.org/0000-0001-9868-6271

BioStudies database
keyword: life science
0000005: S-EPMC6266652
description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.
has prefix: biostudies
is deprecated: false
has responsible: https://orcid.org/0000-0001-9227-8488
has resource example: S-EPMC6266652
has URI prefix: https://www.ebi.ac.uk/biostudies/studies/
is part of: Bioregistry
type: Resource
has provider formatter: https://www.ebi.ac.uk/biostudies/studies/$1
keyword: biomedical science
has local unique identifier pattern: ^S-[A-Z]{4}[\-\_A-Z\d]+$

Electron Microscopy Data Bank
has URI prefix: https://www.ebi.ac.uk/pdbe/entry/emdb/
keyword: virology
0000005: EMD-1001
keyword: epidemiology
type: Resource
has local unique identifier pattern: ^EMD-\d{4,5}$
keyword: structural biology
has identifier space owner: 02catss52
has provider formatter: https://www.ebi.ac.uk/pdbe/entry/emdb/$1
has prefix: emdb
description: The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community.
is deprecated: false
has resource example: EMD-1001
has responsible: https://orcid.org/0000-0001-7663-9028
is part of: Bioregistry

Database of Sequence Tagged Sites
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
keyword: protein
has prefix: unists
has URI prefix: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi
type: Resource
keyword: gene
has resource example: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi
0000005: 456789
description: UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.
is deprecated: true
has provider formatter: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi

NCBI Orthologs
contributor: Terence D. Murphy
has resource example: ortholog
is deprecated: false
description: Database of one-to-one ortholog information provided by the NCBI as a subset of their Gene resource. Used for users to access ortholog information for over 1000 species of vertebrates and arthropods.
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has URI prefix: https://bioregistry.io/ncbiortholog:
has provider formatter: https://www.ncbi.nlm.nih.gov/gene/$1/ortholog
has responsible: Terence D. Murphy
type: Resource
0000005: 2
has prefix: ncbiortholog

NeuronDB
has prefix: neurondb
keyword: anatomy
is deprecated: true
has provider formatter: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx
description: NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.
keyword: neurobiology
keyword: molecular neuroscience
has URI prefix: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx
has resource example: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx
keyword: comparative neurobiology
keyword: neurophysiology
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: computational neuroscience
0000005: 265
type: Resource
keyword: cellular neuroscience
keyword: structure

Golm Metabolome Database Analyte
has URI prefix: http://gmd.mpimp-golm.mpg.de/Analytes/
has provider formatter: http://gmd.mpimp-golm.mpg.de/Analytes/$1
description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.
has local unique identifier pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
is deprecated: false
is part of: Bioregistry
type: Resource
has prefix: gmd.analyte

Babelon
has resource example: translation language
has URI prefix: https://w3id.org/babelon/
git repository: babelon
is deprecated: false
is part of: Bioregistry
contributor: https://orcid.org/0000-0002-7356-1779
description: Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation.
0000005: translation_language
type: Resource
has local unique identifier pattern: ^[a-z][a-z0-9_]+[a-z0-9]$
has provider formatter: https://w3id.org/babelon/$1
has responsible: https://orcid.org/0000-0002-7356-1779
has reviewer: Charles Tapley Hoyt
has prefix: babelon

Cell Signaling Technology Pathways
is deprecated: false
has prefix: cst.pathway
is part of: Bioregistry
has provider formatter: http://www.cellsignal.com/reference/pathway/$1.html
has local unique identifier pattern: ^[A-Za-z0-9_-]+$
has alternative prefix: cst
keyword: biomedical science
type: Resource
0000005: Akt_PKB
has URI prefix: https://bioregistry.io/cst.pathway:
keyword: life science
has resource example: Akt PKB.html
description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.

Fungal Nomenclature and Species Bank
keyword: classification
description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.
0000005: 349124
has local unique identifier pattern: ^\d+$
has provider formatter: https://www.mycobank.org/page/Name%20details%20page/$1
is part of: Bioregistry
contributor: https://orcid.org/0000-0003-0066-1717
has resource example: https://www.mycobank.org/page/Name%20details%20page/349124
type: Resource
has prefix: mycobank
has responsible: Vincent Robert
has URI prefix: https://www.mycobank.org/page/Name%20details%20page/
keyword: biology
is deprecated: false
keyword: taxonomy

Earth Metabolome Ontology
has provider formatter: https://www.dbgi.org/earth_metabolome_ontology/#$1
git repository: earth metabolome ontology
type: Resource
0000005: ChemicalStructure
has responsible: https://orcid.org/0000-0002-3175-5372
has URI prefix: https://www.dbgi.org/earth_metabolome_ontology/#
has download URL: https://w3id.org/emi/version/1.0
has resource example: ChemicalStructure
keyword: ontology
description: The EMI ontology is used to structure spectrum annotation provenance by reusing the PROV-O ontology (a W3C recommendation) and sample and observation data by applying the SOSA ontology. EMI reuses the SOSA ontology as a data schema for struturing the Sample and Observation data. SOSA (Sensor, Observation, Sample, and Actuator) is a subset of SSN (Semantic Sensor Network Ontology) that is a W3C recommendation. [from homepage]
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: emi

openWEMI Vocabulary
has responsible: Karen Coyle
git repository: openwemi
is deprecated: false
has local unique identifier pattern: ^\w+$
has prefix: openwemi
0000005: Endeavor
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item.
has resource example: Endeavor
type: Resource
has provider formatter: https://dcmi.github.io/openwemi/ns#$1
has URI prefix: https://dcmi.github.io/openwemi/ns#

Process Chemistry Ontology
keyword: obo
keyword: chemical and environmental engineering
description: PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry.
keyword: ontology
has prefix: proco
is deprecated: false
depends on: Chemical Information Ontology
has resource example: PROCO_0000001
keyword: chemistry
keyword: nfdi4chem
git repository: PROCO
depends on: Relation Ontology
has provider formatter: http://purl.obolibrary.org/obo/PROCO_$1
has responsible: Wes Schafer
has download URL: proco.owl
is part of: Bioregistry
type: Resource
depends on: Phenotype And Trait Ontology
depends on: Systems Biology Ontology
depends on: Ontology for Biomedical Investigations
has URI prefix: http://purl.obolibrary.org/obo/PROCO_
depends on: Chemical Entities of Biological Interest
0000005: 0000001
has local unique identifier pattern: ^\d{7}$

EM-DAT Disaster Classification Ontology
keyword: life sciences, biology
0000005: Air
type: Resource
keyword: coypu
has URI prefix: https://schema.coypu.org/em-dat#
has provider formatter: https://schema.coypu.org/em-dat#$1
is deprecated: false
is part of: Bioregistry
has resource example: Air
description: Crisis and hazard related taxonomy developed by CRED for disaster preparedness and humanitarian actions at national and international level.
keyword: earth sciences
has prefix: coypu.emdat

Genomic Epidemiology Ontology
keyword: pathogen
has resource example: GENEPIO_0001885
has URI prefix: http://purl.obolibrary.org/obo/GENEPIO_
has prefix: genepio
keyword: obo
keyword: food
keyword: ontology
depends on: Relation Ontology
keyword: genome
is deprecated: false
keyword: genomics
has download URL: genepio.owl
0000005: 0001885
depends on: Uber Anatomy Ontology
has provider formatter: http://purl.obolibrary.org/obo/GENEPIO_$1
description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.
depends on: Chemical Entities of Biological Interest
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
has responsible: Damion Dooley
keyword: epidemiology
git repository: genepio
type: Resource
depends on: NCBI Taxonomy
depends on: Plant Ontology

ISA Programme Location Core Vocabulary
type: Resource
has prefix: locn
is deprecated: false
is part of: Bioregistry
keyword: geography
description: The ISA Programme Location Core Vocabulary provides a minimum set of classes and properties for describing any place in terms of its name, address or geometry. The vocabulary is specifically designed to aid the publication of data that is interoperable with EU INSPIRE Directive.
keyword: geometry
0000005: Address

NeuroLex Dysfunction
contributor: Charles Tapley Hoyt
has resource example: nlx dys 20090602
type: Resource
has prefix: nlx.dys
description: NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc.
has reviewer: Charles Tapley Hoyt
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_dys_
appears in: Mondo Disease Ontology
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1
0000005: 20090602
keyword: disorders
has responsible: Tom Gillespie
is deprecated: false
keyword: disease
keyword: phenotypes
has local unique identifier pattern: ^\d+$
is part of: Bioregistry

WikiGenes
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: http://www.wikigenes.org/e/gene/e/$1.html
has prefix: wikigenes
has resource example: 3771877.html
0000005: 3771877
has URI prefix: https://bioregistry.io/wikigenes:
type: Resource
0000011: NCBI Gene
description: WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.

Cassava Ontology
keyword: agriculture
has local unique identifier pattern: ^\d{7}$
is part of: Bioregistry
has prefix: co_334
type: Resource
git repository: Crop-Ontology
has download URL: CO 334.owl
0000005: 0000070
keyword: nutritional science
has URI prefix: https://cropontology.org/rdf/CO_334:
keyword: food
keyword: ontology
description: Crop-specific trait ontologies enhance the interoperability and effectiveness of data exchange between the data sources which adopt it, by providing standard concepts that are use to describe phenotypes stored in those sources. As one of them, the Cassava Ontology is actively used and shared in different databases such as the BMS (Breeding Management system) of the IBP or the CassavaBase. Cassava, a major staple crop, is the main source of calories for 500 million people across the globe. A perennial woody shrub native to Latin America, cassava is primarily grown as an annual crop in the humid tropics. A cash crop as well as a subsistence crop, cassava's large edible starchy roots are a source of low-cost carbohydrates for millions. Cassava end products range from fresh roots cooked, boiled, baked or fried at the household level, to highly processed starch as a food additive.
has provider formatter: https://cropontology.org/rdf/CO_334:$1
has responsible: Elizabeth Arnaud
is deprecated: false
keyword: plant phenotypes and traits
has resource example: CO 334:0000070
keyword: phenotype
keyword: botany

VirOligo
has provider formatter: http://viroligo.okstate.edu/main.php
0000005: BM0456
description: The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place.
has prefix: viroligo
is deprecated: false
keyword: small molecule
is part of: Bioregistry
type: Resource
has URI prefix: http://viroligo.okstate.edu/main.php
has resource example: http://viroligo.okstate.edu/main.php

NCI Thesaurus
type: Resource
keyword: obo
has alternative prefix: NCIT_Thesaurus
appears in: Sickle Cell Disease Ontology
appears in: Ontology for Avida digital evolution platform
keyword: ontology
has download URL: ncit.owl
keyword: thesaurus
is deprecated: false
keyword: disease
keyword: dataplant
has alternative prefix: NCITm
has provider formatter: http://purl.obolibrary.org/obo/NCIT_$1
has alternative prefix: NCit
has URI prefix: http://purl.obolibrary.org/obo/NCIT_
has alternative prefix: NCI2004_11_17
has alternative prefix: NCI
keyword: nfdi4chem
description: NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code.
keyword: translational medicine
keyword: life sciences, biology
appears in: Environmental conditions, treatments and exposures ontology
keyword: preclinical studies
is part of: Bioregistry
has alternative prefix: NCIt
appears in: Microbial Conditions Ontology
git repository: ncit-obo-edition
has identifier space owner: 040gcmg81
has alternative prefix: NCIT
has alternative prefix: NCIThesaurus
keyword: cancer
has alternative prefix: NCITt
has prefix: ncit
has alternative prefix: ncithesaurus
keyword: biomedical science
0000005: C138986
has responsible: NCI Thesaurus Mailbox
has alternative prefix: NCI_Thesaurus
has local unique identifier pattern: ^[CRPA]\d+$
has resource example: NCIT C138986

Information Objects Ontology
0000005: InformationObject
keyword: computer science
is deprecated: false
has provider formatter: http://bimerr.iot.linkeddata.es/def/information-objects#$1
has resource example: InformationObject
keyword: digital planning and construction
is part of: Bioregistry
has URI prefix: http://bimerr.iot.linkeddata.es/def/information-objects#
has prefix: tib.io
keyword: fid baudigital
description: An ontology for the description of information objects.
type: Resource
keyword: nfdi4ing

NCATS Drugs
has URI prefix: https://drugs.ncats.io/drug/
has alternative prefix: inxight
is deprecated: false
has provider formatter: https://drugs.ncats.io/drug/$1
0000005: 44259
description: The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including: - US Approved Drugs - Marketed Drugs - Investigational Drugs - Other Substances
has resource example: https://drugs.ncats.io/drug/44259
is part of: Bioregistry
contributor: Charles Tapley Hoyt
contributor: Sierra Moxon
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-5970-6660
type: Resource
has alternative prefix: inxight-drugs
has prefix: ncats.drug

Funding, Research Administration and Projects Ontology
has URI prefix: http://purl.org/cerif/frapo/
is part of: Bioregistry
keyword: academy
has provider formatter: http://purl.org/cerif/frapo/$1
git repository: frapo
type: Resource
contributor: Charles Tapley Hoyt
0000005: Grant
has responsible: Silvio Peroni
description: An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc.
keyword: subject agnostic
keyword: funding bodies
has prefix: frapo
keyword: research project
has resource example: Grant
is deprecated: false
keyword: grant application

Sequence Read Archive
has responsible: https://orcid.org/0000-0003-1374-6015
keyword: epidemiology
keyword: biology
type: Resource
has prefix: insdc.sra
0000005: SRX000007
description: The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.
has URI prefix: https://www.ncbi.nlm.nih.gov/sra/
has local unique identifier pattern: ^[SED]R[APRSXZ]\d+$
is deprecated: false
keyword: genomics
has resource example: SRX000007
keyword: virology
has provider formatter: https://www.ncbi.nlm.nih.gov/sra/$1
is part of: Bioregistry

Pocketome
has provider formatter: http://www.pocketome.org/files/$1.html
has resource example: 1433C TOBAC 1 252.html
has URI prefix: https://bioregistry.io/pocketome:
has responsible: Ruben Abagyan
is part of: Bioregistry
has local unique identifier pattern: ^[A-Za-z_0-9]+$
0000005: 1433C_TOBAC_1_252
description: Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries.
has prefix: pocketome
type: Resource
keyword: life science
is deprecated: false

HGNC gene family
is deprecated: false
keyword: gene group
has alternative prefix: hgnc.family
has prefix: hgnc.genefamily
has alternative prefix: GFAM
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
keyword: gene family
description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.
has alternative prefix: HGNC_GROUP
type: Resource
keyword: gene
has responsible: Elspeth Bruford
0000005: 2029
has provider formatter: https://www.genenames.org/cgi-bin/genefamilies/set/$1
has URI prefix: https://www.genenames.org/cgi-bin/genefamilies/set/
has resource example: https://www.genenames.org/cgi-bin/genefamilies/set/2029
has canonical: HGNC Gene Group

Semantic Web Context
has part: Simple Knowledge Organization System eXtension for Labels
has part: Data Catalog
has part: Resource Description Framework
has part: Web Ontology Language
has part: Feature Annotation Location Description Ontology
has part: Quantities, Units, Dimensions, and Types Ontology
has part: Shape Expression Vocabulary
has part: Friend of a Friend
has part: Web Annotation Ontology
has part: Dublin Core Metadata Initiative Terms
has part: XML Schema Definition
has part: A Semantic Web Rule Language Combining OWL and RuleML
has part: Shapes Constraint Language
has part: OASIS Open Services for Lifecycle Collaboration Core Vocabulary
has part: Simple Knowledge Organization System
has part: Dublin Core Elements (1.1)
has part: RDF Schema
has part: The Bibliographic Ontology
has part: Dublin Core Types
has part: PROV Namespace
has part: The data cube vocabulary
has part: Schema.org
description: Resources used in the semantic web, drawing from lists in [BioContext](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) and [LinkML](https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/data/linked_data.curated.yaml) as well as W3C recommendations.
has part: A vocabulary for annotating vocabulary descriptions
creator: Charles Tapley Hoyt
type: Collection
has part: Identifiers.org Terms
has part: Description of a Project
has part: OBO in OWL
has part: Activity Streams
has part: Vocabulary of Interlinked Datasets
has part: Provenance, Authoring, and Versioning Vocabulary

CIViC Molecular Profile
type: Resource
has resource example: https://civicdb.org/links/molecular_profile/559
has local unique identifier pattern: ^[0-9]+$
has URI prefix: https://civicdb.org/links/molecular_profile/
has alternative prefix: civic.molecularprofile
is deprecated: false
0000005: 559
has prefix: civic.mpid
is part of: Bioregistry
has responsible: Malachi Griffith
has provider formatter: https://civicdb.org/links/molecular_profile/$1
description: CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC.

High-quality Automated and Manual Annotation of microbial Proteomes
has provider formatter: https://hamap.expasy.org/unirule/$1
description: HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.
has URI prefix: https://hamap.expasy.org/unirule/
0000005: MF_01400
is deprecated: false
keyword: protein
is part of: Bioregistry
has responsible: https://orcid.org/0000-0003-2148-9135
has prefix: hamap
type: Resource
has resource example: MF_01400
has local unique identifier pattern: ^MF_\d+$
keyword: life science

SWEET Ontology Phenomena Geologic Tectonic
has resource example: AsymmetricHeatFlow
0000005: AsymmetricHeatFlow
is deprecated: false
has alternative prefix: sophgt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Tectonic
has URI prefix: http://sweetontology.net/phenGeolTectonic/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: phenomena
has provider formatter: http://sweetontology.net/phenGeolTectonic/$1
has prefix: sweet.phgt
keyword: geologic tectonic
type: Resource

SWEET Ontology Representation Data Service
is part of: Bioregistry
keyword: representation data service
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Service
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has alternative prefix: sorepds
has resource example: Access
is deprecated: false
has URI prefix: http://sweetontology.net/reprDataService/
0000005: Access
has provider formatter: http://sweetontology.net/reprDataService/$1
has prefix: sweet.repds

RiceNetDB Reaction
description: RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.
has prefix: ricenetdb.reaction
is deprecated: false
has local unique identifier pattern: ^OSR\d{4}$
has URI prefix: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php
is part of: Bioregistry
type: Resource
has resource example: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php
0000005: OSR0818
has provider formatter: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php

TarBase
has local unique identifier pattern: ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)?$
type: Resource
has prefix: tarbase
has resource example: http://diana.imis.athena-innovation.gr/DianaTools/index.php
has provider formatter: http://diana.imis.athena-innovation.gr/DianaTools/index.php
keyword: biomedical science
0000005: hsa-let-7a-2-3p
keyword: life science
description: TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used.
is deprecated: false
is part of: Bioregistry
has URI prefix: http://diana.imis.athena-innovation.gr/DianaTools/index.php

Physico-chemical methods and properties
has local unique identifier pattern: ^\d{7}$
type: Resource
keyword: experimental measurement
has prefix: fix
0000005: 0000390
has identifier space owner: 02catss52
description: An ontology of physico-chemical methods and properties.
has responsible: https://orcid.org/0000-0001-8123-5351
keyword: property
has download URL: fix.owl
is deprecated: true
keyword: obo
has URI prefix: http://purl.obolibrary.org/obo/FIX_
keyword: experiment
keyword: ontology
has resource example: FIX_0000390
has provider formatter: http://purl.obolibrary.org/obo/FIX_$1
is part of: Bioregistry
keyword: chemistry

eVOC mouse development stage
contributor: Charles Tapley Hoyt
has prefix: evm
type: Resource
is deprecated: true
is part of: Bioregistry

Anatomical Therapeutic Chemical Vetinary
has URI prefix: http://www.whocc.no/atcvet/atcvet_index/
is part of: Bioregistry
description: The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.
has local unique identifier pattern: ^Q[A-Z0-9]+$
has prefix: atcvet
type: Resource
has resource example: http://www.whocc.no/atcvet/atcvet_index/
is deprecated: false
0000005: QJ51RV02
has provider formatter: http://www.whocc.no/atcvet/atcvet_index/

Vertebrate Skeletal Anatomy Ontology
has alternative prefix: VSAO_RETIRED
keyword: obo
description: Vertebrate skeletal anatomy ontology.
has prefix: vsao
keyword: ontology
has resource example: VSAO_0000183
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/VSAO_
has download URL: vsao.owl
keyword: vertebrate
has local unique identifier pattern: ^\d{7}$
has responsible: https://orcid.org/0000-0003-3162-7490
type: Resource
is deprecated: true
0000005: 0000183
has provider formatter: http://purl.obolibrary.org/obo/VSAO_$1
keyword: anatomy

New Zealand Threat Classification System
keyword: taxon
contributor: https://orcid.org/0000-0002-1216-4761
has local unique identifier pattern: ^[1-9]\d{2,6}$
keyword: taxonomy
is deprecated: false
0000005: 11061
has URI prefix: https://nztcs.org.nz/nztcs-species/
has prefix: nztcs
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: https://nztcs.org.nz/nztcs-species/11061
description: identifier for species classified under the New Zealand Threat Classification System
type: Resource
has provider formatter: https://nztcs.org.nz/nztcs-species/$1

Digital Competence Framework
type: Resource
has prefix: europa.dcf
is deprecated: false
description: The Digital Competence Framework for Citizens standard list identifies the key components of digital competence in 5 broader, and a total of 21 narrower areas, with eight proficiency levels for each concept and a few contextualising examples of use. It is maintained by DG EMPL and published by the Publications Office of the European Union on the EU Vocabularies website.
keyword: social sciences
has provider formatter: http://data.europa.eu/snb/dcf/$1
keyword: educational resources
is part of: Bioregistry
keyword: literature
has URI prefix: http://data.europa.eu/snb/dcf/
has resource example: 00b51s9rc5
0000005: 00b51s9rc5

The World-2DPAGE database
keyword: structure
has reviewer: Charles Tapley Hoyt
has prefix: world2dpage
is deprecated: true
has provider formatter: http://world-2dpage.expasy.org/repository/database=$1
has resource example: http://world-2dpage.expasy.org/repository/database=0020
has URI prefix: http://world-2dpage.expasy.org/repository/database=
keyword: protein
keyword: 2d-page
0000005: 0020
description: A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots.
is part of: Bioregistry
type: Resource

Mass spectrometry ontology
keyword: nfdi4chem
depends on: Phenotype And Trait Ontology
0000005: 1000560
is part of: Bioregistry
has responsible: Joshua Klein
has provider formatter: http://purl.obolibrary.org/obo/MS_$1
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/MS_
has resource example: MS_1000560
has local unique identifier pattern: ^\d{7}$
has prefix: ms
has download URL: ms.owl
description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.
keyword: obo
keyword: ontology
git repository: psi-ms-CV
is deprecated: false
keyword: dataplant
keyword: chemistry
keyword: nfdi4cat
depends on: Units of measurement ontology

neXtProt family
description: NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. (Developed by the SIB Swiss Institute of Bioinformatics)
has prefix: nextprot.family
has provider formatter: https://www.nextprot.org/term/FA-$1
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: https://www.nextprot.org/term/FA-
type: Resource
contributor: Charles Tapley Hoyt
has alternative prefix: NXPFA
0000005: 01406
has resource example: https://www.nextprot.org/term/FA-01406
is deprecated: false

CIÊNCIAVITAE ID
is deprecated: false
description: identifier of scientific author in www.cienciavitae.pt
is part of: Bioregistry
0000005: 0C1F-DA6C-4B02
keyword: person
keyword: researcher
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: https://www.cienciavitae.pt/
has local unique identifier pattern: ^([0-9A-F]{4}-){2}[0-9A-F]{4}$
has resource example: https://www.cienciavitae.pt/0C1F-DA6C-4B02
has provider formatter: https://www.cienciavitae.pt/$1
has prefix: cienciavitae

The Arabidopsis Information Resource
has responsible: 0000-0003-3871-858X
has prefix: tair.locus
0000005: 2200950
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has provider formatter: https://www.arabidopsis.org/locus
type: Resource
description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.
has URI prefix: https://www.arabidopsis.org/locus
keyword: genome
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has resource example: https://www.arabidopsis.org/locus

Friend of a Friend
keyword: ontology
is part of: Bioregistry
description: FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world.
has prefix: foaf
contributor: Charles Tapley Hoyt
has resource example: familyName
keyword: people
has URI prefix: http://xmlns.com/foaf/0.1/
type: Resource
has responsible: Rafael Gonçalves
0000005: familyName
has provider formatter: http://xmlns.com/foaf/0.1/$1
is deprecated: false
has download URL: foaf.owl

Gene Regulation Ontology
keyword: obo
has alternative prefix: bootstrep
keyword: ontology
has resource example: Lipid
is part of: Bioregistry
description: The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes.
type: Resource
has provider formatter: http://www.bootstrep.eu/ontology/GRO#$1
is deprecated: true
has download URL: gro.owl
has URI prefix: http://www.bootstrep.eu/ontology/GRO#
has prefix: gro
0000005: Lipid

HL7 V3 Code System
has provider formatter: https://terminology.hl7.org/CodeSystem-v3-$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has prefix: hl7.v3codesystem
is part of: Bioregistry
description: A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.
has URI prefix: https://terminology.hl7.org/CodeSystem-v3-
type: Resource
0000005: AcknowledgementCondition
contributor: Charles Tapley Hoyt
has resource example: CodeSystem-v3-AcknowledgementCondition

Proteomics Identification Database Ontology
has local unique identifier pattern: ^\d{7}$
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/PRIDE_$1
is deprecated: true
has URI prefix: http://purl.obolibrary.org/obo/PRIDE_
keyword: ontology
has download URL: pride.owl
description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays.
has responsible: Yasset Perez-Riverol
keyword: protein
0000005: 0000006
keyword: proteomics
is part of: Bioregistry
has prefix: pride
has resource example: PRIDE_0000006
git repository: pride-ontology

MolGlueDB
has URI prefix: https://www.molgluedb.com/browseDB/
keyword: compound
is deprecated: false
contributor: Kangho Ji
description: Identifiers correspond to molecular glue compounds in the MolGlueDB which is a free and open-access online database dedicated to the collection and integration of molecular glue compound information.
0000005: 1
has reviewer: https://orcid.org/0000-0001-9439-5346
has responsible: Chong Qin
has prefix: molgluedb
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: proteolysis
type: Resource
keyword: degraders
has provider formatter: https://www.molgluedb.com/browseDB/$1
has resource example: https://www.molgluedb.com/browseDB/1

FID BAUdigital Subject Headings
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
keyword: architecture
keyword: civil engineering
has prefix: fidbaudigital.subject
has URI prefix: https://purl.org/fidbaudigital/subjects#
is deprecated: false
keyword: digital planning and construction
keyword: fid baudigital
has provider formatter: https://purl.org/fidbaudigital/subjects#$1
description: This subject heading system has beeen developed for use in FID BAUdigital and its future web services. It covers scientific fields of Civil Engineering, Architecture and Urban Studies with a special section on digitization. This subject classification has been mapped to several other classification systems. The latest version of the subject classification including these mappings is available at https://gitlab.com/fid-bau/terminologie/fid-baudigital-faecherklassifikation/-/raw/main/Subject_Headings_all_mappings.owl.

PDB Structure
keyword: epidemiology
type: Resource
0000005: 2gc4
keyword: structure
has local unique identifier pattern: ^[0-9][A-Za-z0-9]{3}$
keyword: structural biology
has resource example: https://www.wwpdb.org/pdb
has responsible: https://orcid.org/0000-0001-6690-5863
is deprecated: false
has alternative prefix: pdbj
has provider formatter: https://www.wwpdb.org/pdb
has prefix: pdb
has alternative prefix: pdbe
has alternative prefix: wwpdb
has URI prefix: https://www.wwpdb.org/pdb
is part of: Bioregistry
keyword: protein
has alternative prefix: RCSB_PDB
keyword: bioinformatics
keyword: virology
keyword: proteomics
description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.

Multiplexed Assays of Variant Effect Database
has provider formatter: https://www.mavedb.org/#/experiments/urn:mavedb:$1
git repository: mavedb-api
is part of: Bioregistry
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
has prefix: mavedb
has reviewer: Charles Tapley Hoyt
has responsible: Alan Rubin
0000005: 00000011-a
has local unique identifier pattern: ^\S+$
is deprecated: false
has resource example: experiments/urn:mavedb:00000011-a
description: Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a
has URI prefix: https://www.mavedb.org/#/experiments/urn:mavedb:

Degree of Establishment Controlled Vocabulary
has prefix: dwc.doe
keyword: fair data spaces
has provider formatter: http://rs.tdwg.org/dwcdoe/$1
0000005: d001
has resource example: d001
is deprecated: false
description: The Darwin Core term degreeOfEstablishment provides information about degree to which an Organism survives, reproduces, and expands its range at the given place and time. The Degree of Establishment Controlled Vocabulary provides term that should be used as values for dwc:degreeOfEstablishment and dwciri:degreeOfEstablishment
has URI prefix: http://rs.tdwg.org/dwcdoe/
is part of: Bioregistry
keyword: life sciences, biology
type: Resource

StreptomeDB
has prefix: streptomedb
has resource example: http://streptomedb.vm.uni-freiburg.de/streptomedb/get_drugcard/15753
0000005: 15753
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: Identifers for natural products isolated or mutasynthesized by bacteria of the genus Streptomyces.
has reviewer: https://orcid.org/0000-0001-9439-5346
type: Resource
has provider formatter: http://streptomedb.vm.uni-freiburg.de/streptomedb/get_drugcard/$1
has responsible: Stefan Günther
contributor: Mufaddal Naguthanawala
has URI prefix: http://streptomedb.vm.uni-freiburg.de/streptomedb/get_drugcard/

CranioMaxilloFacial ontology
has prefix: cmf
has responsible: https://orcid.org/0000-0001-5889-4463
has URI prefix: http://purl.obolibrary.org/obo/CMF_
is part of: Bioregistry
type: Resource
description: This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain
is deprecated: true
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/CMF_$1

Country Names and Codes
type: Resource
description: ISO 3166-1 alpha-2 country codes and names.
has prefix: cessda.countrynamesandcodes
has identifier space owner: 02wg9xc72
has resource example: code AF
0000005: AF
has provider formatter: https://vocabularies.cessda.eu/vocabulary/CountryNamesAndCodes#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/CountryNamesAndCodes#code_
is part of: Bioregistry
contributor: Charles Tapley Hoyt

Cell Image Library
keyword: image
has provider formatter: http://cellimagelibrary.org/images/$1
keyword: cell biology
0000005: 24801
is deprecated: false
has responsible: David N. Orloff
has resource example: http://cellimagelibrary.org/images/24801
description: The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has prefix: cellimage
has URI prefix: http://cellimagelibrary.org/images/
type: Resource
keyword: life science

National Microbial Pathogen Data Resource
type: Resource
description: The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.
has reviewer: Charles Tapley Hoyt
has prefix: nmpdr
0000005: fig|306254.1.peg.183
has provider formatter: http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer
is deprecated: true
has URI prefix: http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer
keyword: genome
is part of: Bioregistry

Taconic Biosciences
description: Supplier of mice for research purposes. [from RRID]
has provider formatter: https://scicrunch.org/resolver/RRID:IMSR_TAC_$1
keyword: supply
0000005: 1178
keyword: model
keyword: mouse
is deprecated: false
keyword: strain
keyword: mice
is part of: Bioregistry
keyword: transgenic
has prefix: imsr_tac
keyword: repository
has URI prefix: https://scicrunch.org/resolver/RRID:IMSR_TAC_
type: Resource
keyword: genetic engineering
keyword: gene
keyword: subject
keyword: research
has resource example: RRID:IMSR TAC 1178
keyword: knockout

BioModels Database
has local unique identifier pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$
description: BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.
has resource example: BIOMD0000000048
has provider formatter: https://biomodels.org/$1
keyword: model
is deprecated: false
has URI prefix: https://biomodels.org/
is part of: Bioregistry
has alternative prefix: BIOMD
0000005: BIOMD0000000048
has prefix: biomodels.db
has responsible: Michael Hucka
type: Resource

SupraBank Solvent
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: suprabank.solvent
keyword: chemical
0000005: 57
description: Identifiers for chemicals used as solvents in SupraBank
type: Resource
keyword: molecule
has URI prefix: https://suprabank.org/solvents/
has provider formatter: https://suprabank.org/solvents/$1
has resource example: https://suprabank.org/solvents/57
is deprecated: false
has responsible: https://orcid.org/0000-0002-9676-9839

Gene Ontology Rules
description: GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio.
0000005: 0000004
is deprecated: false
has provider formatter: https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md
has resource example: gorule-0000004.md
is part of: Bioregistry
type: Resource
has URI prefix: https://bioregistry.io/go.rule:
contributor: Charles Tapley Hoyt
has prefix: go.rule
has local unique identifier pattern: ^\d{7}$

International Generic Sample Number
is deprecated: false
has provider formatter: http://igsn.org/$1
keyword: centrally registered identifier
keyword: geochemistry
0000005: AU124
has resource example: AU124
keyword: omics
keyword: environmental material
description: IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents.
has prefix: igsn
has local unique identifier pattern: ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$
is part of: Bioregistry
has responsible: https://orcid.org/0000-0001-5911-6022
has URI prefix: http://igsn.org/
git repository: igsn.github.io
keyword: earth science
keyword: hydrogeology
keyword: geology
keyword: environmental science
type: Resource
keyword: archaeology
keyword: biospecimen

Maize gross anatomy
has local unique identifier pattern: ^\d{7}$
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/ZEA_$1
description: Maize gross anatomy
keyword: anatomy
has download URL: zea.obo
has responsible: https://orcid.org/0000-0002-9316-2919
is deprecated: true
keyword: obo
has URI prefix: http://purl.obolibrary.org/obo/ZEA_
keyword: ontology
keyword: maize
has resource example: ZEA_0015177
is part of: Bioregistry
has prefix: zea
0000005: 0015177

Drosophila development
keyword: life science
keyword: obo
has download URL: fbdv.owl
has URI prefix: http://purl.obolibrary.org/obo/FBdv_
keyword: ontology
has local unique identifier pattern: ^\d{8}$
git repository: drosophila-developmental-ontology
keyword: life cycle stage
has resource example: FBdv_00000000
is deprecated: false
keyword: developmental biology
has provider formatter: http://purl.obolibrary.org/obo/FBdv_$1
keyword: life cycle
is part of: Bioregistry
type: Resource
description: A structured controlled vocabulary of the development of Drosophila melanogaster.
has prefix: fbdv
keyword: fly
has alternative prefix: FBdv
0000005: 00000000
keyword: development
has responsible: Clare Pilgrim

XML Schema Definition
is deprecated: false
has URI prefix: http://www.w3.org/2001/XMLSchema#
0000005: decimal
keyword: w3c rec
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: http://www.w3.org/2001/XMLSchema#$1
has resource example: decimal
has prefix: xsd
description: This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language.

Thermo Fisher Scientific
keyword: vendor
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
description: ThermoFisher is a life sciences supply vendor.
has URI prefix: https://www.thermofisher.com/antibody/product/
keyword: life sciences
keyword: biology
has resource example: OSR00185W
has prefix: thermofisher
0000005: OSR00185W
is deprecated: false
keyword: chemistry
has provider formatter: https://www.thermofisher.com/antibody/product/$1
has local unique identifier pattern: ^\w+$

Chan Zuckerberg CELLxGENE Collection
has prefix: cellxgene.collection
has reviewer: Charles Tapley Hoyt
type: Resource
description: Assigns identifiers to collections of datasets indexed by CELLxGENE. CELLxGENE is an interactive data visualization and exploration tool developed by the Chan Zuckerberg Initiative that enables researchers to analyze and share single-cell genomics datasets. It provides a user-friendly interface for biologists and computational scientists to interrogate gene expression patterns across different cell types.
has responsible: Ambrose Carr
has URI prefix: https://cellxgene.cziscience.com/collections/
is deprecated: false
has local unique identifier pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
contributor: https://orcid.org/0000-0003-3573-3565
has provider formatter: https://cellxgene.cziscience.com/collections/$1

Online Mendelian Inheritance in Animals
has resource example: omia:001000
has alternative prefix: OMIA
keyword: traits
is part of: Bioregistry
has responsible: Imke Tammen
type: Resource
has provider formatter: https://omia.org/phene/omia:$1
has local unique identifier pattern: ^\d{6}(-\d+)?$
keyword: gene
has prefix: omia
description: Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia' prefix is used for phenes, either across species (omia:001000) or in a specific species (omia:001000-9615)
has URI prefix: https://omia.org/phene/omia:
keyword: model organism database
contributor: Imke Tammen
keyword: classification
keyword: disorders
0000005: 001000
is deprecated: false

SWEET Ontology Property Temperature Gradient
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has alternative prefix: soproptg
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Temperature Gradient
keyword: temperature gradient
has resource example: AutoConvectiveLapseRate
has provider formatter: http://sweetontology.net/propTemperatureGradient/$1
has prefix: sweet.proptg
is deprecated: false
0000005: AutoConvectiveLapseRate
has URI prefix: http://sweetontology.net/propTemperatureGradient/
is part of: Bioregistry

Software Package Repositories
description: These resources represent software repositories
has part: Node Package Manager
has part: The Comprehensive R Archive Network
has part: Crates.io
type: Collection
has part: Packagist
has part: RubyGems
has part: PyPI
creator: Charles Tapley Hoyt

CORDIS Project
description: The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).
is part of: Bioregistry
has resource example: https://cordis.europa.eu/project/id/817732
has provider formatter: https://cordis.europa.eu/project/id/$1
has prefix: cordis.project
type: Resource
has URI prefix: https://cordis.europa.eu/project/id/
has reviewer: Charles Tapley Hoyt
0000005: 817732
is deprecated: false
has local unique identifier pattern: ^\d+$
contributor: https://orcid.org/0000-0001-9439-5346

MassBank
is deprecated: false
keyword: chemistry
has resource example: https://massbank.jp/MassBank/RecordDisplay
has local unique identifier pattern: ^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$
0000005: MSBNK-IPB_Halle-PB000166
has prefix: massbank
is part of: Bioregistry
has provider formatter: https://massbank.jp/MassBank/RecordDisplay
has responsible: https://orcid.org/0000-0002-9744-8914
has URI prefix: https://massbank.jp/MassBank/RecordDisplay
type: Resource
description: MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).
keyword: life science
git repository: MassBank
keyword: physics

CESSDA Topic Classification
is part of: Bioregistry
description: A typology of main themes or subjects of data.
contributor: Charles Tapley Hoyt
has provider formatter: https://vocabularies.cessda.eu/vocabulary/TopicClassification#code_$1
has prefix: cessda.topicclassification
type: Resource
0000005: Demography
has identifier space owner: 02wg9xc72
is deprecated: false
has resource example: code Demography
has URI prefix: https://vocabularies.cessda.eu/vocabulary/TopicClassification#code_

Obstetric and Neonatal Ontology
0000005: 00000098
type: Resource
git repository: Ontoneo
has resource example: ONTONEO_00000098
has provider formatter: http://purl.obolibrary.org/obo/ONTONEO_$1
has URI prefix: http://purl.obolibrary.org/obo/ONTONEO_
is deprecated: false
has responsible: https://orcid.org/0000-0003-2338-8872
keyword: obo
description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.
keyword: ontology
has local unique identifier pattern: ^\d{8}$
keyword: obstetrics
keyword: electronic health record
has prefix: ontoneo
is part of: Bioregistry
has download URL: ontoneo.owl

Orphanet
has URI prefix: http://www.orpha.net/ORDO/Orphanet_
keyword: ontology and terminology
keyword: human
keyword: ontology
is deprecated: false
keyword: disease
has provider formatter: http://www.orpha.net/ORDO/Orphanet_$1
0000005: 85163
is part of: Bioregistry
contributor: https://orcid.org/0000-0002-7356-1779
has alternative prefix: Orphanet
has resource example: Orphanet_85163
has prefix: orpha
has alternative prefix: orphanet
has download URL: ordo orphanet.owl
has local unique identifier pattern: ^C?\d+$
has responsible: Marc Hanauer
description: Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases.
type: Resource
keyword: life science
keyword: drug

CIDOC Conceptual Reference Model
keyword: coypu
keyword: nfdi4culture
keyword: history
description: The CIDOC Conceptual Reference Model (CRM) is a theoretical and practical tool for information integration in the field of cultural heritage. It can help researchers, administrators and the public explore complex questions with regards to our past across diverse and dispersed datasets. The CIDOC CRM achieves this by providing definitions and a formal structure for describing the implicit and explicit concepts and relationships used in cultural heritage documentation and of general interest for the querying and exploration of such data. Such models are also known as formal ontologies. These formal descriptions allow the integration of data from multiple sources in a software and schema agnostic fashion. [from homepage]
keyword: culture
has prefix: cidoc.crm
keyword: ontology
keyword: anthropology
has resource example: E1
is deprecated: false
keyword: digital planning and construction
is part of: Bioregistry
has URI prefix: http://www.cidoc-crm.org/cidoc-crm/
keyword: humanities and social science
keyword: fid baudigital
0000005: E1
has provider formatter: http://www.cidoc-crm.org/cidoc-crm/$1
has download URL: cidoc-crm.owl
keyword: cultural studies
type: Resource
contributor: Charles Tapley Hoyt

Cell Markers Ontology
has provider formatter: http://purl.obolibrary.org/obo/CLM_$1
has URI prefix: http://purl.obolibrary.org/obo/CLM_
git repository: CellMark
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: This ontology integrates cell type markers for cells in the Cell Ontology from various sources along with details of marker context (anatomical context, assay), confidence (where available) and provenance. [from repository]
0000005: 1000003
has local unique identifier pattern: ^\d{7}$
has prefix: clm
has download URL: clm.owl
has responsible: David Osumi-Sutherland
keyword: ontology
is deprecated: false
has resource example: CLM_1000003

Hypertension Ontology
has prefix: htn
has responsible: Amanda Hicks
is deprecated: false
keyword: obo
keyword: ontology
has local unique identifier pattern: ^\d{8}$
is part of: Bioregistry
has URI prefix: http://purl.obolibrary.org/obo/HTN_
git repository: htn owl
description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines
has download URL: htn.owl
has provider formatter: http://purl.obolibrary.org/obo/HTN_$1
0000005: 00000014
has resource example: HTN_00000014
type: Resource

BridgeDb Vocabulary
type: Resource
has URI prefix: http://vocabularies.bridgedb.org/ops#
has prefix: bridgedb
is deprecated: false
is part of: Bioregistry
description: A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc.
has provider formatter: http://vocabularies.bridgedb.org/ops#$1
contributor: Charles Tapley Hoyt
has resource example: hasPrimaryUriPattern
0000005: hasPrimaryUriPattern

Clinical Trials Information System
0000005: 2023-503698-40-00
has URI prefix: https://euclinicaltrials.eu/app/#/view/
is deprecated: false
has local unique identifier pattern: ^\d{4}-\d+-\d+-\d+$
has prefix: ctis
is part of: Bioregistry
description: This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). It is part of a broad initiative to transform the EU/EEA clinical trials environment in support of large clinical trials in multiple European countries, to the benefit of medical innovation and patients. (from homepage)
has resource example: view/2023-503698-40-00
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: https://euclinicaltrials.eu/app/#/view/$1

ProDom
keyword: life science
has provider formatter: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl
is deprecated: true
keyword: classification
has responsible: https://orcid.org/0000-0003-1644-0169
has resource example: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl
keyword: protein
has prefix: prodom
has local unique identifier pattern: ^PD\d+$
has URI prefix: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl
is part of: Bioregistry
description: ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.
type: Resource
0000005: PD10000

NIF Standard Ontology: Neurolex
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_$1
has prefix: neurolex
has alternative prefix: nlx
has part: NIF Standard Ontology: Subcellular Entities
keyword: classification
has alternative prefix: NLX
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_
keyword: ontology
has responsible: Tom Gillespie
is deprecated: false
has local unique identifier pattern: ^\d+$
git repository: NIF-Ontology
is part of: Bioregistry
has resource example: nlx 4
type: Resource
description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex).
keyword: neuroscience
0000005: 4

DragonDB DNA
has URI prefix: https://bioregistry.io/dragondb.dna:
0000005: 3hB06
has provider formatter: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
has prefix: dragondb.dna
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^\d\w+$
is deprecated: true
has resource example: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information.

SAREF extension for Smart City
keyword: fid move
type: Resource
keyword: iot
description: This ontology extends the SAREF ontology for the Smart City domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Smart City domain.
keyword: government
keyword: computer science
has prefix: saref.city
has provider formatter: https://saref.etsi.org/saref4city/$1
has alternative prefix: s4city
has URI prefix: https://saref.etsi.org/saref4city/
keyword: civil engineering
is deprecated: false
keyword: traffic engineering
has resource example: AccessibilityConcept
keyword: digital planning and construction
is part of: Bioregistry
0000005: AccessibilityConcept

Medaka Developmental Stages
keyword: ontology
keyword: life cycle stage
keyword: developmental biology
has URI prefix: http://purl.obolibrary.org/obo/OlatDv_
has responsible: Frédéric Bastian
is part of: Bioregistry
git repository: developmental-stage-ontologies
description: Life cycle stages for Medaka
has prefix: olatdv
keyword: aquaculture
has local unique identifier pattern: ^\d{7}$
has provider formatter: http://purl.obolibrary.org/obo/OlatDv_$1
type: Resource
0000005: 0000210
keyword: life science
has download URL: olatdv.owl
has resource example: OlatDv_0000210
is deprecated: true
keyword: obo

Analysis Unit
has resource example: code Individual
description: Describes the entity being analyzed in the study or variable. This vocabulary can also be used to describe the unit of observation, which is the unit being observed, or from which data are collected. The unit of observation can be the same as, or different from the unit of analysis.
0000005: Individual
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: https://vocabularies.cessda.eu/vocabulary/AnalysisUnit#code_$1
has identifier space owner: 015em2733
has prefix: ddi.analysisunit
has URI prefix: https://vocabularies.cessda.eu/vocabulary/AnalysisUnit#code_
is deprecated: false
is part of: Bioregistry

Bactibase
has prefix: bactibase
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: BAC045
has provider formatter: http://bactibase.hammamilab.org/$1
has resource example: BAC045
type: Resource
keyword: life science
is deprecated: false
has responsible: https://orcid.org/0000-0002-8467-9414
description: Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria.
keyword: protein
has URI prefix: http://bactibase.hammamilab.org/

Reaxys
has prefix: reaxys
description: Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier.
is deprecated: false
has local unique identifier pattern: ^\d+$
has alternative prefix: Beilstein
is part of: Bioregistry
has alternative prefix: Reaxys
type: Resource
contributor: Charles Tapley Hoyt
0000005: 1257009

The Behaviour Change Intervention Ontology
has prefix: bcio
keyword: ontology
has resource example: https://w3id.org/BCI-ontology#040000
is deprecated: false
is part of: Bioregistry
has download URL: bcio.owl
has responsible: https://orcid.org/0000-0001-7203-8399
description: The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.
has local unique identifier pattern: ^\d{6}$
type: Resource
has provider formatter: https://w3id.org/BCI-ontology#$1
0000005: 040000
has URI prefix: https://w3id.org/BCI-ontology#

ProtoNet Cluster
keyword: clustering
is deprecated: true
keyword: classification
has resource example: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php
keyword: protein
description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.
0000005: 4349895
is part of: Bioregistry
has prefix: protonet.cluster
has local unique identifier pattern: ^\d+$
has provider formatter: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php
has URI prefix: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php
type: Resource
has responsible: https://orcid.org/0000-0002-9357-4526

Foundational Model of Anatomy
has local unique identifier pattern: ^\d+$
has resource example: https://www.ebi.ac.uk/ols4/ontologies/fma/terms
has responsible: Onard Mejino
keyword: phenotype
has provider formatter: https://www.ebi.ac.uk/ols4/ontologies/fma/terms
has alternative prefix: FMA_RETIRED
has alternative prefix: FMAID
has download URL: fma.owl
keyword: owl
is part of: Bioregistry
0000005: 63189
has prefix: fma
type: Resource
keyword: radiology
keyword: neuroimaging measurement
git repository: fma
keyword: biomedical science
keyword: anatomy
description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.
is deprecated: true
keyword: obo
keyword: ontology
has URI prefix: https://www.ebi.ac.uk/ols4/ontologies/fma/terms
keyword: human

SWEET Ontology Phenomena Heliosphere
is deprecated: false
has provider formatter: http://sweetontology.net/phenHelio/$1
keyword: heliosphere
is part of: Bioregistry
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Heliosphere
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
keyword: phenomena
has URI prefix: http://sweetontology.net/phenHelio/
has resource example: Airglow
0000005: Airglow
has alternative prefix: sophhe
has prefix: sweet.phhe

International Standard Classification of Education, 1997 Edition
keyword: open educational resources
type: Resource
has resource example: level1
has provider formatter: https://w3id.org/kim/isced-1997/level$1
description: ISCED is designed to serve as a framework to classify educational activities as defined in programmes and the resulting qualifications into internationally agreed categories. The basic concepts and definitions of ISCED are therefore intended to be internationally valid and comprehensive of the full range of education systems.
0000005: 1
has URI prefix: https://w3id.org/kim/isced-1997/level
is deprecated: false
is part of: Bioregistry
has prefix: isced1997
keyword: education level
contributor: Charles Tapley Hoyt

Response Unit
has provider formatter: https://vocabularies.cessda.eu/vocabulary/ResponseUnit#code_$1
is deprecated: false
has prefix: ddi.responseunit
0000005: Self
is part of: Bioregistry
description: Indicates the entity that provided the information carried by the variable.
type: Resource
contributor: Charles Tapley Hoyt
has resource example: code Self
has identifier space owner: 015em2733
has URI prefix: https://vocabularies.cessda.eu/vocabulary/ResponseUnit#code_

Minimal Anatomical Terminology
has prefix: mat
keyword: obo
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/MAT_
description: Minimal set of terms for anatomy
has download URL: mat.obo
is part of: Bioregistry
has resource example: MAT_0000000
has local unique identifier pattern: ^\d{7}$
has responsible: Jonathan Bard
type: Resource
0000005: 0000000
is deprecated: true
has provider formatter: http://purl.obolibrary.org/obo/MAT_$1

Spider Ontology
is deprecated: false
description: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).
has resource example: SPD_0000001
keyword: behavior
has prefix: spd
has responsible: https://orcid.org/0000-0002-0358-0130
has URI prefix: http://purl.obolibrary.org/obo/SPD_
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/SPD_$1
has download URL: spd.owl
type: Resource
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
keyword: spider
keyword: anatomy
keyword: life science
git repository: spider-ontology
keyword: obo
keyword: ontology

NHMRC Australian PhenomeBank
keyword: embryo
keyword: murine
keyword: database
keyword: allele
has URI prefix: https://pb.apf.edu.au/phenbank/strain.html
keyword: transgene
is deprecated: false
keyword: strain
description: The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]
keyword: phenotype
keyword: transgenic
0000005: 7345
keyword: sperm
has prefix: imsr.apb
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
keyword: gene
keyword: chromosome
has provider formatter: https://pb.apf.edu.au/phenbank/strain.html
keyword: live mouse
keyword: alteration
has resource example: https://pb.apf.edu.au/phenbank/strain.html
keyword: mutation

ChemFOnt Ontology
has reviewer: Charles Tapley Hoyt
has local unique identifier pattern: ^CFo\d{9}$
has responsible: David Wishart
type: Resource
keyword: ontology
description: The Chemical Functional Ontology (ChemFOnt) is a hierarchical, OWL-compatible ontology describing the functions and actions of biologically important chemicals including primary metabolites, secondary metabolites, natural products, food chemicals, synthetic food additives, drugs, herbicides, pesticides and environmental chemicals. The identifiers in this semantic space correspond to entries in the ChemFOnt ontology that are used to organize individual chemicals. Terms can be looked up using the following URL (https://www.chemfont.ca/ontology_browse/term_info/18), but not directly by ID
contributor: https://orcid.org/0000-0001-9439-5346
is deprecated: false
has download URL: chemfont.owl.zip
has prefix: chemfont.ontology
keyword: chemical
0000005: CFo000000197
is part of: Bioregistry

PolBase
has responsible: 0000-0003-4497-423X
keyword: genetics
has resource example: sequences
is deprecated: false
0000005: 19-T4
has URI prefix: https://bioregistry.io/polbase:
has prefix: polbase
is part of: Bioregistry
has provider formatter: https://polbase.neb.com/polymerases/$1#sequences
type: Resource
has local unique identifier pattern: ^[A-Za-z-0-9]+$
keyword: biochemistry
description: Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity.

FunderRegistry
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: http://data.crossref.org/fundingdata/funder/10.13039/$1
has prefix: funderregistry
description: The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.
type: Resource
has alternative prefix: crossref.funder
0000005: 100000001
has alternative prefix: FundRef
has URI prefix: http://data.crossref.org/fundingdata/funder/10.13039/
has resource example: http://data.crossref.org/fundingdata/funder/10.13039/100000001

BioKC
has prefix: biokc
has provider formatter: https://biokb.lcsb.uni.lu/fact/$1
type: Resource
0000005: bkc640
has local unique identifier pattern: ^bkc[0-9]*$
has resource example: bkc640
has URI prefix: https://biokb.lcsb.uni.lu/fact/
description: BioKC (Biological Knowledge Curation), is a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML).
is deprecated: false
is part of: Bioregistry

Lentil Ontology
keyword: life science
keyword: food
0000005: 0000032
keyword: ontology
has responsible: Elizabeth Arnaud
has provider formatter: https://cropontology.org/rdf/CO_339:$1
is deprecated: false
keyword: plant phenotypes and traits
is part of: Bioregistry
description: The Lentil Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
has resource example: CO 339:0000032
git repository: Crop-Ontology
keyword: phenotype
has download URL: CO 339.owl
keyword: botany
has URI prefix: https://cropontology.org/rdf/CO_339:
keyword: agriculture
has prefix: co_339
has local unique identifier pattern: ^\d{7}$
type: Resource

Mental Disease Ontology
description: The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF).
has local unique identifier pattern: ^\d{7}$
type: Resource
has prefix: mfomd
keyword: psychiatry
has URI prefix: http://purl.obolibrary.org/obo/MFOMD_
0000005: 0000046
has resource example: MFOMD_0000046
has download URL: mfomd.owl
keyword: obo
has responsible: https://orcid.org/0000-0002-3469-4923
keyword: ontology
is deprecated: false
keyword: disease
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/MFOMD_$1
git repository: mental-functioning-ontology

Polygenic Score Catalog
is deprecated: false
is part of: Bioregistry
has URI prefix: https://www.pgscatalog.org/pgs/
has prefix: pgs
description: The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation.
type: Resource
has local unique identifier pattern: ^PGS[0-9]{6}$
0000005: PGS000018
has provider formatter: https://www.pgscatalog.org/pgs/$1
has resource example: PGS000018

NIA Mouse cDNA Project
type: Resource
keyword: life science
description: A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones.
has local unique identifier pattern: ^\w\d{4}\w\d{2}(\-[35])?$
has prefix: niaest
has resource example: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3
is deprecated: true
has responsible: Dawood B. Dudekula
has provider formatter: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3
keyword: dna
is part of: Bioregistry
has URI prefix: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3
0000005: J0705A10

Web of Science work ID
is deprecated: false
is part of: Bioregistry
has URI prefix: https://www.webofscience.com/wos/woscc/full-record/WOS:
0000005: 000177759000002
description: unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix)
has resource example: WOS:000177759000002
has alternative prefix: wos
has alternative prefix: wosuid
type: Resource
has provider formatter: https://www.webofscience.com/wos/woscc/full-record/WOS:$1
has alternative prefix: wosid
has prefix: wos.work

Microbial Protein Interaction Database
has responsible: https://orcid.org/0000-0002-9968-4080
has URI prefix: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-
has alternative prefix: mpidb
keyword: small molecule
0000005: 1776
is deprecated: false
keyword: protein
has provider formatter: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1
description: The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: mpid
has resource example: interaction id:MPIDB-INT-1776
type: Resource
keyword: interaction
keyword: life science

HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
has prefix: xlmod
0000005: 00050
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/XLMOD_
keyword: reagent
keyword: experimental measurement
has provider formatter: http://purl.obolibrary.org/obo/XLMOD_$1
keyword: mass spectrum
keyword: mass spectrometry assay
git repository: xlmod-CV
keyword: obo
keyword: ontology
has download URL: xlmod.owl
has resource example: XLMOD_00050
has local unique identifier pattern: ^\d{5}$
is deprecated: false
keyword: gas chromatography
is part of: Bioregistry
has responsible: Gerhard Mayer
keyword: chemical biology
keyword: metabolomics
description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.
keyword: omics

PLOS Thesaurus
has URI prefix: http://localhost/plosthes.2017-1#
has prefix: plos
keyword: subject agnostic
has resource example: http://localhost/plosthes.2017-1#1443
keyword: ontology
has alternative prefix: PLOSTHES
has provider formatter: http://localhost/plosthes.2017-1#$1
is deprecated: false
description: An ontologization of Public Library of Science (PLOS) journal keywords and topics. It's not clear how the IDs correspond to the actual pages. Appears in ADCAD.
has local unique identifier pattern: ^\d+$
0000005: 1443
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt

FooDB compound
0000005: FDB002100
has provider formatter: http://foodb.ca/compounds/$1
type: Resource
description: FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.
is deprecated: false
has prefix: foodb.compound
is part of: Bioregistry
has local unique identifier pattern: ^FDB\d+$
has resource example: http://foodb.ca/compounds/FDB002100
has URI prefix: http://foodb.ca/compounds/
has alternative prefix: foodb

Protein covalent bond
keyword: small molecule
keyword: protein
0000005: AA0001
is part of: Bioregistry
has responsible: 0000-0002-4131-735X
keyword: structure
has prefix: resid
has provider formatter: https://proteininformationresource.org/cgi-bin/resid
description: The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
type: Resource
is deprecated: true
keyword: obo
has URI prefix: https://proteininformationresource.org/cgi-bin/resid
has local unique identifier pattern: ^AA\d{4}$
has resource example: https://proteininformationresource.org/cgi-bin/resid
keyword: ontology

Software Package
has URI prefix: https://vocabularies.cessda.eu/vocabulary/SoftwarePackage#code_
is deprecated: false
has prefix: ddi.softwarepackage
is part of: Bioregistry
0000005: AcaStat
contributor: Charles Tapley Hoyt
has provider formatter: https://vocabularies.cessda.eu/vocabulary/SoftwarePackage#code_$1
type: Resource
description: Indicates the statistical software package used in the production/processing/dissemination of the data. Data collection software is not covered in this list.
has resource example: code AcaStat
has identifier space owner: 015em2733

Wikidata Property
is part of: Wikidata
is deprecated: false
has provider formatter: http://www.wikidata.org/entity/$1
is part of: Bioregistry
description: Wikidata is a free and open knowledge base that can be read and edited by both humans and machines. Wikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others.
contributor: Charles Tapley Hoyt
type: Resource
0000005: P4355
has prefix: wikidata.property
has URI prefix: http://www.wikidata.org/entity/
has local unique identifier pattern: ^P\d+$
has resource example: P4355

Homeodomain Research
type: Resource
has resource example: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi
has URI prefix: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi
is deprecated: true
keyword: genome
has local unique identifier pattern: ^\d+$
0000005: 63
is part of: Bioregistry
description: The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.
has provider formatter: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi
has prefix: hdr

Apple Ontology
has local unique identifier pattern: ^\d{7}$
has prefix: co_370
description: Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales. This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 894215.
has URI prefix: https://cropontology.org/rdf/CO_370:
has download URL: CO 370.owl
keyword: ontology
is deprecated: false
has provider formatter: https://cropontology.org/rdf/CO_370:$1
0000005: 0000890
has resource example: CO 370:0000890
is part of: Bioregistry
type: Resource
git repository: Crop-Ontology
has responsible: https://orcid.org/0000-0002-8981-0442

GitHub account
has resource example: bioregistry
keyword: knowledge and information systems
is part of: Bioregistry
description: GitHub is an online host of Git source code repositories.
type: Resource
0000005: biopragmatics/bioregistry
keyword: subject agnostic
has provider formatter: https://github.com/$1
git repository: services.github.com
has prefix: github
keyword: software engineering
is deprecated: false
has local unique identifier pattern: ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$
has URI prefix: https://github.com/

DragonDB Protein
has provider formatter: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
0000005: AMDEFA
has URI prefix: https://bioregistry.io/dragondb.protein:
has resource example: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
is deprecated: true
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.
has prefix: dragondb.protein
has local unique identifier pattern: ^\w+$
is part of: Bioregistry
type: Resource

Bioregistry
has prefix: bioregistry
keyword: life science
keyword: ontology and terminology
git repository: bioregistry
keyword: computational chemistry
has responsible: Charles Tapley Hoyt
is deprecated: false
keyword: computational biology
has URI prefix: https://bioregistry.io/registry/
keyword: cheminformatics
keyword: bioinformatics
has provider formatter: https://bioregistry.io/registry/$1
description: The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database.
has local unique identifier pattern: ^[A-Za-z_][A-Za-z0-9\.\-_]*$
is part of: Bioregistry
0000005: bioregistry
type: Resource
contributor: Charles Tapley Hoyt

Educational Resource Discovery Index Schema
has provider formatter: http://www.bigdatau.org/schema#$1
is deprecated: false
has URI prefix: http://www.bigdatau.org/schema#
description: A metadata stadnard to model data science training materials. Later, was replaced by Bioschemas' [training materials specification](http://bioschemas.org/specifications/TrainingMaterial/specification/).
keyword: educational resource
0000005: enables
has resource example: enables
keyword: learning material
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: erudite
keyword: schema
keyword: open educational resource
type: Resource

LINCS Small Molecule
has local unique identifier pattern: ^LSM-\d+$
has resource example: view/LSM-6306
is part of: Bioregistry
0000005: LSM-6306
has alternative prefix: lincs
has prefix: lincs.smallmolecule
type: Resource
has URI prefix: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/
description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).
is deprecated: false
has provider formatter: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1

SWEET Ontology Property Diffusivity
has prefix: sweet.propdifu
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Diffusivity
is deprecated: false
0000005: Confluence
has resource example: Confluence
has alternative prefix: sopropdifu
has provider formatter: http://sweetontology.net/propDiffusivity/$1
has URI prefix: http://sweetontology.net/propDiffusivity/
is part of: Bioregistry
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
type: Resource
keyword: diffusivity

National Swine Resource and Research Center
0000005: 0005
description: Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. [from RRID]
type: Resource
has provider formatter: https://nsrrc.missouri.edu/nsrrc$1info/
keyword: tissue
keyword: live animal
keyword: consulting
keyword: genotyping
keyword: genetically modified pig
has resource example: nsrrc0005info
keyword: breeding
is deprecated: false
keyword: cryopreservation
keyword: reproduction
keyword: fibroblast
keyword: phenotyping
has URI prefix: https://bioregistry.io/nsrrc:
keyword: pig
keyword: biomaterial manufacture
keyword: health monitoring
keyword: genetics
has prefix: nsrrc
keyword: genome
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: fetus
keyword: fetal fibroblast

Units of measurement ontology
has responsible: George Gkoutos
has URI prefix: http://purl.obolibrary.org/obo/UO_
keyword: nfdi4chem
keyword: earth sciences
git repository: unit-ontology
has resource example: UO_0000080
keyword: life sciences, biology
keyword: unit
appears in: Mass spectrometry ontology
has local unique identifier pattern: ^\d{7}$
description: Ontology of standardized units
type: Resource
keyword: nfdi4ing
appears in: Radiation Biology Ontology
has provider formatter: http://purl.obolibrary.org/obo/UO_$1
appears in: Sickle Cell Disease Ontology
appears in: Agronomy Ontology
keyword: life science
keyword: ess
is deprecated: false
keyword: units
has download URL: uo.owl
keyword: physics
keyword: obo
keyword: measurement
keyword: ontology
0000005: 0000080
has prefix: uo
keyword: mathematics
is part of: Bioregistry
keyword: dataplant

Database of Genotypes and Phenotypes
keyword: genetics
has resource example: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi
is deprecated: false
0000005: phs000768.v2.p1
has provider formatter: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi
is part of: Bioregistry
type: Resource
has URI prefix: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi
keyword: biomedical science
has prefix: dbgap
keyword: epigenetics
description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.
has local unique identifier pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$
has responsible: Michael Feolo

Distributed Archives for Neurophysiology Data Integration
has prefix: dandi
has provider formatter: https://dandiarchive.org/dandiset/$1
has resource example: https://dandiarchive.org/dandiset/000017
has URI prefix: https://dandiarchive.org/dandiset/
has local unique identifier pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$
git repository: dandiarchive
is deprecated: false
description: DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). DANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.
0000005: 000017
has responsible: https://orcid.org/0000-0003-3456-2493
is part of: Bioregistry
keyword: neurophysiology
type: Resource

SWEET Ontology Human Research
0000005: Analysis
has prefix: sweet.hur
has resource example: Analysis
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Research
is deprecated: false
has URI prefix: http://sweetontology.net/humanResearch/
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/humanResearch/$1
has alternative prefix: sohur
keyword: research

SWEET Ontology Human Jurisdiction
has URI prefix: http://sweetontology.net/humanJurisdiction/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Jurisdiction
has prefix: sweet.huj
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
0000005: AdministrativeRegion
has resource example: AdministrativeRegion
has provider formatter: http://sweetontology.net/humanJurisdiction/$1
keyword: jurisdiction
is deprecated: false
has alternative prefix: sohuj

Immune Epitope Database Assays
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: iedb.assay
is part of: Bioregistry
type: Resource
has responsible: https://orcid.org/0000-0001-8957-7612
0000005: 1691753
keyword: life science
has resource example: https://www.iedb.org/assay/1691753
description: Identifiers for specific experimental assays that serve as evidence for immune-related studies.
contributor: Mufaddal Naguthanawala
keyword: immunology
is deprecated: false
has local unique identifier pattern: ^\d+$
has URI prefix: https://www.iedb.org/assay/
keyword: bioinformatics
has provider formatter: https://www.iedb.org/assay/$1

The Bibliographic Ontology
is deprecated: false
git repository: bibo
keyword: bibliometrics
has provider formatter: http://purl.org/ontology/bibo/$1
is part of: Bioregistry
keyword: catalogs
type: Resource
has resource example: authorList
contributor: Charles Tapley Hoyt
has URI prefix: http://purl.org/ontology/bibo/
has prefix: bibo
0000005: authorList
has download URL: bibo.rdf.xml
description: The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web.
keyword: ontology

Ontology of Core Data Mining Entities
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
appears in: Experimental Factor Ontology
has download URL: OntoDM.owl
has resource example: OntoDM_000072
has provider formatter: http://www.ontodm.com/OntoDM-core/OntoDM_$1
0000005: 000072
type: Resource
contributor: Charles Tapley Hoyt
has prefix: ontodm
git repository: ontodm-core
has URI prefix: http://www.ontodm.com/OntoDM-core/OntoDM_
description: OntoDM-core defines the most essential data mining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. (from abstract)
keyword: ontology

Assembling the Fungal Tree of Life - Taxonomy
has prefix: aftol.taxonomy
has URI prefix: http://wasabi.lutzonilab.net/pub/displayTaxonInfo
0000005: 959
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
has provider formatter: http://wasabi.lutzonilab.net/pub/displayTaxonInfo
contributor: 0000-0002-5798-662X
has responsible: David J. McLaughlin
description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.
is deprecated: true
has resource example: http://wasabi.lutzonilab.net/pub/displayTaxonInfo

Salk Institute for Biological Studies
has prefix: salk
has URI prefix: https://abrc.osu.edu/stocks/number/SALK_
is deprecated: false
description: Scientific research institute for neuroscience, genetics, immunology, plant biology and more.
appears in: Experimental Factor Ontology
has resource example: SALK_037727
0000005: 037727
is part of: Bioregistry
has local unique identifier pattern: ^\d{6}$
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: https://abrc.osu.edu/stocks/number/SALK_$1

SWEET Ontology Realm Land Fluvial
is part of: Bioregistry
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has prefix: sweet.realf
keyword: fluvialland
has URI prefix: http://sweetontology.net/realmLandFluvial/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Fluvial
has provider formatter: http://sweetontology.net/realmLandFluvial/$1
has resource example: Alluvial
0000005: Alluvial
has alternative prefix: sorealf
is deprecated: false

Manufacturers of Vaccines
type: Resource
contributor: https://orcid.org/0000-0002-8741-7823
description: The CDC's National Center for Immunization and Respiratory Diseases ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers of vaccines in the US. Inactive MVX codes allow transmission of historical immunization records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename) (vaccine administered code), the specific trade named vaccine may be indicated.
has provider formatter: https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action
has reviewer: Charles Tapley Hoyt
has resource example: https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action
is deprecated: false
0000005: ASZ
has local unique identifier pattern: ^\w+$
has URI prefix: https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action
is part of: Bioregistry
has prefix: mvx

GenBank
keyword: genomics
is deprecated: false
keyword: dna
keyword: bioinformatics
keyword: virology
has URI prefix: https://www.ncbi.nlm.nih.gov/nucleotide/
keyword: functional genomics
is part of: Bioregistry
description: GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).
has resource example: U49845
keyword: transcriptomics
type: Resource
contributor: Charles Tapley Hoyt
keyword: epidemiology
has provider formatter: https://www.ncbi.nlm.nih.gov/nucleotide/$1
keyword: metagenomics
has prefix: genbank
keyword: data management
0000005: U49845
has responsible: https://orcid.org/0000-0002-2497-3427

KEGG LIGAND
is deprecated: true
has prefix: kegg.ligand
has provider formatter: http://www.genome.jp/dbget-bin/www_bget
is part of: Bioregistry
type: Resource
is part of: Kyoto Encyclopedia of Genes and Genomes
has URI prefix: http://www.genome.jp/dbget-bin/www_bget

SWEET Ontology Phenomena Atmosphere Lightning
keyword: phenomena
has URI prefix: http://sweetontology.net/phenAtmoLightning/
0000005: BallLightning
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Lightning
has resource example: BallLightning
has alternative prefix: sophatmol
keyword: atmosphere lightning
is deprecated: false
is part of: Bioregistry
has provider formatter: http://sweetontology.net/phenAtmoLightning/$1
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has prefix: sweet.phatmol
type: Resource

Domain Resource Application Ontology
keyword: agriculture
keyword: humanities
is part of: Bioregistry
has download URL: DRAO.owl
type: Resource
contributor: Charles Tapley Hoyt
keyword: biomedical science
keyword: earth science
keyword: fair
keyword: computer science
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
keyword: environmental science
has URI prefix: http://www.fairsharing.org/ontology/domain/DRAO_
has resource example: DRAO_0000001
keyword: life science
git repository: domain-ontology
keyword: metadata standardization
keyword: natural science
keyword: classification
description: A project supporting the DRAO application ontology, a hierarchy of specific research domains and descriptors which imports subsets of terms from over 40 publicly-available terminologies. (from repository)
has prefix: drao
keyword: ontology
has responsible: https://orcid.org/0000-0002-7702-4495
keyword: resource metadata
is deprecated: false
has provider formatter: http://www.fairsharing.org/ontology/domain/DRAO_$1

Genome Aggregation Database
has responsible: Heidi L. Rehm
has provider formatter: https://gnomad.broadinstitute.org/variant/$1
has resource example: 1-55516888-G-GA
has URI prefix: https://gnomad.broadinstitute.org/variant/
is deprecated: false
has prefix: gnomad
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
0000005: 1-55516888-G-GA
description: The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community (from https://gnomad.broadinstitute.org).

Antibiotic Resistance Genes Database
type: Resource
description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.
has provider formatter: http://ardb.cbcb.umd.edu/cgi/search.cgi
is deprecated: true
has URI prefix: http://ardb.cbcb.umd.edu/cgi/search.cgi
0000005: CAE46076
has prefix: ardb
has resource example: http://ardb.cbcb.umd.edu/cgi/search.cgi
has local unique identifier pattern: ^[A-Z_]{3}[0-9]{4,}$
is part of: Bioregistry

Unified Astronomy Thesaurus
has provider formatter: http://astrothesaurus.org/uat/$1
0000005: 0
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
has resource example: http://astrothesaurus.org/uat/0
keyword: ess
description: The Unified Astronomy Thesaurus (UAT) is an open, interoperable and community-supported thesaurus being developed to unify the existing divergent and isolated Astronomy & Astrophysics thesauri into a single high-quality, freely-available open-source thesaurus which will be of immediate value to both research and research support, and provide a mechanism for reviewing, discussing and evaluating the continuous evolution of terminology in these fields.
has URI prefix: http://astrothesaurus.org/uat/
keyword: astronomy and astrophysics
keyword: physics
has prefix: uat
git repository: UAT
is deprecated: false

Yeast Genome Order Browser
description: YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes.
has URI prefix: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl
is part of: Bioregistry
type: Resource
keyword: gene
has reviewer: Charles Tapley Hoyt
0000011: HGNC gene symbol
has resource example: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl
is deprecated: true
has provider formatter: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl
keyword: genome
has prefix: ygob
0000005: ADH1

BRENDA Enzyme
description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.
has local unique identifier pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$
0000005: 1.1.1.1
0000011: Enzyme Nomenclature
has provider formatter: https://www.brenda-enzymes.org/php/result_flat.php4
has resource example: https://www.brenda-enzymes.org/php/result_flat.php4
is part of: Bioregistry
has URI prefix: https://www.brenda-enzymes.org/php/result_flat.php4
has responsible: Dietmar Schomburg
has prefix: brenda
type: Resource
keyword: life science
keyword: enzyme
is deprecated: false

SABIO-RK Reaction
has URI prefix: http://sabiork.h-its.org/reacdetails.jsp
keyword: pathway
has prefix: sabiork.reaction
has responsible: Ulrike Wittig
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has resource example: http://sabiork.h-its.org/reacdetails.jsp
type: Resource
description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information.
has alternative prefix: SABIO-RK
keyword: biochemistry
keyword: life science
is deprecated: false
has provider formatter: http://sabiork.h-its.org/reacdetails.jsp
keyword: reaction
keyword: kinetics
0000005: 75

GeneDB
has resource example: LinJ.20.0070
0000005: LinJ.20.0070
has URI prefix: https://www.genedb.org/gene/
type: Resource
description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.
has provider formatter: https://www.genedb.org/gene/$1
keyword: life science
has prefix: genedb
is deprecated: true
keyword: sequence
has local unique identifier pattern: ^[\w\d\.-]*$
keyword: genome
is part of: Bioregistry

Ensembl Glossary
has download URL: ensembl-glossary.owl
has prefix: ensemblglossary
has local unique identifier pattern: ^\d{7}$
type: Resource
has resource example: ENSGLOSSARY_0000198
description: The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used.
has URI prefix: http://ensembl.org/glossary/ENSGLOSSARY_
has provider formatter: http://ensembl.org/glossary/ENSGLOSSARY_$1
is deprecated: false
keyword: ontology
0000005: 0000198
is part of: Bioregistry

Reagent Ontology
git repository: reagent-ontology
has provider formatter: http://purl.obolibrary.org/obo/REO_$11
has download URL: reo reasoned 9-6-12.owl
description: The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: 0000079
has prefix: reo
has resource example: REO_00000791
has local unique identifier pattern: ^\d{7}$
type: Resource
has URI prefix: https://bioregistry.io/reo:
has responsible: Matthew Brush
keyword: ontology
is deprecated: false

Enabling and Unlocking Biology in the Open
has responsible: https://orcid.org/0000-0001-6518-3344
is part of: Bioregistry
has local unique identifier pattern: ^EUB\d{7}$
has reviewer: https://orcid.org/0000-0001-9439-5346
0000005: EUB0000221
type: Resource
has URI prefix: https://gateway.eubopen.org/compound/
has prefix: eubopen
has resource example: EUB0000221
description: EUbOPEN is a project focusing on organizing chemogenic library collections, advancing chemical probe discovery, profiling bioactive compounds, and making project data more accessible.
is deprecated: false
has provider formatter: https://gateway.eubopen.org/compound/$1
contributor: 0009-0008-8406-631X

Human Medical Genetics
has URI prefix: https://www.ncbi.nlm.nih.gov/medgen/
type: Resource
0000005: 760050
has prefix: medgen
has alternative prefix: medgen.uid
contributor: https://orcid.org/0000-0002-7356-1779
is deprecated: false
is part of: Bioregistry
description: MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder.
has responsible: Megan S. Kane
has resource example: https://www.ncbi.nlm.nih.gov/medgen/760050
has provider formatter: https://www.ncbi.nlm.nih.gov/medgen/$1
has local unique identifier pattern: ^(CN)?\d{2,7}$

Biological and Environmental Research Variable Ontology
has responsible: Harry Caufield
keyword: ontology
is deprecated: false
has prefix: bervo
has provider formatter: https://w3id.org/bervo/BERVO_$1
has download URL: bervo.owl
description: A representation of variables appearing in models in the environmental research space.
git repository: bervo
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: https://w3id.org/bervo/BERVO_
has resource example: BERVO_0000001
0000005: 0000001

Fossilworks Journal
0000005: 61467
has resource example: http://fossilworks.org/
description: Identifier for a journal article in the fossilworks website
contributor: https://orcid.org/0000-0003-2699-3066
has URI prefix: http://fossilworks.org/
is deprecated: false
has local unique identifier pattern: ^\d+$
has provider formatter: http://fossilworks.org/
is part of: Bioregistry
type: Resource
has prefix: fossilworks.journal
has reviewer: Charles Tapley Hoyt

Small Angle Scattering Biological Data Bank
has prefix: sasbdb
is deprecated: false
keyword: molecular biology
has URI prefix: http://www.sasbdb.org/data/
has resource example: SASDAX8
is part of: Bioregistry
has local unique identifier pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$
type: Resource
has responsible: Al Kikhney
0000005: SASDAX8
has provider formatter: http://www.sasbdb.org/data/$1
keyword: life science
description: Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.

Database of protein-protein complexes
has URI prefix: http://www.ces.clemson.edu/compbio/protcom/print_file.cgi
is part of: Bioregistry
keyword: protein
has prefix: protcom
type: Resource
description: This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures).
keyword: structure
has reviewer: Charles Tapley Hoyt
0000005: 12e8LH
has resource example: http://www.ces.clemson.edu/compbio/protcom/print_file.cgi
is deprecated: true
has provider formatter: http://www.ces.clemson.edu/compbio/protcom/print_file.cgi

Neurofibromatosis Data Portal Tools
has prefix: nfportal.tool
keyword: research resources
keyword: neurofibromatosis
has resource example: https://nf.synapse.org/Explore/Tools/DetailsPage
has provider formatter: https://nf.synapse.org/Explore/Tools/DetailsPage
has responsible: https://orcid.org/0000-0003-3573-3565
is deprecated: false
contributor: Kangho Ji
has local unique identifier pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
has URI prefix: https://nf.synapse.org/Explore/Tools/DetailsPage
has reviewer: https://orcid.org/0000-0001-9439-5346
keyword: experimental tools
is part of: Bioregistry
description: Identifiers represent experimental tools and resources for neurofibromatosis (NF) research in the NF Data Portal Tools catalog.
type: Resource

Collection
type: Class
description: A type for entries in the Bioregistry's collections

SWEET Ontology Phenomena Ecology
type: Resource
0000005: Adaptation
keyword: phenomena
has URI prefix: http://sweetontology.net/phenEcology/
has prefix: sweet.phec
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Ecology
is part of: Bioregistry
has alternative prefix: sophec
keyword: ecology
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/phenEcology/$1
has resource example: Adaptation

Scientific Information Retrieval and Exchange Network
has alternative prefix: SUBSET_SIREN
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^F\d+$
has responsible: Patrice Buche
contributor: Charles Tapley Hoyt
has prefix: siren
description: A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods
type: Resource
0000005: F11903

iRefWeb
has resource example: http://wodaklab.org/iRefWeb/interaction/show/617102
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: protein
0000005: 617102
has URI prefix: http://wodaklab.org/iRefWeb/interaction/show/
description: iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.
has provider formatter: http://wodaklab.org/iRefWeb/interaction/show/$1
type: Resource
has responsible: Shoshana J. Wodak
keyword: interaction
is deprecated: true
has prefix: irefweb
keyword: life science

Integrated Genomic Resources of human Cell Lines for Identification
has provider formatter: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi
type: Resource
description: Cell line databases/resources
has URI prefix: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi
0000005: ACHN
is deprecated: false
is part of: Bioregistry
has resource example: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi
has prefix: igrhcellid

SWEET Ontology Property Speed
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Speed
type: Resource
keyword: speed
has alternative prefix: sopropsp
0000005: Acceleration
has resource example: Acceleration
has provider formatter: http://sweetontology.net/propSpeed/$1
is deprecated: false
has URI prefix: http://sweetontology.net/propSpeed/
is part of: Bioregistry
has prefix: sweet.propsp
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology

Protein Ensemble Database ensemble
has provider formatter: https://proteinensemble.org/$1
has resource example: PED00017e001
0000005: PED00017e001
is deprecated: false
description: The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins.
has prefix: ped.ensemble
has URI prefix: https://proteinensemble.org/
is part of: Protein Ensemble Database
is part of: Bioregistry
has local unique identifier pattern: ^PED\d{5}e\d{3}$
type: Resource

Protein Affinity Reagents
has provider formatter: https://www.ebi.ac.uk/ontology-lookup/
has URI prefix: https://www.ebi.ac.uk/ontology-lookup/
type: Resource
is deprecated: true
has prefix: psipar
has resource example: https://www.ebi.ac.uk/ontology-lookup/
0000005: 0116
has local unique identifier pattern: ^\d+$
description: Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.
is part of: Bioregistry

Molecular Signatures Database
has responsible: https://orcid.org/0000-0002-9755-2818
keyword: reaction
keyword: gene group
0000005: M1
has download URL: msigdb.owl.gz
has prefix: msigdb
has local unique identifier pattern: ^M\d+$
has alternative prefix: msig
keyword: ontology
has URI prefix: https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/
keyword: pathway
has provider formatter: https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/$1
is deprecated: false
description: The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can
has resource example: M1
keyword: gene family
keyword: gene set
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

Mouse Brain Atlas
git repository: mouse brain atlas ontology
description: A controlled vocabulary to support the study of transcription in the mouse brain
0000005: 688
has prefix: mba
keyword: ontology
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: https://purl.brain-bican.org/ontology/mbao/MBA_
has resource example: MBA 688
has download URL: mbao.owl
has provider formatter: https://purl.brain-bican.org/ontology/mbao/MBA_$1
type: Resource
contributor: Charles Tapley Hoyt
has responsible: Allen Institute for Brain Science

Phylogenomic Analysis of Human Genome
keyword: phylogenomics
has prefix: pahg
has provider formatter: https://www.pahgncb.com/genomedb/public/genefamily/$1
keyword: gene duplication
keyword: multigene families
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Kangho Ji
has responsible: https://orcid.org/0000-0002-9922-9723
keyword: vertebrate evolution
description: Identifiers correspond to curated multigene families in the human genome from the Phylogenomic Analysis of Human Genome (PAHG) database, focusing on evolutionary relationships and gene duplication events across vertebrates.
type: Resource
keyword: human genome
has URI prefix: https://www.pahgncb.com/genomedb/public/genefamily/
keyword: paralogons
has resource example: https://www.pahgncb.com/genomedb/public/genefamily/92
has reviewer: Charles Tapley Hoyt
0000005: 92

Arabidopsis Information Portal
0000005: AT5G05330
is deprecated: false
has resource example: https://www.arabidopsis.org/servlets/TairObject
is part of: Bioregistry
has prefix: araport
type: Resource
has URI prefix: https://www.arabidopsis.org/servlets/TairObject
has responsible: https://orcid.org/0000-0002-5227-0200
has provider formatter: https://www.arabidopsis.org/servlets/TairObject
has local unique identifier pattern: ^AT.G[0-9]{5}$
description: Website with general information about Arabidopsis and functionalities such as a genomic viewer

NFDI4Culture Metadata API
has resource example: E4330
0000005: E4330
is deprecated: false
has URI prefix: https://nfdi4culture.de/id/
has prefix: nfdi4culture.id
keyword: digital humanities
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: The NFDI4Culture portal offers all content as Linked Open Data over this RESTful API. The API implements the Hydra-Specification of the W3C Hydra Community Group. The semantic description of this API can be retrieved by clients via the Hydra documentation file (JSON). Each metadata record offered via this API can also be retrieved in one of following machine-readable LOD serializations. The API is the basis for the Culture Research Information Graph, which together with the Culture Research Data Graph forms the [Culture Knowledge Graph](https://nfdi4culture.de/services/details/culture-knowledge-graph.html) (for more details see [this presentation](https://doi.org/10.5281/zenodo.7748740)) (from homepage).
has provider formatter: https://nfdi4culture.de/id/$1
keyword: organization
keyword: generic

PharmGKB Gene
is deprecated: false
keyword: pharmacogenomics
has resource example: PA131
has prefix: pharmgkb.gene
has responsible: Teri E Klein
is part of: Bioregistry
has download URL: pharmgkb.gene.owl
type: Resource
description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.
keyword: gene
0000005: PA131
has local unique identifier pattern: ^PA\w+$
has provider formatter: http://www.pharmgkb.org/gene/$1
has URI prefix: http://www.pharmgkb.org/gene/
keyword: ontology

ExAC Transcript
is deprecated: false
has URI prefix: http://exac.broadinstitute.org/transcript/
description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.
0000005: ENST00000407236
is part of: Bioregistry
has resource example: ENST00000407236
has provider formatter: http://exac.broadinstitute.org/transcript/$1
type: Resource
has local unique identifier pattern: ^ENST\d{11}$
has prefix: exac.transcript

MicrosporidiaDB
is part of: Bioregistry
0000005: ECU03_0820i
has resource example: http://microsporidiadb.org/micro/showRecord.do
type: Resource
keyword: eukaryotic
has prefix: microsporidia
has responsible: Omar S. Harb
has provider formatter: http://microsporidiadb.org/micro/showRecord.do
description: MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
is deprecated: false
keyword: genome
has local unique identifier pattern: ^\w+$
has URI prefix: http://microsporidiadb.org/micro/showRecord.do

Darwin-SW
has provider formatter: http://purl.org/dsw/$1
has resource example: DriedSpecimen
keyword: ess
is deprecated: false
keyword: fair data spaces
has URI prefix: http://purl.org/dsw/
0000005: DriedSpecimen
is part of: Bioregistry
git repository: dsw
has responsible: Steve Baskauf
keyword: earth sciences
keyword: life sciences, biology
has prefix: dsw
type: Resource
description: Version 0.4 to 1.0 fixed reversed dsw:locates and dsw:locatedAt. Added labels. Changed comments and descriptions to conform to DC and DwC precedent. Added subClassOf relations to RO hasEvidence and isEvidenceFor. Specified preferred direction for inverse object property pairs., Changes from version 0.2.1 to version 0.3: removal of all functional and inverse function properties of object property terms, use of dwctype classes, deprecation of terms replaced by dwciri: terms, removal of references to TDWG Ontology., Changes from version 0.3 to 0.4 change DwC class namespace from dwctype: to dwc: to follow class proposal, removed references to TDWG TaxonConcept ontology; deprecated terms that now have equivalent terms in Darwin Core., Change from version 1.0 to 1.0.1 Add CC0 license.

Description of Plant Viruses
has resource example: https://www.dpvweb.net/dpv/showdpv/
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: dpv
has URI prefix: https://www.dpvweb.net/dpv/showdpv/
type: Resource
contributor: Charles Tapley Hoyt
description: Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.
keyword: gene
0000005: 100
keyword: classification
contributor: https://orcid.org/0000-0002-2404-1582
is deprecated: false
has provider formatter: https://www.dpvweb.net/dpv/showdpv/

DiabetesOmic
is deprecated: false
description: DiabetesOmic is a multi-omics database designed to collect and analyze transcriptional regulatory information across five high-throughput sequencing modalities, including ChIP-seq, RNA-seq, ATAC-seq, scATAC-seq, and scRNA-seq. This database's identifiers each represent a single sample. It contains clinical complication annotations including diabetic nephropathy, retinopathy, and atherosclerosis to enhance translational relevance. It enables the identification of disease-associated regulatory elements, epigenetic modifications, and cell type-specific molecular signatures, providing valuable insights into the molecular mechanisms of diabetes and its complications.
is part of: Bioregistry
has prefix: diabetesomic
keyword: omics
has reviewer: https://orcid.org/0000-0001-9439-5346
has local unique identifier pattern: ^sample_\d{3}$
type: Resource
contributor: https://orcid.org/0009-0000-6974-6386
has URI prefix: https://bio.liclab.net/diabetesOmicdb/RNA-seq
has provider formatter: https://bio.liclab.net/diabetesOmicdb/RNA-seq
has resource example: https://bio.liclab.net/diabetesOmicdb/RNA-seq
0000005: sample_002
has responsible: Jiang-hua Liu
keyword: sample
keyword: diabetes

P3DB Site
has URI prefix: https://bioregistry.io/p3db.site:
type: Resource
has resource example: http://www.p3db.org/phosphosite.php
description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.
has provider formatter: http://www.p3db.org/phosphosite.php
is deprecated: false
0000005: 65
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: p3db.site

Hölzel Diagnostika
is deprecated: false
has prefix: hoelzel
keyword: antibodies
0000005: 40592-R001-100
keyword: inhibitors
description: Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog.
keyword: proteins
keyword: vendor
is part of: Bioregistry
keyword: assays
contributor: Charles Tapley Hoyt
has resource example: https://www.hoelzel-biotech.com/de/catalogsearch/result/
has alternative prefix: hölzel
has responsible: https://orcid.org/0009-0009-3816-8777
keyword: life sciences
has provider formatter: https://www.hoelzel-biotech.com/de/catalogsearch/result/
keyword: elisa-kits
type: Resource
has URI prefix: https://www.hoelzel-biotech.com/de/catalogsearch/result/
keyword: biologics

Bitbucket
is deprecated: false
is part of: Bioregistry
description: Bitbucket is a Git-based source code repository hosting service owned by Atlassian.
has provider formatter: https://bitbucket.org/$1
keyword: knowledge and information systems
has URI prefix: https://bitbucket.org/
has prefix: bitbucket
type: Resource
0000005: andreadega/systems-biology-compiler
has local unique identifier pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$
keyword: subject agnostic
has resource example: systems-biology-compiler
keyword: software engineering

Animal natural history and life history
keyword: ontology
contributor: https://orcid.org/0000-0002-1216-4761
keyword: taxonomic classification
has local unique identifier pattern: ^[A-Z_a-z]+$
0000005: Lycalopex_vetulus
is part of: Bioregistry
type: Resource
has prefix: adw
has download URL: adw.owl
has resource example: Lycalopex vetulus
keyword: anatomy
has provider formatter: https://animaldiversity.org/accounts/$1
keyword: life science
description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.
is deprecated: true
has URI prefix: https://animaldiversity.org/accounts/
keyword: obo

Radiomics Ontology
has provider formatter: http://www.radiomics.org/RO/$1
has resource example: LK99
keyword: ontology
description: The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]
is deprecated: false
has URI prefix: http://www.radiomics.org/RO/
is part of: Bioregistry
type: Resource
0000005: LK99
has prefix: radiomics
has responsible: https://orcid.org/0000-0001-6183-4429

SWEET Ontology State Role Biological
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Biological
has resource example: Autotroph
has URI prefix: http://sweetontology.net/stateRoleBiological/
has provider formatter: http://sweetontology.net/stateRoleBiological/$1
is deprecated: false
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sostrb
type: Resource
keyword: state role biological
has prefix: sweet.strb
0000005: Autotroph

CIViC Source
is deprecated: false
0000005: 62
is part of: Bioregistry
has resource example: https://civicdb.org/links/sources/62
has responsible: Malachi Griffith
has prefix: civic.sid
has provider formatter: https://civicdb.org/links/sources/$1
type: Resource
has alternative prefix: civic.source
has local unique identifier pattern: ^[0-9]+$
has URI prefix: https://civicdb.org/links/sources/
description: In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.

Pennsieve
has prefix: pennsieve
has URI prefix: https://discover.pennsieve.io/package/
has provider formatter: https://discover.pennsieve.io/package/$1
is deprecated: false
description: Pennsieve is a publicly accessible Scientific Data Management and publication platform. The platform supports data curation, sharing and publishing complex scientific datasets with a focus on integration between graph-based metadata and file-archival. The platform provides a "peer"-reviewed publication mechanism and public datasets are available through its Discover Web Application and APIs.
is part of: Bioregistry
has local unique identifier pattern: ^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$
type: Resource

Health Canada Clinical Trials Database
description: Health Canada, through its Clinical Trials Database, is providing to the public a listing of specific information relating to phase I, II and III clinical trials in patients. The database is managed by Health Canada and provides a source of information about Canadian clinical trials involving human pharmaceutical and biological drugs. [from website]
has resource example: https://health-products.canada.ca/ctdb-bdec/brand/
0000005: 239287
type: Resource
has provider formatter: https://health-products.canada.ca/ctdb-bdec/brand/
has prefix: hc.trial
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has URI prefix: https://health-products.canada.ca/ctdb-bdec/brand/

PMADS
type: Resource
has local unique identifier pattern: ^acc\d{4}$
has URI prefix: https://pmads-db.org/result/
description: Identifiers correspond to curated and proteomics-inferred associations between protein post-translational modifications (PTM) and drug sensitivity.
has prefix: pmads
has resource example: https://pmads-db.org/result/
contributor: Kangho Ji
keyword: drug sensitivity
is deprecated: false
0000005: acc0079
is part of: Bioregistry
keyword: modification
has provider formatter: https://pmads-db.org/result/
has responsible: https://orcid.org/0000-0001-8364-8328
keyword: proteomics
has reviewer: https://orcid.org/0000-0001-9439-5346

EAWAG Biocatalysis/Biodegradation Database pathway
has alternative prefix: UM-BBD_pathwayID
has resource example: http://umbbd.ethz.ch/servlets/pageservlet
has URI prefix: http://umbbd.ethz.ch/servlets/pageservlet
has local unique identifier pattern: ^\w+$
is part of: Bioregistry
is deprecated: false
0000005: ala
has provider formatter: http://umbbd.ethz.ch/servlets/pageservlet
type: Resource
description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information.
has prefix: umbbd.pathway

Insertion sequence elements database
has resource example: https://www-is.biotoul.fr/scripts/ficheIS.php
has URI prefix: https://www-is.biotoul.fr/scripts/ficheIS.php
description: ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.
is part of: Bioregistry
has local unique identifier pattern: ^IS\w+(\-\d)?$
type: Resource
0000005: ISA1083-2
keyword: gene
keyword: life science
has responsible: Patricia Siguier
is deprecated: true
has prefix: isfinder
keyword: sequence
has provider formatter: https://www-is.biotoul.fr/scripts/ficheIS.php

PhosphoSite Protein
has resource example: http://www.phosphosite.org/proteinAction.do
has URI prefix: http://www.phosphosite.org/proteinAction.do
0000005: 12300
is deprecated: false
has prefix: phosphosite.protein
has local unique identifier pattern: ^\d{5}$
has provider formatter: http://www.phosphosite.org/proteinAction.do
is part of: Bioregistry
type: Resource
description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.

SWEET Ontology Material Ion
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Ion
is deprecated: false
has URI prefix: http://sweetontology.net/matrIon/
has alternative prefix: somaio
keyword: ion
has resource example: Anion
is part of: Bioregistry
has prefix: sweet.maio
type: Resource
has provider formatter: http://sweetontology.net/matrIon/$1
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: materials
0000005: Anion

SWEET Ontology Material Natural Resource
has URI prefix: http://sweetontology.net/matrNaturalResource/
has alternative prefix: somanr
0000005: Anthracite
keyword: natural resource
has resource example: Anthracite
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Natural Resource
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: materials
has provider formatter: http://sweetontology.net/matrNaturalResource/$1
has prefix: sweet.manr

William Hogan
label: Bill Hogan

Physics Subject Headings
has prefix: physh
description: PhySH (Physics Subject Headings) is a physics classification scheme developed by the American Physical Society to organize journals, meetings, and other content by topic. The development of PhySH is motivated by the lack of a fully open, high quality classification scheme for physics. It is intended initially to meet the specific goals of the APS for our journal, meeting, and other content. A longer term goal is to make it available for use by the broader community. (...) Right now, the main use of PhySH is to classify manuscripts within the APS peer-review process and, ultimately, published journal articles. The assigned concepts will be used for ensuring articles are routed to the most appropriate handling editor who is knowledgeable in that area. They also help editors in finding similar articles previously submitted and in finding suitable referees. As one might expect with something so new, the refinement of PhySH is still very much underway. The facets and disciplines have been identified and almost 3,000 concepts have been added to PhySH through an iterative process that is still ongoing. Many APS journal editors are involved in this process, primarily by lending their expertise in the various subfields in physics. The assignment of concepts to the various facets can be rather subjective. Thus, we expect to make many adjustments to PhySH as we receive feedback from the community (especially authors using PhySH to classify their submissions) and as we incorporate PhySH into the APS journal websites. As we iteratively refine PhySH over the coming months, the rate of new concept additions, concept reassignments within facets, and new relationships among concepts should abate significantly.
type: Resource
keyword: nfdi4ing
has URI prefix: https://doi.org/10.29172/
has local unique identifier pattern: ^[0-9a-z-]+$
is deprecated: false
keyword: physics
has provider formatter: https://doi.org/10.29172/$1
is part of: Bioregistry

Research Resource Identification
keyword: life science
keyword: biochemistry
is deprecated: false
has URI prefix: https://scicrunch.org/resolver/RRID:
has responsible: https://orcid.org/0000-0002-5497-0243
keyword: community resource
has resource example: RRID:AB 262044
keyword: resource discovery
keyword: centrally registered identifier
keyword: resource metadata
is part of: Bioregistry
keyword: chemistry
keyword: omics
0000005: AB_262044
contributor: https://orcid.org/0000-0002-5497-0243
has provider formatter: https://scicrunch.org/resolver/RRID:$1
type: Resource
description: The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools. The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.
keyword: data retrieval
keyword: annotation
has prefix: rrid
keyword: fair
has local unique identifier pattern: ^[a-zA-Z]+.+$
keyword: biology

DragonDB Allele
0000005: cho
has local unique identifier pattern: ^\w+$
is part of: Bioregistry
has provider formatter: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
has URI prefix: https://bioregistry.io/dragondb.allele:
has resource example: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
type: Resource
has prefix: dragondb.allele
is deprecated: true
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information.

BioSimulators
has resource example: vcell
has responsible: Jonathan Karr
is deprecated: false
keyword: computational biology
git repository: choose
has prefix: biosimulators
description: BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML).
is part of: Bioregistry
type: Resource
has URI prefix: https://biosimulators.org/simulators/
0000005: vcell
has local unique identifier pattern: ^[a-zA-Z0-9-_]+$
has provider formatter: https://biosimulators.org/simulators/$1
keyword: systems biology

Carbohydrate Active EnZYmes
has prefix: cazy
is part of: Bioregistry
has local unique identifier pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$
has resource example: GT10.html
description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features.
0000005: GT10
keyword: polysaccharide
type: Resource
has responsible: Nicolas Terrapon
keyword: life science
keyword: classification
keyword: glycomics
is deprecated: false
has provider formatter: http://www.cazy.org/$1.html
has URI prefix: https://bioregistry.io/cazy:

Model Card Report Ontology
0000005: 0000001
git repository: MCRO
has local unique identifier pattern: ^\d{7}$
keyword: obo
description: An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.).
keyword: ontology
has URI prefix: https://www.ebi.ac.uk/ols4/ontologies/mcro/classes
is deprecated: false
depends on: Software ontology
has responsible: Tuan Amith
has resource example: https://www.ebi.ac.uk/ols4/ontologies/mcro/classes
depends on: Information Artifact Ontology
is part of: Bioregistry
has download URL: mcro.owl
type: Resource
has provider formatter: https://www.ebi.ac.uk/ols4/ontologies/mcro/classes
has prefix: mcro

SWEET Ontology Property Binary
type: Resource
has URI prefix: http://sweetontology.net/propBinary/
has provider formatter: http://sweetontology.net/propBinary/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Binary
has alternative prefix: sopropb
is deprecated: false
0000005: BinaryProperty
keyword: binary
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
has resource example: BinaryProperty
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.propb

MediaDive Medium
has resource example: https://mediadive.dsmz.de/medium/77
type: Resource
0000005: 77
has URI prefix: https://mediadive.dsmz.de/medium/
has reviewer: Charles Tapley Hoyt
has responsible: Jörg Overmann
is deprecated: false
has prefix: mediadive.medium
description: The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]
is part of: Bioregistry
contributor: https://orcid.org/0000-0002-6601-2165
has local unique identifier pattern: ^\d+\w?$
has provider formatter: https://mediadive.dsmz.de/medium/$1

NITE Biological Resource Center
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has URI prefix: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet
has prefix: nbrc
has resource example: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet
keyword: microbiology
type: Resource
0000005: 00001234
description: NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information.
has provider formatter: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet
keyword: microbial
keyword: taxonomy

Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi.
is part of: Bioregistry
0000005: CADAFLAT00006211
type: Resource
has URI prefix: https://fungi.ensembl.org/id/
has resource example: CADAFLAT00006211
keyword: comparative genomics
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes.
has provider formatter: https://fungi.ensembl.org/id/$1
has prefix: ensembl.fungi
has local unique identifier pattern: ^[A-Z-a-z0-9]+$
keyword: genome
keyword: genomics
is deprecated: false
has responsible: Paul Flicek

AAindex
has resource example: http://www.genome.jp/dbget-bin/www_bget
type: Resource
has URI prefix: http://www.genome.jp/dbget-bin/www_bget
has reviewer: Charles Tapley Hoyt
contributor: https://orcid.org/0000-0002-1216-4761
is deprecated: false
description: Identifier of an entry from the AAindex database.
is part of: Bioregistry
keyword: protein
has provider formatter: http://www.genome.jp/dbget-bin/www_bget
0000005: BUNA790102
has responsible: Shuichi Kawashima
has prefix: aaindex

Association-Rule-Based Annotator
has alternative prefix: arba
contributor: https://orcid.org/0000-0002-6601-2165
has reviewer: Charles Tapley Hoyt
has responsible: Alex Bateman
has provider formatter: https://www.uniprot.org/arba/$1
has local unique identifier pattern: ^ARBA\d+$
has resource example: ARBA00000001
is deprecated: false
has URI prefix: https://www.uniprot.org/arba/
description: Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins. This replaces the previous rule-based SAAS system.
has prefix: uniprot.arba
is part of: Bioregistry
type: Resource
0000005: ARBA00000001

Integrated Canine Data Commons
type: Resource
description: The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer.
has URI prefix: https://caninecommons.cancer.gov/#/study/
is deprecated: false
has prefix: icdc
has provider formatter: https://caninecommons.cancer.gov/#/study/$1
is part of: Bioregistry
0000005: 000009
has resource example: study/000009
has local unique identifier pattern: ^\d{6}$

PubMed
keyword: bibliography
has resource example: https://pubmed.ncbi.nlm.nih.gov/16333295/
has provider formatter: https://pubmed.ncbi.nlm.nih.gov/$1/
has alternative prefix: MEDLINE
description: PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.
has alternative prefix: PMID
has alternative prefix: PubMed ID
is deprecated: false
has URI prefix: https://bioregistry.io/pubmed:
has alternative prefix: PubMed
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has responsible: Jeff Beck
has prefix: pubmed
type: Resource
keyword: biomedical science
has alternative prefix: pmid
0000005: 16333295

Database of structurally defined protein interfaces
0000005: 21692
is part of: Bioregistry
description: PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected.
type: Resource
keyword: structure
has provider formatter: http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl
has reviewer: Charles Tapley Hoyt
has prefix: pibase
has URI prefix: http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl
is deprecated: false
keyword: protein
has resource example: http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl

WormBase
has local unique identifier pattern: ^(CE[0-9]{5}|WB[A-Z][a-z]+\d+)$
has alternative prefix: WB
keyword: phenotype
keyword: gene function
keyword: roundworm
keyword: catalog
has responsible: 0000-0003-3406-163X
keyword: gene expression
is part of: Bioregistry
keyword: orthology assignment
keyword: ortholog
has alternative prefix: wormbase
keyword: wormmart
keyword: gene
contributor: https://orcid.org/0000-0002-6601-2165
keyword: geneotype
keyword: gene mapping
keyword: gene prediction
has resource example: https://www.wormbase.org/get
keyword: anatomy
has alternative prefix: wb
keyword: blast
0000005: WBGene00000001
type: Resource
has prefix: wormbase
keyword: life science
keyword: faseb list
keyword: database
has provider formatter: https://www.wormbase.org/get
has alternative prefix: WB_REF
keyword: genomic sequence
keyword: transposon family
has URI prefix: https://www.wormbase.org/get
keyword: c elegans
keyword: genome
description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities.
keyword: genomics
is deprecated: false

VIRsiRNA
has prefix: virsirna
is part of: Bioregistry
has provider formatter: http://crdd.osdd.net/servers/virsirnadb/record.php
type: Resource
has URI prefix: http://crdd.osdd.net/servers/virsirnadb/record.php
has local unique identifier pattern: ^virsi\d+$
has resource example: http://crdd.osdd.net/servers/virsirnadb/record.php
description: The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.
is deprecated: false
0000005: virsi1909

Fischertechnik Ontology
description: The FTOnto enables reseachers to sematically describe a physical fischertechnik factory simulation environment. This is archieved by aligning concepts from MASON and SOSA with own concepts. Furthermore the FTOnto can capture knowledge about semantic web services which are used to interact between the service-layer and the cyber-physical layer in a cyber-physical production system. This includes precondition which have to be met before a webservice can be performed, postconditions which check if the webservice execution was performed successfully and effects which describe the changed state of the domain after performing a service. [from homepage]
has URI prefix: http://iot.uni-trier.de/FTOnto#
has provider formatter: http://iot.uni-trier.de/FTOnto#$1
0000005: ADXL345_Pi_1_AccSensor_1_Result_2019-02-26_14_53_54.97
is deprecated: false
has prefix: ftonto
keyword: engineering
git repository: ftonto
has resource example: ADXL345 Pi 1 AccSensor 1 Result 2019-02-26 14 53 54.97
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
keyword: coypu

OMIA variants
has provider formatter: https://omia.org/variant/omia.variant:$1
contributor: Imke Tammen
keyword: model organism database
keyword: disorders
description: Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia.variant' prefix is used for genetic variants associated with phenes listed in OMIA
is deprecated: false
has prefix: omia.variant
0000005: 1710
has reviewer: https://orcid.org/0000-0001-9439-5346
keyword: traits
has resource example: omia.variant:1710
is part of: Bioregistry
has URI prefix: https://omia.org/variant/omia.variant:
has responsible: Imke Tammen
has local unique identifier pattern: ^\d+$
type: Resource

SWAP Logic Ontology
has prefix: log
type: Resource
description: Une ontologie "historique" utilisée par l'outil en ligne de commande cwm, au temps des balbutiements du web sémantique (~ 2000 - 2003 ?)
keyword: rdf
is deprecated: false
0000005: dtlit
is part of: Bioregistry

Database of Quantitative Cellular Signaling: Pathway
has responsible: Upinder S. Bhalla
has prefix: doqcs.pathway
has URI prefix: http://doqcs.ncbs.res.in/template.php
is deprecated: false
keyword: pathway
description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways.
has provider formatter: http://doqcs.ncbs.res.in/template.php
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has resource example: http://doqcs.ncbs.res.in/template.php
0000005: 131

PK-DB
has prefix: pkdb
is deprecated: false
keyword: pharmacogenomics
keyword: pharmacology
keyword: clinical veterinary medicine
has provider formatter: https://pk-db.com/data/$1
keyword: preclinical studies
has resource example: PKDB00198
is part of: Bioregistry
type: Resource
keyword: clinical studies
git repository: issues
has responsible: 0000-0003-1725-179X
keyword: life science
description: PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration.
has local unique identifier pattern: ^PKDB[0-9]{5}$
0000005: PKDB00198
keyword: personalized medicine
has URI prefix: https://pk-db.com/data/

Human Proteome Map Peptide
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: http://www.humanproteomemap.org/spectrum.php
has prefix: hpm.peptide
has URI prefix: http://www.humanproteomemap.org/spectrum.php
0000005: 9606117
type: Resource
has provider formatter: http://www.humanproteomemap.org/spectrum.php
description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.

SWEET Ontology Phenomena Atmosphere Fog
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
0000005: AdvectionFog
git repository: sweet
has resource example: AdvectionFog
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Fog
has provider formatter: http://sweetontology.net/phenAtmoFog/$1
keyword: phenomena
has alternative prefix: sophatmofo
keyword: atmosphere fog
has prefix: sweet.phatmofo
is deprecated: false
has URI prefix: http://sweetontology.net/phenAtmoFog/

re3data
type: Resource
has resource example: r3d100010772
has URI prefix: https://www.re3data.org/repository/
description: Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines.
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^r3d\d{9,9}$
0000005: r3d100010772
has prefix: re3data
has provider formatter: https://www.re3data.org/repository/$1

DevTox
description: The DevTox Project harmonizes the nomenclature used to describe developmental anomalies in laboratory animals, assists in the visual recognition of developmental anomalies with the aid of photographs, and provides a historical control database of developmental effects in laboratory animals.
has responsible: https://orcid.org/0000-0002-6807-8731
is deprecated: false
has prefix: devtox
contributor: https://orcid.org/0000-0001-9439-5346
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: https://www.devtox.org/nomenclature/ml_manus.php
type: Resource
0000005: 311935300
has URI prefix: https://www.devtox.org/nomenclature/ml_manus.php
has reviewer: Charles Tapley Hoyt
has provider formatter: https://www.devtox.org/nomenclature/ml_manus.php

SWEET Ontology Property Mass Flux
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Mass Flux
has resource example: DarcyFlux
has prefix: sweet.propmf
is part of: Bioregistry
type: Resource
git repository: sweet
0000005: DarcyFlux
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sopropmf
has provider formatter: http://sweetontology.net/propMassFlux/$1
has URI prefix: http://sweetontology.net/propMassFlux/
keyword: mass flux

PicTar
is deprecated: true
is part of: Bioregistry
has alternative prefix: pictar-vert
0000005: hsa-let-7a
has prefix: pictar
contributor: Charles Tapley Hoyt
type: Resource

Sensitive Data Ontology
has responsible: Bryce Mecum
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
0000005: 00000003
type: Resource
has URI prefix: http://purl.dataone.org/odo/SENSO_
has provider formatter: http://purl.dataone.org/odo/SENSO_$1
has resource example: SENSO_00000003
description: The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing.
has prefix: senso
keyword: ontology
is deprecated: false
has download URL: senso.owl

iNaturalist User
type: Resource
has resource example: https://www.inaturalist.org/users/1426686
is deprecated: false
has URI prefix: https://www.inaturalist.org/users/
description: Identifier for a user in iNaturalist
has local unique identifier pattern: ^[1-9]\d*$
is part of: Bioregistry
has provider formatter: https://www.inaturalist.org/users/$1
0000005: 1426686
contributor: Charles Tapley Hoyt
keyword: person
has prefix: inaturalist.user

CutDB
keyword: enzyme
description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).
keyword: pathway
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: protein
has prefix: pmap.cutdb
has URI prefix: http://cutdb.burnham.org/relation/show/
has provider formatter: http://cutdb.burnham.org/relation/show/$1
0000005: 25782
type: Resource
has resource example: http://cutdb.burnham.org/relation/show/25782
has responsible: Adam Godzik
is deprecated: true

Loop ID
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: loop
keyword: person
has provider formatter: https://loop.frontiersin.org/people/$1
description: identifier for a person, in the Loop database of researcher impact
keyword: researcher
has URI prefix: https://loop.frontiersin.org/people/
type: Resource
has resource example: https://loop.frontiersin.org/people/1859
is deprecated: false
has local unique identifier pattern: ^[1-9]\d*$
0000005: 1859

SBML RDF Vocabulary
0000005: rateRule
has prefix: biomodels.vocabulary
type: Resource
has URI prefix: http://biomodels.net/rdf/vocabulary.rdf#
is deprecated: false
description: Vocabulary used in the RDF representation of SBML models.
has provider formatter: http://biomodels.net/rdf/vocabulary.rdf#$1
has resource example: rateRule
has local unique identifier pattern: ^[A-Za-z]+$
is part of: Bioregistry

Integbio
description: Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)
is part of: Bioregistry
has local unique identifier pattern: ^nbdc\d+$
0000005: nbdc01071
type: Resource
contributor: Charles Tapley Hoyt
has responsible: Shuichi Kawashima
has resource example: nbdc01071
has provider formatter: https://catalog.integbio.jp/dbcatalog/en/record/$1
has URI prefix: https://catalog.integbio.jp/dbcatalog/en/record/
has prefix: integbio
is deprecated: false

MassIVE
has provider formatter: https://www.omicsdi.org/dataset/massive/$1
0000005: MSV000082131
has URI prefix: https://www.omicsdi.org/dataset/massive/
has responsible: Mingxun Wang
is deprecated: false
keyword: metaproteomics
is part of: Bioregistry
git repository: MassIVEDocumentation
keyword: metabolomics
has resource example: MSV000082131
keyword: omics
keyword: proteomics
has prefix: massive
keyword: functional genomics
has local unique identifier pattern: ^MSV\d+$
keyword: phenomics
type: Resource
description: MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data.

SWEET Ontology Realm Land Orographic
keyword: orographicland
0000005: Alpine
is deprecated: false
has resource example: Alpine
has provider formatter: http://sweetontology.net/realmLandOrographic/$1
has alternative prefix: sorealo
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Orographic
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.realo
has URI prefix: http://sweetontology.net/realmLandOrographic/

Atomistic
is deprecated: false
is part of: Bioregistry
keyword: engineering
has provider formatter: https://w3id.org/emmo/domain/atomistic#$1
git repository: domain-atomistic
description: An EMMO-based domain ontology for atomistic and electronic modelling.
type: Resource
keyword: nfdi4ing
has URI prefix: https://w3id.org/emmo/domain/atomistic#
has prefix: atomistic

Asteraceae Genome Database - Plant
0000005: 0016
has provider formatter: https://cbcb.cdutcm.edu.cn/AGD/plant/details/
has URI prefix: https://cbcb.cdutcm.edu.cn/AGD/plant/details/
has prefix: asteraceaegd.plant
type: Resource
contributor: Mufaddal Naguthanawala
is deprecated: false
has responsible: Wei Chen
description: The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collections refers to the broader phenotypic and genetic resources of Asteraceae plants.
has resource example: https://cbcb.cdutcm.edu.cn/AGD/plant/details/
has local unique identifier pattern: ^\d{4}$
is part of: Bioregistry
has reviewer: https://orcid.org/0000-0001-9439-5346

Integrative and Conjugative Element Ontology
keyword: ontology
has prefix: iceo
git repository: ICEO
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/ICEO_$1
has URI prefix: http://purl.obolibrary.org/obo/ICEO_
has download URL: iceo.owl
has responsible: https://orcid.org/0000-0003-3781-6962
description: A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.
type: Resource
has resource example: ICEO 0000712 1
has local unique identifier pattern: ^\d{7}(_\d)?$
0000005: 0000712_1
is deprecated: false
keyword: obo

4D Nucleome Data Portal Biosource
has alternative prefix: 4DN
is deprecated: false
keyword: dna
has provider formatter: https://data.4dnucleome.org/biosources/$1
keyword: protein
has local unique identifier pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$
has URI prefix: https://data.4dnucleome.org/biosources/
has responsible: https://orcid.org/0000-0001-5631-0698
0000005: 4DNSR73BT2A2
has resource example: 4DNSR73BT2A2
has prefix: _4dn.biosource
is part of: Bioregistry
type: Resource
has alternative prefix: 4dn.biosource
keyword: life science
description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases.

United States Patent and Trademark Office
is part of: Bioregistry
description: The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.
type: Resource
has provider formatter: http://patft.uspto.gov/netacgi/nph-Parser
has resource example: http://patft.uspto.gov/netacgi/nph-Parser
0000005: 4145692
has prefix: uspto
has local unique identifier pattern: ^(\d{1,2},?\d{3},?\d{3}|(PP|RE|AI|RX)\d{2},?\d{3}|(D|T|H|X)\d{3},?\d{3})$
is deprecated: false
has URI prefix: http://patft.uspto.gov/netacgi/nph-Parser
contributor: https://orcid.org/0000-0002-3012-7446

Genome assembly database - INSDC accessions
has prefix: insdc.gca
has local unique identifier pattern: ^GCA_[0-9]{9}(\.[0-9]+)?$
is part of: Bioregistry
type: Resource
has URI prefix: https://www.ncbi.nlm.nih.gov/datasets/genome/
0000005: GCA_000155495.1
has provider formatter: https://www.ncbi.nlm.nih.gov/datasets/genome/$1
has canonical: Assembly
has resource example: GCA 000155495.1
description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.
is deprecated: false

Regulation of Gene Expression Ontology
description: Regulation of Gene Expression
is part of: Bioregistry
type: Resource
has prefix: rexo
has download URL: rexo.owl
keyword: life science
keyword: orthologous
keyword: ontology
has responsible: Martin Kuiper
keyword: expression data
is deprecated: false
keyword: regulation of gene expression

SWEET Ontology State Energy Flux
keyword: state energy flux
has alternative prefix: sostef
is deprecated: false
is part of: Bioregistry
has prefix: sweet.stef
is part of: Semantic Web for Earth and Environment Technology Ontology
0000005: AClass
has resource example: AClass
has provider formatter: http://sweetontology.net/stateEnergyFlux/$1
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
has URI prefix: http://sweetontology.net/stateEnergyFlux/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Energy Flux

Citation Counting and Context Characterisation Ontology
keyword: subject agnostic
is deprecated: false
has provider formatter: http://purl.org/spar/c4o/$1
description: An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date.
is part of: Bioregistry
git repository: c4o
contributor: Charles Tapley Hoyt
has responsible: Silvio Peroni
0000005: InTextReferencePointer
has resource example: InTextReferencePointer
has URI prefix: http://purl.org/spar/c4o/
type: Resource
keyword: spar
has prefix: c4o

Industrial Foundational Classes
type: Resource
keyword: architecture
keyword: nfdi4ing
keyword: computer science
has resource example: IfcAbsorbedDoseMeasure
0000005: IfcAbsorbedDoseMeasure
keyword: civil engineering
is deprecated: false
keyword: digital planning and construction
is part of: Bioregistry
has provider formatter: https://standards.buildingsmart.org/IFC/DEV/IFC4/ADD2_TC1/OWL#$1
keyword: fid baudigital
has prefix: tib.ifc
description: OWL ontology for the IFC conceptual data schema and exchange file format for Building Information Model (BIM) data
has URI prefix: https://standards.buildingsmart.org/IFC/DEV/IFC4/ADD2_TC1/OWL#

Nucleic Acids Phylogenetic Profiling
has responsible: Daniel Gautheret
has URI prefix: http://rssf.i2bc.paris-saclay.fr/NAPP/Niveau2.php
keyword: clustering
has resource example: http://rssf.i2bc.paris-saclay.fr/NAPP/Niveau2.php
has prefix: napp
has provider formatter: http://rssf.i2bc.paris-saclay.fr/NAPP/Niveau2.php
is deprecated: false
description: NAPP (Nucleic Acids Phylogenetic Profiling) is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters.
keyword: genomics
0000005: 351
has local unique identifier pattern: ^\d+$
keyword: nucleotide
is part of: Bioregistry
type: Resource

Data Object Service
has provider formatter: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1
is deprecated: false
is part of: Bioregistry
has URI prefix: https://dataguids.org/ga4gh/dos/v1/dataobjects/
type: Resource
has local unique identifier pattern: ^[a-zA-Z0-9\-:#/\.]+$
has prefix: ga4ghdos
description: Assists in resolving data across cloud resources.

SWEET Ontology Human Commerce
has alternative prefix: sohuc
has provider formatter: http://sweetontology.net/humanCommerce/$1
is part of: Bioregistry
keyword: commerce
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
0000005: Assembly
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Commerce
has prefix: sweet.huc
type: Resource
has resource example: Assembly
is deprecated: false
has URI prefix: http://sweetontology.net/humanCommerce/

National Drug Data File
has responsible: First DataBank Customer Support
keyword: medicinal chemistry
is part of: Bioregistry
has URI prefix: http://purl.bioontology.org/ontology/NDDF/
contributor: Charles Tapley Hoyt
keyword: chemical entity
has local unique identifier pattern: ^\d{6}$
type: Resource
0000005: 002678
keyword: biomedical science
has resource example: http://purl.bioontology.org/ontology/NDDF/002678
has provider formatter: http://purl.bioontology.org/ontology/NDDF/$1
has prefix: nddf
is deprecated: false
description: FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements.
keyword: drug
keyword: ontology

International Standard Serial Number
has provider formatter: https://portal.issn.org/resource/ISSN/$1
description: The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books.
has resource example: https://portal.issn.org/resource/ISSN/0745-4570
has URI prefix: https://portal.issn.org/resource/ISSN/
is deprecated: false
0000005: 0745-4570
has prefix: issn
has local unique identifier pattern: ^\d{4}-\d{3}[\dX]$
is part of: Bioregistry
type: Resource

OntoSpecies - Chemical Species Ontology for Data Integration and Knowledge Discovery
0000005: Charge
has resource example: Charge
type: Resource
has prefix: worldavatar.os
description: OntoSpecies is an ontology developed for representing chemical species.
is deprecated: false
keyword: chemistry
keyword: nfdi4chem
is part of: Bioregistry
has provider formatter: http://www.theworldavatar.com/ontology/ontospecies/OntoSpecies.owl#$1
has URI prefix: http://www.theworldavatar.com/ontology/ontospecies/OntoSpecies.owl#

TreeHub
type: Resource
contributor: https://orcid.org/0009-0000-6974-6386
has provider formatter: https://www.plantplus.cn/treehub/tree/$1
has responsible: Hui Wu
has local unique identifier pattern: ^T\d{8}$
keyword: taxonomy
has URI prefix: https://www.plantplus.cn/treehub/tree/
description: TreeHub is a taxonomical database for trees. TreeHub contains extracted phylogenetic data and integrates relevant species information for each identifier.
is deprecated: false
keyword: dendrology
is part of: Bioregistry
has prefix: treehub
has resource example: T00232742
keyword: tree
0000005: T00232742
has reviewer: https://orcid.org/0000-0001-9439-5346

Epilepsy and Seizure Ontology
has download URL: epso.owl
is part of: Bioregistry
keyword: epilepsy
0000005: 0000400
has resource example: http://www.case.edu/EpilepsyOntology.owl#0000400
has responsible: Satya S. Sahoo
has local unique identifier pattern: ^\d{7}$
type: Resource
has URI prefix: http://www.case.edu/EpilepsyOntology.owl#
description: The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research.
keyword: neurology
keyword: patient care
is deprecated: false
has provider formatter: http://www.case.edu/EpilepsyOntology.owl#$1
has prefix: epso
keyword: ontology

Cancer Data Standards Registry and Repository
is part of: Bioregistry
type: Resource
description: The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR.
has prefix: cadsr
0000005: 3771992
has resource example: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML
has local unique identifier pattern: ^[0-9]*$
has provider formatter: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML
is deprecated: false
has URI prefix: https://bioregistry.io/cadsr:

Learning Resource Metadata Innovation Terms
has URI prefix: http://purl.org/dcx/lrmi-terms/
keyword: education
has provider formatter: http://purl.org/dcx/lrmi-terms/$1
keyword: educational resource
has prefix: lrmi
0000005: AlignmentObject
has resource example: AlignmentObject
is deprecated: false
description: The Learning Resource Metadata Innovation (LRMI) specification is a collection of classes and properties for markup and description of educational resources. The specification builds on the extensive vocabulary provided by Schema.org and other standards. LRMI terms not included in schema.org may nevertheless be used to augment and enrich Schema.org markup. (from homepage)
keyword: open educational resources
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt

Thesaurus for long-term ecological research, monitoring, experiments
has provider formatter: http://vocabs.lter-europe.net/EnvThes/$1
description: The Environmental Thesaurus is a controlled vocabulary built to aid integration of the data resulting from long term ecological research and monitoring in Europe (eLTER). It provides described and semantically well defined terms for later analysis and it serves as harmonized specification of parameters in the observation and measurement of ecosystem processes.
keyword: ontology
is deprecated: false
is part of: Bioregistry
keyword: ecology
keyword: geochemistry
has prefix: envthes
has URI prefix: http://vocabs.lter-europe.net/EnvThes/
keyword: monitoring
keyword: earth sciences
type: Resource
keyword: geographic location
has responsible: Barbara Magagna
keyword: environmental science
keyword: observations
keyword: ess
keyword: natural science
git repository: issues

NFDI4DataScience Collection
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4DataScience
has part: Bioregistry
type: Collection
creator: Charles Tapley Hoyt

Common Core Ontologies
keyword: ontology
is deprecated: false
description: The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest. CCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.
is part of: Bioregistry
keyword: engineering
has responsible: https://orcid.org/0000-0001-9228-8838
contributor: Charles Tapley Hoyt
git repository: CommonCoreOntologies
0000005: DirectiveInformationContentEntity
type: Resource
keyword: nfdi4ing
has provider formatter: http://www.ontologyrepository.com/CommonCoreOntologies/$1
has URI prefix: http://www.ontologyrepository.com/CommonCoreOntologies/
has prefix: commoncoreontology
keyword: upper-level ontology
has resource example: DirectiveInformationContentEntity

RNA Modification Database
is deprecated: false
has provider formatter: http://rna.rega.kuleuven.be/rnamods/rnashow.pl
has URI prefix: http://rna.rega.kuleuven.be/rnamods/rnashow.pl
is part of: Bioregistry
has resource example: http://rna.rega.kuleuven.be/rnamods/rnashow.pl
type: Resource
keyword: structure
has prefix: rnamods
has local unique identifier pattern: ^\d{3}$
description: The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA.
keyword: rna
0000005: 101

SWEET Ontology Realm Cryosphere
has alternative prefix: soreac
has prefix: sweet.reac
has URI prefix: http://sweetontology.net/realmCryo/
is part of: Bioregistry
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Cryosphere
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
0000005: AblationZone
keyword: realm
keyword: cryosphere
has provider formatter: http://sweetontology.net/realmCryo/$1
has resource example: AblationZone
is deprecated: false

PlasmoDB
has alternative prefix: ApiDB_PlasmoDB
keyword: genome
is part of: Bioregistry
keyword: genomics
description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
type: Resource
has URI prefix: http://plasmodb.org/plasmo/showRecord.do
has provider formatter: http://plasmodb.org/plasmo/showRecord.do
has responsible: Omar S. Harb
has resource example: http://plasmodb.org/plasmo/showRecord.do
0000005: PF11_0344
has prefix: plasmodb
is deprecated: false
keyword: infectious disease medicine
has local unique identifier pattern: ^\w+$

Allotrope result
type: Resource
has resource example: AFR_0001055
has prefix: allotrope.result
has provider formatter: http://purl.allotrope.org/ontologies/result#AFR_$1
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: http://purl.allotrope.org/ontologies/result#AFR_
0000005: 0001055
is part of: Allotrope Merged Ontology Suite
description: The result component of the Allotrope ontology suite

Influenza Sequence and Epitope Database
is part of: Bioregistry
keyword: protein
description: ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea.
0000005: AY209920
type: Resource
is deprecated: false
has prefix: ised

ArrayExpress
keyword: functional genomics
keyword: microarray
has local unique identifier pattern: ^[AEP]-\w{4}-\d+$
is part of: Bioregistry
has prefix: arrayexpress
keyword: nucleotide
type: Resource
keyword: expression
has responsible: https://orcid.org/0000-0001-5988-7409
has resource example: E-MEXP-1712
has provider formatter: https://www.ebi.ac.uk/arrayexpress/experiments/$1
contributor: https://orcid.org/0000-0002-1216-4761
has URI prefix: https://www.ebi.ac.uk/arrayexpress/experiments/
is deprecated: false
description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.
0000005: E-MEXP-1712

CAMEO Chemicals ID
has resource example: https://cameochemicals.noaa.gov/chemical/19757
is deprecated: false
has provider formatter: https://cameochemicals.noaa.gov/chemical/$1
is part of: Bioregistry
has URI prefix: https://cameochemicals.noaa.gov/chemical/
0000005: 19757
type: Resource
has prefix: noaa.cameo
has local unique identifier pattern: ^\d*$
description: CAMEO Chemicals is a database of hazardous chemical datasheets that emergency responders and planners can use to get response recommendations and predict hazards—such as explosions or toxic fumes.

Intrinsically Disordered proteins with Extensive Annotations and Literature
type: Resource
has responsible: Satoshi Fukuchi
has prefix: ideal
keyword: biology
description: IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.
has URI prefix: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php
is deprecated: false
has provider formatter: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php
has local unique identifier pattern: ^IID\d+$
0000005: IID00001
has resource example: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php
is part of: Bioregistry

SWEET Ontology Property Space
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space
keyword: space
has URI prefix: http://sweetontology.net/propSpace/
has prefix: sweet.props
has resource example: AngularDistribution
is part of: Bioregistry
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/propSpace/$1
has alternative prefix: soprops
0000005: AngularDistribution

The Hydra Core Vocabulary
has prefix: hydra
type: Resource
0000005: TemplatedLink
is deprecated: false
keyword: rdf
description: A lightweight vocabulary for hypermedia-driven Web APIs
is part of: Bioregistry

Cowpea Ontology
keyword: food
has URI prefix: https://cropontology.org/rdf/CO_340:
keyword: ontology
is deprecated: false
keyword: plant phenotypes and traits
keyword: phenotype
keyword: botany
keyword: agriculture
has responsible: Elizabeth Arnaud
is part of: Bioregistry
has download URL: CO 340.owl
type: Resource
git repository: Crop-Ontology
0000005: 0000639
has resource example: CO 340:0000639
has prefix: co_340
has local unique identifier pattern: ^\d{7}$
has provider formatter: https://cropontology.org/rdf/CO_340:$1
description: The Cowpea Trait Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.

ChEMBL target
0000005: CHEMBL3467
keyword: cell
has URI prefix: https://www.ebi.ac.uk/chembl/target/inspect/
has prefix: chembl.target
description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.
keyword: cell line
keyword: ontology
is deprecated: false
has alternative prefix: ChEMBL-Targets
is part of: Bioregistry
keyword: protein
has local unique identifier pattern: ^CHEMBL\d+$
has responsible: David Mendez Lopez
has provider formatter: https://www.ebi.ac.uk/chembl/target/inspect/$1
has resource example: CHEMBL3467
has download URL: chembl.target.owl
type: Resource
keyword: protein complex

KEGG Metagenome
description: The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.
has resource example: T30002
has provider formatter: http://www.kegg.jp/entry/$1
has prefix: kegg.metagenome
has URI prefix: http://www.kegg.jp/entry/
keyword: genome
is deprecated: false
is part of: Bioregistry
is part of: Kyoto Encyclopedia of Genes and Genomes
has local unique identifier pattern: ^T3\d+$
has responsible: Minoru Kanehisa
0000005: T30002
type: Resource

MIRIAM Registry collection
has resource example: https://www.ebi.ac.uk/miriam/main/00000008
is deprecated: true
has URI prefix: https://www.ebi.ac.uk/miriam/main/
description: MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.
has prefix: miriam.collection
has local unique identifier pattern: ^000\d{5}$
is part of: Bioregistry
0000005: 00000008
has provider formatter: https://www.ebi.ac.uk/miriam/main/$1
type: Resource

EndlessForms Studio Element
has URI prefix: https://graphics.endlessforms.info/element
type: Resource
contributor: Charles Tapley Hoyt
has prefix: endlessforms.element
has resource example: https://graphics.endlessforms.info/element
0000005: HUMAN0000174
description: A reusable element of a vector graphic for an anatomical entity useful for biological and biomedical informatics applications.
has provider formatter: https://graphics.endlessforms.info/element
is deprecated: false
is part of: Bioregistry
has responsible: Melissa D Clarkson

Financial Industry Business Ontology
has URI prefix: https://spec.edmcouncil.org/fibo/ontology/
is deprecated: false
description: FIBO defines the sets of things that are of interest in financial business applications and the ways that those things can relate to one another. In this way, FIBO can give meaning to any data (e.g., spreadsheets, relational databases, XML documents) that describe the business of finance
keyword: economics
is part of: Bioregistry
type: Resource
has provider formatter: https://spec.edmcouncil.org/fibo/ontology/$1
has resource example: BEDomain
git repository: fibo
keyword: coypu
has prefix: edm.fibo
0000005: BE/MetadataBE/BEDomain

Thin-film Solar Cells Ontology
git repository: autoperosol
0000005: 00000001
has URI prefix: https://purl.archive.org/tfsco/TFSCO_
keyword: physics
has provider formatter: https://purl.archive.org/tfsco/TFSCO_$1
is deprecated: false
is part of: Bioregistry
has resource example: TFSCO_00000001
keyword: mechanical engineering, energy technology
description: Domain ontology for thin-film solar cells and related tandem solar cells. Contains relevant terms and concepts from BFO, IAO, UO, PATO, OBI, CHMO.
keyword: fairmat
type: Resource
keyword: material science
has prefix: tfsco

UniPathway Compound
has resource example: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc
0000005: UPC04349
is part of: Bioregistry
has provider formatter: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc
has URI prefix: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc
type: Resource
has local unique identifier pattern: ^UPC\d{5}$
is deprecated: false
description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds.
has prefix: unipathway.compound

Mouse Developmental Anatomy Ontology with Theiler Stage
has prefix: emaps
is deprecated: false
has responsible: https://orcid.org/0000-0002-0956-8634
has local unique identifier pattern: ^\d+$
contributor: https://orcid.org/0000-0001-9439-5346
has provider formatter: https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1
has URI prefix: https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:
description: EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number. For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823
is part of: Bioregistry
type: Resource
depends on: Mouse Developmental Anatomy Ontology
has reviewer: Charles Tapley Hoyt
0000005: 3517823
has resource example: EMAPS:3517823

ESCO - International Standard Classification of Occupations
contributor: Charles Tapley Hoyt
has resource example: C4
0000005: C4
description: The European Skills, Competences, Qualifications and Occupations (ESCO) International Standard Classification of Occupations (ISCO).
type: Resource
has URI prefix: http://data.europa.eu/esco/isco/
has provider formatter: http://data.europa.eu/esco/isco/$1
is deprecated: false
has prefix: esco.isco
is part of: Bioregistry

Chinese Clinical Trial Registry
is deprecated: false
is part of: Bioregistry
has prefix: chictr
0000005: ChiCTR2300070727
contributor: Charles Tapley Hoyt
type: Resource
description: Established in 2005 by professor Wu Taixiang and Li Youping team, West China Hospital, Sichuan University, and the Ministry of Health of China assigned it to be the representative of China to join WHO ICTRP in 2007. The Chinese Clinical Trial Registry provides the services include register for trials, consultation for trial design, central randomization for an allocation sequence, peer review for draft articles and training for peer reviewers. (from website)
has local unique identifier pattern: ^ChiCTR(-[A-Z]+-)?\d+$

Ontology for Avida digital evolution platform
0000005: 00000001
has resource example: ONTOAVIDA_00000001
git repository: ontoavida
depends on: NCI Thesaurus
keyword: obo
depends on: The Statistical Methods Ontology
keyword: ontology
has local unique identifier pattern: ^\d{8}$
has download URL: ontoavida.owl
depends on: Relation Ontology
description: The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment). The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight. OntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA). More information can be found at https://obofoundry.org/ontology/ontoavida.html
has responsible: Miguel A. Fortuna
has prefix: ontoavida
depends on: Gender, Sex, and Sexual Orientation Ontology
is part of: Bioregistry
depends on: FlyBase Controlled Vocabulary
is deprecated: false
has provider formatter: http://purl.obolibrary.org/obo/ONTOAVIDA_$1
has URI prefix: http://purl.obolibrary.org/obo/ONTOAVIDA_
type: Resource

MeSH 2013
has URI prefix: https://bioregistry.io/mesh.2013:
0000011: Medical Subject Headings
has resource example: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi
is deprecated: false
description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013.
has provider formatter: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi
is part of: Bioregistry
0000005: 17165
has prefix: mesh.2013
has local unique identifier pattern: ^[A-Za-z0-9]+$
type: Resource

PeptideAtlas Dataset
has provider formatter: http://www.peptideatlas.org/PASS/$1
0000005: PASS01237
has URI prefix: http://www.peptideatlas.org/PASS/
has resource example: PASS01237
has local unique identifier pattern: ^PASS\d{5}$
has prefix: peptideatlas.dataset
is deprecated: false
is part of: Bioregistry
type: Resource
description: Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas.

Arabidopsis Small RNA Project
0000005: ASRP1423
contributor: Charles Tapley Hoyt
is part of: Bioregistry
type: Resource
has provider formatter: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html
has resource example: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html
has URI prefix: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html
keyword: rna
keyword: genome
is deprecated: false
keyword: regulation
description: Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes.
has prefix: asrp

PomBase
has alternative prefix: PomBase
keyword: ontology
has local unique identifier pattern: ^S\w+(\.)?\w+(\.)?$
is part of: Bioregistry
has download URL: pombase.owl
has responsible: Valerie Wood
0000005: SPCC13B11.01
type: Resource
has provider formatter: https://www.pombase.org/gene/$1
description: PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets.
has prefix: pombase
has resource example: SPCC13B11.01
has URI prefix: https://www.pombase.org/gene/
is deprecated: false
keyword: life science

Unified Phenotype Ontology
keyword: phenotype
keyword: omics
has provider formatter: http://purl.obolibrary.org/obo/UPHENO_$1
is part of: Bioregistry
keyword: phenomics
git repository: upheno
keyword: evolutionary biology
type: Resource
has responsible: https://orcid.org/0000-0002-8361-2795
description: The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
keyword: data analysis
has prefix: upheno
keyword: obo
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/UPHENO_
has download URL: upheno.owl
keyword: expression data
is deprecated: false

GitHub Issue
keyword: software engineering
keyword: version control
is part of: Bioregistry
description: An issue in any public repository on GitHub.
contributor: Charles Tapley Hoyt
keyword: knowledge and information systems
type: Resource
has URI prefix: https://bioregistry.io/resolve/github/issue/
0000005: biopragmatics/bioregistry/424
has prefix: github.issue
is deprecated: false
has provider formatter: https://bioregistry.io/resolve/github/issue/$1
keyword: project management
has resource example: https://bioregistry.io/resolve/github/issue/biopragmatics/bioregistry/424

Terminologia Histologica
contributor: Charles Tapley Hoyt
keyword: cytology
keyword: life sciences
keyword: biology
type: Resource
0000005: H3.03.00.0.00007
has local unique identifier pattern: ^H\d\.\d{2}\.\d{2}\.\d\.\d{5}$
is deprecated: false
keyword: histology
description: The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]
has prefix: th
is part of: Bioregistry

iNaturalist Observation
type: Resource
has resource example: https://www.inaturalist.org/observations/36010371
is deprecated: false
0000005: 36010371
has URI prefix: https://www.inaturalist.org/observations/
has local unique identifier pattern: ^[1-9]\d*$
has provider formatter: https://www.inaturalist.org/observations/$1
is part of: Bioregistry
description: The identifier for an observation in iNaturalist
has prefix: inaturalist.observation
contributor: Pierre-Marie Allard
has reviewer: Charles Tapley Hoyt

SWEET Ontology State Time Frequency
has alternative prefix: sosttf
keyword: state time frequency
has resource example: Annual
type: Resource
has provider formatter: http://sweetontology.net/stateTimeFrequency/$1
has URI prefix: http://sweetontology.net/stateTimeFrequency/
has prefix: sweet.sttf
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Time Frequency
is deprecated: false
0000005: Annual
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology

mirTarBase
has local unique identifier pattern: ^MIRT\d{6}$
has responsible: Sheng-Da Hsu
keyword: life science
contributor: https://orcid.org/0000-0001-9439-5346
is deprecated: true
0000005: MIRT000002
has provider formatter: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: mirtarbase
has URI prefix: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php
has resource example: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php
description: miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.
type: Resource

Educational Context
description: educational levels
has URI prefix: http://w3id.org/openeduhub/vocabs/educationalContext/
has resource example: sekundarstufe 2
has provider formatter: http://w3id.org/openeduhub/vocabs/educationalContext/$1
is deprecated: false
keyword: education level
0000005: sekundarstufe_2
keyword: open educational resources
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has prefix: openeduhub.context

Japan Consortium for Glycobiology and Glycotechnology Database
has resource example: JCGG-STR008690
has local unique identifier pattern: ^JCGG-STR\d{6}$
has provider formatter: http://jcggdb.jp/idb/jcggdb/$1
has URI prefix: http://jcggdb.jp/idb/jcggdb/
is part of: Bioregistry
description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.
0000005: JCGG-STR008690
has prefix: jcggdb
type: Resource
is deprecated: true

ProGlycProt
has local unique identifier pattern: ^[A-Z]C\d{1,3}$
is deprecated: true
has URI prefix: http://www.proglycprot.org/detail.aspx
description: ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information.
has resource example: http://www.proglycprot.org/detail.aspx
has provider formatter: http://www.proglycprot.org/detail.aspx
0000005: AC119
is part of: Bioregistry
type: Resource
has prefix: proglyc

COMBINE specifications
has URI prefix: https://bioregistry.io/combine.specifications:
description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.
is deprecated: false
has resource example: sed-ml.level-1.version-1.md
has provider formatter: https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md
0000005: sed-ml.level-1.version-1
has prefix: combine.specifications
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^\w+(\-|\.|\w)*$

Database of Anti-Microbial Peptides
has reviewer: https://orcid.org/0000-0001-9439-5346
has responsible: https://orcid.org/0000-0001-8475-7868
type: Resource
has provider formatter: https://awi.cuhk.edu.cn/dbAMP/information.php
description: Identifiers represent antimicrobial peptides in the Database of Antimicrobial Peptides (dbAMP) which is an open-access, manually curated database of antimicrobial peptides (AMPs).
has resource example: https://awi.cuhk.edu.cn/dbAMP/information.php
has reviewer: Charles Tapley Hoyt
0000005: 28463
has URI prefix: https://awi.cuhk.edu.cn/dbAMP/information.php
contributor: Kangho Ji
has local unique identifier pattern: ^\d{5}$
is deprecated: false
is part of: Bioregistry
keyword: antimicrobial peptides
has prefix: dbamp

Philippine Health Research Registry
description: The Philippine Health Research Registry (PHRR), managed by the Philippine Council for Health Research and Development, is a tool for good governance to promote transparency and accountability in health research. PHRR is a publicly accessible database on newly approved health researches. It includes clinical trials and non-clinical studies conducted in the Philippines. The registry is compliant with the World Health Organization (WHO) standard for clinical trials registry. [from website]
0000005: 4195
has prefix: phrr
type: Resource
has resource example: https://registry.healthresearch.ph/index.php/registry
has provider formatter: https://registry.healthresearch.ph/index.php/registry
is deprecated: false
has URI prefix: https://registry.healthresearch.ph/index.php/registry
is part of: Bioregistry
contributor: Charles Tapley Hoyt

DSSTox substance
0000005: DTXSID2021028
is deprecated: false
has prefix: comptox
has resource example: DTXSID2021028
has provider formatter: https://comptox.epa.gov/dashboard/$1
is part of: Bioregistry
has URI prefix: https://comptox.epa.gov/dashboard/
type: Resource
has local unique identifier pattern: ^DTXSID\d+$
description: The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks.

NameRXN
has prefix: namerxn
has responsible: https://orcid.org/0000-0001-6279-4481
description: The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO).
0000005: 4.2.78
keyword: reactions
is deprecated: false
keyword: chemistry
keyword: text mining
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt

AOPWiki (Stressor)
0000005: 9
description: International repository of Adverse Outcome Pathways.
is deprecated: false
has prefix: aop.stressor
has URI prefix: https://aopwiki.org/stressors/
has resource example: https://aopwiki.org/stressors/9
has provider formatter: https://aopwiki.org/stressors/$1
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource

Japan Chemical Substance Dictionary
keyword: drug
has URI prefix: http://jglobal.jst.go.jp/en/redirect
has alternative prefix: nikkaji
description: The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).
0000005: J55.713G
has prefix: jcsd
is deprecated: false
has local unique identifier pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$
contributor: https://orcid.org/0000-0001-9439-5346
has resource example: http://jglobal.jst.go.jp/en/redirect
has provider formatter: http://jglobal.jst.go.jp/en/redirect
is part of: Bioregistry
type: Resource
has alternative prefix: Nikkaji number

Resources mentioned in "Sharing biological data: why, when, and how"
has part: European Genome-phenome Archive Dataset
has part: BioStudies database
has part: System Science of Biological Dynamics dataset
has part: Electron Microscopy Public Image Archive
creator: Charles Tapley Hoyt
type: Collection
has part: PeptideAtlas Dataset
has part: Panorama Public
has part: Proteomics Identification Database Ontology
has part: European Genome-phenome Archive Study
has part: Biological Magnetic Resonance Data Bank
has part: Electron Microscopy Data Bank
has part: GenBank
has part: PDB Structure
has part: System Science of Biological Dynamics project
description: These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible.
has part: Sequence Read Archive
has part: NCBI Gene Expression Omnibus
has part: Cell Image Library
has part: MassIVE
has part: Image Data Resource

Nematode & Neglected Genomics
is deprecated: true
keyword: rna
keyword: dna
0000005: NBC00001
keyword: protein
description: NEMBASE is a comprehensive Nematode Transcriptome Database. NEMBASE4 includes robust protein predictions (NemPep4), and protein families for 63 nematode species, over 600,000 ESTs and over 250,000 proteins.
has URI prefix: http://www.nematodes.org/nembase4/cluster.php
is part of: Bioregistry
has provider formatter: http://www.nematodes.org/nembase4/cluster.php
has prefix: nembase
has reviewer: Charles Tapley Hoyt
type: Resource
has resource example: http://www.nematodes.org/nembase4/cluster.php

Identifiers.org Ontology
is part of: Bioregistry
type: Resource
0000005: DataCollection
has prefix: idoo
has URI prefix: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#
has provider formatter: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1
has resource example: DataCollection
has local unique identifier pattern: ^[0-9a-zA-Z]+$
is deprecated: false
description: Identifiers.org Ontology

NCBI PubChem database of bioassay records
has alternative prefix: pubchem.aid
has resource example: https://pubchem.ncbi.nlm.nih.gov/bioassay/1018
0000005: 1018
has responsible: https://orcid.org/0000-0001-7950-1374
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/bioassay/
keyword: small molecule
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has prefix: pubchem.bioassay
has alternative prefix: pubchem.assay
description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results.
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/bioassay/$1
type: Resource

NASA Open Science Data Repository Hardware
description: Identifiers for hardware used in experiments that investigate biological and health responses of terrestrial life to spaceflight
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-8542-2389
type: Resource
has resource example: https://osdr.nasa.gov/bio/repo/data/hardware/2011
has provider formatter: https://osdr.nasa.gov/bio/repo/data/hardware/$1
contributor: Mufaddal Naguthanawala
0000005: 2011
is deprecated: false
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://osdr.nasa.gov/bio/repo/data/hardware/
has prefix: nasaosdr.hardware

Sharkipedia Species
0000005: 983
has prefix: sharkipedia.species
has reviewer: Charles Tapley Hoyt
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has provider formatter: https://www.sharkipedia.org/species/$1
has responsible: Christopher Mull
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has resource example: https://www.sharkipedia.org/species/983
has URI prefix: https://www.sharkipedia.org/species/
git repository: sharkipedia
type: Resource
description: Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone.

Experimental Factor Ontology
keyword: genome-wide association study
keyword: experimental measurement
has provider formatter: http://www.ebi.ac.uk/efo/EFO_$1
has resource example: EFO_0005147
has identifier space owner: 02catss52
has download URL: efo.owl
keyword: ess
keyword: medicine
keyword: study design
git repository: efo
keyword: study design independent variable
has URI prefix: http://www.ebi.ac.uk/efo/EFO_
keyword: ontology
is deprecated: false
0000005: 0005147
keyword: dataplant
keyword: experimental condition
keyword: genomics
keyword: assay
keyword: nfdi4chem
description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.
keyword: omics
keyword: proteomics
keyword: earth sciences
has local unique identifier pattern: ^\d{7}$
keyword: life sciences, biology
has prefix: efo
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-3458-4839
type: Resource

AOPWiki
has URI prefix: https://aopwiki.org/aops/
has prefix: aop
contributor: https://orcid.org/0000-0002-1216-4761
has provider formatter: https://aopwiki.org/aops/$1
is deprecated: false
description: International repository of Adverse Outcome Pathways.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
0000005: 98
has resource example: https://aopwiki.org/aops/98

SWEET Ontology Human Environmental Assessment
has URI prefix: http://sweetontology.net/humanEnvirAssessment/
is part of: Bioregistry
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Environmental Assessment
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has resource example: CEMS
has alternative prefix: sohuea
type: Resource
keyword: environmental assessment
0000005: CEMS
is deprecated: false
has prefix: sweet.huea
has provider formatter: http://sweetontology.net/humanEnvirAssessment/$1

MultiCellDS
keyword: life science
has provider formatter: http://multicellds.org/MultiCellDB/$1
description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.
has responsible: Samuel Friedman
has URI prefix: http://multicellds.org/MultiCellDB/
0000005: MCDS_S_0000000001
is deprecated: false
has part: MultiCellDS Digital Cell Line
has prefix: multicellds
has part: MultiCellDS Digital snapshot
has part: MultiCellDS collection
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has resource example: MCDS S 0000000001

MarDB
is part of: Bioregistry
has provider formatter: https://mmp.sfb.uit.no/databases/mardb/#/records/$1
type: Resource
0000005: MMP02954345.1
has local unique identifier pattern: ^MMP\d+.\d+$
description: MarDB includes all sequenced marine microbial genomes regardless of level of completeness.
is deprecated: false
has prefix: mmp.db
has URI prefix: https://mmp.sfb.uit.no/databases/mardb/#/records/
has resource example: records/MMP02954345.1

Food-Biomarker Ontology
keyword: ontology
has local unique identifier pattern: ^\d{4,6}$
has download URL: fobi.owl
is part of: Bioregistry
description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data
has provider formatter: http://purl.obolibrary.org/obo/FOBI_$1
depends on: Chemical Entities of Biological Interest
type: Resource
has responsible: 0000-0001-6466-877X
0000005: 030719
has prefix: fobi
has resource example: FOBI_030719
has URI prefix: http://purl.obolibrary.org/obo/FOBI_
depends on: The Food Ontology
is deprecated: false
git repository: FoodBiomarkerOntology
keyword: obo

Getty Iconography Authority
has provider formatter: http://vocab.getty.edu/page/ia/$1
is deprecated: false
has URI prefix: http://vocab.getty.edu/page/ia/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: http://vocab.getty.edu/page/ia/901001034
description: The Getty Iconography Authority ™ (IA), Cultural Objects Name Authority ® (CONA), the Union List of Artist Names ® (ULAN), the Art & Architecture Thesaurus ® (AAT), the Getty Thesaurus of Geographic Names ® (TGN) are structured resources that can be used to improve access to information about art, architecture, and other material culture. The Vocabularies are not simply 'value vocabularies,' but knowledge bases. Through rich metadata and links, the Getty Vocabularies provide powerful conduits for knowledge creation, complex research, and discovery for digital art history and related disciplines. [from https://www.getty.edu/research/tools/vocabularies/cona/about.html#purpose_ia]
type: Resource
0000005: 901001034
has prefix: getty.ia

SED-ML model format
description: Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).
has resource example: language:sbml.level-3.version-2
type: Resource
has provider formatter: https://sed-ml.org/urns.html#language:$1
is deprecated: false
has URI prefix: https://sed-ml.org/urns.html#language:
has local unique identifier pattern: ^[a-z]+(\..*?)?$
0000005: sbml.level-3.version-2
is part of: Bioregistry
has prefix: sedml.language

GWAS Central Marker
has prefix: gwascentral.marker
is part of: Bioregistry
has provider formatter: https://www.gwascentral.org/marker/$1
has local unique identifier pattern: ^HGVM\d+$
has responsible: https://orcid.org/0000-0002-0292-7972
type: Resource
has resource example: HGVM15354
is deprecated: false
0000005: HGVM15354
description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.
has URI prefix: https://www.gwascentral.org/marker/

StoreDB Dataset
description: Datasets inside StoreDB at University of Cambridge
is deprecated: true
has URI prefix: https://www.storedb.org/
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has resource example: https://www.storedb.org/
has provider formatter: https://www.storedb.org/
has prefix: storedb.dataset
type: Resource
0000005: 1251

National Uniform Claim Committee Characteristic
0000005: 2A
is deprecated: false
has local unique identifier pattern: ^\d(\d|\w)$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan.
has prefix: nucc.characteristic

UBERON Issue Tracker
has prefix: uberon.issue
0000005: 530
has resource example: https://github.com/obophenotype/uberon/issues/530
is deprecated: false
description: An issue on the UBERON GitHub Issue tracker
has local unique identifier pattern: ^\d+$
has URI prefix: https://github.com/obophenotype/uberon/issues/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://github.com/obophenotype/uberon/issues/$1
type: Resource

Software Heritage
is part of: Bioregistry
description: Software Heritage is the universal archive of software source code.
type: Resource
has URI prefix: https://archive.softwareheritage.org/browse/swh:
has provider formatter: https://archive.softwareheritage.org/browse/swh:$1
has prefix: swh
has local unique identifier pattern: ^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$
is deprecated: false

Golm Metabolome Database Reference Substance
has local unique identifier pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
has URI prefix: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/
is deprecated: false
has prefix: gmd.ref
description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.
is part of: Bioregistry
has provider formatter: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1
type: Resource

BioDolphin
is part of: Bioregistry
has local unique identifier pattern: ^BD\d[a-zA-Z0-9]+-[A-Za-z]-[A-Za-z]-[A-Za-z0-9]+$
has responsible: https://orcid.org/0000-0002-3212-9867
type: Resource
has provider formatter: https://biodolphin.chemistry.gatech.edu/detail/$1
has prefix: biodolphin
contributor: Mufaddal Naguthanawala
0000005: BD1a05-A-A-IPM1
is deprecated: false
has resource example: BD1a05-A-A-IPM1
has URI prefix: https://biodolphin.chemistry.gatech.edu/detail/
description: Identifiers for lipid-protein interactions, including details about protein functions, protein families, lipid classifications, lipid-protein binding affinities, membrane association type, and atomic structures.
has reviewer: https://orcid.org/0000-0001-9439-5346

SWEET Ontology Representation Scientific Model
has URI prefix: http://sweetontology.net/reprSciModel/
has prefix: sweet.repsmo
is deprecated: false
has resource example: BoussinesqApproximation
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Model
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sorepsmo
has provider formatter: http://sweetontology.net/reprSciModel/$1
0000005: BoussinesqApproximation
keyword: representation scientific model

GrassBase
type: Resource
has provider formatter: https://www.kew.org/data/grasses-db/www/$1
description: GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species.
has URI prefix: https://www.kew.org/data/grasses-db/www/
has local unique identifier pattern: ^(imp|gen)\d{5}$
has resource example: imp10873
0000005: imp10873
has prefix: grassbase
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt

Terminology of Anatomy of Human Histology
has provider formatter: http://purl.obolibrary.org/obo/TAHH_$1
is part of: Bioregistry
type: Resource
has prefix: tahh
has URI prefix: http://purl.obolibrary.org/obo/TAHH_
is deprecated: true
keyword: obo
keyword: ontology

NINDS Human Cell and Data Repository
has URI prefix: https://stemcells.nindsgenetics.org
0000005: ND50028
has provider formatter: https://stemcells.nindsgenetics.org
is deprecated: false
description: Cell line collections (Providers)
has prefix: nhcdr
is part of: Bioregistry
has resource example: https://stemcells.nindsgenetics.org
type: Resource

SAREF4LIFT: an extension of SAREF for the Smart Lifts domain
is deprecated: false
keyword: digital planning and construction
keyword: engineering
description: This ontology extends the SAREF ontology for the Smart Lifts domain.
keyword: fid baudigital
has prefix: saref.lift
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
0000005: AlarmSignal
has provider formatter: https://saref.etsi.org/saref4lift/$1
has resource example: AlarmSignal
has alternative prefix: s4lift
has URI prefix: https://saref.etsi.org/saref4lift/

eukaryotic Subcellular Localization database
has URI prefix: http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi
0000005: HS000015122
has prefix: esldb
has resource example: http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi
is deprecated: false
description: eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.
keyword: protein
has provider formatter: http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi
is part of: Bioregistry
type: Resource
has reviewer: Charles Tapley Hoyt

SWEET Ontology Realm Geologic Basin
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Basin
has prefix: sweet.reagb
has resource example: BackArcBasin
is part of: Bioregistry
has alternative prefix: soreagb
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: realm
0000005: BackArcBasin
has provider formatter: http://sweetontology.net/realmGeolBasin/$1
has URI prefix: http://sweetontology.net/realmGeolBasin/
type: Resource
keyword: geologic basin

RiceNetDB miRNA
is deprecated: false
has provider formatter: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php
is part of: Bioregistry
0000005: osa-miR446
type: Resource
has local unique identifier pattern: ^osa-miR\d{3,5}[a-z]{0,1}$
has prefix: ricenetdb.mirna
has resource example: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php
description: RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.
has URI prefix: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php

Sigma Aldrich
has provider formatter: https://www.sigmaaldrich.com/US/en/product/sigma/$1
has resource example: HPA000698
is part of: Bioregistry
keyword: chemistry
contributor: Charles Tapley Hoyt
keyword: vendor
0000005: HPA000698
type: Resource
has prefix: sigmaaldrich
has URI prefix: https://www.sigmaaldrich.com/US/en/product/sigma/
keyword: life sciences
keyword: biology
description: Sigma Aldrich is a life sciences supply vendor.
is deprecated: false

UTRdb
has resource example: https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb
has provider formatter: https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb
has local unique identifier pattern: ^([3-5][A-Z])\w+[^A-Z][0-9]$
has prefix: utrdb
0000005: 5UTR_107_ENST00000517291.2
has URI prefix: https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb
is deprecated: false
description: A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets.
is part of: Bioregistry
type: Resource

United States Department of Agriculture Veterinary Biological Product Code Number
description: A Product Code Number (PCN) assigned by the Animal and Plant Health Inspection Service (APHIS)'s Center for Veterinary Biologics (CVB) to veterinary biological products such as vaccines, bacterins, antibodies, diagnostic products, antitoxins, bacterin-toxoids, and toxioids approved for veterinary use by the United States Department of Agriculture Veterinary (USDA). A quarterly release, as PDF, can be found [here](https://www.aphis.usda.gov/sites/default/files/currentprodcodebook.pdf). The PDF document states (verbatim): The alphanumeric system used for product codes provides for a six-digit number of number-letter combination to be assigned to each product, i.e., the first digit denotes product types; second and third, group by agents; fourth, the viability of vaccine, (live, killed, modified live, etc.); fifth, substrates; and sixth, miscellaneous variables
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: vaccine
keyword: diagnostic product
type: Resource
keyword: bacterin
0000005: 1011.00
has prefix: usda.cvb.pcn
has identifier space owner: 0599wfz09
keyword: toxoid
is deprecated: false
appears in: Vaccine Ontology
has local unique identifier pattern: ^[A-Z0-9]{4}\.[A-Z0-9]{2}$
keyword: bacterin-toxoid
keyword: antitoxin

Immunology Database and Analysis Portal (ImmPort)
description: ImmPort is a scientific data resource funded by the National Institutes of Health (NIH) to preserve and share immunology research and clinical trials data generated by NIH researchers and external organizations. ImmPort uses FAIR principles to maximize reuse of deposited data for advancement of biomedical sciences.
is deprecated: false
is part of: Bioregistry
has provider formatter: https://immport.org/shared/study/$1
has resource example: sdy998
has local unique identifier pattern: ^[sS][dD][yY]\d+$
type: Resource
0000005: sdy998
has prefix: sdy
has URI prefix: https://immport.org/shared/study/

Deutsche Sammlung von Mikroorganismen und Zellkulturen
has resource example: ACC-1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers: - `PC`: positive control - `NC`: negative control - `AS`: antiserum - `PV`: plant viruses - `RT`: recommended test - `ACC`: human or animal cell line - `DSM`: microorganism cell line
0000005: ACC-1
has provider formatter: https://www.dsmz.de/collection/catalogue/details/culture/$1
type: Resource
has alternative prefix: DSMZCellDive
has local unique identifier pattern: ^(ACC|DSM|NC|PC|RT|AS|PV)-\d+$
has prefix: dsmz
is deprecated: false
has URI prefix: https://www.dsmz.de/collection/catalogue/details/culture/

Cuban Registry of Clinical Trials
description: The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage)
has provider formatter: https://rpcec.sld.cu/en/trials/$1
is part of: Bioregistry
has resource example: RPCEC00000423
type: Resource
has URI prefix: https://rpcec.sld.cu/en/trials/
contributor: Charles Tapley Hoyt
has prefix: rpcec
has local unique identifier pattern: ^RPCEC\d+$
0000005: RPCEC00000423
is deprecated: false

ProteomicsDB Peptide
has provider formatter: https://www.proteomicsdb.org/#human/proteinDetails/$1
type: Resource
has prefix: proteomicsdb.peptide
has URI prefix: https://www.proteomicsdb.org/#human/proteinDetails/
0000005: 53504
description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.
has resource example: human/proteinDetails/53504
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$

MetaCyc Reaction
has prefix: metacyc.reaction
0000005: RXN-14904
has local unique identifier pattern: ^[A-Za-z0-9+_.%-:]+$
is deprecated: false
is part of: Bioregistry
has resource example: https://metacyc.org/META/NEW-IMAGE
type: Resource
has responsible: https://orcid.org/0000-0002-5876-6418
description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.
has URI prefix: https://metacyc.org/META/NEW-IMAGE
has provider formatter: https://metacyc.org/META/NEW-IMAGE

ChemBioSys Dataset
type: Resource
has URI prefix: https://data.chembiosys.de/data_files/
description: A dataset in the ChemBioSys data platform
0000005: 103
has prefix: chembiosys.data
is deprecated: false
has local unique identifier pattern: ^\d+$
has resource example: https://data.chembiosys.de/data_files/103
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://data.chembiosys.de/data_files/$1

AOPWiki (Key Event)
has prefix: aop.events
has resource example: https://aopwiki.org/events/3
is deprecated: false
has URI prefix: https://aopwiki.org/events/
description: International repository of Adverse Outcome Pathways.
0000005: 3
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has provider formatter: https://aopwiki.org/events/$1
type: Resource

HL7 V2 Code System
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: v2-0778
has URI prefix: http://terminology.hl7.org/CodeSystem/v2-
description: A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.
has prefix: hl7.v2codesystem
type: Resource
0000005: 0778
has provider formatter: http://terminology.hl7.org/CodeSystem/v2-$1

Ontology of Prokaryotic Phenotypic and Metabolic Characters
has URI prefix: http://purl.obolibrary.org/obo/MICRO_
description: An ontology of prokaryotic phenotypic and metabolic characters
is deprecated: true
git repository: MicrO
keyword: obo
keyword: ontology
has resource example: MICRO_0002999
has provider formatter: http://purl.obolibrary.org/obo/MICRO_$1
has download URL: micro.owl
keyword: bioinformatics
keyword: assay
keyword: phenotype
keyword: cell culture
is part of: Bioregistry
keyword: microbiology
type: Resource
appears in: Microbial Conditions Ontology
has responsible: https://orcid.org/0000-0002-2100-6351
has local unique identifier pattern: ^\d{7}$
0000005: 0002999
has prefix: micro

KEGG Orthology
0000005: K00001
type: Resource
has provider formatter: http://www.kegg.jp/entry/$1
keyword: classification
keyword: pathway
is deprecated: false
has URI prefix: http://www.kegg.jp/entry/
description: KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.
has prefix: kegg.orthology
is part of: Bioregistry
is part of: Kyoto Encyclopedia of Genes and Genomes
has local unique identifier pattern: ^K\d+$
has resource example: K00001

SWEET Ontology Material Rock Igneous
is deprecated: false
has alternative prefix: somarocki
has URI prefix: http://sweetontology.net/matrRockIgneous/
has resource example: Aa
is part of: Bioregistry
has prefix: sweet.marocki
0000005: Aa
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/matrRockIgneous/$1
keyword: rock igneous
type: Resource
keyword: materials
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Rock Igneous

SWEET Ontology State Role
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sostro
has URI prefix: http://sweetontology.net/stateRole/
has provider formatter: http://sweetontology.net/stateRole/$1
has resource example: ConductionRole
0000005: ConductionRole
keyword: state role
has prefix: sweet.stro
is deprecated: false

GXA Gene
is deprecated: false
has local unique identifier pattern: ^\w+$
has prefix: gxa.gene
0000005: AT4G01080
has resource example: AT4G01080
has URI prefix: https://www.ebi.ac.uk/gxa/genes/
is part of: Bioregistry
description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes.
has provider formatter: https://www.ebi.ac.uk/gxa/genes/$1
type: Resource
has identifier space owner: 02catss52

Audubon Core Subtype Controlled Vocabulary
keyword: fair data spaces
0000005: Animation
description: Audubon Core uses the terms ac:subtype and ac:subtypeLiteral to refine the type of a media item to a level more specific than the Dublin Core Type Vocabulary, http://purl.org/dc/dcmitype/. This controlled vocabulary provides values for ac:subtype and ac:subtypeLiteral.
is deprecated: false
has prefix: ac.subtype
keyword: life sciences, biology
is part of: Bioregistry
has resource example: Animation
has URI prefix: http://rs.tdwg.org/acsubtype/
has provider formatter: http://rs.tdwg.org/acsubtype/$1
type: Resource

Lehrplan Ontology
has provider formatter: https://w3id.org/lehrplan/ontology/LP_$1
has resource example: LP_0000141
keyword: ontology
has prefix: kim.lp
is deprecated: false
has download URL: lp.owl
description: This ontology is a formal representation that captures the fundamental concepts and their relationships to one another in the field of curriculum design and implementation of the German school system.
0000005: 0000141
git repository: school-curriculum-pg
has local unique identifier pattern: ^\d{7}$
is part of: Bioregistry
has URI prefix: https://w3id.org/lehrplan/ontology/LP_
type: Resource
contributor: Charles Tapley Hoyt

BioTop
description: Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network
git repository: biotop
contributor: Charles Tapley Hoyt
is part of: Bioregistry
has resource example: attachedTo
type: Resource
keyword: biology
has provider formatter: http://purl.org/biotop/biotop.owl#$1
0000005: attachedTo
has prefix: biotop
has URI prefix: http://purl.org/biotop/biotop.owl#
has download URL: biotop.owl
keyword: ontology
has responsible: https://orcid.org/0000-0001-7222-3287
is deprecated: false

ResearcherID
is deprecated: false
is part of: Bioregistry
has URI prefix: https://www.webofscience.com/wos/author/record/
has resource example: https://www.webofscience.com/wos/author/record/B-5720-2018
has provider formatter: https://www.webofscience.com/wos/author/record/$1
type: Resource
has local unique identifier pattern: ^[A-Z]{1,3}-\d{4}-(19|20)\d\d$
has prefix: wos.researcher
description: identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829
0000005: B-5720-2018

Biomedical Informatics Research Network Lexicon
keyword: anatomy
keyword: study design
keyword: ontology
has prefix: birnlex
is deprecated: false
keyword: disease
has download URL: birnlex.owl
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.
type: Resource
0000005: 2023
contributor: Charles Tapley Hoyt
has URI prefix: http://uri.neuinfo.org/nif/nifstd/birnlex_
has provider formatter: http://uri.neuinfo.org/nif/nifstd/birnlex_$1
keyword: biomedical science
has resource example: birnlex 2023

Nicolas Le Novere
label: Nicolas Le Novère

Dynamic Ecological Information Management System - Site and Dataset Registry - Network
has prefix: deims.network
has provider formatter: https://deims.org/networks/$1
has URI prefix: https://deims.org/networks/
is deprecated: false
has local unique identifier pattern: ^[0-9a-f\-]+$
is part of: Bioregistry
description: Networks in DEIMS SDR
type: Resource
contributor: Charles Tapley Hoyt
has responsible: Christoph Wohner

PhosphoSite Site Group
has reviewer: Charles Tapley Hoyt
keyword: grouping
keyword: biochemistry
contributor: https://orcid.org/0000-0001-9439-5346
has prefix: phosphosite.sitegroup
description: Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur.
0000005: 447860
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: post-translational modification
type: Resource

Establishment Means Controlled Vocabulary
keyword: fair data spaces
is deprecated: false
has provider formatter: http://rs.tdwg.org/dwcem/$1
has prefix: dwc.em
is part of: Bioregistry
keyword: life sciences, biology
0000005: e001
type: Resource
has URI prefix: http://rs.tdwg.org/dwcem/
has resource example: e001
description: The Darwin Core term establishmentMeans provides information about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans. The Establishment Means Controlled Vocabulary provides terms that should be used as values for dwc:establishmentMeans and dwciri:establishmentMeans.

Semantic Sensor Network Ontology
has provider formatter: http://www.w3.org/ns/ssn/$1
keyword: methods
has download URL: ssn.owl
0000005: hasProperty
keyword: ontology
keyword: imaging
contributor: https://orcid.org/0000-0002-1595-3213
keyword: resource metadata
is deprecated: false
keyword: engineering
git repository: sdw-sosa-ssn
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-3884-3420
description: This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.
keyword: w3c rec
has URI prefix: http://www.w3.org/ns/ssn/
keyword: nfdi4chem
has resource example: hasProperty
keyword: monitoring
has prefix: ssn
keyword: iot
keyword: remote sensing
type: Resource
keyword: nfdi4ing
keyword: sensor data
has reviewer: Charles Tapley Hoyt
keyword: web of things
keyword: ess

nmrXiv sample
has local unique identifier pattern: ^S\d+$
is deprecated: false
0000005: S1295
has responsible: https://orcid.org/0000-0002-2564-3243
is part of: Bioregistry
keyword: spectrum
type: Resource
contributor: Charles Tapley Hoyt
has resource example: S1295
description: spectra (samples) in the nmrXiv database
keyword: nmr
has prefix: nmrxiv.sample
keyword: spectra
has provider formatter: https://nmrxiv.org/sample/$1
has URI prefix: https://nmrxiv.org/sample/
keyword: sample

BiGG Metabolite
is deprecated: false
keyword: small molecule
has provider formatter: http://bigg.ucsd.edu/models/universal/metabolites/$1
keyword: chemical
has download URL: bigg.metabolite.owl
is part of: Bioregistry
keyword: metabolite
0000005: 12dgr161
has prefix: bigg.metabolite
has responsible: https://orcid.org/0000-0003-1238-1499
has resource example: 12dgr161
type: Resource
keyword: compound
has URI prefix: http://bigg.ucsd.edu/models/universal/metabolites/
has local unique identifier pattern: ^[a-z_A-Z0-9]+(\[[c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y]\])?$
description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolites.
keyword: ontology

depends on
description: The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix
domain: Resource
range: Resource
type: Property

NLFFF Database
description: Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database
is part of: Bioregistry
has URI prefix: http://database.deepsolar.space:18080/dbs/nlfff/
has prefix: nlfff
type: Resource
has provider formatter: http://database.deepsolar.space:18080/dbs/nlfff/$1
0000005: 345201101230312003
has local unique identifier pattern: ^[0-9]+$
has resource example: http://database.deepsolar.space:18080/dbs/nlfff/345201101230312003
is deprecated: false

Leafsnap
has prefix: leafsnap
has URI prefix: https://bioregistry.io/leafsnap:
is deprecated: false
0000005: Amelanchier laevis
is part of: Bioregistry
description: identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide
type: Resource
has provider formatter: http://leafsnap.com/species/$1/

SWEET Ontology State Chemical
type: Resource
git repository: sweet
has alternative prefix: sostc
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Chemical
has resource example: BiochemicalState
has provider formatter: http://sweetontology.net/stateChemical/$1
has prefix: sweet.stc
has URI prefix: http://sweetontology.net/stateChemical/
is deprecated: false
0000005: BiochemicalState
is part of: Bioregistry
keyword: state chemical
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt

LifeWatch Metadata Catalogue
has provider formatter: https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/$1
is deprecated: false
has local unique identifier pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$
has URI prefix: https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/
description: The LifeWatch Metadata Catalogues plays a crucial role in managing metadata for digital objects, including Datasets, Services, Workflows and Virtual Research Environments. This catalogue serves as the central repository, ensuring that resources are accessible and reusable by stakeholders.
is part of: Bioregistry
type: Resource
has prefix: lw

Minimum Information about a Biosynthetic Gene Cluster data repository
has provider formatter: https://mibig.secondarymetabolites.org/go/$1
is part of: Bioregistry
git repository: mibig-json
type: Resource
has prefix: mibig
has reviewer: Charles Tapley Hoyt
0000005: BGC0000001
has responsible: Kai Blin
contributor: https://orcid.org/0000-0001-6534-6609
has resource example: BGC0000001
is deprecated: false
has URI prefix: https://mibig.secondarymetabolites.org/go/
has local unique identifier pattern: ^BGC\d{7}$
description: MIBiG (Minimum Information about a Biosynthetic Gene Cluster) is a data repository and associated data standard designed to describe biosynthetic gene clusters involved in the production of specialized metabolites. It also stores data on measured biological activities and links to other resources such as NCBI, NPAtlas, and ChEBI. MIBiG is used as a reference database, knowledgebase, and training dataset for machine learning.

Odor Molecules DataBase
has prefix: odor
description: OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors
is deprecated: false
0000005: 74
has provider formatter: https://ordb.biotech.ttu.edu/OdorDB/Data/$1
has resource example: https://ordb.biotech.ttu.edu/OdorDB/Data/74
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: https://ordb.biotech.ttu.edu/OdorDB/Data/
type: Resource

NERC Vocabulary Server
has resource example: P06
0000005: P06
description: SKOS concept collections held in the NERC Vocabulary Server. A concept collection is useful where a group of concepts shares something in common, and it is convenient to group them under a common label. In the NVS, concept collections are synonymous with controlled vocabularies or code lists. Each collection is associated with its governance body. An external website link is displayed when applicable.
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://vocab.nerc.ac.uk/collection/$1
has URI prefix: https://vocab.nerc.ac.uk/collection/
has prefix: nvs
type: Resource

UniProt Keywords
has provider formatter: https://www.uniprot.org/keywords/$1
has resource example: KW-1273
type: Resource
has prefix: uniprot.keyword
has alternative prefix: SP_KW
has responsible: Alex Bateman
has alternative prefix: UniProtKB-KW
has download URL: https://rest.uniprot.org/keywords/stream
has URI prefix: https://www.uniprot.org/keywords/
is deprecated: false
keyword: classification
has alternative prefix: uniprot.kw
description: UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries.
has alternative prefix: uniprot.keyword
keyword: ontology
0000005: KW-1273
has local unique identifier pattern: ^KW-\d{4}$
is part of: Bioregistry

Chemical Component Dictionary
has alternative prefix: pdbechem
has responsible: Helen Berman
has canonical: PDB ligand
type: Resource
has resource example: AB0
has provider formatter: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1
0000005: AB0
has prefix: pdb-ccd
has alternative prefix: PDBeChem
is deprecated: false
keyword: classification
has local unique identifier pattern: ^\w{1,3}$
has URI prefix: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/
description: The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.
is part of: Bioregistry
contributor: Birgit Meldal
keyword: chemical

MetaboLights Compound
has resource example: MTBLS1
is deprecated: false
is part of: Bioregistry
has prefix: metabolights
has provider formatter: https://www.ebi.ac.uk/metabolights/$1
type: Resource
has URI prefix: https://www.ebi.ac.uk/metabolights/
has local unique identifier pattern: ^MTBL[CS]\d+$
0000005: MTBLS1
description: MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.

Audubon Core Variant Controlled Vocabulary
has responsible: Steve Baskauf
is deprecated: false
has prefix: ac.variant
description: Audubon Core uses the terms ac:variant and ac:variantLiteral to provide information about the size, extent, and availability of the Service Access Point of a media item. This controlled vocabulary provides values for those terms.
keyword: life sciences, biology
is part of: Bioregistry
type: Resource
0000005: v001
keyword: fair data spaces

KIM Education Level
is deprecated: false
keyword: educational science
has resource example: level 6
is part of: Bioregistry
has prefix: kim.educationlevel
keyword: education level
contributor: Charles Tapley Hoyt
has provider formatter: https://w3id.org/kim/educationalLevel/level_$1
git repository: educationalLevel
keyword: educational resources
keyword: open educational resources
type: Resource
has URI prefix: https://w3id.org/kim/educationalLevel/level_
description: A controlled vocabulary for education levels, such as primary eduation, secondary education, and post-secondary education
0000005: 6

Alzheimer's Disease Ontology
keyword: ontology
has responsible: Alpha Tom Kodamullil
is part of: Bioregistry
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
has prefix: ado
type: Resource
depends on: Basic Formal Ontology
has URI prefix: http://purl.obolibrary.org/obo/ADO_
has provider formatter: http://purl.obolibrary.org/obo/ADO_$1
keyword: alzheimer's disease
git repository: ADO
has resource example: ADO_0000001
contributor: https://orcid.org/0000-0002-1216-4761
description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.
keyword: health science
has download URL: ado.owl
is deprecated: false
keyword: obo

GLIDA Ligand
type: Resource
is deprecated: true
has prefix: glida.ligand
0000005: L000001
has resource example: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php
has URI prefix: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php
description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands.
is part of: Bioregistry
has local unique identifier pattern: ^L\d+$
has provider formatter: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php

PolyMat Ontology
has URI prefix: https://w3id.org/polymat/
type: Resource
description: PolyMat is a domain ontology designed for polymer membrane research and tailored for immediate integration within Electronic Laboratory Notebooks (ELNs), facilitating efficient documentation of laboratory experiments and advancing the domain's FAIRification process.
has prefix: polymat
0000005: 4PointResistanceSetup
is deprecated: false
keyword: chemistry
has provider formatter: https://w3id.org/polymat/$1
is part of: Bioregistry
has resource example: 4PointResistanceSetup
keyword: material science
keyword: nfdi4ing

Liver Cancer Model Repository
type: Resource
has resource example: https://www.picb.ac.cn/limore/cellLines/single
has URI prefix: https://www.picb.ac.cn/limore/cellLines/single
is deprecated: false
description: Cell line databases/resources
0000005: Li7
is part of: Bioregistry
has provider formatter: https://www.picb.ac.cn/limore/cellLines/single
has prefix: limore

Core Ontology for Biology and Biomedicine
type: Resource
description: COB brings together key terms from a wide range of OBO projects to improve interoperability.
has local unique identifier pattern: ^\d{7}$
has responsible: Bjoern Peters
has provider formatter: http://purl.obolibrary.org/obo/COB_$1
git repository: COB
keyword: obo
has resource example: COB_0000080
keyword: ontology
has prefix: cob
has URI prefix: http://purl.obolibrary.org/obo/COB_
is deprecated: false
keyword: dataplant
0000005: 0000080
has download URL: cob.owl
keyword: life sciences, biology
is part of: Bioregistry

Gramene Gene
0000005: GR:0080039
has local unique identifier pattern: ^GR\:\d+$
is deprecated: false
has resource example: http://www.gramene.org/db/genes/search_gene
is part of: Bioregistry
has prefix: gramene.gene
has URI prefix: http://www.gramene.org/db/genes/search_gene
has provider formatter: http://www.gramene.org/db/genes/search_gene
description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.
type: Resource
has alternative prefix: GR_GENE

EchoBASE post-genomic database for Escherichia coli
has URI prefix: http://www.york.ac.uk/res/thomas/Gene.cfm
is deprecated: false
has provider formatter: http://www.york.ac.uk/res/thomas/Gene.cfm
keyword: gene expression
is part of: Bioregistry
type: Resource
has prefix: echobase
has local unique identifier pattern: ^EB\d+$
0000005: EB0170
keyword: gene
has responsible: Gavin H. Thomas
description: EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.
has resource example: http://www.york.ac.uk/res/thomas/Gene.cfm

IntAct Molecule
is part of: Bioregistry
has local unique identifier pattern: ^EBI\-[0-9]+$
has prefix: intact.molecule
type: Resource
has provider formatter: https://www.ebi.ac.uk/intact/search
has resource example: https://www.ebi.ac.uk/intact/search
0000005: EBI-366083
has URI prefix: https://www.ebi.ac.uk/intact/search
description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.
is deprecated: false

DALIA Resources
has part: Dublin Core Metadata Initiative Terms
has part: MoDALIA Ontology
has part: Software Package Data Exchange RDF Vocabulary
description: Prefixes relevant for the [Data Literacy Alliance (DALIA)](https://dalia.education/en) project
has part: International Standard Classification of Education, 1997 Edition
has part: International Standard Classification of Education, 2011 Edition
has part: Elementary Multiperspective Material Ontology
has part: Common Entity Data Standards - Domain Entity Schema
has part: U.S. Education Level Vocabulary
type: Collection
has part: DataCite Ontology
has part: CODATA Research Data Management Terminology
has part: Bibliographic Framework Initiative Vocabulary
has part: terms4FAIRskills
has part: DBPedia Resource
has part: Library of Congress Format Description Document
has part: The Bibliographic Ontology
has part: PROV Namespace
has part: Machine-readable Cataloging (MARC) List for Languages
has part: Metadata4Ing
creator: Charles Tapley Hoyt
has part: Schema.org
has part: Wikidata
has part: German Archaeological Institute Thesaurus
has part: German Federal Ministry of Education and Research Glossary
has part: Media Types
has part: NFDI4DS Ontology
has part: Software Package Data Exchange License
has part: FaBiO, the FRBR-aligned Bibliographic Ontology
has part: UNESCO Thesaurus
has part: DataCite to DCAT-AP Mapping
has part: SAGE Social Science Thesaurus
has part: Protocol for Web Description Resources (POWDER): POWDER-S Vocabulary
has part: Semanticscience Integrated Ontology
has part: Web Ontology Language

ProtoNet ProteinCard
description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has resource example: http://www.protonet.cs.huji.ac.il/requested/protein_card.php
has responsible: https://orcid.org/0000-0002-9357-4526
has prefix: protonet.proteincard
has provider formatter: http://www.protonet.cs.huji.ac.il/requested/protein_card.php
is deprecated: true
0000005: 16941567
has URI prefix: http://www.protonet.cs.huji.ac.il/requested/protein_card.php
keyword: protein

The COVID-19 Infectious Disease Ontology
keyword: ontology
has download URL: ido covid-19
has resource example: COVIDO_0001191
is deprecated: false
has responsible: John Beverly
git repository: ido-covid-19
description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.
is part of: Bioregistry
type: Resource
0000005: 0001191
has prefix: idocovid19
has local unique identifier pattern: ^\d{7}$
has provider formatter: http://purl.obolibrary.org/obo/COVIDO_$1
has URI prefix: http://purl.obolibrary.org/obo/COVIDO_

Language Proficiency
has provider formatter: https://vocabularies.cessda.eu/vocabulary/LanguageProficiency#code_$1
has prefix: ddi.languageproficiency
has identifier space owner: 015em2733
is deprecated: false
0000005: Native
has resource example: code Native
description: Describes the level of proficiency of an individual in a natural language.
has URI prefix: https://vocabularies.cessda.eu/vocabulary/LanguageProficiency#code_
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

GeneFarm
has provider formatter: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl
has URI prefix: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
keyword: nucleotide
has responsible: https://orcid.org/0000-0002-0695-4767
0000005: 4892
has resource example: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl
has prefix: genefarm
keyword: expression
keyword: life science
is deprecated: true
description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.
keyword: sequence
keyword: genome

Australian New Zealand Clinical Trials Registry
contributor: https://orcid.org/0000-0002-1216-4761
is deprecated: false
has URI prefix: https://anzctr.org.au/Trial/Registration/TrialReview.aspx
is part of: Bioregistry
has local unique identifier pattern: ^ACTRN\d+$
0000005: ACTRN12623000498695
type: Resource
contributor: Charles Tapley Hoyt
has prefix: anzctr
has resource example: https://anzctr.org.au/Trial/Registration/TrialReview.aspx
has alternative prefix: ACTRN
has provider formatter: https://anzctr.org.au/Trial/Registration/TrialReview.aspx
description: The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. In 2007 the ANZCTR was one of the first three trial registries to be recognised by the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries if they fulfil certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch. (from website)

Benchmark Energy & Geometry Database
has resource example: http://www.begdb.com/index.php
type: Resource
has local unique identifier pattern: ^[0-9]+$
has responsible: https://orcid.org/0000-0001-5292-6719
0000005: 4214
has prefix: begdb
keyword: life science
is deprecated: false
has provider formatter: http://www.begdb.com/index.php
description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.
has URI prefix: http://www.begdb.com/index.php
is part of: Bioregistry

Prefix.cc
type: Registry
has responsible: Richard Cyganiak
0000005: foaf
description: A web-developer centric archive of prefixes and URI prefixes
has provider formatter: https://prefix.cc/$1

TTD Drug
type: Resource
description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.
has local unique identifier pattern: ^\w+$
has URI prefix: https://db.idrblab.net/ttd/data/drug/details/
is deprecated: false
is part of: Bioregistry
has resource example: D0N5OV
has prefix: ttd.drug
has provider formatter: https://db.idrblab.net/ttd/data/drug/details/$1
0000005: D0N5OV

EPA Hazardous Wastes
is deprecated: false
has local unique identifier pattern: ^[FKPU]\d{3}$
has prefix: epawaste
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
0000005: F001
type: Resource
description: This resource provides identifiers for listed hazardous wastes which are substances explicitly identified due to their potential harm to human health and the environment. These are categorized into four groups (F, K, P, and U) based on specific criteria, such as their source or inherent properties.
contributor: Mufaddal Naguthanawala

OncoTree
keyword: oncology
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: oncotree
type: Resource
keyword: cancer
has URI prefix: http://oncotree.mskcc.org/api/tumorTypes/search/code/
0000005: BLL
has provider formatter: http://oncotree.mskcc.org/api/tumorTypes/search/code/$1
description: OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.
has responsible: https://orcid.org/0000-0002-0131-4904
is deprecated: false
has resource example: BLL
appears in: Experimental Factor Ontology
keyword: clinical decision support systems

Digical Object Container Identifier
has provider formatter: https://docid.africapidalliance.org/docid/$1
has resource example: https://docid.africapidalliance.org/docid/20.500.14351/5a7cdd09d9b65bc39697
is deprecated: false
has alternative prefix: DOCiD
keyword: cultural heritage
has identifier space owner: 02y9nww90
has responsible: Joy Owango
description: Assigns persistent identifiers to multidisciplinary research outputs with focus on research originating in Africa, such as in cultural heritage and indigenous knowledge.
is part of: Bioregistry
keyword: publishing
0000005: 20.500.14351/5a7cdd09d9b65bc39697
contributor: Charles Tapley Hoyt
keyword: bibliometrics
has prefix: docid
has URI prefix: https://docid.africapidalliance.org/docid/
keyword: digital humanities
type: Resource

SWEET Ontology Realm Land Coastal
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Coastal
has URI prefix: http://sweetontology.net/realmLandCoastal/
has alternative prefix: sorealc
has provider formatter: http://sweetontology.net/realmLandCoastal/$1
has resource example: Atoll
is deprecated: false
keyword: coastalland
has prefix: sweet.realc
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
0000005: Atoll

Schema.org
0000005: Person
has alternative prefix: sdo
has provider formatter: https://schema.org/$1
is part of: Bioregistry
has resource example: Person
contributor: Charles Tapley Hoyt
keyword: catalogs
type: Resource
description: Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond.
has URI prefix: https://schema.org/
keyword: ess
keyword: fair data spaces
has alternative prefix: schemaorg
has download URL: schemaorg.owl
has prefix: schema
keyword: ontology
is deprecated: false

BlastRule
has URI prefix: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/
has prefix: blastrule
is deprecated: false
description: BlastRules (identifiers starting with the “NBR” prefix) are a type of evidence for functional classification of proteins based on BLAST (Basic Local Alignment Search Tool). A BlastRule consists of one or more 'model' proteins with known biological function, and BLAST identity and coverage cutoffs. Any protein aligning to a model protein above the cutoffs is considered a BlastRule hit. [from homepage]
has local unique identifier pattern: ^NBR\d+$
is part of: Bioregistry
has provider formatter: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/$1
has resource example: NBR016799
contributor: Charles Tapley Hoyt
type: Resource
0000005: NBR016799

GlycoEpitope
description: GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.
has prefix: glycoepitope
is part of: Bioregistry
has URI prefix: https://www.glycoepitope.jp/epitopes/
type: Resource
has local unique identifier pattern: ^EP\d{4}$
0000005: EP0311
has provider formatter: https://www.glycoepitope.jp/epitopes/$1
has resource example: EP0311
is deprecated: false

SAREF extension for environment
has provider formatter: https://saref.etsi.org/saref4envi/$1
0000005: AirEmissionKind
has resource example: AirEmissionKind
keyword: iot
type: Resource
keyword: nfdi4ing
has prefix: saref.environment
description: This ontology extends the SAREF ontology for the environment domain, specifically for the light pollution domain, including concepts like photometers, light, etc.
is deprecated: false
is part of: Bioregistry
has URI prefix: https://saref.etsi.org/saref4envi/
keyword: engineering
has alternative prefix: s4envi
keyword: environment

Integrated Microbial Genomes Taxon
keyword: genome
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has responsible: Nikos C. Kyrpides
has prefix: img.taxon
type: Resource
has resource example: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
has provider formatter: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
keyword: taxonomy
description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.
0000005: 648028003
has URI prefix: http://img.jgi.doe.gov/cgi-bin/w/main.cgi

SWEET Ontology Phenomena System
has provider formatter: http://sweetontology.net/phenSystem/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena System
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
0000005: Accumulation
type: Resource
has URI prefix: http://sweetontology.net/phenSystem/
keyword: system
keyword: phenomena
has prefix: sweet.phsy
has alternative prefix: sophsy
is deprecated: false
has resource example: Accumulation

CLAVAS: ISO 639-3 Language Codes
type: Resource
has prefix: clarin.clavas
keyword: language
has provider formatter: http://cdb.iso.org/lg/$1
has resource example: http://cdb.iso.org/lg/CDB-00133756-001
0000005: CDB-00133756-001
is deprecated: false
is part of: Bioregistry
description: Representation of languages
has URI prefix: http://cdb.iso.org/lg/
contributor: Charles Tapley Hoyt

International Nucleotide Sequence Database Collaboration (INSDC) Run
description: An experimental run, served thrugh the ENA
type: Resource
has provider formatter: https://www.ebi.ac.uk/ena/browser/view/$1
contributor: https://orcid.org/0000-0002-6601-2165
has reviewer: Charles Tapley Hoyt
has resource example: ERR436051
0000005: ERR436051
has URI prefix: https://www.ebi.ac.uk/ena/browser/view/
is deprecated: false
has prefix: insdc.run
is part of: Bioregistry
has local unique identifier pattern: ^(E|D|S)RR[0-9]{6,}$

The localization and quantitation atlas of the yeast proteome
type: Resource
has URI prefix: http://www.weizmann.ac.il/molgen/loqate/gene/view/
has reviewer: Charles Tapley Hoyt
has provider formatter: http://www.weizmann.ac.il/molgen/loqate/gene/view/$1
has resource example: http://www.weizmann.ac.il/molgen/loqate/gene/view/1001
has prefix: loqate
is deprecated: false
is part of: Bioregistry
0000005: 1001
has responsible: Maya Schuldiner
description: The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library

NeuroNames
description: BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it.
has prefix: neuronames
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has resource example: http://braininfo.rprc.washington.edu/centraldirectory.aspx
contributor: Charles Tapley Hoyt
type: Resource
has alternative prefix: neuroname
0000005: 268
has provider formatter: http://braininfo.rprc.washington.edu/centraldirectory.aspx
has URI prefix: http://braininfo.rprc.washington.edu/centraldirectory.aspx
is deprecated: false

Sample processing and separation techniques
is part of: Bioregistry
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/SEP_
has responsible: SEP developers via the PSI and MSI mailing lists
0000005: 00073
is deprecated: true
has download URL: sep.owl
keyword: obo
has provider formatter: http://purl.obolibrary.org/obo/SEP_$1
keyword: ontology
has prefix: sep
has resource example: SEP_00073
keyword: protein
description: A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.
has local unique identifier pattern: ^\d{5,6}$

Kyoto Stock Center
has prefix: dggr
keyword: genetic resource
is deprecated: false
keyword: genomics
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
has provider formatter: https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi
has resource example: https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi
keyword: drosophila
keyword: organism supplier
0000005: 918902
has URI prefix: https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi
description: Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. [from RRID]

snoRNABase
keyword: rna
has resource example: http://www-snorna.biotoul.fr/plus.php
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: SR0000178
description: A comprehensive database of human H/ACA and C/D box snoRNAs.
type: Resource
has prefix: snornabase
has URI prefix: http://www-snorna.biotoul.fr/plus.php
is deprecated: false
has provider formatter: http://www-snorna.biotoul.fr/plus.php

ChemBioSys Organism
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://data.chembiosys.de/organisms/$1
has prefix: chembiosys.organism
description: An organism in the ChemBioSys data platform
type: Resource
0000005: 604090889
is deprecated: false
has URI prefix: https://data.chembiosys.de/organisms/
has resource example: https://data.chembiosys.de/organisms/604090889

AntiBody Sequence Database
has provider formatter: https://absd.pasteur.cloud/antibody/$1
has URI prefix: https://absd.pasteur.cloud/antibody/
contributor: 0009-0008-8406-631X
is part of: Bioregistry
description: The AntiBody Sequence Database is a public dataset for antibody sequence data. It provides unique identifiers for antibody sequences, including both immunoglobulin and single-chain variable fragment sequences. These are are critical for immunological studies, and allows users to search and retrieve antibody sequences based on sequence similarity and specificity, and other biological properties.
has reviewer: https://orcid.org/0000-0001-9439-5346
has responsible: https://orcid.org/0000-0003-1611-5243
type: Resource
has prefix: absd
has local unique identifier pattern: ^[a-f0-9]{64}$
is deprecated: false

has alternative prefix
sub property of: hasExactSynonym
type: Property
range: string
description: An alternative or synonymous prefix
domain: Resource
equivalent property: alternatePrefix

Mobility Theme
has URI prefix: https://w3id.org/mobilitydcat-ap/mobility-theme/
keyword: traffic engineering
is deprecated: false
has prefix: tib.mt
has resource example: accesibility-information-for-vehicles
0000005: accesibility-information-for-vehicles
keyword: fid move
is part of: Bioregistry
description: Controlled vocabulary for the classification of the theme for a mobility dataset.
type: Resource
keyword: nfdi4ing
has provider formatter: https://w3id.org/mobilitydcat-ap/mobility-theme/$1

Human Genome Variation Society Nomenclature
type: Resource
has reviewer: Charles Tapley Hoyt
description: The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the [Human Genome Organization (HUGO)](https://hugo-int.org/).
contributor: 0000-0002-0548-891X
has resource example: http://reg.clinicalgenome.org/allele
has URI prefix: http://reg.clinicalgenome.org/allele
has responsible: Reece Hart
is deprecated: false
has provider formatter: http://reg.clinicalgenome.org/allele
git repository: hgvs-nomenclature
has prefix: hgvs
0000005: NP_003997.1:p.Trp24Cys
is part of: Bioregistry

Guide to Pharmacology Target
has alternative prefix: IUPHAR_GPCR
0000005: 101
description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits.
has resource example: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward
is deprecated: false
has prefix: iuphar.receptor
has provider formatter: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
has responsible: Simon Douglas Harding
has URI prefix: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward
has alternative prefix: IUPHARobj

SEED Compound
description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.
has prefix: seed.compound
has resource example: cpd15380
is deprecated: false
has local unique identifier pattern: ^cpd\d+$
0000005: cpd15380
is part of: Bioregistry
has URI prefix: http://modelseed.org/biochem/compounds/
git repository: TheSEED
type: Resource
has provider formatter: http://modelseed.org/biochem/compounds/$1

Bibliographic Reference Ontology
keyword: subject agnostic
has URI prefix: http://purl.org/spar/biro/
has resource example: BibliographicRecord
git repository: biro
is deprecated: false
0000005: BibliographicRecord
description: An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.
is part of: Bioregistry
has provider formatter: http://purl.org/spar/biro/$1
has prefix: biro
contributor: Charles Tapley Hoyt
keyword: spar
type: Resource
has responsible: Silvio Peroni

Structural Classification of Proteins - Unique Identifier
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
keyword: structure
has resource example: http://scop.berkeley.edu/sunid=47419
0000005: 47419
has alternative prefix: scop.sunid
has prefix: scop
has URI prefix: http://scop.berkeley.edu/sunid=
has alternative prefix: scop.sun
has provider formatter: http://scop.berkeley.edu/sunid=$1
is deprecated: false
has local unique identifier pattern: ^\d+$
keyword: protein
has responsible: https://orcid.org/0000-0002-5153-9079
description: SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.).

Saccharomyces Genome Database
has download URL: sgd.owl
keyword: proteomics
has responsible: J. Michael Cherry
keyword: nucleotide
keyword: transcriptomics
has provider formatter: https://www.yeastgenome.org/locus/$1
type: Resource
has URI prefix: https://www.yeastgenome.org/locus/
description: The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.
keyword: epigenetics
has prefix: sgd
0000005: S000002493
keyword: life science
is deprecated: false
keyword: eukaryotic
has local unique identifier pattern: ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$
keyword: ontology
is part of: Bioregistry
has resource example: S000002493
keyword: genome

KEGG Module
has local unique identifier pattern: ^([a-z]{3,5}_)?M\d{5}$
is part of: Bioregistry
type: Resource
0000005: M00002
is part of: Kyoto Encyclopedia of Genes and Genomes
has provider formatter: http://www.kegg.jp/entry/$1
has resource example: M00002
has prefix: kegg.module
has URI prefix: http://www.kegg.jp/entry/
is deprecated: false
description: KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.

PubChem Element
type: Resource
is deprecated: false
has resource example: https://pubchem.ncbi.nlm.nih.gov/element/1
description: PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number.
0000005: 1
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/element/$1
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has prefix: pubchem.element
keyword: chemistry
contributor: Charles Tapley Hoyt
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/element/

microRNA Ontology
has prefix: mirnao
has URI prefix: http://purl.obolibrary.org/obo/MIRNAO_
is part of: Bioregistry
type: Resource
has download URL: mirnao.owl
description: An application ontology for use with miRNA databases.
has responsible: Pantelis Topalis
has provider formatter: http://purl.obolibrary.org/obo/MIRNAO_$1
keyword: obo
is deprecated: true
keyword: ontology

COEXISTENCE
has URI prefix: https://mamoura.eci.ufmg.br/tematres/vocab/index.php
type: Resource
has resource example: https://mamoura.eci.ufmg.br/tematres/vocab/index.php
has prefix: coexistence
has provider formatter: https://mamoura.eci.ufmg.br/tematres/vocab/index.php
0000005: 163
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
description: COEXISTENCE - Thesaurus of intersectionality and decolonial issues: black studies, gender, sexuality and feminist studies

Big Open Network of Sustainability Assessment Information Ontology
has URI prefix: http://ontology.bonsai.uno/core#
has prefix: bonsai
has provider formatter: http://ontology.bonsai.uno/core#$1
is deprecated: false
0000005: Activity
is part of: Bioregistry
description: The BONSAI ontologies provides elements of description for product footprint concepts defined in the bonsai.uno data base
keyword: engineering
has resource example: Activity
git repository: ontology
keyword: nfdi4energy
type: Resource
keyword: nfdi4ing

Molecular Interaction Database
keyword: proteomics
has provider formatter: https://mint.bio.uniroma2.it/index.php/detailed-curation/
0000005: 6978836
type: Resource
keyword: interaction
has responsible: https://orcid.org/0000-0001-5084-9000
has URI prefix: https://mint.bio.uniroma2.it/index.php/detailed-curation/
keyword: life science
is deprecated: false
has resource example: https://mint.bio.uniroma2.it/index.php/detailed-curation/
has prefix: mint
is part of: Bioregistry
keyword: protein
has local unique identifier pattern: ^\d{1,7}$
description: The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.

Drosophila Genomics Resource Center
has prefix: dgrc
type: Resource
0000005: 215
has resource example: https://dgrc.bio.indiana.edu/product/View
is deprecated: false
has provider formatter: https://dgrc.bio.indiana.edu/product/View
description: Cell line collections (Providers)
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: https://dgrc.bio.indiana.edu/product/View

OpenCitations Meta Identifier
has local unique identifier pattern: ^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$
has provider formatter: https://w3id.org/oc/meta/$1
has prefix: omid
description: Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure entity_type_abbreviation/supplier_prefixsequential_number. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted.
has URI prefix: https://w3id.org/oc/meta/
0000005: br/0601
is deprecated: false
is part of: Bioregistry
has resource example: https://w3id.org/oc/meta/br/0601
type: Resource

Feature Type Thesaurus
0000005: 273
has URI prefix: https://apps.usgs.gov/thesaurus/term-simple.php
is deprecated: false
has prefix: ftt
has provider formatter: https://apps.usgs.gov/thesaurus/term-simple.php
has resource example: https://apps.usgs.gov/thesaurus/term-simple.php
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific.

Dutch Research Council File Number
has provider formatter: https://www.nwo.nl/en/projects/$1
type: Resource
has resource example: osf232097
has reviewer: Charles Tapley Hoyt
has prefix: drc.filenumber
contributor: Tim Vandermeersch
0000005: osf232097
is deprecated: false
is part of: Bioregistry
description: Dutch Research Council file numbers are used for approved grants.
has URI prefix: https://www.nwo.nl/en/projects/

NFDI4Immuno Collection
has part: Bioregistry
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Immuno
type: Collection
creator: Charles Tapley Hoyt

Biomarker Ontology
type: Resource
description: An application ontology that represents comprehensive knowledge involving a variety of fields of medical and biological aspects.
has URI prefix: http://purl.obolibrary.org/obo/BMONT_
has download URL: bmont.owl
has prefix: bmont
is deprecated: false
0000005: 0000006
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/BMONT_$1
has responsible: Alpha Tom Kodamullil
is part of: Bioregistry
git repository: BiomarkerOntology

NASA Open Science Data Repository Payload
0000005: VEG-03D
contributor: Mufaddal Naguthanawala
has prefix: nasaosdr.payload
has URI prefix: https://osdr.nasa.gov/bio/repo/data/payloads/
is deprecated: false
has provider formatter: https://osdr.nasa.gov/bio/repo/data/payloads/$1
has resource example: VEG-03D
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-8542-2389
description: Identifiers for payloads associated with experiments that investigate biological and health responses of terrestrial life to spaceflight
type: Resource
has local unique identifier pattern: ^.+$

Chicken Gene Nomenclature Consortium
is deprecated: false
has download URL: cgnc.owl
has alternative prefix: BirdBase
0000005: 10087
has URI prefix: http://birdgenenames.org/cgnc/GeneReport
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has responsible: https://orcid.org/0000-0003-2175-5464
has resource example: http://birdgenenames.org/cgnc/GeneReport
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: http://birdgenenames.org/cgnc/GeneReport
keyword: gene
description: Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)
has prefix: cgnc
has alternative prefix: CGNC
keyword: ontology

Time Method
has resource example: code Longitudinal
0000005: Longitudinal
description: Describes the time dimension of the data collection.
has URI prefix: https://vocabularies.cessda.eu/vocabulary/TimeMethod#code_
has prefix: ddi.timemethod
is deprecated: false
is part of: Bioregistry
has provider formatter: https://vocabularies.cessda.eu/vocabulary/TimeMethod#code_$1
type: Resource
contributor: Charles Tapley Hoyt
has identifier space owner: 015em2733

ConoServer
has prefix: conoserver
keyword: neurophysiology
has URI prefix: http://www.conoserver.org/
has resource example: http://www.conoserver.org/
description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.
type: Resource
0000005: 2639
keyword: life science
has responsible: David Craik
has provider formatter: http://www.conoserver.org/
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
keyword: statistics
keyword: synthetic biology

General Multilingual Environmental Thesaurus Group
contributor: Charles Tapley Hoyt
is part of: Bioregistry
has prefix: gemet.group
type: Resource
has provider formatter: https://www.eionet.europa.eu/gemet/en/group/$1
description: Groups listed in GEMET
0000005: 893
has URI prefix: https://www.eionet.europa.eu/gemet/en/group/
has resource example: https://www.eionet.europa.eu/gemet/en/group/893
is deprecated: false
has local unique identifier pattern: ^\d+$

Database of RNA Junctions and Kissing loop Structures
description: RNAJunction is a database of RNA junctions and kissing loop structures. It contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. It allows searching by PDB code, structural classification, sequence, keyword or inter-helix angles. RNAJunction is designed to aid analysis of RNA structures as well as design of novel RNA structures on a nanoscale.
type: Resource
has prefix: rnajunction
keyword: structure
has resource example: https://rnajunction.ncifcrf.gov/JunctionPage.php
keyword: structural biology
has reviewer: Charles Tapley Hoyt
has URI prefix: https://rnajunction.ncifcrf.gov/JunctionPage.php
has responsible: https://orcid.org/0000-0002-8557-9992
0000005: 8668
has provider formatter: https://rnajunction.ncifcrf.gov/JunctionPage.php
keyword: rna
is deprecated: false
is part of: Bioregistry

Tick Cell Biobank
is deprecated: false
has prefix: tcb
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: A cell line collection
has resource example: https://www.pirbright.ac.uk/node/2966
has URI prefix: https://www.pirbright.ac.uk/node/
has provider formatter: https://www.pirbright.ac.uk/node/$1
0000005: 2966

BOLD Systems taxon
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has provider formatter: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage
has URI prefix: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage
has prefix: bold.taxonomy
description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.
has responsible: https://orcid.org/0000-0002-3081-6700
0000005: 27267
is deprecated: false
keyword: dna
has resource example: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage

KEGG pathway
is part of: Bioregistry
has provider formatter: https://www.kegg.jp/pathway/$1
type: Resource
0000005: rsk00410
has alternative prefix: KEGG-path
has responsible: Minoru Kanehisa
has alternative prefix: KEGG_PATHWAY
has URI prefix: https://www.kegg.jp/pathway/
description: KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
has local unique identifier pattern: ^\w{2,4}\d{5}$
keyword: pathway
has prefix: kegg.pathway
is deprecated: false
has resource example: rsk00410

SWEET Ontology Realm Hydrosphere
keyword: hydrosphere
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Hydrosphere
has alternative prefix: soreah
type: Resource
has URI prefix: http://sweetontology.net/realmHydro/
0000005: Aquiclude
keyword: realm
has resource example: Aquiclude
is deprecated: false
has prefix: sweet.reah
has provider formatter: http://sweetontology.net/realmHydro/$1

NASA Open Science Data Repository Biospecimen
0000005: 7943
has reviewer: https://orcid.org/0000-0001-9439-5346
has provider formatter: https://osdr.nasa.gov/bio/repo/data/biospecimens/$1
has responsible: https://orcid.org/0000-0002-8542-2389
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has prefix: nasaosdr.biospecimen
has URI prefix: https://osdr.nasa.gov/bio/repo/data/biospecimens/
type: Resource
description: Identifiers for biospecimens used in experiments that investigate biological and health responses of terrestrial life to spaceflight
has resource example: https://osdr.nasa.gov/bio/repo/data/biospecimens/7943
contributor: Mufaddal Naguthanawala
is deprecated: false

SWEET Ontology Relationships Provenance
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: fillValue
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Provenance
type: Resource
has provider formatter: http://sweetontology.net/relaProvenance/$1
keyword: provenance
has prefix: sweet.relpr
has alternative prefix: sorelpr
has URI prefix: http://sweetontology.net/relaProvenance/
0000005: fillValue

SILVA Taxon
has reviewer: Charles Tapley Hoyt
type: Resource
contributor: Jose P. Faria
has responsible: Lorenz Reimer
has prefix: silva.taxon
0000005: 11084
is deprecated: false
description: SILVA is a resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes. It assigns internal, auto-incremented integer identifiers to taxa. However, these identifiers are not persistent nor unique - if the label for a taxon is changed, it assigned a new identifier and the old identifier is removed.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry

WGS84 Geo Positioning
has provider formatter: http://www.w3.org/2003/01/geo/wgs84_pos#$1
keyword: geography
is part of: Bioregistry
has prefix: wgs84
contributor: Charles Tapley Hoyt
has URI prefix: http://www.w3.org/2003/01/geo/wgs84_pos#
type: Resource
0000005: latitude
description: A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum
has resource example: latitude
is deprecated: false

Ontologized MIABIS
0000005: 0001079
has local unique identifier pattern: ^\d{7}$
has provider formatter: http://purl.obolibrary.org/obo/OMIABIS_$1
type: Resource
has prefix: omiabis
is deprecated: true
description: An ontological version of MIABIS (Minimum Information About BIobank data Sharing)
appears in: clinical LABoratory Ontology
has resource example: OMIABIS_0001079
git repository: omiabis-dev
has download URL: omiabis.owl
has URI prefix: http://purl.obolibrary.org/obo/OMIABIS_
keyword: obo
keyword: ontology
has responsible: https://orcid.org/0000-0003-1834-3856
is part of: Bioregistry

ICEberg cis-integrative and mobilizable element
is deprecated: false
keyword: genomics
has provider formatter: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php
has URI prefix: https://bioregistry.io/iceberg.cime:
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has responsible: Hong-Yu Ou
has prefix: iceberg.cime
keyword: biology
description: ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.
has resource example: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php
0000005: 6

Base Ontology
is deprecated: false
has provider formatter: https://git.onem2m.org/MAS/BaseOntology/raw/master/base_ontology.owl#$1
is part of: Bioregistry
keyword: engineering
has URI prefix: https://git.onem2m.org/MAS/BaseOntology/raw/master/base_ontology.owl#
has prefix: tib.bo
0000005: AreaNetwork
type: Resource
keyword: nfdi4ing
has resource example: AreaNetwork
description: This file contains the Base Ontology of oneM2M as specified in TS-0012

BioCarta Pathway
is deprecated: false
has local unique identifier pattern: ^([hm]\_)?\w+Pathway$
description: BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps.
has URI prefix: https://cgap.nci.nih.gov/Pathways/BioCarta/
has resource example: h aktPathway
is part of: Bioregistry
0000005: h_aktPathway
type: Resource
has provider formatter: https://cgap.nci.nih.gov/Pathways/BioCarta/$1
has prefix: biocarta.pathway

ChemSpider
keyword: life science
has responsible: Harry E. Pence
has alternative prefix: ChemSpiderID
has prefix: chemspider
keyword: molecules
is deprecated: false
0000005: 56586
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: chemistry
has alternative prefix: Chemspider
has resource example: Chemical-Structure.56586.html
has provider formatter: http://www.chemspider.com/Chemical-Structure.$1.html
description: ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.
type: Resource
has URI prefix: https://bioregistry.io/chemspider:
keyword: structure

EcoLexicon
keyword: environmental science
is deprecated: false
description: EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology.
is part of: Bioregistry
keyword: ecology
contributor: Charles Tapley Hoyt
type: Resource
0000005: canal
has prefix: ecolexicon

General Standard for Food Additives Online Database
has provider formatter: http://www.fao.org/gsfaonline/additives/details.html
has prefix: gsfa
has alternative prefix: FAO/WHO_standards
has URI prefix: http://www.fao.org/gsfaonline/additives/details.html
is deprecated: false
0000005: 174
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: The "Codex General Standard for Food Additives" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database.
contributor: Charles Tapley Hoyt
type: Resource
has resource example: http://www.fao.org/gsfaonline/additives/details.html

Yeast Phenotype Ontology
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/YPO_$1
is deprecated: true
keyword: obo
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/YPO_
has prefix: ypo
is part of: Bioregistry
has responsible: J. Michael Cherry

Mammalia Polymorphism Database
description: The Mammalia Polymorphism Database is a secondary database designed to provide a collection of all the existing polymorphic sequences in the MammaliaOnline query interfaces facilitate data interrogation by different polymorphism parameter values and keyword queries (based on SQL searches).
keyword: dna
is part of: Bioregistry
has URI prefix: http://mampol.uab.es/cgi-bin/MamPol_s2.pl
has resource example: http://mampol.uab.es/cgi-bin/MamPol_s2.pl
type: Resource
has reviewer: Charles Tapley Hoyt
has provider formatter: http://mampol.uab.es/cgi-bin/MamPol_s2.pl
0000005: MAMpol005339
is deprecated: false
has prefix: mampol

Pearl Millet Ontology
has provider formatter: https://cropontology.org/rdf/CO_327:$1
is deprecated: false
has download URL: CO 327.owl
has prefix: co_327
keyword: ontology
has responsible: Elizabeth Arnaud
keyword: plant phenotypes and traits
is part of: Bioregistry
keyword: phenotype
git repository: Crop-Ontology
keyword: botany
0000005: 0000095
keyword: agriculture
has local unique identifier pattern: ^\d{7}$
type: Resource
has resource example: CO 327:0000095
description: The goal of the CGIAR Pearl Millet Ontology is to help improve food security for subsistence smallholder farmers in East and West Africa with productive and nutritious pearl millet food and fodder production technologies.
has URI prefix: https://cropontology.org/rdf/CO_327:

Dendritic cell
has resource example: DC CL 0000003
has local unique identifier pattern: ^\d{7}$
has provider formatter: http://purl.obolibrary.org/obo/DC_CL_$1
has prefix: dc_cl
is deprecated: true
keyword: obo
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/DC_CL_
is part of: Bioregistry
has responsible: Lindsay Cowell
type: Resource
0000005: 0000003

Software Package Data Exchange RDF Vocabulary
has provider formatter: http://spdx.org/rdf/terms#$1
has prefix: spdx.term
has URI prefix: http://spdx.org/rdf/terms#
is part of: Bioregistry
description: A dictionary of named properties and classes for Software Package Data Exchange (SPDX) - an open standard for communicating software bill of material information, including components, licenses, copyrights, and security references. SPDX reduces redundant work by providing a common format for companies and communities to share important data, thereby streamlining and improving compliance. [from homepage]
contributor: Charles Tapley Hoyt
has resource example: annotation
type: Resource
has alternative prefix: spdx.terms
0000005: annotation
is deprecated: false

Publons publication
description: identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID)
has URI prefix: https://publons.com/publon/
is deprecated: false
has resource example: https://publons.com/publon/18466622
has prefix: publons.publication
is part of: Bioregistry
type: Resource
0000005: 18466622
has provider formatter: https://publons.com/publon/$1

MultiCellDS collection
has prefix: multicellds.collection
has URI prefix: http://multicellds.org/MultiCellDB/
has resource example: MCDS C 0000000001
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$
type: Resource
description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).
is part of: MultiCellDS
0000005: MCDS_C_0000000001
has provider formatter: http://multicellds.org/MultiCellDB/$1

EAWAG Biocatalysis/Biodegradation Database reaction
is part of: Bioregistry
has resource example: http://eawag-bbd.ethz.ch/servlets/pageservlet
has prefix: umbbd.reaction
type: Resource
has local unique identifier pattern: ^r\d+$
description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information.
has alternative prefix: UM-BBD_reactionID
has URI prefix: http://eawag-bbd.ethz.ch/servlets/pageservlet
is deprecated: false
0000005: r0001
has provider formatter: http://eawag-bbd.ethz.ch/servlets/pageservlet

LRMI Interact Type Vocabulary
description: A concept scheme that defines the predominate interact mode of the learning resource being described.
has URI prefix: http://purl.org/dcx/lrmi-vocabs/interactivityType/
type: Resource
is deprecated: false
has resource example: active
keyword: learning resource
0000005: active
has provider formatter: http://purl.org/dcx/lrmi-vocabs/interactivityType/$1
is part of: Bioregistry
has prefix: lrmi.interact
keyword: open educational resource
contributor: Charles Tapley Hoyt
git repository: lrmi

Bio-MINDER Tissue Database
description: Database of the dielectric properties of biological tissues.
is part of: Bioregistry
type: Resource
has prefix: biominder
has URI prefix: https://datalab.rwth-aachen.de/MINDER/resource/
has local unique identifier pattern: ^[a-z0-9\-]+$
has provider formatter: https://datalab.rwth-aachen.de/MINDER/resource/$1
is deprecated: false

GitLab
is part of: Bioregistry
keyword: knowledge and information systems
has provider formatter: https://gitlab.com/$1
has prefix: gitlab
type: Resource
keyword: subject agnostic
has resource example: morpheus
0000005: morpheus.lab/morpheus
description: GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability.
is deprecated: false
has local unique identifier pattern: ^.*/.*$
keyword: software engineering
has URI prefix: https://gitlab.com/

Microarray experimental conditions
has prefix: mo
has URI prefix: https://mged.sourceforge.net/ontologies/MGEDontology.php#
0000005: ArrayGroup
is deprecated: true
keyword: obo
has local unique identifier pattern: ^\w+$
keyword: ontology
has download URL: mo.owl
has provider formatter: https://mged.sourceforge.net/ontologies/MGEDontology.php#$1
is part of: Bioregistry
has resource example: ArrayGroup
description: The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data.
type: Resource
has responsible: 0000-0002-5714-991X

Emotion Ontology
keyword: ontology
has download URL: mfoem.owl
is part of: Bioregistry
has prefix: mfoem
has resource example: MFOEM_000204
has local unique identifier pattern: ^\d{6}$
type: Resource
git repository: emotion-ontology
description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.
keyword: biomedical science
0000005: 000204
has provider formatter: http://purl.obolibrary.org/obo/MFOEM_$1
keyword: mental health
keyword: emotion process
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/MFOEM_
keyword: obo
has responsible: https://orcid.org/0000-0002-3469-4923

Antibiotic Resistance Ontology
has local unique identifier pattern: ^\d{7}$
keyword: mutation
keyword: antibiotic resistance
keyword: obo
git repository: aro
has provider formatter: http://purl.obolibrary.org/obo/ARO_$1
appears in: Sickle Cell Disease Ontology
0000005: 1000001
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/ARO_
has prefix: aro
contributor: https://orcid.org/0000-0002-1216-4761
has responsible: https://orcid.org/0000-0002-1142-3063
keyword: genetics
is deprecated: false
has download URL: aro.owl
has resource example: ARO_1000001
description: Antibiotic resistance genes and mutations
is part of: Bioregistry
type: Resource
keyword: gene
keyword: antimicrobial agent

IEEE Xplore document ID
has resource example: https://ieeexplore.ieee.org/document/1580791
has provider formatter: https://ieeexplore.ieee.org/document/$1
type: Resource
has URI prefix: https://ieeexplore.ieee.org/document/
description: identifier for a document in IEEE Xplore
is deprecated: false
has prefix: ieee.document
has local unique identifier pattern: ^[1-9]\d*$
is part of: Bioregistry
0000005: 1580791
contributor: Charles Tapley Hoyt

PerkinElmer
is deprecated: false
0000005: SCC111
has resource example: https://www.perkinelmer.com/searchresult
is part of: Bioregistry
description: A product catalog for PerkinElmer, a laboratory supplies vendor
type: Resource
contributor: Charles Tapley Hoyt
has URI prefix: https://www.perkinelmer.com/searchresult
has provider formatter: https://www.perkinelmer.com/searchresult
has prefix: perkinelmer

Plasmodium Life Cycle
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/PLO_$1
has URI prefix: http://purl.obolibrary.org/obo/PLO_
type: Resource
is deprecated: true
has prefix: plo
keyword: obo
keyword: ontology

FINDEX Bau as a SKOS Thesaurus - Facetted Indexing System for Civil Engineering
has prefix: findex.bau
git repository: terminologie
has provider formatter: https://terminology.fraunhofer.de/voc/bau#$1
has resource example: B10000000000 3
keyword: civil engineering
description: SKOS Model of FINDEX Bau by Fraunhofer-Informationszentrum Raum und Bau IRB
is deprecated: false
keyword: digital planning and construction
keyword: fid baudigital
0000005: B10000000000_3
has URI prefix: https://terminology.fraunhofer.de/voc/bau#
is part of: Bioregistry
type: Resource
keyword: nfdi4ing

SemWeb Vocab Status ontology
keyword: ontology
has resource example: term status
is deprecated: false
is part of: Bioregistry
0000005: term_status
has download URL: ns
has URI prefix: http://www.w3.org/2003/06/sw-vocab-status/ns#
has prefix: vs
type: Resource
contributor: Charles Tapley Hoyt
description: This vocabulary was created in the FOAF project, based on experience with FOAF, Dublin Core and other early RDF vocabularies. Deployment experience shows that changing namespace URIs is expensive and unrewarding, so this vocabulary provides terms to support in-place evolution of structured data vocabularies. By indicating status at the level of terms rather than vocabularies, dictionary-style, fine grained improvements become easier. Different organizations and parties can agree or disagree on the status of a vocabulary term; however the status published alongside the term may deserve special attention. Future work could include patterns for citing announcements and decisions, or using SKOS to decentralise the extension of the basic status levels. (from artifact)
keyword: semantic web
keyword: metadata
has provider formatter: http://www.w3.org/2003/06/sw-vocab-status/ns#$1

Ligand-Gated Ion Channel database
0000005: 5HT3Arano
is part of: Bioregistry
type: Resource
keyword: gene
description: The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.
has prefix: lgic
has resource example: 5HT3Arano.php
is deprecated: true
has provider formatter: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php
keyword: sequence
keyword: protein
has local unique identifier pattern: ^\w+$
has URI prefix: https://bioregistry.io/lgic:

Ximbio
is deprecated: false
description: Cell line collections (Providers)
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: ximbio
has provider formatter: https://ximbio.com/reagent/$1
type: Resource
has URI prefix: https://ximbio.com/reagent/
has resource example: https://ximbio.com/reagent/151022
0000005: 151022

Immune Epitope Database References
keyword: immunology
0000005: 1038233
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
keyword: bioinformatics
has resource example: https://www.iedb.org/reference/1038233
has prefix: iedb.reference
has reviewer: https://orcid.org/0000-0001-9439-5346
type: Resource
has provider formatter: https://www.iedb.org/reference/$1
has URI prefix: https://www.iedb.org/reference/
has responsible: https://orcid.org/0000-0001-8957-7612
contributor: Mufaddal Naguthanawala
keyword: life science
description: Identifiers for references, typically linking to sources of evidence such as publications that support data within IEDB.

CoVoc Coronavirus Vocabulary
is deprecated: false
is part of: Bioregistry
git repository: covoc
has resource example: COVOC_0010034
has local unique identifier pattern: ^\d{7}$
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/COVOC_$1
0000005: 0010034
description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
has download URL: covoc.owl
has prefix: covoc
has URI prefix: http://purl.obolibrary.org/obo/COVOC_
has responsible: Zoë May Pendlington
keyword: ontology

Sri Lanka Clinical Trials Registry
contributor: Charles Tapley Hoyt
0000005: SLCTR/2023/010
type: Resource
has local unique identifier pattern: ^SLCTR/\d{4}/\d+$
description: The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage)
is deprecated: false
has prefix: slctr
is part of: Bioregistry

DASHR expression
has resource example: exprPerTissueTable
0000005: hsa-mir-200a
is deprecated: false
description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.
has prefix: dashr.expression
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
has URI prefix: https://bioregistry.io/dashr.expression:
has provider formatter: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable

SWEET Ontology State Ordinal
0000005: Acute
is deprecated: false
keyword: state ordinal
is part of: Bioregistry
has prefix: sweet.sto
git repository: sweet
contributor: Charles Tapley Hoyt
has alternative prefix: sosto
has URI prefix: http://sweetontology.net/stateOrdinal/
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Ordinal
type: Resource
has resource example: Acute
has provider formatter: http://sweetontology.net/stateOrdinal/$1

GWAS Catalog
has identifier space owner: 02catss52
description: The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.
is deprecated: false
has local unique identifier pattern: ^GCST\d{6}\d*$
has provider formatter: https://www.ebi.ac.uk/gwas/studies/$1
has URI prefix: https://www.ebi.ac.uk/gwas/studies/
has prefix: gcst
is part of: Bioregistry
type: Resource
has resource example: GCST000035
0000005: GCST000035

Getty Vocabulary Program ontology
description: The GVP Ontology defines classes, properties and values (skos:Concepts) used in GVP LOD. As of version 3.0, it is complete regarding AAT, TGN and ULAN, and will be extended in time with more elements needed for other GVP vocabularies (CONA).
has prefix: getty.gvp
has URI prefix: http://vocab.getty.edu/ontology#
is deprecated: false
has provider formatter: http://vocab.getty.edu/ontology#$1
0000005: prefLabelGVP
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has resource example: prefLabelGVP

Amphibian taxonomy
is part of: Bioregistry
has download URL: ato.obo
keyword: taxonomic classification
has local unique identifier pattern: ^\d{7}$
type: Resource
0000005: 0000000
has provider formatter: http://purl.obolibrary.org/obo/ATO_$1
is deprecated: true
has URI prefix: http://purl.obolibrary.org/obo/ATO_
has responsible: David Blackburn
keyword: taxonomy
has prefix: ato
keyword: obo
has resource example: ATO_0000000
keyword: ontology
description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource

Vaccine Adjuvant Compendium
keyword: vaccines
has URI prefix: https://vac.niaid.nih.gov/view
keyword: immunology
0000005: 15
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://vac.niaid.nih.gov/view
description: The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations between NIAID-supported adjuvant researchers and the broader scientific community. The VAC displays adjuvant characteristics or metadata defined through NIAID-supported adjuvant studies to help vaccine developers identify suitable adjuvants for various vaccine indications, including immune-mediated and infectious diseases. In addition, the VAC welcomes the inclusion of adjuvant metadata generated by other research programs.
type: Resource
has resource example: https://vac.niaid.nih.gov/view
keyword: biology
has prefix: vac

BioGRID
has provider formatter: http://thebiogrid.org/$1
keyword: proteomics
has resource example: http://thebiogrid.org/31623
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has prefix: biogrid
type: Resource
keyword: gene
keyword: interaction
has responsible: Mike Tyers
description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.
git repository: BioGRID
keyword: life science
keyword: biochemistry
keyword: systems biology
0000005: 31623
has URI prefix: http://thebiogrid.org/
keyword: chemical biology
is deprecated: false
keyword: cheminformatics
keyword: protein
keyword: bioinformatics

RNA SSTRAND
has URI prefix: http://www.rnasoft.ca/sstrand/show_results.php
keyword: rna
is deprecated: false
has prefix: rna_sstrand
has resource example: http://www.rnasoft.ca/sstrand/show_results.php
0000005: CRW_00469
is part of: Bioregistry
type: Resource
keyword: structure
description: RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database.
has reviewer: Charles Tapley Hoyt
has provider formatter: http://www.rnasoft.ca/sstrand/show_results.php

ESCO Ontology
description: The ontology of the taxonomy "European Skills, Competences, qualifications and Occupations". The ontology considers three ESCO pillars (or taxonomy) and 2 registers. The three pillars are: 1) Occupation, 2) Skill (and competences), and 3) Qualification
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has resource example: Occupation
has prefix: esco.model
has URI prefix: https://ec.europa.eu/esco/lod/static/model.html#
has provider formatter: https://ec.europa.eu/esco/lod/static/model.html#$1
0000005: Occupation
is deprecated: false

SWEET Ontology Representation Time Season
is deprecated: false
has provider formatter: http://sweetontology.net/reprTimeSeason/$1
has URI prefix: http://sweetontology.net/reprTimeSeason/
keyword: representation time season
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.repts
has resource example: ColdestMonth
0000005: ColdestMonth
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Time Season
has alternative prefix: sorepts

The Comprehensive R Archive Network
has URI prefix: https://cran.r-project.org/web/packages/
has resource example: ggplot2
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: Repository of packages for the R programming language
0000005: ggplot2
has prefix: cran
type: Resource
has provider formatter: https://cran.r-project.org/web/packages/$1
is deprecated: false

BDGP insertion DB
has responsible: Allan Spradling
has URI prefix: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php
description: BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.
has prefix: bdgp.insertion
is deprecated: false
keyword: sequence
0000005: KG09531
has local unique identifier pattern: ^\w+$
has provider formatter: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php
is part of: Bioregistry
type: Resource
keyword: gene
has resource example: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php

NASA Open Science Data Repository Subject
has reviewer: https://orcid.org/0000-0001-9439-5346
has resource example: https://osdr.nasa.gov/bio/repo/data/subjects/58
has local unique identifier pattern: ^\d+$
0000005: 58
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-8542-2389
type: Resource
has provider formatter: https://osdr.nasa.gov/bio/repo/data/subjects/$1
has prefix: nasaosdr.subject
has URI prefix: https://osdr.nasa.gov/bio/repo/data/subjects/
contributor: Mufaddal Naguthanawala
is deprecated: false
description: Identifiers for subjects of experiments that investigate biological and health responses of terrestrial life to spaceflight

Provenance, Authoring, and Versioning Vocabulary
has URI prefix: http://purl.org/pav/
has reviewer: Charles Tapley Hoyt
has download URL: pav.owl
keyword: subject agnostic
keyword: data management
description: PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources.
has provider formatter: http://purl.org/pav/$1
keyword: ontology
0000005: authoredBy
is deprecated: false
keyword: resource metadata
git repository: pav
keyword: quality
has local unique identifier pattern: ^[a-z][a-zA-Z]+$
has responsible: https://orcid.org/0000-0001-9842-9718
has resource example: authoredBy
is part of: Bioregistry
contributor: https://orcid.org/0000-0002-7356-1779
has prefix: pav
type: Resource
contributor: Charles Tapley Hoyt

Identifiers.org Registry
has prefix: mir
is deprecated: false
has local unique identifier pattern: ^\d{8}$
0000005: 00100037
is part of: Bioregistry
has provider formatter: https://registry.identifiers.org/registry
has resource example: https://registry.identifiers.org/registry
type: Resource
has URI prefix: https://registry.identifiers.org/registry
description: The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources.

RDF Schema
type: Resource
has prefix: rdfs
has URI prefix: http://www.w3.org/2000/01/rdf-schema#
has responsible: Dan Brickley
has resource example: label
keyword: life science
keyword: ontology and terminology
has download URL: download.trig.gz
keyword: ontology
is deprecated: false
0000005: label
description: RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary.
is part of: Bioregistry
keyword: bioinformatics
keyword: w3c rec
contributor: Charles Tapley Hoyt
has provider formatter: http://www.w3.org/2000/01/rdf-schema#$1
keyword: linguistics

UniProt Isoform
has responsible: Alex Bateman
has local unique identifier pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$
is deprecated: false
has provider formatter: http://purl.uniprot.org/isoforms/$1
has resource example: Q5BJF6-3
0000005: Q5BJF6-3
is part of: Bioregistry
type: Resource
has URI prefix: http://purl.uniprot.org/isoforms/
has alternative prefix: UPISO
has prefix: uniprot.isoform
description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information.

Sugar Kelp Ontology
keyword: ontology
has provider formatter: https://cropontology.org/rdf/CO_360:$1
keyword: marine environment
has download URL: CO 360.owl
has responsible: Elizabeth Arnaud
is deprecated: false
keyword: plant phenotypes and traits
keyword: phenotype
keyword: botany
description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Sugar Kelp Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
0000005: 0000071
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
type: Resource
has resource example: CO 360:0000071
git repository: Crop-Ontology
has URI prefix: https://cropontology.org/rdf/CO_360:
has prefix: co_360
keyword: life science

Health Data Research Innovation Gateway
has local unique identifier pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$
has prefix: gateway
has URI prefix: https://web.www.healthdatagateway.org/dataset/
is deprecated: false
description: The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.
is part of: Bioregistry
has provider formatter: https://web.www.healthdatagateway.org/dataset/$1
type: Resource

Database of experimentally verified IRES structures
has reviewer: Charles Tapley Hoyt
has provider formatter: http://www.iresite.org/IRESite_web.php
keyword: life science
has resource example: http://www.iresite.org/IRESite_web.php
keyword: rna
is deprecated: false
has prefix: iresite
is part of: Bioregistry
keyword: regulation
has responsible: https://orcid.org/0000-0002-9490-8911
0000005: 322
has URI prefix: http://www.iresite.org/IRESite_web.php
type: Resource
description: The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.

GWAS Central Study
has URI prefix: https://www.gwascentral.org/study/
keyword: genome
is deprecated: false
is part of: Bioregistry
description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.
has prefix: gwascentral.study
has responsible: https://orcid.org/0000-0002-0292-7972
has resource example: HGVST1828
type: Resource
keyword: gene
has local unique identifier pattern: ^HGVST\d+$
0000005: HGVST1828
has provider formatter: https://www.gwascentral.org/study/$1

Library of Congress Resource Types Scheme
keyword: data classification
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: dig
type: Resource
has provider formatter: http://id.loc.gov/vocabulary/resourceTypes/$1
description: A controlled vocabulary of media resources, such as audio, cartographic, manuscript, multimedia, etc.
has resource example: dig
has prefix: loc.resourcetype
has URI prefix: http://id.loc.gov/vocabulary/resourceTypes/
contributor: https://orcid.org/0000-0001-8997-2620

SWEET Ontology State Role Trust
has URI prefix: http://sweetontology.net/stateRoleTrust/
keyword: state role trust
has alternative prefix: sostrt
has resource example: Accurate
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Trust
is part of: Bioregistry
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
0000005: Accurate
has provider formatter: http://sweetontology.net/stateRoleTrust/$1
has prefix: sweet.strt

MediaDive Ingredient
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has URI prefix: https://mediadive.dsmz.de/ingredients/
has prefix: mediadive.ingredient
has resource example: https://mediadive.dsmz.de/ingredients/13
type: Resource
0000005: 13
has provider formatter: https://mediadive.dsmz.de/ingredients/$1
has responsible: Jörg Overmann
is deprecated: false
description: The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]

Zenodo
has prefix: zenodo.record
description: Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts.
0000005: 4390079
has URI prefix: https://zenodo.org/record/
type: Resource
has resource example: https://zenodo.org/record/4390079
has alternative prefix: zenodo
has reviewer: Charles Tapley Hoyt
has provider formatter: https://zenodo.org/record/$1
keyword: subject agnostic
keyword: data management
contributor: https://orcid.org/0000-0001-9439-5346
has responsible: Lars Holm Nielsen
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$

ChemBioSys Tag
has prefix: chembiosys.tag
is deprecated: false
has provider formatter: https://data.chembiosys.de/tags/$1
has URI prefix: https://data.chembiosys.de/tags/
0000005: 59
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
contributor: Charles Tapley Hoyt
has resource example: https://data.chembiosys.de/tags/59
description: A tag in the ChemBioSys data platform

Index Fungorum
is part of: Bioregistry
description: identifier for a fungus taxon in Index Fungorum
contributor: Charles Tapley Hoyt
has prefix: fungorum
type: Resource
has local unique identifier pattern: ^[1-9]\d{0,5}$
has provider formatter: http://www.indexfungorum.org/names/NamesRecord.asp
0000005: 154022
is deprecated: false
has URI prefix: http://www.indexfungorum.org/names/NamesRecord.asp
has resource example: http://www.indexfungorum.org/names/NamesRecord.asp

ChemPro Competitor
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: chempro.competitor
is part of: Bioregistry
type: Resource
0000005: LDCM0160
has resource example: LDCM0160
has local unique identifier pattern: ^LDCM\d+$
has URI prefix: https://chemprosquare.idrblab.net/data/competitor/details/
contributor: Mufaddal Naguthanawala
description: ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for compounds that compete with probes for binding to target proteins.
has responsible: https://orcid.org/0000-0001-8069-0053
is deprecated: false
has provider formatter: https://chemprosquare.idrblab.net/data/competitor/details/$1

Resource
type: Class
description: A type for entries in the Bioregistry's registry.

Cell Line Database
is deprecated: false
has URI prefix: https://bioregistry.io/cldb:
description: The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.
has provider formatter: http://bioinformatics.hsanmartino.it/hypercldb/$1.html
0000005: cl3603
is part of: Bioregistry
type: Resource
has alternative prefix: hypercldb
has resource example: cl3603.html
has prefix: cldb
has local unique identifier pattern: ^(cl|tum)\d+$

Gramene QTL
is part of: Bioregistry
type: Resource
has provider formatter: http://www.gramene.org/db/qtl/qtl_display
has URI prefix: http://www.gramene.org/db/qtl/qtl_display
description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.
has prefix: gramene.qtl
has alternative prefix: GR_QTL
has resource example: http://www.gramene.org/db/qtl/qtl_display
is deprecated: false
has local unique identifier pattern: ^\w+$
0000005: CQG5

Swiss National Clinical Trials Portal
is part of: Bioregistry
description: The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage]
contributor: Charles Tapley Hoyt
has prefix: snctp
type: Resource
is deprecated: false
0000005: SNCTP000005580

International Data Spaces Information Model
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
description: This ontology defines classes and properties for describing participants, infrastructure, data and services of the International Data Spaces (formerly known as Industrial Data Space).
has URI prefix: https://w3id.org/idsa/core/
is deprecated: true
has provider formatter: https://w3id.org/idsa/core/$1
git repository: InformationModel
keyword: engineering
has prefix: idsa

dictyBase Expressed Sequence Tag
has provider formatter: http://dictybase.org/db/cgi-bin/feature_page.pl
is deprecated: false
description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information.
is part of: Bioregistry
0000005: DDB0016567
has prefix: dictybase.est
has local unique identifier pattern: ^DDB\d+$
type: Resource
has URI prefix: http://dictybase.org/db/cgi-bin/feature_page.pl
has resource example: http://dictybase.org/db/cgi-bin/feature_page.pl

GO Relations
has resource example: GOREL_0002005
has local unique identifier pattern: ^\d{7}$
type: Resource
0000005: 0002005
has download URL: gorel.owl
description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.
has provider formatter: http://purl.obolibrary.org/obo/GOREL_$1
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/GOREL_
keyword: ontology
has prefix: gorel
is part of: Bioregistry
contributor: Charles Tapley Hoyt
contributor: https://orcid.org/0009-0006-4842-7427

Simple Modular Architecture Research Tool
has responsible: https://orcid.org/0000-0003-0202-7816
keyword: structure
type: Resource
has URI prefix: http://smart.embl-heidelberg.de/smart/do_annotation.pl
keyword: life science
0000005: SM00015
has provider formatter: http://smart.embl-heidelberg.de/smart/do_annotation.pl
keyword: domain
has resource example: http://smart.embl-heidelberg.de/smart/do_annotation.pl
has local unique identifier pattern: ^SM\d{5}$
is deprecated: false
keyword: protein
description: The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.
has prefix: smart
is part of: Bioregistry

Mammalian Feeding Muscle Ontology
depends on: Uber Anatomy Ontology
has responsible: https://orcid.org/0000-0002-1572-1316
has local unique identifier pattern: ^\d{7}$
description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.
type: Resource
keyword: anatomy
has resource example: MFMO_0000208
is deprecated: true
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/MFMO_$1
git repository: feedontology
0000005: 0000208
has download URL: mfmo.owl
is part of: Bioregistry
has prefix: mfmo
has URI prefix: http://purl.obolibrary.org/obo/MFMO_

FAIRsharing Subject Ontology
0000005: 0000400
has prefix: srao
keyword: agriculture
keyword: humanities
has local unique identifier pattern: ^\d{7}$
description: The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies.
type: Resource
keyword: earth science
keyword: biomedical science
has URI prefix: http://www.fairsharing.org/ontology/subject/SRAO_
keyword: fair
keyword: computer science
has responsible: https://orcid.org/0000-0002-7702-4495
git repository: subject-ontology
keyword: environmental science
keyword: metadata standardization
is deprecated: false
keyword: natural science
keyword: life science
keyword: classification
has provider formatter: http://www.fairsharing.org/ontology/subject/SRAO_$1
has download URL: SRAO.owl
keyword: metascience
keyword: ontology
keyword: topics
has resource example: SRAO_0000400
keyword: resource metadata
is part of: Bioregistry

Individual Organism Information Ontology
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: IOIO_0000001
has download URL: IOIO.owl
has local unique identifier pattern: ^\d{7}$
0000005: 0000001
type: Resource
description: An ontology of information entities about an individual
has provider formatter: http://purl.obolibrary.org/obo/IOIO_$1
git repository: IOIO
has URI prefix: http://purl.obolibrary.org/obo/IOIO_
is deprecated: false
has prefix: ioio
keyword: ontology

Social Insect Behavior Ontology
has local unique identifier pattern: ^\d{7}$
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/SIBO_
keyword: biology
has download URL: sibo.owl
has prefix: sibo
has responsible: https://orcid.org/0000-0002-6601-2165
is deprecated: true
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/SIBO_$1
has resource example: SIBO_0000509
is part of: Bioregistry
0000005: 0000509
description: Social Behavior in insects
git repository: sibo

Fababean Ontology
keyword: ontology
has responsible: Elizabeth Arnaud
is deprecated: false
is part of: Bioregistry
has prefix: co_365
has URI prefix: https://cropontology.org/rdf/CO_365:
has resource example: CO 365:0000205
git repository: Crop-Ontology
has download URL: CO 365.owl
description: to add
has provider formatter: https://cropontology.org/rdf/CO_365:$1
has local unique identifier pattern: ^\d{7}$
type: Resource
0000005: 0000205

Pharmacogene Variation Consortium
has URI prefix: https://www.pharmvar.org/gene/
has responsible: Andrea Gaedigk
0000005: CYP2A6
is deprecated: false
keyword: pharmacogenomics
is part of: Bioregistry
keyword: variant
0000011: HGNC gene symbol
description: The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium.
has provider formatter: https://www.pharmvar.org/gene/$1
type: Resource
keyword: gene
has prefix: pharmvar
has resource example: CYP2A6
has reviewer: Charles Tapley Hoyt

UNESCO Thesaurus
has URI prefix: http://vocabularies.unesco.org/thesaurus/concept
keyword: political science
is deprecated: false
has provider formatter: http://vocabularies.unesco.org/thesaurus/concept$1
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
keyword: education science
has prefix: unesco.thesaurus
type: Resource
has resource example: concept585
0000005: 585
keyword: culture
keyword: subject agnostic
keyword: communication science
description: The UNESCO Thesaurus is a controlled and structured list of terms used in subject analysis and retrieval of documents and publications in the fields of education, culture, natural sciences, social and human sciences, communication and information. Continuously enriched and updated, its multidisciplinary terminology reflects the evolution of UNESCO's programmes and activities. [from homepage]

PharmGKB Drug
has provider formatter: http://www.pharmgkb.org/drug/$1
has responsible: Teri E Klein
has URI prefix: http://www.pharmgkb.org/drug/
type: Resource
description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.
has download URL: pharmgkb.drug.owl
keyword: drug
has resource example: PA448710
keyword: ontology
has local unique identifier pattern: ^PA\d+$
is deprecated: false
keyword: pharmacogenomics
is part of: Bioregistry
has prefix: pharmgkb.drug
0000005: PA448710

MGnify Sample
has resource example: SRS086444
is deprecated: false
has prefix: mgnify.samp
is part of: Bioregistry
has URI prefix: https://www.ebi.ac.uk/metagenomics/samples/
has local unique identifier pattern: ^[A-Z]+[0-9]+$
0000005: SRS086444
type: Resource
description: The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.
has provider formatter: https://www.ebi.ac.uk/metagenomics/samples/$1

Rice Genome Annotation Project
type: Resource
has local unique identifier pattern: ^LOC\_Os\d{1,2}g\d{5}$
has alternative prefix: rgap
description: The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.
has prefix: ricegap
has provider formatter: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi
has resource example: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi
is deprecated: false
keyword: dna
is part of: Bioregistry
keyword: genome
has responsible: https://orcid.org/0000-0002-6727-4677
0000005: LOC_Os02g13300
has URI prefix: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi

SWEET Ontology Material Sediment
has URI prefix: http://sweetontology.net/matrSediment/
keyword: sediment
has prefix: sweet.mas
is deprecated: false
has alternative prefix: somas
has resource example: Alluvium
0000005: Alluvium
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Sediment
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: materials
has provider formatter: http://sweetontology.net/matrSediment/$1

VMH Gene
0000005: 8639.1
has provider formatter: https://www.vmh.life/#gene/$1
has prefix: vmhgene
is deprecated: false
has local unique identifier pattern: ^[0-9]+\.[0-9]+$
has resource example: gene/8639.1
is part of: Bioregistry
type: Resource
description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.
has URI prefix: https://www.vmh.life/#gene/

COG Pathways
has prefix: cog.pathway
has responsible: Michael Y Galperin
is deprecated: false
description: Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera.
has resource example: NAD biosynthesis
has provider formatter: https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1
0000005: NAD%20biosynthesis
has URI prefix: https://www.ncbi.nlm.nih.gov/research/cog/pathway/
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt

Wormpep
is deprecated: false
description: Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.
is part of: Bioregistry
keyword: protein
has local unique identifier pattern: ^CE\d{5}$
has URI prefix: https://www.wormbase.org/db/seq/protein
type: Resource
has resource example: https://www.wormbase.org/db/seq/protein
has provider formatter: https://www.wormbase.org/db/seq/protein
keyword: structure
0000005: CE28239
has prefix: wormpep

Bgee stage
type: Resource
has provider formatter: http://bgee.unil.ch/bgee/bgee
is deprecated: true
description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages.
has prefix: bgee.stage
is part of: Bioregistry
has URI prefix: http://bgee.unil.ch/bgee/bgee
has resource example: http://bgee.unil.ch/bgee/bgee
has local unique identifier pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$
0000005: HsapDO:0000004
contributor: 0000-0003-3947-488X

Sunflower Ontology
keyword: ontology
has responsible: Elizabeth Arnaud
description: To add
is part of: Bioregistry
git repository: Crop-Ontology
has download URL: CO 359.owl
has resource example: CO 359:0000947
has local unique identifier pattern: ^\d{7}$
has provider formatter: https://cropontology.org/rdf/CO_359:$1
type: Resource
0000005: 0000947
has prefix: co_359
is deprecated: false
has URI prefix: https://cropontology.org/rdf/CO_359:

FishBase
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has alternative prefix: fishbase
contributor: Charles Tapley Hoyt
description: Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years.
type: Resource
has URI prefix: https://www.fishbase.ca/summary/
has provider formatter: https://www.fishbase.ca/summary/$1
has prefix: fishbase.species
0000005: 6472
is deprecated: false
has resource example: https://www.fishbase.ca/summary/6472

FDA Submission Tracking Number
0000005: 125768
type: Resource
is deprecated: false
description: The pre-IND tracking number for submissions to the FDA
is part of: Bioregistry
has prefix: stn
contributor: Charles Tapley Hoyt

has provider formatter
equivalent property: accessPattern
domain: Resource
equivalent property: hasPrimaryUriPattern
type: Property
range: string
description: The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved.
equivalent property: P1630

Oryzabase Mutant
has provider formatter: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/
type: Resource
description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.
has resource example: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/21393
has prefix: oryzabase.mutant
0000005: 21393
is deprecated: false

Synthetic Binding Protein Protein Scaffold
has resource example: ps048
has local unique identifier pattern: ^ps\d+$
has provider formatter: http://synbip.idrblab.net/data/scaffold/details/$1
description: Identifiers for the protein scaffolds of synthetic binding proteins (SBP), detailing their structural frameworks and roles in facilitating SBP function.
is part of: Bioregistry
has responsible: 0000-0002-1846-639X
has URI prefix: http://synbip.idrblab.net/data/scaffold/details/
0000005: ps048
has reviewer: https://orcid.org/0000-0001-9439-5346
type: Resource
has prefix: synbip.pss
contributor: Mufaddal Naguthanawala
is deprecated: false

16S rRNA gene database
0000005: 100000
keyword: rna
keyword: genetics
has local unique identifier pattern: ^\d+$
has provider formatter: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl
is part of: Bioregistry
has prefix: greengenes
description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.
type: Resource
has resource example: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl
is deprecated: true
has URI prefix: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl
has responsible: Gary L Andersen
keyword: life science

Genetics Home Reference
type: Resource
has provider formatter: https://medlineplus.gov/genetics/condition/$1
description: MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA).
is deprecated: false
has prefix: ghr
is part of: Bioregistry
0000005: saddan
has URI prefix: https://medlineplus.gov/genetics/condition/
contributor: Charles Tapley Hoyt
has resource example: saddan

CiteXplore
is part of: Bioregistry
description: One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes.
type: Resource
has URI prefix: https://europepmc.org/article/CTX/
contributor: Charles Tapley Hoyt
has resource example: C6155
0000005: C6155
has prefix: citexplore
has provider formatter: https://europepmc.org/article/CTX/$1
is deprecated: false
has alternative prefix: CTX

UniProt Proteomes
has local unique identifier pattern: ^UP\d{9}$
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
contributor: JervenBolleman
0000005: UP000005640
description: UniProt provides proteome sets of proteins whose genomes have been completely sequenced.
has URI prefix: https://www.uniprot.org/proteomes/
is part of: Bioregistry
type: Resource
has prefix: uniprot.proteome
contributor: Charles Tapley Hoyt
has provider formatter: https://www.uniprot.org/proteomes/$1
has resource example: UP000005640
has reviewer: Charles Tapley Hoyt

DrugBank Target v4
has URI prefix: https://go.drugbank.com/bio_entities/
has responsible: David Wishart
description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.
has prefix: drugbank.bioentity
has local unique identifier pattern: ^BE\d{7}$
has provider formatter: https://go.drugbank.com/bio_entities/$1
is deprecated: false
has alternative prefix: drugbankv4.target
has alternative prefix: drugbank.target
0000005: BE0000048
is part of: Bioregistry
type: Resource
has resource example: https://go.drugbank.com/bio_entities/BE0000048

Bioregistry Collections
has resource example: Resources mentioned in "Sharing biological data: why, when, and how"
has URI prefix: https://bioregistry.io/collection/
keyword: registry
has responsible: Charles Tapley Hoyt
is deprecated: false
description: Manually curated collections of resources stored in the bioregistry
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: bioregistry.collection
has provider formatter: https://bioregistry.io/collection/$1
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
type: Resource

Universal Spectrum Identifier
description: The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it.
0000005: PXD002255:ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2
has provider formatter: http://proteomecentral.proteomexchange.org/usi/
git repository: usi
is part of: Bioregistry
has responsible: Gerhard Mayer
keyword: metabolomics
keyword: proteomics
has prefix: mzspec
has URI prefix: http://proteomecentral.proteomexchange.org/usi/
has local unique identifier pattern: ^.+$
has resource example: http://proteomecentral.proteomexchange.org/usi/
keyword: lipidomics
type: Resource
keyword: data retrieval
keyword: data analysis
contributor: https://orcid.org/0000-0002-8741-7823
keyword: mass spectrum
keyword: data identity and mapping
is deprecated: false

Wiktionary
has prefix: wiktionary
0000005: pharmacist
has URI prefix: https://en.wiktionary.org/wiki/
description: A free dictionary
is deprecated: false
has resource example: pharmacist
has provider formatter: https://en.wiktionary.org/wiki/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

OntoRXN
description: OntoRXN is an ontology for the description of reaction networks as undirected graphs characterized by energies.
keyword: ontology
is deprecated: false
is part of: Bioregistry
has download URL: OntoRXN.owl
keyword: chemistry
contributor: Charles Tapley Hoyt
keyword: nfdi4chem
has prefix: ontorxn
type: Resource
0000005: hasCalculation

UniProt
has local unique identifier pattern: ^[A-Z0-9]{1,10}_[A-Z0-9]{1,5}$
has responsible: Alex Bateman
has prefix: uniprot.mnemonic
has provider formatter: https://www.uniprot.org/uniprotkb/$1
has reviewer: https://orcid.org/0000-0003-2473-2313
0000005: BRAF_HUMAN
has URI prefix: https://www.uniprot.org/uniprotkb/
is deprecated: false
is part of: Bioregistry
contributor: https://orcid.org/0000-0001-9439-5346
has resource example: BRAF HUMAN
description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. This entry represents UniProt mnemonics which combine an alphanumeric representation the protein name and a species identification code representing the biological source of the protein.
type: Resource

SWEET Ontology Human Transportation
has prefix: sweet.hut
has provider formatter: http://sweetontology.net/humanTransportation/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Transportation
keyword: transportation
has alternative prefix: sohut
0000005: AirTraffic
is deprecated: false
has resource example: AirTraffic
is part of: Bioregistry
has URI prefix: http://sweetontology.net/humanTransportation/
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt

AutDB
is part of: Bioregistry
description: AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.
type: Resource
has provider formatter: http://autism.mindspec.org/GeneDetail/$1
is deprecated: true
has resource example: ADA
has local unique identifier pattern: ^[A-Z]+[A-Z-0-9]{2,}$
0000005: ADA
has URI prefix: http://autism.mindspec.org/GeneDetail/
has prefix: autdb

has identifier space owner
range: https://bioregistry.io/schema/#0000025
type: Property
domain: Resource
description: An organization

SWEET Ontology Realm Geologic Oceanic
keyword: geologic oceanic
has URI prefix: http://sweetontology.net/realmGeolOceanic/
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Oceanic
0000005: AccretionaryPrism
is part of: Bioregistry
has provider formatter: http://sweetontology.net/realmGeolOceanic/$1
has prefix: sweet.reagoc
git repository: sweet
contributor: Charles Tapley Hoyt
keyword: realm
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: soreagoc
type: Resource
has resource example: AccretionaryPrism

SWEET Ontology Material Energy
0000005: Battery
is deprecated: false
has alternative prefix: somaen
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Energy
has URI prefix: http://sweetontology.net/matrEnergy/
keyword: energy
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
type: Resource
has resource example: Battery
has provider formatter: http://sweetontology.net/matrEnergy/$1
keyword: materials
has prefix: sweet.maen

Citation Typing Ontology
contributor: Charles Tapley Hoyt
keyword: spar
type: Resource
description: An ontology that enables characterization of the nature or type of citations, both factually and rhetorically.
0000005: sharesAuthorInstitutionWith
has prefix: cito
has URI prefix: http://purl.org/spar/cito/
has download URL: cito.owl
git repository: cito
keyword: miscellaneous
keyword: ontology
is deprecated: false
is part of: Bioregistry
has resource example: sharesAuthorInstitutionWith
has responsible: Silvio Peroni
has provider formatter: http://purl.org/spar/cito/$1
keyword: knowledge and information systems

Building Ontology
is part of: Bioregistry
type: Resource
has download URL: building.owl
keyword: nfdi4ing
keyword: architecture
description: The Building ontology has been developed to perform as the core module of the BIMERR Ontology Network, containing information related to building topology, and components. The model is constructed as an extention of the BOT ontology that provides the vocabulary to describe the topology of a building as well as the relationships between their main components such as zones, spaces, and building elements. The taxonomy of building components is based on the proposed by the IFC 4.1 standard.
has prefix: building
has URI prefix: http://bimerr.iot.linkeddata.es/def/building#
keyword: civil engineering
has resource example: AirConditioningUnit
keyword: ontology
has provider formatter: http://bimerr.iot.linkeddata.es/def/building#$1
is deprecated: false
keyword: digital planning and construction
keyword: fid baudigital
0000005: AirConditioningUnit

ICEberg integrative and mobilizable element
0000005: 1
has resource example: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php
keyword: genomics
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has responsible: Hong-Yu Ou
description: ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.
type: Resource
has URI prefix: https://bioregistry.io/iceberg.ime:
keyword: biology
has provider formatter: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php
has prefix: iceberg.ime
is deprecated: false

Virus-HostDB
has reviewer: Charles Tapley Hoyt
description: Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys.
type: Resource
has responsible: 0000-0001-6594-377X
has provider formatter: https://www.genome.jp/virushostdb/$1
0000011: NCBI Taxonomy
has prefix: virushostdb
keyword: virus
is deprecated: false
has URI prefix: https://www.genome.jp/virushostdb/
is part of: Bioregistry
has resource example: https://www.genome.jp/virushostdb/438782
0000005: 438782

Olfactory Receptor Database
keyword: gene
0000005: 8497
has provider formatter: https://ordb.biotech.ttu.edu/ORDB/Data/$1
type: Resource
keyword: life science
is deprecated: false
has prefix: ordb
has URI prefix: https://ordb.biotech.ttu.edu/ORDB/Data/
keyword: protein
has resource example: https://ordb.biotech.ttu.edu/ORDB/Data/8497
is part of: Bioregistry
description: The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs).
has local unique identifier pattern: ^\d+$

Metabolic Atlas
type: Resource
has responsible: Mihail Anton
has part: Metabolic Atlas Metabolite
has local unique identifier pattern: ^(MAM\d{5}\w)|(MAR\d{5})$
0000005: MAM01234c
has URI prefix: https://metabolicatlas.org/identifier/MetabolicAtlas/
has part: Metabolic Atlas Reaction
is deprecated: false
keyword: reactions
contributor: Mihail Anton
keyword: metabolites
has provider formatter: https://metabolicatlas.org/identifier/MetabolicAtlas/$1
is part of: Bioregistry
has resource example: MAM01234c
keyword: chemistry
has prefix: metatlas
description: A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis.
has reviewer: Charles Tapley Hoyt

has responsible
type: Property
domain: Resource
range: Person
description: The responsible person for a resource

Basic Register of Thesauri, Ontologies & Classifications
type: Resource
has responsible: Jakob Voß
git repository: bartoc.org
has prefix: bartoc
has resource example: https://bartoc.org/en/node/241
description: The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries. The main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).
is deprecated: false
0000005: 241
keyword: ontology and terminology
contributor: Jakob Voß
has identifier space owner: 048vdhs48
is part of: Bioregistry
has URI prefix: https://bartoc.org/en/node/
has provider formatter: https://bartoc.org/en/node/$1
contributor: Charles Tapley Hoyt
keyword: knowledge and information systems
has local unique identifier pattern: ^[1-9][0-9]*$

Xenbase
is part of: Bioregistry
has prefix: xenbase
has resource example: XB-GENE-922462
type: Resource
has alternative prefix: Xenbase
keyword: expression
description: Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions.
has responsible: Troy Pells
keyword: anatomy
has URI prefix: https://www.xenbase.org/entry/
keyword: cell biology
keyword: genome
keyword: genetics
is deprecated: false
keyword: developmental biology
0000005: XB-GENE-922462
keyword: genomics
has provider formatter: https://www.xenbase.org/entry/$1
has local unique identifier pattern: ^XB\-\w+\-\d+$
keyword: proteomics
keyword: functional genomics

MarkerDB
has responsible: David Wishart
has local unique identifier pattern: ^MDB\d{8}$
contributor: Mufaddal Naguthanawala
is deprecated: false
has prefix: markerdb
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
type: Resource
description: MarkerDB is a freely available electronic database that attempts to consolidate information on all known clinical and pre-clinical biomarkers into a single resource. It provides identifiers for known clinical and pre-clinical biomarkers. Each entry provides detailed annotations, including biomarker descriptions, associated conditions, specificity, sensitivity, molecular structures, chromosomal locations, and clinical approval status.
0000005: MDB00000001

Blue Brain Project Topological sampling Knowledge Graph
is part of: Bioregistry
has provider formatter: https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1
type: Resource
description: Input data and analysis results for the paper "Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ).
has prefix: bbtp
is deprecated: true
has local unique identifier pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$
has URI prefix: https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:

Google Patents
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.google.com/patents/
has prefix: google.patent
has alternative prefix: Patent
has provider formatter: https://www.google.com/patents/$1
0000005: US4145692
has alternative prefix: patent
is part of: Bioregistry
type: Resource
description: Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.
has local unique identifier pattern: ^[A-Z]{2,4}\d+([A-Z])?([0-9])?$
has resource example: US4145692

Dialnet journal ID
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: https://dialnet.unirioja.es/servlet/revista
has local unique identifier pattern: ^[1-9]\d{0,6}$
has URI prefix: https://dialnet.unirioja.es/servlet/revista
0000005: 1119
has prefix: dialnet.journal
has resource example: https://dialnet.unirioja.es/servlet/revista
is deprecated: false
description: identifier of a journal in Dialnet

SWEET Ontology Representation Mathematics Graph
keyword: representation mathematics graph
type: Resource
has alternative prefix: sorepmg
has provider formatter: http://sweetontology.net/reprMathGraph/$1
is deprecated: false
has URI prefix: http://sweetontology.net/reprMathGraph/
has resource example: Arc
0000005: Arc
is part of: Bioregistry
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Graph
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.repmg

enviPath
has URI prefix: https://envipath.org/package/
keyword: environmental science
has responsible: Jörg Wicker
has prefix: envipath
is deprecated: false
has local unique identifier pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$
description: enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products.
has provider formatter: https://envipath.org/package/$1
is part of: Bioregistry
type: Resource

WikiPathways Ontology
git repository: WpVocabularies
has URI prefix: https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/
keyword: ontology
has resource example: https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/
is deprecated: false
has prefix: wikipathways.vocab
0000005: DataNode
description: An ontology supporting data modeling in WikiPathways
has provider formatter: https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has download URL: wp.owl
has responsible: Tim Vandermeersch

Human Dermatological Disease Ontology
has provider formatter: http://purl.obolibrary.org/obo/DERMO_$1
is deprecated: false
keyword: disease
has download URL: dermo.obo
has prefix: dermo
description: DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: dermatology
has responsible: Dr Paul Schofield
has resource example: DERMO_0000000
has local unique identifier pattern: ^\d{7}$
type: Resource
0000005: 0000000
git repository: dermatology
has URI prefix: http://purl.obolibrary.org/obo/DERMO_
keyword: ontology

MoDALIA Ontology
0000005: belongsToCluster
is deprecated: false
keyword: educational science
git repository: dalia-ontology
has prefix: modalia
keyword: ontology
has URI prefix: https://purl.org/ontology/modalia#
has provider formatter: https://purl.org/ontology/modalia#$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: belongsToCluster
has download URL: modalia.obo
description: The aim of DALIA project is to build a platform for learning material for Research Data Management (RDM) and Data Science. The platform is based on a knowledge graph. We introduce MoDalia, the base ontology of DALIA knowledge graph. Modalia inherits some modules from EduCOR. It includes also modelling of micro -credentials and certificates
has responsible: https://orcid.org/0000-0003-2083-1277
keyword: educational resources
type: Resource

Neuroscience Multi-Omic BRAIN Initiative Data
description: This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects.
has prefix: nemo
0000005: smp-m3w9hbe
has resource example: smp-m3w9hbe
has local unique identifier pattern: ^[a-z]{3}-[a-km-z0-9]{7}$
is deprecated: false
has provider formatter: https://assets.nemoarchive.org/$1
is part of: Bioregistry
has URI prefix: https://assets.nemoarchive.org/
type: Resource

Telethon Network of Genetic Biobanks
is deprecated: false
0000005: 67035
description: Cell line collections (Providers)
has local unique identifier pattern: ^\d+$
has provider formatter: https://biobanknetwork.telethon.it/Sample/View
has prefix: tngb
has URI prefix: https://biobanknetwork.telethon.it/Sample/View
is part of: Bioregistry
has resource example: https://biobanknetwork.telethon.it/Sample/View
type: Resource

Central concepts of R|EX research
has identifier space owner: 018afyw53
has provider formatter: https://vocabularies.cessda.eu/vocabulary/rexconcepts#code_$1
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has resource example: code 33
description: This CV, developed within the framework of the DP-R|EX joint project, involving the partner institutions DeZIM, Qualiservice and GESIS, maps the central concepts and theoretical approaches in research on racism and right-wing extremism. The compilation is based on a systematic evaluation of the relevant national and international empirical research literature. The CV equally takes into account the different thematic (racism, right-wing extremism, discrimination) as well as methodological (qualitative research, standardised surveys, data from social media and messaging services) research strands.
0000005: 33
has prefix: gesis.rexconcepts
has URI prefix: https://vocabularies.cessda.eu/vocabulary/rexconcepts#code_
is deprecated: false

Search Tool for Retrieval of Interacting Genes/Proteins
type: Resource
has URI prefix: https://string-db.org/cgi/network
keyword: interaction
keyword: biology
has responsible: 0000-0002-2627-833X
has local unique identifier pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$
keyword: life science
has resource example: https://string-db.org/cgi/network
is deprecated: false
has provider formatter: https://string-db.org/cgi/network
0000005: P53350
0000011: UniProt Protein
is part of: Bioregistry
keyword: protein
has prefix: string
description: STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.

Chickpea Ontology
is deprecated: false
has URI prefix: https://cropontology.org/rdf/CO_338:
has resource example: CO 338:0000138
keyword: food
has provider formatter: https://cropontology.org/rdf/CO_338:$1
has responsible: https://orcid.org/0000-0002-0091-7981
keyword: ontology
is part of: Bioregistry
keyword: plant phenotypes and traits
git repository: Crop-Ontology
keyword: phenotype
has prefix: co_338
keyword: botany
keyword: agriculture
has local unique identifier pattern: ^\d{7}$
0000005: 0000138
has download URL: CO 338.owl
type: Resource
description: Development of crop-specific trait ontologies including the Chickpea Ontology began in 2008 as part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.

appears in
description: Terms from the source appear in the target resource
type: Property
domain: Resource
range: Resource

YRC PDR
keyword: computational biology
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
keyword: protein
has URI prefix: http://yeastrc.org/pdr/viewProtein.do
has responsible: Michael Riffle
0000005: 2673500
type: Resource
has resource example: http://yeastrc.org/pdr/viewProtein.do
has prefix: yrcpdr
description: The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.
keyword: life science
is deprecated: false
has provider formatter: http://yeastrc.org/pdr/viewProtein.do

Contextual Ontology-based Repository Analysis Library - Context and Measurement Ontology
keyword: ontology
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has responsible: https://orcid.org/0000-0002-5153-9079
type: Resource
has prefix: coral.como
has download URL: context measurement ontology.obo
description: The Context and Measurement Ontology (COMO) contains ontological terms to describe the context for various types of experimental data and measurements. It is useful in its current state for several different environmental microbiology projects. This ontology is used in multiple CORAL (Contextual Ontology-based Repository Analysis Library) deployments.
has reviewer: Charles Tapley Hoyt
0000005: 0000001
git repository: CORAL
contributor: https://orcid.org/0000-0002-5153-9079

Valerie Wood
label: Val Wood

SWEET Ontology State Thermodynamic
is deprecated: false
keyword: state thermodynamic
has provider formatter: http://sweetontology.net/stateThermodynamic/$1
has prefix: sweet.stth
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
0000005: ThermodynamicState
has alternative prefix: sostth
has URI prefix: http://sweetontology.net/stateThermodynamic/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Thermodynamic
has resource example: ThermodynamicState

Unified Code for Units of Measure
keyword: subject agnostic
keyword: data identity and mapping
0000005: aBq
keyword: measurement
has URI prefix: https://units-of-measurement.org/
keyword: general & upper
has resource example: aBq
is deprecated: false
has prefix: ucum
is part of: Bioregistry
description: Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business.
git repository: ucum
has responsible: https://orcid.org/0000-0002-3884-3420
contributor: Charles Tapley Hoyt
keyword: unit
type: Resource
has provider formatter: https://units-of-measurement.org/$1

ChEMBL mechanism
has responsible: David Mendez Lopez
has local unique identifier pattern: ^activator|agonist|allosteric-antagonist|antagonist|antisense-inhibitor|binding-agent|blocker|chelating-agent|cross-linking-agent|degrader|disrupting-agent|exogenous-gene|exogenous-protein|hydrolytic-enzyme|inhibitor|inverse-agonist|methylating-agent|modulator|negative-allosteric-modulator|negative-modulator|opener|other|oxidative-enzyme|partial-agonist|positive-allosteric-modulator|positive-modulator|proteolytic-enzyme|reducing-agent|releasing-agent|rnai-inhibitor|sequestering-agent|stabiliser|substrate|vaccine-antigen$
is part of: ChEMBL
has prefix: chembl.mechanism
is deprecated: false
0000005: activator
description: This controlled vocabulary contains terms to describe the mechanism of action for a chemical-target interaction. The terms can be retrieved from ACTION_TYPE table in ChEMBL's SQL dump and are used to annotate the DRUG_MECHANISM table. Because these aren't really identifiers, they are transformed by lowercasing and replacing spaces with dashes to form 'identifiers'. The pattern in the Bioregistry record contains an enumeration of the 33 allowed values as of ChEMBL v35.
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt

GO Chemicals
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has download URL: chebi roles.owl
has resource example: https://biopragmatics.github.io/providers/goche/25512
has alternative prefix: go.chemicals
0000005: 25512
has URI prefix: https://biopragmatics.github.io/providers/goche/
description: Represent chemical entities having particular CHEBI roles
keyword: ontology
has alternative prefix: go.chemical
is deprecated: false
has prefix: goche
has provider formatter: https://biopragmatics.github.io/providers/goche/$1
git repository: go-ontology
has alternative prefix: go.chebi

CIViC Variant Group
description: Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance
type: Resource
has prefix: civic.vgid
has local unique identifier pattern: ^[0-9]+$
has provider formatter: https://civicdb.org/links/variant_group/$1
has alternative prefix: civic.variantgroup
is deprecated: false
has URI prefix: https://civicdb.org/links/variant_group/
0000005: 16
is part of: Bioregistry
has responsible: Malachi Griffith
has resource example: https://civicdb.org/links/variant_group/16

HGNC gene symbol
has prefix: hgnc.symbol
is part of: Bioregistry
0000005: DAPK1
has URI prefix: https://www.genenames.org/data/gene-symbol-report/#!/symbol/
type: Resource
description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.
has local unique identifier pattern: ^[A-Za-z-0-9_]+(\@)?$
has resource example: !/symbol/DAPK1
is deprecated: false
has provider formatter: https://www.genenames.org/data/gene-symbol-report/#!/symbol/$1

MONDO Issue Tracker
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: https://github.com/monarch-initiative/mondo/issues/$1
has URI prefix: https://github.com/monarch-initiative/mondo/issues/
description: An issue on the MONDO GitHub issue tracker
0000005: 832
is deprecated: false
has prefix: mondo.issue
has resource example: https://github.com/monarch-initiative/mondo/issues/832

SWEET Ontology Phenomena Atmosphere Front
has alternative prefix: sophatmofr
has URI prefix: http://sweetontology.net/phenAtmoFront/
is part of: Bioregistry
git repository: sweet
has provider formatter: http://sweetontology.net/phenAtmoFront/$1
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Front
type: Resource
has prefix: sweet.phatmofr
keyword: phenomena
0000005: ColdFront
has resource example: ColdFront
is deprecated: false
keyword: atmosphere front

Creative Commons Rights Expression Language
has local unique identifier pattern: ^\w+$
is part of: Bioregistry
has provider formatter: https://creativecommons.org/ns#$1
has URI prefix: https://creativecommons.org/ns#
contributor: Charles Tapley Hoyt
has alternative prefix: ccrel
0000005: Work
has resource example: Work
has prefix: cc
description: The Creative Commons Rights Expression Language (ccREL) lets you describe copyright licenses in RDF. For more information on describing licenses in RDF and attaching those descriptions to digital works, see [ccREL](https://wiki.creativecommons.org/CC_REL) in the [Creative Commons wiki](https://wiki.creativecommons.org/).
type: Resource
keyword: nfdi4ing
keyword: metadata
is deprecated: false
keyword: law

Type of Note
description: Includes a typology of notes.
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: code Processing
has prefix: ddi.typeofnote
has identifier space owner: 015em2733
type: Resource
0000005: Processing
has URI prefix: https://vocabularies.cessda.eu/vocabulary/TypeOfNote#code_
is deprecated: false
has provider formatter: https://vocabularies.cessda.eu/vocabulary/TypeOfNote#code_$1

GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray
keyword: microarray
0000005: GE86325
is part of: Bioregistry
keyword: transcriptomics
type: Resource
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^GE\d+$
description: GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).
is deprecated: false
has prefix: codelink

Data Quality Vocabulary
type: Resource
0000005: QualityAnnotation
description: The Data Quality Vocabulary (DQV) is seen as an extension to DCAT to cover the quality of the data, how frequently is it updated, whether it accepts user corrections, persistence commitments etc. When used by publishers, this vocabulary will foster trust in the data amongst developers.
has prefix: dqv
is deprecated: false
is part of: Bioregistry
keyword: quality

The data cube vocabulary
has provider formatter: http://purl.org/linked-data/cube#$1
is deprecated: false
0000005: Observation
has local unique identifier pattern: ^\w+$
keyword: w3c rec
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has URI prefix: http://purl.org/linked-data/cube#
has prefix: qb
has resource example: Observation
keyword: methods
description: This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI).
has responsible: Richard Cyganiak
git repository: publishing-statistical-data

Nucleotide
description: The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
has prefix: nucleotide
0000005: 880798137
has provider formatter: https://www.ncbi.nlm.nih.gov/nuccore/$1
is deprecated: false
is part of: Bioregistry
has URI prefix: https://www.ncbi.nlm.nih.gov/nuccore/
has canonical: Nucleotide Sequence Database
has resource example: https://www.ncbi.nlm.nih.gov/nuccore/880798137
type: Resource
has local unique identifier pattern: ^[a-zA-Z0-9_\.]+$

Wheat Ontology
0000005: 0000449
keyword: phenotype
keyword: agriculture
description: This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor. The Wheat Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
has provider formatter: https://cropontology.org/rdf/CO_321:$1
is part of: Bioregistry
git repository: Crop-Ontology
has resource example: CO 321:0000449
has local unique identifier pattern: ^\d{7}$
type: Resource
has download URL: CO 321.owl
keyword: life science
keyword: food
has URI prefix: https://cropontology.org/rdf/CO_321:
keyword: ontology
has responsible: https://orcid.org/0000-0002-9399-8003
has prefix: co_321
is deprecated: false

Creative Biolabs antibody
description: Creative Biolabs Antigen provides identifiers for antibody-based entities such as recombinant, functional, engineered, and format-specific antibodies as well as antibody processing tools, which are essential for applications in diagnostics, therapeutics, and immunology.
0000005: TAB-884
is deprecated: false
has prefix: creativebiolabs.antibody
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
has local unique identifier pattern: ^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$
type: Resource
contributor: Mufaddal Naguthanawala

International Committee on Taxonomy of Viruses Ontology
has URI prefix: http://ictv.global/id/MSL40/
git repository: ictv-ontology
type: Resource
0000005: ICTV19990991
description: Ontology representation of the [International Committee on Taxonomy of Viruses (ICTV)](https://ictv.global/) for the [EVORA project](https://evora-project.eu/)
has provider formatter: http://ictv.global/id/MSL40/$1
has resource example: ICTV19990991
has prefix: ictv
is deprecated: false
is part of: Bioregistry

Disease Drivers Ontology
has download URL: disdriv.owl
has responsible: https://orcid.org/0000-0001-8910-9851
description: Drivers of human diseases including environmental, maternal and social exposures.
has resource example: DISDRIV_0000000
type: Resource
0000005: 0000000
has URI prefix: http://purl.obolibrary.org/obo/DISDRIV_
is deprecated: false
keyword: obo
has prefix: disdriv
keyword: ontology
git repository: DiseaseDriversOntology
has local unique identifier pattern: ^\d+$
has provider formatter: http://purl.obolibrary.org/obo/DISDRIV_$1
is part of: Bioregistry

Corpus Vitrearum
description: A digital photo archive
has URI prefix: https://corpusvitrearum.de/id/
is deprecated: false
has resource example: F3436
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: corpusvitrearum
has responsible: https://orcid.org/0000-0002-5101-5275
type: Resource
has provider formatter: https://corpusvitrearum.de/id/$1
0000005: F3436

H-InvDb Transcript
is deprecated: true
has local unique identifier pattern: ^HIT\d{9}(\.\d+)?$
has resource example: http://h-invitational.jp/hinv/spsoup/transcript_view
is part of: Bioregistry
has prefix: hinv.transcript
0000005: HIT000195363
type: Resource
has URI prefix: http://h-invitational.jp/hinv/spsoup/transcript_view
description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.
has provider formatter: http://h-invitational.jp/hinv/spsoup/transcript_view

Veterans Administration National Drug File
has prefix: vandf
keyword: ontology
is deprecated: false
keyword: pharmacology
has URI prefix: http://purl.bioontology.org/ontology/VANDF/
has resource example: http://purl.bioontology.org/ontology/VANDF/4019477
has local unique identifier pattern: ^\d+$
has provider formatter: http://purl.bioontology.org/ontology/VANDF/$1
description: The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
keyword: biomedical science
keyword: drug interaction
0000005: 4019477
keyword: drug

Synthetic Binding Protein Epitope
0000005: mt002305
has prefix: synbip.epitope
type: Resource
contributor: Mufaddal Naguthanawala
has resource example: mt002305
description: Identifiers for synthetic binding protein-target complexes, detailing their components, 3D structures and docking statistics
is deprecated: false
has local unique identifier pattern: ^mt\d+$
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: http://synbip.idrblab.net/data/sbp-target-complex/details/
has responsible: 0000-0002-1846-639X
is part of: Bioregistry
has provider formatter: http://synbip.idrblab.net/data/sbp-target-complex/details/$1

SPARQL Operation
description: Used for operations in SPARQL, such as ceil() and bound().
has URI prefix: http://www.w3.org/ns/sparql#
is deprecated: false
has resource example: ceil
has provider formatter: http://www.w3.org/ns/sparql#$1
is part of: Bioregistry
0000005: ceil
type: Resource
contributor: Charles Tapley Hoyt
has prefix: sparql

International Clinical Trials Registry Platform
has provider formatter: https://www.isrctn.com/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: https://www.isrctn.com/
has resource example: ISRCTN10175490
description: The International Clinical Trials Registry Platform, originally called International Standard Randomised Controlled Trial Number (ISRCTN) registry, is a primary clinical study registry recognised by the World Health Organisation (WHO) and the International Committee of Medical Journal Editors (ICMJE) that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. All study records in the database are freely accessible and searchable. (from homepage)
type: Resource
has prefix: isrctn
has local unique identifier pattern: ^ISRCTN\d+$
0000005: ISRCTN10175490
is deprecated: false

National Bibliography Number
has URI prefix: http://nbn-resolving.org/
is part of: Bioregistry
0000005: urn:nbn:fi:tkk-004781
has resource example: urn:nbn:fi:tkk-004781
has prefix: nbn
has local unique identifier pattern: ^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$
type: Resource
has provider formatter: http://nbn-resolving.org/$1
description: The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier.
is deprecated: false

Guide to Pharmacology Ligand
has URI prefix: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward
description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
0000005: 1755
has provider formatter: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward
has prefix: iuphar.ligand
has alternative prefix: IUPHAR_LIGAND_ID
type: Resource
has alternative prefix: IUPHAR_LIGAND
has resource example: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward

Dictybase Gene
has local unique identifier pattern: ^DDB_G\d+$
has provider formatter: http://dictybase.org/gene/$1
0000005: DDB_G0267522
is part of: Bioregistry
is part of: dictyBase
type: Resource
has URI prefix: http://dictybase.org/gene/
keyword: gene
has prefix: dictybase.gene
has responsible: https://orcid.org/0000-0002-4532-2703
description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information.
has resource example: DDB G0267522
has download URL: dictybase.gene.owl
keyword: ontology
is deprecated: false

Crates.io
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: curies
type: Resource
description: A repository of software packages written in Rust.
has provider formatter: https://crates.io/crates/$1
has resource example: curies
is deprecated: false
has URI prefix: https://crates.io/crates/
has prefix: crates

Database of Genomic Structural Variation - Study
has provider formatter: https://www.ncbi.nlm.nih.gov/dbvar/studies/$1
0000005: nstd102
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: dbvar.study
has resource example: nstd102
has URI prefix: https://www.ncbi.nlm.nih.gov/dbvar/studies/
type: Resource
description: Studies in dbVar.
has alternative prefix: dbvar.studies
is deprecated: false

Energy Market Roles ontology
has provider formatter: http://www.purl.org/dabgeo/conceptual/energymarketroles#$1
description: The 'Energy Market Roles' ontology module represents the energy market roles of energy agents. Additionally, it includes the consumer role, as it is reused in most of Smart Grid scenarios. This ontology module reuses the knowledge of the 'Actor' ontology module.
is deprecated: false
is part of: Bioregistry
has prefix: energymarketroles
has URI prefix: http://www.purl.org/dabgeo/conceptual/energymarketroles#
keyword: nfdi4energy
type: Resource

SABIO Reaction Kinetics
keyword: classification
keyword: enzyme
keyword: kinetics
has responsible: Ulrike Wittig
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information.
type: Resource
has URI prefix: http://sabiork.h-its.org/kineticLawEntry.jsp
has prefix: sabiork.kineticrecord
has provider formatter: http://sabiork.h-its.org/kineticLawEntry.jsp
has resource example: http://sabiork.h-its.org/kineticLawEntry.jsp
0000005: 5046

Rat Genome Database qTL
has prefix: rgd.qtl
description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes.
0000005: 1354581
type: Resource
has URI prefix: http://rgd.mcw.edu/rgdweb/report/qtl/main.html
has resource example: http://rgd.mcw.edu/rgdweb/report/qtl/main.html
is deprecated: false
has provider formatter: http://rgd.mcw.edu/rgdweb/report/qtl/main.html
has local unique identifier pattern: ^\d+$
is part of: Bioregistry

Rhea reaction
keyword: biochemistry
keyword: life science
is deprecated: false
has resource example: https://www.rhea-db.org/rhea/12345
keyword: reaction
has URI prefix: https://www.rhea-db.org/rhea/
keyword: ontology
has download URL: rhea.owl.gz
0000005: 12345
has local unique identifier pattern: ^\d{5}$
keyword: small molecule
has prefix: rhea
is part of: Bioregistry
has alternative prefix: RHEA
has responsible: https://orcid.org/0000-0002-1216-2969
type: Resource
has provider formatter: https://www.rhea-db.org/rhea/$1
description: Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants. Rhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB.

SWEET Ontology Representation Scientific Component
keyword: representation scientific component
is deprecated: false
0000005: Component
has alternative prefix: sorepsc
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Component
has prefix: sweet.repsc
is part of: Bioregistry
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has URI prefix: http://sweetontology.net/reprSciComponent/
has resource example: Component
type: Resource
has provider formatter: http://sweetontology.net/reprSciComponent/$1

General Multilingual Environmental Thesaurus Relation
has prefix: gemet.relation
0000005: 6237
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: https://www.eionet.europa.eu/gemet/en/relations/
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: https://www.eionet.europa.eu/gemet/en/relations/$1
description: Relations in GEMET
has resource example: https://www.eionet.europa.eu/gemet/en/relations/6237

SWEET Ontology Realm
0000005: Atmosphere
has alternative prefix: SWEETRealm
has URI prefix: http://sweetontology.net/realm/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm
is deprecated: false
has alternative prefix: sorea
has resource example: Atmosphere
has prefix: sweet.rea
is part of: Bioregistry
has provider formatter: http://sweetontology.net/realm/$1
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
keyword: realm
is part of: Semantic Web for Earth and Environment Technology Ontology

National Experimental Cell Resource Sharing Platform
is part of: Bioregistry
type: Resource
has prefix: ccrid
contributor: Charles Tapley Hoyt
has provider formatter: http://www.cellresource.cn/cellsearch.aspx
has resource example: http://www.cellresource.cn/cellsearch.aspx
0000005: 4201PAT-CCTCC00348
is deprecated: false
has URI prefix: http://www.cellresource.cn/cellsearch.aspx
description: Cell line databases/resources

Biomarker Knowledgebase - Canonical Biomarker
contributor: Charles Tapley Hoyt
has resource example: AN6278
has responsible: https://orcid.org/0000-0001-8823-9945
0000005: AN6278
has URI prefix: https://biomarkerkb.org/canonical/
type: Resource
has local unique identifier pattern: ^A(N|O)\d+$
contributor: Jeet Kiran Vora
has prefix: biomarkerkb.canonical
keyword: biomarker
has provider formatter: https://biomarkerkb.org/canonical/$1
description: A canonical biomarker, which describes the composition of a measurement on a change to an entity. For example, the increase in IL6 level
is deprecated: false
is part of: Bioregistry

iCalendar in RDF
description: A vocabulary for calendar events and related objects
type: Resource
0000005: Vevent
is deprecated: false
is part of: Bioregistry
has prefix: ical

Global LEI Index
has provider formatter: https://www.gleif.org/lei/$1
is deprecated: false
has local unique identifier pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$
has prefix: lei
has resource example: HWUPKR0MPOU8FGXBT394
0000005: HWUPKR0MPOU8FGXBT394
description: Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland.
is part of: Bioregistry
type: Resource
has URI prefix: https://www.gleif.org/lei/

VIVO Ontology
description: An ontology about scholarship
0000005: Laboratory
git repository: vivo-ontology
keyword: natural science
keyword: study design
keyword: miscellaneous
has resource example: Laboratory
keyword: ontology
is deprecated: false
has URI prefix: http://vivoweb.org/ontology/core#
keyword: resource metadata
has provider formatter: http://vivoweb.org/ontology/core#$1
has prefix: vivo
has download URL: vivo.owl
keyword: academy
is part of: Bioregistry
has responsible: Christian Hauschke
contributor: Charles Tapley Hoyt
type: Resource

Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse
description: The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.
type: Resource
keyword: gene
has prefix: vbase2
has provider formatter: http://www.vbase2.org/vgene.php
keyword: life science
is deprecated: false
has local unique identifier pattern: ^\w+$
has URI prefix: http://www.vbase2.org/vgene.php
has resource example: http://www.vbase2.org/vgene.php
has responsible: https://orcid.org/0000-0002-1297-9725
is part of: Bioregistry
0000005: humIGHV025

SWEET Ontology Representation Data Service Geospatial
has prefix: sweet.repdsg
has provider formatter: http://sweetontology.net/reprDataServiceGeospatial/$1
has alternative prefix: sorepdsg
0000005: Buffer
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Service Geospatial
has URI prefix: http://sweetontology.net/reprDataServiceGeospatial/
keyword: representation data service geospatial
has resource example: Buffer
is deprecated: false
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
type: Resource

SWEET Ontology Human Environmental Conservation
has URI prefix: http://sweetontology.net/humanEnvirConservation/
type: Resource
git repository: sweet
has prefix: sweet.huecons
has provider formatter: http://sweetontology.net/humanEnvirConservation/$1
has alternative prefix: sohuecons
keyword: environmental conservation
has resource example: Conservation
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
0000005: Conservation
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Environmental Conservation

SWEET Ontology Property Ordinal
has provider formatter: http://sweetontology.net/propOrdinal/$1
0000005: ActivityLevel
has alternative prefix: sopropo
keyword: ordinal
is deprecated: false
has URI prefix: http://sweetontology.net/propOrdinal/
has prefix: sweet.propo
is part of: Bioregistry
has resource example: ActivityLevel
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Ordinal
type: Resource

MarCat
is deprecated: false
is part of: Bioregistry
has URI prefix: https://mmp.sfb.uit.no/databases/marcat/#/records/
has prefix: mmp.cat
type: Resource
0000005: MMP743597.11
has resource example: records/MMP743597.11
has local unique identifier pattern: ^MMP\d+.\d+$
has provider formatter: https://mmp.sfb.uit.no/databases/marcat/#/records/$1
description: MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.

Representing Content in RDF
description: This vocabulary is intended to provide a flexible framework within different usage scenarios to semantically represent any type of content, be it on the Web or in local storage media. For example, it can be used by web quality assurance tools such as web accessibility evaluation tools to record a representation of the assessed web content, including text, images, or other types of formats. In many cases, it can be used together with HTTP Vocabulary in RDF 1.0, which allows quality assurance tools to record the HTTP headers that have been exchanged between a client and a server. This is particularly useful for quality assurance testing, conformance claims, and reporting languages like the W3C Evaluation And Report Language (EARL). [from homepage]
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has prefix: cnt
has provider formatter: http://www.w3.org/2011/content#$1
has URI prefix: http://www.w3.org/2011/content#
has resource example: Content
keyword: rdf
0000005: Content
is deprecated: false

Snapshot
has resource example: Quality
has prefix: snap
description: Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality.
is deprecated: false
has alternative prefix: bfo11snap
0000005: Quality
is part of: Bioregistry
has URI prefix: http://www.ifomis.org/bfo/1.1/snap#
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: http://www.ifomis.org/bfo/1.1/snap#$1

Healthcare Common Procedure Coding System
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: business administration
has responsible: Cynthia Hake
description: HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers.
type: Resource
has prefix: hcpcs
keyword: biomedical science
is deprecated: false
keyword: ontology
has resource example: G8944
0000005: G8944
has provider formatter: http://purl.bioontology.org/ontology/HCPCS/$1
has URI prefix: http://purl.bioontology.org/ontology/HCPCS/

Digital Humanities
has part: Europeana Data Model vocabulary
has part: Iconclass Classification
has part: Cultural Objects Names Authority
type: Collection
has part: Union List of Artist Names
has part: CIDOC Conceptual Reference Model
has part: Getty Vocabulary Program ontology
creator: Charles Tapley Hoyt
has part: Getty Thesaurus of Geographic Names
has part: Getty Iconography Authority
has part: Art and Architecture Thesaurus
description: Prefixes relevant for the digital humanities

Immune Epitope Database Epitopes
has URI prefix: https://www.iedb.org/epitope/
type: Resource
has resource example: https://www.iedb.org/epitope/117395
has responsible: https://orcid.org/0000-0001-8957-7612
keyword: life science
contributor: Mufaddal Naguthanawala
keyword: immunology
is deprecated: false
keyword: small molecule
is part of: Bioregistry
keyword: protein
0000005: 117395
has local unique identifier pattern: ^\d+$
keyword: bioinformatics
has prefix: iedb.epitope
has reviewer: https://orcid.org/0000-0001-9439-5346
description: Identifiers for epitopes, which are the specific parts of antigens recognized by the immune system.
has provider formatter: https://www.iedb.org/epitope/$1

Integrated Chemical Environment - Chemical data
description: The Integrated Chemical Environment (ICE) provides high-quality curated data and appropriate tools to support development and evaluation of new, revised, and alternative methods. ICE provides free online access to curated in vivo and in vitro test data, in silico toxicity predictions and chemical property data, reference chemical lists, and computational tools for chemical characterization and predicting toxicity. ICE supports the following: (i) Data integration: brings together available data, including data on formulations; (ii) Results exploration: enables dynamic, graphical exploration with publication-quality graphics; (iii) Data analysis: allows characterization of data using online workflows, and (iv) FAIR data access: data are findable, accessible, interoperable, and reusable.
has local unique identifier pattern: ^\d{2,7}-\d{2}-\d|DTXSID\d{7,9}|[A-Z]{14}-[A-Z]{8}[SN][A-Z]-[A-Z]$
has resource example: https://ice.ntp.niehs.nih.gov/api/v1/search
has prefix: icechem
type: Resource
has URI prefix: https://ice.ntp.niehs.nih.gov/api/v1/search
has provider formatter: https://ice.ntp.niehs.nih.gov/api/v1/search
is deprecated: false
0000005: DTXSID7032004
is part of: Bioregistry

OMA HOGs
is part of: Bioregistry
has prefix: oma.hog
type: Resource
has local unique identifier pattern: ^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$
has provider formatter: https://omabrowser.org/oma/hog/HOG:$1
has URI prefix: https://omabrowser.org/oma/hog/HOG:
has resource example: HOG:0459895
0000005: 0459895
description: Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference.
is deprecated: false

NMR Restraints Grid
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
keyword: nmr
has prefix: bmrb.restraint
has resource example: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
0000005: 28789
is deprecated: false
description: The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively.
keyword: chemistry
keyword: spectrometry

SWEET Ontology Phenomena Geologic Seismicity
has resource example: Aftershock
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: phenomena
has prefix: sweet.phgs
keyword: geologic seismicity
has provider formatter: http://sweetontology.net/phenGeolSeismicity/$1
0000005: Aftershock
has alternative prefix: sophgs
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Seismicity
is deprecated: false
has URI prefix: http://sweetontology.net/phenGeolSeismicity/

Human Endogenous Retrovirus Database
description: Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features.
has provider formatter: https://herv.img.cas.cz/s/$1
is deprecated: false
0000005: THE1B
has local unique identifier pattern: ^[A-Za-z0-9\-\_]+$
is part of: Bioregistry
type: Resource
has URI prefix: https://herv.img.cas.cz/s/
has prefix: erv
has resource example: THE1B

VMH metabolite
has URI prefix: https://www.vmh.life/#metabolite/
is part of: Bioregistry
description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.
has prefix: vmhmetabolite
type: Resource
0000005: h2o
has local unique identifier pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$
is deprecated: false
has resource example: metabolite/h2o
has provider formatter: https://www.vmh.life/#metabolite/$1

IOC: Internet of Construction Ontology
is deprecated: false
keyword: digital planning and construction
is part of: Bioregistry
description: The Internet of Construction Ontology (IoC) construction process ontology is intended to represent a comprehensive solution of how processes in the construction industry can be modelled. Due to the iterative nature of creating an ontology, the construction process ontology presented here can at best be considered a working state at the time of publication. Our approach emphasizes the simplest and most comprehensive mapping possible, which is only extended based on insights from practical use when otherwise compelling limitations in usability and applicability arise. Thus, the extension and refinement of the developed construction process ontology strongly depends on the integration of further areas of the construction value chain and the connection of further domain ontologies.
has URI prefix: http://w3id.org/ioc#
keyword: fid baudigital
has prefix: tib.ioc
type: Resource
keyword: nfdi4ing
has provider formatter: http://w3id.org/ioc#$1
has resource example: Actor
keyword: civil engineering
0000005: Actor

Encyclopedia of DNA Elements
is deprecated: false
is part of: Bioregistry
has URI prefix: https://www.encodeproject.org/
has responsible: Idan Gabdank
has prefix: encode
keyword: functional genomics
0000005: ENCSR163RYW
has provider formatter: https://www.encodeproject.org/$1
type: Resource
description: The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.
keyword: epigenetics
has local unique identifier pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$
has resource example: ENCSR163RYW

Internet Engineering Task Force Language Tag
has local unique identifier pattern: ^\w{2,3}(-\w+)?$
has prefix: ietf.language
description: Shorthand representations of languages and their subtypes
0000005: en-GB
has alternative prefix: bcp47
is deprecated: false
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt

Lifestyle Factors Ontology
description: In this ontology, we defined nine distinct categories that encompass various aspects of lifestyle factors (LSFs), creating a unified Lifestyle Factors Ontology (LSFO) across these categories. Within the context of lifestyle, we have identified nine categories that can collectively describe all LSFs, namely: 1-Nutrition, a category that covers different branches such as dietary habits, food groups, food processing and preparation, macronutrients, and micronutrients, among others. 2-Socioeconomic factors, which includes social and economic conditions such as income, wealth, education and socioeconomic status. 3-Environmental exposures, includes exposure to various environmental factors, such as air pollution, water quality, and workplace hazards, that can impact an individual’s health. 4-Substance use, covers concepts such as smoking, as well as illicit drug use. 5-Physical activities, includes regular exercise and physically demanding activities like leisure time, occupational, and household physical activities. 6-Non-physical leisure time activities, describes any activity an individual might engage in during their free time that is not a physical activity. 7-Personal care products and cosmetic procedures, covers activities related to hygiene, use of cosmetic and cleaning products as well as invasive procedures that people undergo to improve their appearance, such as cosmetic surgery. 8-Sleep, covers sleep quality, stages, and habits. 9-Mental health practices, includes the behaviors and habits related to maintaining good mental health and emotional well-being such as meditation, and psychotherapy.
has provider formatter: http://purl.obolibrary.org/obo/LFID_$1
has URI prefix: http://purl.obolibrary.org/obo/LFID_
keyword: ontology
0000005: 0000015
is deprecated: false
has download URL: LSFO.owl
has resource example: LFID_0000015
is part of: Bioregistry
type: Resource
has prefix: lifestylefactors
has responsible: Lars Juhl Jensen

NIF Standard Ontology
type: Resource
has prefix: nif.std
has resource example: BAMSC981
keyword: neuroscience
has URI prefix: http://uri.neuinfo.org/nif/nifstd/
has alternative prefix: NIFSTD
has local unique identifier pattern: ^BAMSC\d+$
has reviewer: Charles Tapley Hoyt
contributor: Tom Gillespie
has provider formatter: http://uri.neuinfo.org/nif/nifstd/$1
description: NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing.
keyword: ontology
has responsible: Tom Gillespie
has download URL: nifstd.owl
is deprecated: false
keyword: disease
git repository: NIF-Ontology
is part of: Bioregistry
0000005: BAMSC981
keyword: brain

miRNA Target Prediction at EMBL
has prefix: mirte
is deprecated: false
description: This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: miR-1
type: Resource

FlyBrain Neuron Database
description: A database of fly neurons and pathways with an associated 3D viewer.
has provider formatter: https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html
type: Resource
is deprecated: false
has URI prefix: https://bioregistry.io/flybrain.ndb:
0000005: 10531
has resource example: https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=10531&-find=-find.html
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has prefix: flybrain.ndb

SWEET Ontology Phenomena Atmosphere
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere
is part of: Bioregistry
type: Resource
0000005: AirMass
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: phenomena
has prefix: sweet.phatmo
has alternative prefix: sophatmo
keyword: atmosphere
has URI prefix: http://sweetontology.net/phenAtmo/
has provider formatter: http://sweetontology.net/phenAtmo/$1
is deprecated: false
has resource example: AirMass

Saccharomyces genome database pathways
has local unique identifier pattern: ^PWY\w{2}\-\d{3}$
has resource example: http://pathway.yeastgenome.org/YEAST/new-image
description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD).
has provider formatter: http://pathway.yeastgenome.org/YEAST/new-image
keyword: pathway
keyword: sequence
keyword: genome
has responsible: Karen R. Christie
is deprecated: false
has URI prefix: http://pathway.yeastgenome.org/YEAST/new-image
0000005: PWY3O-214
is part of: Bioregistry
has prefix: sgd.pathways
type: Resource

Protocol for Web Description Resources (POWDER) Schema
has prefix: wdr
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: http://www.w3.org/2007/05/powder#$1
description: Underlying schema for POWDER
type: Resource
0000005: tag
has resource example: tag
has URI prefix: http://www.w3.org/2007/05/powder#

SWEET Ontology Process
type: Resource
0000005: Force
has URI prefix: http://sweetontology.net/proc/
has prefix: sweet.proc
has provider formatter: http://sweetontology.net/proc/$1
has alternative prefix: soproc
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process
has resource example: Force
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: process
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology

Core Ontology for Robotics and Automation
0000005: -bare#CollectiveRoboticSystem
has provider formatter: http://purl.org/ieee1872-owl/cora$1
is deprecated: false
is part of: Bioregistry
keyword: engineering
description: This is the OWL implementation of CORA in IEEE 1872-2015. It only includes the taxonomy of concepts and relations, with some few axioms reggarding disjointness, property characteristics and property ranges/domains. The OWL implementation is an underspecified version of the SUO-KIF implementation in IEEE 1872-2015. That is, the set of allowed models of the SUO-KIF implementation is a proper subset of the allowed models by the OWL implementation. Concept definitions in natural language and othe clarifications can be found in the IEEE 1872-2015 standard.
has resource example: CollectiveRoboticSystem
has URI prefix: http://purl.org/ieee1872-owl/cora
type: Resource
has prefix: cora
keyword: nfdi4ing

OriDB Saccharomyces
has URI prefix: http://cerevisiae.oridb.org/details.php
type: Resource
has prefix: oridb.sacch
has provider formatter: http://cerevisiae.oridb.org/details.php
0000005: 1
has resource example: http://cerevisiae.oridb.org/details.php
is deprecated: false
has local unique identifier pattern: ^\d+$
description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.
is part of: Bioregistry

Golm Metabolome Database GC-MS spectra
has provider formatter: http://gmd.mpimp-golm.mpg.de/Spectrums/$1
has local unique identifier pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
is deprecated: false
description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.
has prefix: gmd.gcms
has URI prefix: http://gmd.mpimp-golm.mpg.de/Spectrums/
is part of: Bioregistry
type: Resource

SciCrunch Registry
keyword: life science
keyword: interactive portal
has responsible: https://orcid.org/0000-0002-5497-0243
keyword: neurobiology
0000005: 022586
has provider formatter: http://scicrunch.org/resolver/SCR_$1
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has alternative prefix: scicrunch
description: The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources.
keyword: rrid
has prefix: scr
has URI prefix: http://scicrunch.org/resolver/SCR_
type: Resource
keyword: nih initiative
has resource example: SCR_022586

NFDI Knowledge Graph Registry
has URI prefix: http://kgi.services.base4nfdi.de/entity/
has provider formatter: http://kgi.services.base4nfdi.de/entity/$1
description: Assigns identifiers to knowledge graphs (KGs) that are used and/or maintained within any NFDI consortium.
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has responsible: Lozana Rossenova
has local unique identifier pattern: ^KGR\d+$
has resource example: KGR1
keyword: knowledge graph
type: Resource
git repository: kgi4nfdi registry data
0000005: KGR1
has prefix: nfdi.kgi
is deprecated: false

ClinVar Submitter
is part of: Bioregistry
has URI prefix: https://www.ncbi.nlm.nih.gov/clinvar/submitters/
has local unique identifier pattern: ^\d+$
description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs).
has provider formatter: https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1
0000005: 26957
has prefix: clinvar.submitter
type: Resource
has resource example: https://www.ncbi.nlm.nih.gov/clinvar/submitters/26957
is deprecated: false

Current Dental Terminology
has download URL: CDTCodes as Classes pruned.owl
has prefix: cdt
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
contributor: Charles Tapley Hoyt
type: Resource
description: The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment. Note that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D.
appears in: Oral Health and Disease Ontology
0000005: 1000001
keyword: ontology
is deprecated: false

National Library of Medicine Catalog
has URI prefix: https://www.ncbi.nlm.nih.gov/nlmcatalog/
description: The NLM Catalog provides access to NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials. Links to the library's holdings in LocatorPlus, NLM's online public access catalog, are also provided. [from homepage]
0000005: 101775319
has prefix: nlm
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: https://www.ncbi.nlm.nih.gov/nlmcatalog/$1
has download URL: nlm.owl
has resource example: https://www.ncbi.nlm.nih.gov/nlmcatalog/101775319
keyword: ontology
is deprecated: false
keyword: journal

Data Privacy Vocabulary
has prefix: dpvocab
keyword: security
keyword: people
has provider formatter: https://w3id.org/dpv#$1
has URI prefix: https://w3id.org/dpv#
type: Resource
keyword: nfdi4ing
has resource example: Duration
0000005: Duration
contributor: Mufaddal Naguthanawala
contributor: Harry Caufield
has reviewer: Charles Tapley Hoyt
description: The Data Privacy Vocabulary provides an ontology (classes and properties) and taxonomies of concepts to represent information regarding how personal data is processed in the form of an ontology or a knowledge graph.
keyword: ess
contributor: https://orcid.org/0000-0001-9439-5346
keyword: law
contributor: https://orcid.org/0000-0002-9698-1899
has responsible: https://orcid.org/0000-0002-5068-3714
git repository: dpv
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt

PubChem Substance ID (SID)
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/substance/$1
type: Resource
keyword: structure
0000005: 100101
is deprecated: false
has alternative prefix: DSSTox_Generic_SID
has resource example: https://pubchem.ncbi.nlm.nih.gov/substance/100101
description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records.
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/substance/
keyword: small molecule
is part of: Bioregistry
keyword: protein
has local unique identifier pattern: ^\d+$
has prefix: pubchem.substance

Wildlife Monitoring Ontology
keyword: ess
has prefix: wlmo
has resource example: Annotation
is deprecated: false
has provider formatter: https://wildlive.senckenberg.de/wlmo/$1
is part of: Bioregistry
keyword: earth sciences
has URI prefix: https://wildlive.senckenberg.de/wlmo/
type: Resource
description: This semantic artifact describes the semantic relationships between entities which model the setup of a biodiversity monitoring project based on capturing audiovisual digital recordings. It encodes the semantics of the Wildlife Monitoring Ontology and at the same time provides the datamodel behind the wildlive.senckenberg.de platform.
0000005: Annotation

Human BioMolecular Atlas Program Collection
description: The collections section of HuBMAP groups related datasets, samples, and metadata into organized categories. Each collection has a unique identifier that links it to its constituent datasets.
has URI prefix: https://portal.hubmapconsortium.org/browse/collection/
contributor: 0009-0008-8406-631X
is deprecated: false
has prefix: hubmap.collection
is part of: Bioregistry
has local unique identifier pattern: ^[a-f0-9]{32}$
has reviewer: https://orcid.org/0000-0001-9439-5346
type: Resource
has responsible: Katy Börner
has provider formatter: https://portal.hubmapconsortium.org/browse/collection/$1

Joint Genome Institute Proposals
0000005: 502930
contributor: https://orcid.org/0000-0002-5004-3362
is deprecated: false
has URI prefix: https://genome.jgi.doe.gov/portal/lookup
has resource example: https://genome.jgi.doe.gov/portal/lookup
description: Identifiers for proposals/projects at the Joint Genome Institute
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
has responsible: 0000-0002-8489-208X
has reviewer: Charles Tapley Hoyt
has prefix: jgi.proposal
has provider formatter: https://genome.jgi.doe.gov/portal/lookup

Darwin Core pathway controlled vocabulary
keyword: life sciences, biology
has prefix: dwc.pw
is part of: Bioregistry
has URI prefix: http://rs.tdwg.org/dwcpw/
type: Resource
0000005: p001
keyword: fair data spaces
has resource example: p001
description: The Darwin Core term pathway provides information about the process by which an Organism came to be in a given place at a given time. The Pathway Controlled Vocabulary provides terms that should be used as values for dwc:pathway and dwciri:pathway.
is deprecated: false
has provider formatter: http://rs.tdwg.org/dwcpw/$1

Canadian Drug Product Database
has URI prefix: https://health-products.canada.ca/dpd-bdpp/info
0000005: 63250
is deprecated: false
has provider formatter: https://health-products.canada.ca/dpd-bdpp/info
description: The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).
has local unique identifier pattern: ^\d+$
has resource example: https://health-products.canada.ca/dpd-bdpp/info
is part of: Bioregistry
has prefix: cdpd
type: Resource

Human Cell Atlas Ontology
is deprecated: false
has download URL: hcao.owl
is part of: Bioregistry
type: Resource
has prefix: hcao
description: Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.
keyword: ontology

Mechanism, Annotation and Classification in Enzymes
has local unique identifier pattern: ^M\d{4}$
has URI prefix: https://www.ebi.ac.uk/thornton-srv/m-csa/search/
has responsible: Gemma L. Holliday
description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.
type: Resource
has resource example: https://www.ebi.ac.uk/thornton-srv/m-csa/search/
keyword: life science
is deprecated: false
keyword: enzyme
has prefix: macie
keyword: pathway
0000005: M0001
is part of: Bioregistry
has provider formatter: https://www.ebi.ac.uk/thornton-srv/m-csa/search/

OECD TIVA Ontology
has resource example: hasExport
description: An ontology for modeling international trade flows.
type: Resource
keyword: coypu
0000005: hasExport
is deprecated: false
has URI prefix: https://schema.coypu.org/vtf#
has provider formatter: https://schema.coypu.org/vtf#$1
keyword: economics
has prefix: coypu.tiva
is part of: Bioregistry

Datanator Metabolite
is deprecated: false
is part of: Bioregistry
has prefix: datanator.metabolite
0000005: OUYCCCASQSFEME-MRVPVSSYSA-N
has resource example: OUYCCCASQSFEME-MRVPVSSYSA-N
type: Resource
has local unique identifier pattern: ^[A-Z\-]+$
description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.
has provider formatter: https://www.datanator.info/metabolite/$1
has URI prefix: https://www.datanator.info/metabolite/

SWEET Ontology Property Temperature
type: Resource
has URI prefix: http://sweetontology.net/propTemperature/
keyword: temperature
is deprecated: false
is part of: Bioregistry
has provider formatter: http://sweetontology.net/propTemperature/$1
has resource example: AntennaTemperature
0000005: AntennaTemperature
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Temperature
has prefix: sweet.propt
has alternative prefix: sopropt

Database of Aligned Ribosomal Complexes
is deprecated: true
has URI prefix: http://darcsite.genzentrum.lmu.de/darc/view.php
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.
has responsible: https://orcid.org/0000-0003-3816-3828
type: Resource
has prefix: darc
0000005: 1250
has provider formatter: http://darcsite.genzentrum.lmu.de/darc/view.php
has resource example: http://darcsite.genzentrum.lmu.de/darc/view.php
keyword: life science

Biomarker Knowledgebase - Biomarker
keyword: biomarker
description: A disease/condition-specific instantiation of a canonical biomarker
contributor: Jeet Kiran Vora
is deprecated: false
has provider formatter: https://biomarkerkb.org/biomarker/$1
has local unique identifier pattern: ^A(N|O)\d+-\d+$
has resource example: AN6278-5
is part of: Bioregistry
has URI prefix: https://biomarkerkb.org/biomarker/
type: Resource
contributor: Charles Tapley Hoyt
has prefix: biomarkerkb.biomarker
has responsible: https://orcid.org/0000-0001-8823-9945
0000005: AN6278-5

Genome assembly database - RefSeq accessions
is part of: Bioregistry
has local unique identifier pattern: ^GCF_[0-9]{9}(\.[0-9]+)?$
description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database RefSeq accessions does not extend to viroids and bacteriophage.
type: Resource
0000005: GCF_000001405
has URI prefix: https://www.ncbi.nlm.nih.gov/datasets/genome/
has alternative prefix: insdc.gcf
has provider formatter: https://www.ncbi.nlm.nih.gov/datasets/genome/$1
has resource example: GCF_000001405
has canonical: Assembly
has prefix: insdc.gcf
is deprecated: false

GeneCards Gene
keyword: transcriptomics
type: Resource
has responsible: https://orcid.org/0000-0001-5424-1393
description: The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene.
has local unique identifier pattern: ^[A-Za-z-0-9_]+(\@)?$
has prefix: genecards.gene
0000005: ABL1
has provider formatter: https://www.genecards.org/cgi-bin/carddisp.pl
keyword: life science
is deprecated: false
has URI prefix: https://www.genecards.org/cgi-bin/carddisp.pl
has resource example: https://www.genecards.org/cgi-bin/carddisp.pl
keyword: genetics
keyword: genome
is part of: Bioregistry
has alternative prefix: genecards

AspGD Protein
has URI prefix: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl
is part of: Bioregistry
has local unique identifier pattern: ^[A-Za-z_0-9]+$
has prefix: aspgd.protein
has resource example: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl
0000005: ASPL0000349247
type: Resource
has provider formatter: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl
is deprecated: true
description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information.

Vitis Ontology
type: Resource
has resource example: CO 356:4000027
has prefix: co_356
description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Vitis Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
keyword: life science
is deprecated: false
has URI prefix: https://cropontology.org/rdf/CO_356:
has provider formatter: https://cropontology.org/rdf/CO_356:$1
keyword: ontology
keyword: plant phenotypes and traits
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
0000005: 4000027
keyword: phenotype
git repository: Crop-Ontology
has download URL: CO 356.owl
keyword: botany
keyword: agriculture

MGnify Genome
is deprecated: false
has resource example: MGYG000004903
description: The free-to-use MGnify platform provides assembly, analysis and archiving of microbiome-derived nucleic acid sequence data from a wide range of biomes, with analysis results providing taxonomic and functional profiles. The platform also includes MGnify Proteins, a database of protein sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes, a resource of biome-specific catalogues of microbial genomes, including extensive functional annotations.
has local unique identifier pattern: ^MGYG\d{9}(\.\d+)?$
is part of: Bioregistry
type: Resource
has provider formatter: https://www.ebi.ac.uk/metagenomics/genomes/$1
0000005: MGYG000004903
has URI prefix: https://www.ebi.ac.uk/metagenomics/genomes/
has prefix: mgnifygenome

SABIO-RK EC Record
0000005: 2.7.1.1
has prefix: sabiork.ec
has resource example: http://sabiork.h-its.org/newSearch
keyword: reaction
has provider formatter: http://sabiork.h-its.org/newSearch
is deprecated: false
description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data.
has URI prefix: http://sabiork.h-its.org/newSearch
has local unique identifier pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$
0000011: Enzyme Nomenclature
has responsible: Ulrike Wittig
is part of: Bioregistry
type: Resource

IMGT/PRIMER-DB
description: The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).
has resource example: http://imgt.org/IMGTPrimerDB/Check_PrDB.pl
is deprecated: false
0000005: IPP900099
is part of: Bioregistry
keyword: dna
has URI prefix: https://bioregistry.io/imgt.primerdb:
has provider formatter: http://imgt.org/IMGTPrimerDB/Check_PrDB.pl
has prefix: imgt.primerdb
type: Resource

MOSAiC Ontology
has prefix: mosaic
contributor: Harry Caufield
keyword: ontology
is deprecated: false
0000005: 00005643
has provider formatter: https://purl.dataone.org/odo/MOSAIC_$1
has download URL: MOSAiC.owl
has responsible: Bryce Mecum
has local unique identifier pattern: ^\d{8}$
has URI prefix: https://purl.dataone.org/odo/MOSAIC_
is part of: Bioregistry
description: An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io).
type: Resource
has resource example: MOSAIC_00005643
git repository: sem-prov-ontologies
has reviewer: Charles Tapley Hoyt

ISO Object Identifier
is deprecated: false
has responsible: https://orcid.org/0009-0001-5055-9262
is part of: Bioregistry
0000005: 2.16.840
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^[\d.]+$
has prefix: oid
type: Resource
contributor: https://orcid.org/0009-0001-5055-9262
has resource example: https://oid-base.com/get/2.16.840
has URI prefix: https://oid-base.com/get/
has provider formatter: https://oid-base.com/get/$1
description: OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes.

Viral Bioinformatics Resource Center
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has URI prefix: http://vbrc.org/gene_detail.asp
has provider formatter: http://vbrc.org/gene_detail.asp
0000005: 35742
description: The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.
has prefix: vbrc
is deprecated: true
has resource example: http://vbrc.org/gene_detail.asp

E-cyanobacterium model
has provider formatter: https://e-cyanobacterium.org/models/model/$1
is deprecated: false
description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.
has resource example: https://e-cyanobacterium.org/models/model/26
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
0000005: 26
type: Resource
has prefix: ecyano.model
has URI prefix: https://e-cyanobacterium.org/models/model/

General Data Format
has URI prefix: https://vocabularies.cessda.eu/vocabulary/GeneralDataFormat#code_
type: Resource
has prefix: ddi.generaldataformat
description: Describes the physical format(s) of the data documented in the logical product(s) of a study unit.
has identifier space owner: 015em2733
is deprecated: false
0000005: Numeric
has resource example: code Numeric
has provider formatter: https://vocabularies.cessda.eu/vocabulary/GeneralDataFormat#code_$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt

MolBiC Cell Line
has responsible: https://orcid.org/0000-0001-8069-0053
is deprecated: false
has resource example: CL000025
has provider formatter: https://molbic.idrblab.net/data/cellline/details/$1
has reviewer: https://orcid.org/0000-0001-9439-5346
is part of: Bioregistry
type: Resource
has local unique identifier pattern: ^CL\d+$
description: MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for cell lines used in assays measuring molecular bioactivity, linking them to associated compounds and proteins.
0000005: CL000025
has URI prefix: https://molbic.idrblab.net/data/cellline/details/
has prefix: molbic.cellline
contributor: Mufaddal Naguthanawala

PUNCH4NFDI Collection
has part: Bioregistry
type: Collection
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for PUNCH4NFDI
creator: Charles Tapley Hoyt

African Population Ontology
git repository: afpo
type: Resource
has download URL: afpo.owl
has provider formatter: http://purl.obolibrary.org/obo/AfPO_$1
is deprecated: false
keyword: obo
has responsible: https://orcid.org/0000-0001-5868-4204
0000005: 0000440
keyword: ontology
description: AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms.
has prefix: afpo
has URI prefix: http://purl.obolibrary.org/obo/AfPO_
is part of: Bioregistry

Yeast Metabolome Database
has local unique identifier pattern: ^YMDB\d+$
has resource example: YMDB00001
0000005: YMDB00001
has responsible: David Wishart
description: The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast).
type: Resource
has prefix: ymdb
keyword: life science
has provider formatter: http://www.ymdb.ca/compounds/$1
is deprecated: false
has URI prefix: http://www.ymdb.ca/compounds/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: metabolomics

Diagnostic and Statistical Manual of Mental Disorders (5th Edition)
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has alternative prefix: dsm-v
0000005: 312.33
has prefix: dsm5
description: A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]
is deprecated: false
has local unique identifier pattern: ^\d{3}\.\d{2}$

E-cyanobacterium Experimental Data
has provider formatter: https://www.e-cyanobacterium.org/experiments-repository/
type: Resource
0000005: 18
has URI prefix: https://www.e-cyanobacterium.org/experiments-repository/
description: E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments.
is deprecated: false
has resource example: https://www.e-cyanobacterium.org/experiments-repository/
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: ecyano.experiment

Role Ontology
has reviewer: Charles Tapley Hoyt
has local unique identifier pattern: ^\d{7}$
has prefix: roleo
is deprecated: true
keyword: obo
keyword: ontology
has download URL: roleo.owl
has responsible: Yongqun Oliver He
description: The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.
has resource example: RoleO_0000002
has URI prefix: http://purl.obolibrary.org/obo/RoleO_
is part of: Bioregistry
0000005: 0000002
has provider formatter: http://purl.obolibrary.org/obo/RoleO_$1
type: Resource

ChemBioSys Investigation
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: https://data.chembiosys.de/investigations/$1
description: An investigation in the ChemBioSys data platform
0000005: 27
has prefix: chembiosys.investigation
has URI prefix: https://data.chembiosys.de/investigations/
is deprecated: false
has resource example: https://data.chembiosys.de/investigations/27

CDC Publisher Names
has prefix: cessda.cdcpublishernames
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
0000005: AUSSDA
description: Names of organisations providing metadata for CESSDA Data Catalogue.
has identifier space owner: 02wg9xc72
has URI prefix: https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames#code_
has resource example: code AUSSDA
has provider formatter: https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames#code_$1
is deprecated: false

Genitourinary Development Molecular Anatomy Project
keyword: cell biology
has local unique identifier pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
has URI prefix: https://gudmap.org/id/
has resource example: Q-2958
is deprecated: false
keyword: developmental biology
keyword: genomics
keyword: molecular biology
has responsible: Simon Douglas Harding
is part of: Bioregistry
has prefix: gudmap
0000005: Q-2958
type: Resource
description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.
has provider formatter: https://gudmap.org/id/$1

KonsortSWD
has part: Date Type
has part: Contributor Role
has part: Numeric Type
has part: CDC Publisher Names
has part: Consortium of European Social Science Data Archives Vocabulary
has part: Summary Statistic Type
has part: Sampling Procedure
has part: Language Proficiency
description: [KonsortSWD (Strengthen, Widen, Deepen)](https://www.nfdi.de/consortia-konsortswd) is the German National Data Infrastructure (NFDI) consortium for social, educational, behavioral, and economic sciences. This collection reflects the prefixes collected by NFDI Section Metadata for ontologies and controlled vocabularies used by members of the consortium.
has part: Software Package
has part: Data Source Type
type: Collection
has part: Type of Address
has part: General Data Format
has part: Character Set
has part: Commonality Type
has part: Response Unit
has part: Data types in R|EX research
has part: Type of Concept Group
has part: Variables relations for Social Sciences research data
has part: Mode Of Collection
has part: Type of Note
creator: Charles Tapley Hoyt
has part: Time Method
has part: Time Zone
has part: Data Type
has part: Type of Instrument
has part: Central concepts of R|EX research
has part: Lifecycle Event Type
has part: CESSDA Topic Classification
has part: Category Scheme Election Studies
has part: CESSDA Data Catalogue Collections
has part: Aggregation Method
has part: Type of Frequency
has part: Type of Telephone
has part: Diversification criteria of R|EX research
has part: Country Names and Codes
has part: CESSDA Persistent Identifier Types
has part: Analysis Unit
has part: Type of Translation Method

Ensembl Protists
is deprecated: false
0000005: PF3D7_1328700
has local unique identifier pattern: ^\w+$
is part of: Bioregistry
keyword: genome
has provider formatter: https://protists.ensembl.org/id/$1
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes.
type: Resource
has prefix: ensembl.protist
has resource example: PF3D7_1328700
has URI prefix: https://protists.ensembl.org/id/

Vertebrate Gene Nomenclature Committee
type: Resource
keyword: life science
is deprecated: false
has URI prefix: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/
has local unique identifier pattern: ^\d{1,9}$
has responsible: Susan Tweedie
has resource example: !/vgnc id/3792
has provider formatter: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1
is part of: Bioregistry
description: The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee.
has prefix: vgnc
0000005: 3792

Datanator Gene
has URI prefix: https://www.datanator.info/gene/
0000005: K00973
is part of: Bioregistry
has local unique identifier pattern: ^K[0-9]+$
has resource example: K00973
has prefix: datanator.gene
type: Resource
has provider formatter: https://www.datanator.info/gene/$1
description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.
is deprecated: false

Ontology for Chemical Kinetic Reaction Mechanisms
description: Represents chemical kinetic reaction mechanisms.
keyword: ontology
keyword: chemical and environmental engineering
has prefix: worldavatar.kin
is deprecated: false
is part of: Bioregistry
keyword: chemistry
keyword: nfdi4cat
0000005: ElementNumber
contributor: Charles Tapley Hoyt
has URI prefix: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#
keyword: nfdi4chem
has download URL: OntoKin.owl
has provider formatter: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1
has resource example: ElementNumber
type: Resource

has reviewer
description: The reviewer of a prefix
type: Property
domain: Resource
range: Person

SWEET Ontology Material Biomass
is part of: Bioregistry
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
keyword: materials
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Biomass
0000005: AnimalWaste
has resource example: AnimalWaste
keyword: biomass
has alternative prefix: somab
has prefix: sweet.mab
is deprecated: false
has URI prefix: http://sweetontology.net/matrBiomass/
has provider formatter: http://sweetontology.net/matrBiomass/$1

Genome Properties
keyword: genome
is deprecated: false
has local unique identifier pattern: ^GenProp\d+$
has provider formatter: https://www.ebi.ac.uk/interpro/genomeproperties/#$1
is part of: Bioregistry
0000005: GenProp0699
type: Resource
has resource example: GenProp0699
has URI prefix: https://www.ebi.ac.uk/interpro/genomeproperties/#
has identifier space owner: 02catss52
has prefix: genprop
keyword: classification
description: Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome.

H-InvDb Locus
has prefix: hinv.locus
is part of: Bioregistry
0000005: HIX0004394
has provider formatter: http://h-invitational.jp/hinv/spsoup/locus_view
description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.
type: Resource
has resource example: http://h-invitational.jp/hinv/spsoup/locus_view
has URI prefix: http://h-invitational.jp/hinv/spsoup/locus_view
is deprecated: true
has local unique identifier pattern: ^HIX\d{7}(\.\d+)?$

CLARIN Concept Registry
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: http://hdl.handle.net/11459/
has provider formatter: http://hdl.handle.net/11459/$1
description: Concepts for encoding bibliometric information
has prefix: clarin.concept

NIF Standard Ontology: OEN Terms in Neurolex
has prefix: nlx.oen
has alternative prefix: NLXOEN
has provider formatter: http://uri.neuinfo.org/nif/nifstd/oen_$1
description: NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results).
has resource example: oen_0001000
is deprecated: false
git repository: NIF-Ontology
0000005: 0001000
has responsible: Tom Gillespie
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
keyword: neuroscience
has URI prefix: http://uri.neuinfo.org/nif/nifstd/oen_
has reviewer: Charles Tapley Hoyt
contributor: Tom Gillespie

Higher Education Resource Types
is deprecated: false
has URI prefix: https://w3id.org/kim/hcrt/
0000005: simulation
keyword: educational resources
has provider formatter: https://w3id.org/kim/hcrt/$1
is part of: Bioregistry
has prefix: kim.hcrt
has resource example: simulation
contributor: Charles Tapley Hoyt
git repository: hcrt
description: A controlled vocbualry of higher education resource types
type: Resource
keyword: educational science

European Food Information Resource Network
has prefix: eurofir
is deprecated: false
is part of: Bioregistry
description: EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries.
contributor: Charles Tapley Hoyt
type: Resource

Saccharomyces cerevisiae promoter database
has reviewer: Charles Tapley Hoyt
is deprecated: true
description: Database containing promotor sequences found in Saccharomyces cerevisiae.
keyword: rna
has URI prefix: http://rulai.cshl.edu/cgi-bin/SCPD/getgene2
keyword: dna
0000005: CDC2
has prefix: scpd
has provider formatter: http://rulai.cshl.edu/cgi-bin/SCPD/getgene2
is part of: Bioregistry
type: Resource
has resource example: http://rulai.cshl.edu/cgi-bin/SCPD/getgene2

Common Science and Technology Resources
has URI prefix: https://cstr.cn/
description: CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources.
is deprecated: false
keyword: centrally registered identifier
is part of: Bioregistry
0000005: 31253.11.sciencedb.j00001.00123
has prefix: cstr
keyword: open science
has provider formatter: https://cstr.cn/$1
type: Resource
has local unique identifier pattern: ^\w{5}\.\d{2}\..*$
keyword: subject agnostic
has resource example: 31253.11.sciencedb.j00001.00123

Plant Reactome
has provider formatter: https://plantreactome.gramene.org/content/detail/$1
has prefix: plant_reactome
type: Resource
has local unique identifier pattern: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$
has resource example: R-ACH-1120024
0000005: R-ACH-1120024
has URI prefix: https://plantreactome.gramene.org/content/detail/
description: PLANT REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Pathway annotations are authored by expert biologists, in collaboration with the Reactome editorial staff and cross-referenced to many bioinformatics databases. These include project databases like Gramene, Ensembl, UniProt, ChEBI small molecule databases, PubMed, and Gene Ontology.
is deprecated: false
is part of: Bioregistry

ChemBioSys Assay
has provider formatter: https://data.chembiosys.de/assays/$1
has URI prefix: https://data.chembiosys.de/assays/
0000005: 31
is part of: Bioregistry
is deprecated: false
has local unique identifier pattern: ^\d+$
has resource example: https://data.chembiosys.de/assays/31
description: A assay in the ChemBioSys data platform
type: Resource
contributor: Charles Tapley Hoyt
has prefix: chembiosys.assay

ResearchGate profile ID
description: identifier for a person, used by ResearchGate profiles
keyword: person
has prefix: researchgate.profile
has local unique identifier pattern: ^[0-9A-Za-z_-]+$
is part of: Bioregistry
keyword: researcher
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: https://www.researchgate.net/profile/$1
0000005: Rita-Heuser
has resource example: Rita-Heuser
has URI prefix: https://www.researchgate.net/profile/
is deprecated: false

SWEET Ontology Representation Space Reference System
keyword: representation space reference system
is deprecated: false
has prefix: sweet.repsrs
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space Reference System
has alternative prefix: sorepsrs
0000005: HorizontalCoordinateSystem
has resource example: HorizontalCoordinateSystem
is part of: Bioregistry
has URI prefix: http://sweetontology.net/reprSpaceReferenceSystem/
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/reprSpaceReferenceSystem/$1
type: Resource

SWEET Ontology Representation Data Format
0000005: ByteOrder
is deprecated: false
has provider formatter: http://sweetontology.net/reprDataFormat/$1
has URI prefix: http://sweetontology.net/reprDataFormat/
keyword: representation data format
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: ByteOrder
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.repdf
type: Resource
has alternative prefix: sorepdf
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Format

FerroLigandDB
has reviewer: https://orcid.org/0000-0001-9439-5346
has resource example: https://ferr.gulab.org.cn/browse/486
is part of: Bioregistry
0000005: 486
has provider formatter: https://ferr.gulab.org.cn/browse/$1
type: Resource
has responsible: Qiong Gu
has prefix: ferroliganddb
contributor: Tanay Shah
description: FerroLigandDB is a meticulously curated, high-quality database of ferroptosis regulators, including inducers and inhibitors.
has URI prefix: https://ferr.gulab.org.cn/browse/
is deprecated: false

Chemical Analysis Ontology
has prefix: cao
has URI prefix: http://champ-project.org/images/ontology/cao.owl#CAO_
keyword: analytical chemistry
keyword: characterisation data heat
has download URL: cao.owl
has responsible: https://orcid.org/0000-0002-2668-4821
description: An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)
keyword: ontology
is deprecated: false
keyword: transport and kinetic data
is part of: Bioregistry
has resource example: CAO_000064
keyword: chemistry
has local unique identifier pattern: ^\d+$
keyword: nfdi4cat
contributor: Charles Tapley Hoyt
git repository: chemical-analysis-ontology
has provider formatter: http://champ-project.org/images/ontology/cao.owl#CAO_$1
0000005: 000064
type: Resource

IUPAC Gold Book Compendium of Chemical Terminology
has local unique identifier pattern: ^(\wT?)?\d{5}$
0000005: G02681
is deprecated: false
is part of: Bioregistry
has prefix: goldbook
contributor: Charles Tapley Hoyt
has provider formatter: https://goldbook.iupac.org/terms/view/$1
has responsible: https://orcid.org/0000-0002-0703-7776
description: The Compendium is popularly referred to as the "Gold Book", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC "Colour Books" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books. Terminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry. The API can be accessed [here](https://goldbook.iupac.org/pages/api)
type: Resource
has URI prefix: https://goldbook.iupac.org/terms/view/
has resource example: G02681

BioSystems
keyword: biology
keyword: pathways
has prefix: biosystems
keyword: systems biology
is deprecated: true
keyword: molecules
contributor: Tim Vandermeersch
has responsible: https://orcid.org/0000-0003-1516-0712
0000005: 001
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: https://www.ncbi.nlm.nih.gov/biosystems/001
description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.
type: Resource
has URI prefix: https://www.ncbi.nlm.nih.gov/biosystems/
has provider formatter: https://www.ncbi.nlm.nih.gov/biosystems/$1

LNCipedia
is part of: Bioregistry
has responsible: Pieter Mestdagh
contributor: Charles Tapley Hoyt
type: Resource
keyword: life science
is deprecated: false
description: A comprehensive compendium of human long non-coding RNAs
has prefix: lncipedia
0000005: SNHG3

The ROSETTA ontology of industrial robotics devices and robotic skills.
description: The ROSETTA ontology of industrial robotics devices and robotic skills.
is deprecated: false
keyword: engineering
0000005: canBePerformedBy
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
has provider formatter: http://kif.cs.lth.se/ontologies/rosetta.owl#$1
has resource example: canBePerformedBy
has URI prefix: http://kif.cs.lth.se/ontologies/rosetta.owl#
has prefix: rosetta
git repository: Rosetta ontology

Selventa Complexes
has local unique identifier pattern: ^C\d{4}$
has provider formatter: https://biopragmatics.github.io/providers/scomp/$1
keyword: protein complexes
has URI prefix: https://biopragmatics.github.io/providers/scomp/
is part of: Bioregistry
has resource example: C0001
keyword: selventa
description: Selventa legacy complex namespace used with the Biological Expression Language
contributor: Charles Tapley Hoyt
0000005: C0001
type: Resource
keyword: bel
has prefix: scomp
is deprecated: false

Supply Chain Operation Reference
has URI prefix: http://purl.org/eis/vocab/scor#
is part of: Bioregistry
type: Resource
description: The Supply Chain Operation Reference (SCOR) is a cross-industry approach to lay the groundwork for more efficient and effective information exchange in supply networks.
keyword: coypu
0000005: ActiviateOrArchiveContract
has prefix: scor
has resource example: ActiviateOrArchiveContract
keyword: economics
is deprecated: false
has provider formatter: http://purl.org/eis/vocab/scor#$1

SWEET Ontology State Physical
is part of: Bioregistry
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Physical
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has prefix: sweet.stp
keyword: state physical
0000005: MoistureState
has provider formatter: http://sweetontology.net/statePhysical/$1
is deprecated: false
has alternative prefix: sostp
has URI prefix: http://sweetontology.net/statePhysical/
has resource example: MoistureState

PlastChem
type: Resource
has prefix: plastchem
description: A database of chemicals relevant for plastics and polymer sciences.
0000005: 1
has responsible: https://orcid.org/0000-0002-4402-3234
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt

SWEET Ontology Realm Atmospheric Weather
is part of: Bioregistry
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has prefix: sweet.reaaw
has resource example: AdiabaticCondensationLevel
keyword: atmospheric weather
0000005: AdiabaticCondensationLevel
type: Resource
keyword: realm
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Atmospheric Weather
has provider formatter: http://sweetontology.net/realmAtmoWeather/$1
has alternative prefix: soreaaw
is deprecated: false
has URI prefix: http://sweetontology.net/realmAtmoWeather/

E. coli Metabolite Database
is deprecated: false
0000005: ECMDB00005
has URI prefix: http://ecmdb.ca/compounds/
is part of: Bioregistry
has alternative prefix: ECMDB
has prefix: ecmdb
contributor: Charles Tapley Hoyt
has provider formatter: http://ecmdb.ca/compounds/$1
description: The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes.
type: Resource
has local unique identifier pattern: ^ECMDB\d+$
has resource example: ECMDB00005

ISO 639 3-Letter Language Code
keyword: linguistics
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
keyword: informatics
keyword: language
has URI prefix: https://iso639-3.sil.org/code/
keyword: computer science
has prefix: iso.639-3
description: Since the introduction of ISO 639-3 in 2007, access to language information has increased tremendously. The code set initially adopted as ISO639-3:2007 was based on a harmonization of ISO 639-2 with the code set of SIL’s Ethnologue 15th edition and languages from Linguist List to form a comprehensive set of code elements for world languages. SIL International, the Language Coding Agency for 639-3, relies on the contributions of linguists, language coding experts, and language users around the world to maintain and improve the code set through the change request process defined in the ISO 639 standard. [from homepage]
has resource example: spa
has provider formatter: https://iso639-3.sil.org/code/$1
0000005: spa
is deprecated: false

UniCarb-DB
is part of: Bioregistry
has prefix: unicarbdb
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: https://unicarb-db.expasy.org/msData/
description: UniCarb-DB stores structural and mass spectrometry (MS) glycomic data, and has now grown to be one of the largest experimental glycomic MS databases. Identifiers correspond to individual glycan structures and corresponding MS spectra.
has provider formatter: https://unicarb-db.expasy.org/msData/$1
has resource example: https://unicarb-db.expasy.org/msData/91
is deprecated: false
0000005: 91
has local unique identifier pattern: ^\d+$
has responsible: https://orcid.org/0000-0002-3045-2628
has reviewer: https://orcid.org/0000-0001-9439-5346

Animal Genome Pig QTL
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
has resource example: https://www.animalgenome.org/QTLdb/q
has provider formatter: https://www.animalgenome.org/QTLdb/q
has prefix: pigqtldb
0000005: 14
description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs.
is part of: Animal Genome QTL
is deprecated: false
has URI prefix: https://www.animalgenome.org/QTLdb/q
keyword: genome
keyword: dna

Human Proteome Map
0000005: 1968
description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: hpm.protein
type: Resource
is deprecated: true
has provider formatter: http://www.humanproteomemap.org/protein.php
has resource example: http://www.humanproteomemap.org/protein.php
has URI prefix: http://www.humanproteomemap.org/protein.php

BugBase Protocol
description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols.
has URI prefix: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
0000005: 67
is deprecated: true
has resource example: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php
has prefix: bugbase.protocol
has provider formatter: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php

SWEET Ontology Phenomena Atmosphere Cloud
has prefix: sweet.phatmoc
has resource example: Altostratus
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: atmosphere cloud
has URI prefix: http://sweetontology.net/phenAtmoCloud/
keyword: phenomena
has provider formatter: http://sweetontology.net/phenAtmoCloud/$1
0000005: Altostratus
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Cloud
has alternative prefix: sophatmoc
is deprecated: false

Nonribosomal Peptides Database
keyword: life science
description: Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings.
has resource example: https://bioinfo.cristal.univ-lille.fr/norine/result.jsp
has URI prefix: https://bioinfo.cristal.univ-lille.fr/norine/result.jsp
has responsible: https://orcid.org/0000-0003-3197-0715
is deprecated: false
keyword: protein
has local unique identifier pattern: ^NOR\d+$
is part of: Bioregistry
type: Resource
has provider formatter: https://bioinfo.cristal.univ-lille.fr/norine/result.jsp
has prefix: norine
0000005: NOR00681

Gramene Taxonomy
is part of: Bioregistry
type: Resource
0000005: 013681
has prefix: gramene.taxonomy
description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.
has resource example: https://archive.gramene.org/db/ontology/search
has provider formatter: https://archive.gramene.org/db/ontology/search
has URI prefix: https://archive.gramene.org/db/ontology/search
is deprecated: false
has local unique identifier pattern: ^\d+$

MaRDI Collection
has part: Bioregistry
type: Collection
creator: Charles Tapley Hoyt
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for MaRDI

SWEET Ontology Human Environmental Control
0000005: Abatement
has resource example: Abatement
has prefix: sweet.hueccont
has alternative prefix: sohueccont
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Environmental Control
has URI prefix: http://sweetontology.net/humanEnvirControl/
has provider formatter: http://sweetontology.net/humanEnvirControl/$1
is part of: Bioregistry
keyword: environmental control
type: Resource
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology

Semantically-Interlinked Online Communities Argumentation Ontology
has URI prefix: http://rdfs.org/sioc/argument#
is deprecated: false
has provider formatter: http://rdfs.org/sioc/argument#$1
0000005: decides
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has prefix: sioc.argument
description: A vocabulary of argumentation predicates for SIOC
has resource example: decides

International Histocompatibility Workshop cell lines
description: The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics.
0000005: IHW09326
is deprecated: false
is part of: Bioregistry
has prefix: ihw
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^IHW\d+$
type: Resource

SWEET Ontology Representation Mathematics Statistics
has provider formatter: http://sweetontology.net/reprMathStatistics/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Statistics
has prefix: sweet.repmst
is deprecated: false
has alternative prefix: sorepmst
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
keyword: representation mathematics statistics
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: ANOVA
type: Resource
has URI prefix: http://sweetontology.net/reprMathStatistics/
0000005: ANOVA

SWEET Ontology Representation Space Geometry
has provider formatter: http://sweetontology.net/reprSpaceGeometry/$1
is deprecated: false
has resource example: Arc
has alternative prefix: sorepsg
0000005: Arc
is part of: Bioregistry
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space Geometry
type: Resource
keyword: representation space geometry
has URI prefix: http://sweetontology.net/reprSpaceGeometry/
has prefix: sweet.repsg

NMRShiftDB structure
has local unique identifier pattern: ^[0-9]+$
has resource example: https://nmrshiftdb.nmr.uni-koeln.de/molecule/234
has URI prefix: https://nmrshiftdb.nmr.uni-koeln.de/molecule/
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
description: NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties.
has responsible: https://orcid.org/0000-0002-5990-4157
is part of: Bioregistry
type: Resource
0000005: 234
has alternative prefix: NMRShiftDB
has provider formatter: https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1
keyword: analytical chemistry
has prefix: nmrshiftdb2

Getty Thesaurus of Geographic Names
has URI prefix: http://vocab.getty.edu/tgn/
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has prefix: getty.tgn
keyword: geography
has resource example: http://vocab.getty.edu/tgn/1023371
keyword: ancient cultures
0000005: 1023371
type: Resource
keyword: architecture
keyword: human geography
keyword: history
keyword: geographic location
description: The Thesaurus of Geographic Names (TGN) is a terminology that focuses on places relevant to art, architecture, and related disciplines, recording names, relationships, place types, dates, notes, and coordinates for current and historical cities, nations, empires, archaeological sites, lost settlements, and physical features. The TGN is one of 5 Getty Vocabularies intended to provide terminology and other information about the objects, artists, concepts, and places important to various disciplines that specialize in art, architecture, and other material culture.
keyword: art history
keyword: culture
is deprecated: false
keyword: fine arts
has alternative prefix: tgn
has provider formatter: http://vocab.getty.edu/tgn/$1

Healthcare Organizations and Services Ontology
is deprecated: false
description: HOSO is an ontology of informational entities and processes related to healthcare organizations and services.
is part of: Bioregistry
has responsible: Paul Fabry
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
has prefix: hoso
type: Resource
contributor: Paul Fabry
git repository: HOSO
has reviewer: Charles Tapley Hoyt

Logical Observation Identifiers Names and Codes
has local unique identifier pattern: ^(\d|\w)+-\d$
keyword: life science
0000005: LL379-9
is deprecated: false
keyword: genetic polymorphism
has alternative prefix: LNC
keyword: ontology
has provider formatter: https://loinc.org/$1
has resource example: LL379-9
is part of: Bioregistry
description: The international standard for identifying health measurements, observations, and documents.
keyword: assay
contributor: Charles Tapley Hoyt
keyword: phenotype
keyword: diagnosis
has prefix: loinc
keyword: preclinical studies
keyword: genetic disorder
type: Resource
has URI prefix: https://loinc.org/
keyword: biomedical science

SWEET Ontology Realm Earth Reference
has alternative prefix: soreaer
type: Resource
0000005: AbyssopelagicZone
has resource example: AbyssopelagicZone
has prefix: sweet.reaer
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Earth Reference
is deprecated: false
keyword: earth reference
has URI prefix: http://sweetontology.net/realmEarthReference/
has provider formatter: http://sweetontology.net/realmEarthReference/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
keyword: realm
is part of: Semantic Web for Earth and Environment Technology Ontology

Sensor, Observation, Sample, and Actuator Ontology
has resource example: FeatureOfInterest
is deprecated: false
contributor: https://orcid.org/0000-0002-1595-3213
description: This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.
keyword: engineering
keyword: environment
has URI prefix: http://www.w3.org/ns/sosa/
keyword: nfdi4chem
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-3884-3420
keyword: iot
has provider formatter: http://www.w3.org/ns/sosa/$1
type: Resource
keyword: nfdi4ing
git repository: sdw
has reviewer: Charles Tapley Hoyt
0000005: FeatureOfInterest
has prefix: sosa
keyword: ess

GeoSPARQL Rule
has prefix: geosparql.rule
type: Resource
0000005: rcc
description: Rules for GeoSPARQL
is deprecated: false
is part of: Bioregistry

DBG2 Introns
has local unique identifier pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$
0000005: Cu.me.I1
type: Resource
has prefix: dbg2introns
is deprecated: true
has provider formatter: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi
has URI prefix: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi
description: The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.
has resource example: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi
keyword: dna
is part of: Bioregistry

NCBI Genome
has provider formatter: https://www.ncbi.nlm.nih.gov/genome/$1
has URI prefix: https://www.ncbi.nlm.nih.gov/genome/
is deprecated: false
has local unique identifier pattern: ^\d+$
has resource example: https://www.ncbi.nlm.nih.gov/genome/51
has prefix: ncbi.genome
0000005: 51
is part of: Bioregistry
description: This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.
contributor: Charles Tapley Hoyt
type: Resource

Virtual Fly Brain
has resource example: http://virtualflybrain.org/reports/00000001
has prefix: vfb
is part of: Bioregistry
type: Resource
has provider formatter: http://virtualflybrain.org/reports/$1
keyword: life science
has local unique identifier pattern: ^[0-9a-zA-Z]{8}$
has URI prefix: http://virtualflybrain.org/reports/
has responsible: Robert Court
keyword: neurobiology
0000005: 00000001
description: An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.
is deprecated: false

SWEET Ontology State Spectral Line
has resource example: CaK
keyword: state spectral line
has prefix: sweet.stsl
0000005: CaK
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Spectral Line
has URI prefix: http://sweetontology.net/stateSpectralLine/
has alternative prefix: sostsl
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/stateSpectralLine/$1

Materials Design Ontology - Full
git repository: Materials-Design-Ontology
is part of: Bioregistry
keyword: material science
keyword: nfdi4ing
has prefix: tib.mdo
description: The Materials Design Ontology is designed to enable semantic query and integrated query over multiple databases. By generating mappings between MDO and the schemas of materials databases, we can create MDO-enabled query interfaces. The querying can occur, for instance, via MDO-based query expansion, MDO-based mediation or through MDO-enabled data warehouses.
type: Resource
has URI prefix: https://w3id.org/mdo/
has provider formatter: https://w3id.org/mdo/$1
is deprecated: false

Shapes Constraint Language
has download URL: download.trig.gz
0000005: NodeShape
keyword: ontology
keyword: ontology and terminology
has provider formatter: http://www.w3.org/ns/shacl#$1
is deprecated: false
keyword: quality
has responsible: https://orcid.org/0000-0002-3884-3420
keyword: w3c rec
keyword: knowledge and information systems
description: A language for validating RDF graphs against a set of conditions
has resource example: NodeShape
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
keyword: nfdi4ing
has prefix: sh
keyword: informatics
has alternative prefix: shacl
git repository: data-shapes
keyword: computer science
has URI prefix: http://www.w3.org/ns/shacl#

Vertebrate Homologous Organ Group Ontology
0000005: 0000411
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/VHOG_$1
type: Resource
has alternative prefix: VHOG_RETIRED
keyword: development
has local unique identifier pattern: ^\d{7}$
keyword: anatomy
is deprecated: true
keyword: obo
has resource example: VHOG_0000411
keyword: ontology
has responsible: Bgee team
has URI prefix: http://purl.obolibrary.org/obo/VHOG_
has download URL: vhog.owl
description: vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 "historical homology". Each mapping has been manually reviewed, and we provide confidence codes and references when available.
has prefix: vhog

Dynamic Ecological Information Management System - Site and Dataset Registry - Sensor
has prefix: deims.sensor
is deprecated: false
has local unique identifier pattern: ^[0-9a-f\-]+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: Sensors in DEIMS SDR
has responsible: Christoph Wohner
has URI prefix: https://deims.org/sensors/
type: Resource
has provider formatter: https://deims.org/sensors/$1

MGnify Protein
has resource example: MGYP000261684433
has local unique identifier pattern: ^MGYP\d{12}$
has URI prefix: https://www.ebi.ac.uk/metagenomics/proteins/
0000005: MGYP000261684433
is deprecated: false
has provider formatter: https://www.ebi.ac.uk/metagenomics/proteins/$1
description: The free-to-use MGnify platform provides assembly, analysis and archiving of microbiome-derived nucleic acid sequence data from a wide range of biomes, with analysis results providing taxonomic and functional profiles. The platform also includes MGnify Proteins, a database of protein sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes, a resource of biome-specific catalogues of microbial genomes, including extensive functional annotations.
is part of: Bioregistry
type: Resource
has prefix: mgnifyprotein

International Classification of Diseases, 11th Revision (Foundation Component)
keyword: ontology
has resource example: http://id.who.int/icd/entity/402558626
keyword: morbidity
is deprecated: false
keyword: disease
keyword: electronic health record
has URI prefix: https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/
has download URL: icd11.owl
has alternative prefix: ICD-11
keyword: diagnosis
has alternative prefix: icd11.foundation
has local unique identifier pattern: ^[1-9]\d*$
has provider formatter: https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1
has alternative prefix: ICD11
contributor: https://orcid.org/0000-0002-7356-1779
keyword: global health
is part of: Bioregistry
contributor: Charles Tapley Hoyt
keyword: epidemiology
type: Resource
description: The ICD-11 Foundation is the comprehensive base layer of the International Classification of Diseases, encompassing all diagnostic concepts, definitions, and semantic relationships, designed for flexibility and adaptability across various use cases, including research, ontology development, and detailed health data analysis.
keyword: biomedical science
0000005: 402558626
keyword: health science
has prefix: icd11

FuncBase Fly
has resource example: http://func.mshri.on.ca/fly/genes/list_functional_scores/10194
type: Resource
description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.
has prefix: funcbase.fly
is deprecated: false
has provider formatter: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
0000005: 10194
has URI prefix: http://func.mshri.on.ca/fly/genes/list_functional_scores/

ChemBioSys Strain
has URI prefix: https://data.chembiosys.de/strains/
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: A strain in the ChemBioSys data platform
has prefix: chembiosys.strain
has resource example: https://data.chembiosys.de/strains/33
0000005: 33
has provider formatter: https://data.chembiosys.de/strains/$1

Platform Material Digital Core Ontology
0000005: 0000000
has URI prefix: https://w3id.org/pmd/co/PMD_
keyword: chemical and environmental engineering
is deprecated: false
keyword: mechanical engineering, energy technology
has prefix: pmdco
git repository: core-ontology
is part of: Bioregistry
has provider formatter: https://w3id.org/pmd/co/PMD_$1
type: Resource
keyword: material science
keyword: nfdi4ing
description: The PMD Core Ontology (PMDco) is a comprehensive framework for representing knowledge that encompasses fundamental concepts from the domains of materials science and engineering (MSE). The PMDco has been designed as a mid-level ontology to establish a connection between specific MSE application ontologies and the domain neutral concepts found in established top-level ontologies. The primary goal of the PMDco is to promote interoperability between diverse domains. PMDco's class structure is both understandable and extensible, making it an efficient tool for organizing MSE knowledge. It serves as a semantic intermediate layer that unifies MSE knowledge representations, enabling data and metadata to be systematically integrated on key terms within the MSE domain. With PMDco, it is possible to seamlessly trace data generation. By building on this foundation, PMDco facilitates the integration of data from various sources and the creation of complex workflows. In summary, PMDco is a valuable tool for researchers and practitioners in the MSE domains. It provides a common language for representing and sharing knowledge, allowing for efficient collaboration and promoting interoperability between diverse domains. Its design allows for the systematic integration of data and metadata, enabling seamless traceability of data generation. Overall, PMDco is a crucial step towards a unified and comprehensive understanding of the MSE domain. PMDco at GitHub: https://github.com/materialdigital/core-ontology Documentation: https://materialdigital.github.io/core-ontology/docs/
has resource example: PMD_0000000

Habronattus courtship
is part of: Bioregistry
has provider formatter: http://purl.obolibrary.org/obo/HABRONATTUS_$1
has responsible: Peter Midford
type: Resource
has URI prefix: http://purl.obolibrary.org/obo/HABRONATTUS_
is deprecated: true
keyword: obo
keyword: ontology
has prefix: habronattus

CATH domain
is part of: Bioregistry
type: Resource
has resource example: 1cukA01
has provider formatter: http://www.cathdb.info/domain/$1
has local unique identifier pattern: ^\w+$
has prefix: cath.domain
description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains.
is deprecated: false
has URI prefix: http://www.cathdb.info/domain/
0000005: 1cukA01

gist
has resource example: Account
0000005: Account
has provider formatter: https://w3id.org/semanticarts/ns/ontology/gist/$1
is deprecated: false
keyword: engineering
description: gist is a minimalist upper ontology created by Semantic Arts.
keyword: foundational ontologies
has URI prefix: https://w3id.org/semanticarts/ns/ontology/gist/
is part of: Bioregistry
type: Resource
has prefix: gist
keyword: nfdi4ing

Vocabulary Maintenance Standard
has provider formatter: http://www.tdwg.org/standards/642$1
is deprecated: false
has URI prefix: http://www.tdwg.org/standards/642
keyword: life sciences, biology
is part of: Bioregistry
type: Resource
has prefix: tdwg.vms
description: The TDWG Vocabulary Maintenance Standard consists of a single document: the Vocabulary Maintenance Specification.
keyword: fair data spaces

Biocuration Conference 2025 Collection
has part: EndlessForms Studio Unit
has part: EndlessForms Studio Element
has part: AntiFam
description: A collection of resources added during Biocuration 2025 in Kansas City, MO, USA.
has part: Biomarker Knowledgebase - Canonical Biomarker
has part: Graphic Descriptor Ontology
has part: BlastRule
has part: EndlessForms Studio Image
has part: EndlessForms Studio Graphic
type: Collection
has part: Earth Metabolome Ontology
creator: Charles Tapley Hoyt
has part: EndlessForms Studio Image Collections
has part: EndlessForms Studio Library
has part: Biomarker Knowledgebase - Biomarker

PhosphoSite Residue
has resource example: http://www.phosphosite.org/siteAction.do
0000005: 2842
description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence.
has provider formatter: http://www.phosphosite.org/siteAction.do
is deprecated: false
has URI prefix: http://www.phosphosite.org/siteAction.do
has prefix: phosphosite.residue
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource

Type of Translation Method
description: A typology of methods used to translate data collection instruments, including questionnaires, individual questions, measurements, data capture flows, etc.
type: Resource
has provider formatter: https://vocabularies.cessda.eu/vocabulary/TypeOfTranslationMethod#code_$1
has identifier space owner: 015em2733
0000005: SingleTranslation
has prefix: ddi.typeoftranslationmethod
has URI prefix: https://vocabularies.cessda.eu/vocabulary/TypeOfTranslationMethod#code_
is deprecated: false
has resource example: code SingleTranslation
is part of: Bioregistry
contributor: Charles Tapley Hoyt

SWEET Ontology Property Time Frequency
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Time Frequency
has URI prefix: http://sweetontology.net/propTimeFrequency/
is deprecated: false
has alternative prefix: soproptf
keyword: time frequency
has provider formatter: http://sweetontology.net/propTimeFrequency/$1
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: Bandwidth
has prefix: sweet.proptf
0000005: Bandwidth
type: Resource

European Registry of Materials
has local unique identifier pattern: ^ERM[0-9]{8}$
has prefix: erm
is deprecated: false
is part of: Bioregistry
has provider formatter: https://nanocommons.github.io/identifiers/registry#$1
keyword: materials science
description: The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project.
has URI prefix: https://nanocommons.github.io/identifiers/registry#
keyword: chemical entity
0000005: ERM00000044
type: Resource
keyword: nanotechnology
keyword: materials informatics
has resource example: ERM00000044
has responsible: Tim Vandermeersch

Sampling Procedure
has resource example: code TotalUniverseCompleteEnumeration
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has identifier space owner: 015em2733
has prefix: ddi.samplingprocedure
description: A typology of sampling methods.
has URI prefix: https://vocabularies.cessda.eu/vocabulary/SamplingProcedure#code_
0000005: TotalUniverseCompleteEnumeration
has provider formatter: https://vocabularies.cessda.eu/vocabulary/SamplingProcedure#code_$1
is deprecated: false

J. Michael Cherry
label: Mike Cherry

NIF Standard Ontology: Chemical
git repository: NIF-Ontology
is deprecated: false
keyword: chemistry
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1
has responsible: Tom Gillespie
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has alternative prefix: NLXCHEM
type: Resource
description: NLXCHEM covers chemicals. Most classes are also in ChEBI.
has resource example: nlx chem 090801
has reviewer: Charles Tapley Hoyt
0000005: 090801
contributor: Tom Gillespie
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_chem_
has prefix: nlx.chem

MolBiC Protein
0000005: PT00819
has responsible: https://orcid.org/0000-0001-8069-0053
contributor: Mufaddal Naguthanawala
has provider formatter: https://molbic.idrblab.net/data/protein/details/$1
is deprecated: false
has prefix: molbic.protein
has local unique identifier pattern: ^PT\d+$
has resource example: PT00819
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://molbic.idrblab.net/data/protein/details/
is part of: Bioregistry
type: Resource
description: MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for proteins that serve as molecular targets in cell-based bioactivity measurements.

Unique Ingredient Identifier
has URI prefix: https://precision.fda.gov/uniisearch/srs/unii/
has local unique identifier pattern: ^[A-Z0-9]+$
has resource example: 3G6A5W338E
has provider formatter: https://precision.fda.gov/uniisearch/srs/unii/$1
0000005: 3G6A5W338E
is deprecated: false
is part of: Bioregistry
description: The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information.
has prefix: unii
type: Resource

Southwestern Environmental Information Network
has URI prefix: https://swbiodiversity.org/seinet/taxa/index.php
has reviewer: https://orcid.org/0000-0002-8169-9049
0000005: 762
type: Resource
description: A vocabulary about species to support the environmental research community in Arizona and New Mexico
has resource example: https://swbiodiversity.org/seinet/taxa/index.php
is deprecated: false
has prefix: seinet
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: https://swbiodiversity.org/seinet/taxa/index.php
contributor: Charles Tapley Hoyt

LigandBox
has local unique identifier pattern: ^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$
0000005: D00001
description: LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.
has prefix: ligandbox
is deprecated: false
has URI prefix: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi
has resource example: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi
is part of: Bioregistry
type: Resource
has provider formatter: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi

Data Repository of Antimicrobial Peptides
0000005: DRAMP00005
type: Resource
has prefix: dramp
description: Identifiers repesent antimicrobial peptides in the Data Repository of Antimicrobial Peptides (DRAMP) database which is an open-access, manually curated database of antimicrobial peptides (AMPs).
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has responsible: Heng Zheng
has resource example: http://dramp.cpu-bioinfor.org/browse/All_Information.php
is part of: Bioregistry
keyword: antimicrobial peptides
has URI prefix: http://dramp.cpu-bioinfor.org/browse/All_Information.php
has local unique identifier pattern: ^DRAMP\d{5}$
has provider formatter: http://dramp.cpu-bioinfor.org/browse/All_Information.php
has reviewer: Charles Tapley Hoyt

SAREF extension for Agriculture
has prefix: saref.agri
has URI prefix: https://saref.etsi.org/saref4agri/
keyword: agriculture
0000005: Animal
is part of: Bioregistry
description: This ontology extends the SAREF ontology for the Agricultural domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Agricultural domain.
type: Resource
keyword: iot
has provider formatter: https://saref.etsi.org/saref4agri/$1
has alternative prefix: s4agri
keyword: miscellaneous
keyword: food
has resource example: Animal
is deprecated: false

ValidatorDB
type: Resource
has provider formatter: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1
has local unique identifier pattern: ^[A-Za-z0-9\/]+$
description: Database of validation results for ligands and non-standard residues in the Protein Data Bank.
keyword: life science
is deprecated: false
has URI prefix: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/
0000005: 2h6o
has resource example: 2h6o
0000011: PDB Structure
has prefix: validatordb
is part of: Bioregistry
has responsible: https://orcid.org/0000-0002-0682-3089

Contributor Role
has resource example: code ProjectOrStudyDesign
0000005: ProjectOrStudyDesign
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/ContributorRole#code_
description: A classification of contributor roles.
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has identifier space owner: 015em2733
has provider formatter: https://vocabularies.cessda.eu/vocabulary/ContributorRole#code_$1
has prefix: ddi.contributorrole

OriDB Schizosaccharomyces
type: Resource
description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe.
is deprecated: false
has provider formatter: http://pombe.oridb.org/details.php
0000005: 1
has URI prefix: http://pombe.oridb.org/details.php
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has prefix: oridb.schizo
has resource example: http://pombe.oridb.org/details.php

Information Artifact Ontology Issue Tracker
is deprecated: false
has URI prefix: https://github.com/information-artifact-ontology/IAO/issues/
description: An issue on the Information Artifact Ontology GitHub issue tracker
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
contributor: Charles Tapley Hoyt
has resource example: https://github.com/information-artifact-ontology/IAO/issues/206
has provider formatter: https://github.com/information-artifact-ontology/IAO/issues/$1
has prefix: iao.issue
0000005: 206

Data types in R|EX research
is deprecated: false
has resource example: code 01a
description: This CV, developed as part of the DP-R|EX joint project, involving the partner institutions DeZIM, Qualiservice and GESIS, maps the data types relevant to the research field. The CV includes data types that can result from a variety of different collection methods. These include, for example, standardised or unstandardised surveys, individual or repeated observations, as well as process-produced or user-generated types of data generation. The data types can be subject-, event-, space- or time-related and refer to the individual or aggregate level.
has identifier space owner: 018afyw53
0000005: 01a
is part of: Bioregistry
type: Resource
has URI prefix: https://vocabularies.cessda.eu/vocabulary/rexdatatype#code_
contributor: Charles Tapley Hoyt
has provider formatter: https://vocabularies.cessda.eu/vocabulary/rexdatatype#code_$1
has prefix: gesis.rexdatatype

AddexBio cell line products
is part of: Bioregistry
type: Resource
has resource example: https://www.addexbio.com/productdetail
0000005: C0020004/4992
has prefix: addexbio
has URI prefix: https://www.addexbio.com/productdetail
is deprecated: false
description: Cell line collections (Providers)
has provider formatter: https://www.addexbio.com/productdetail

Glottolog
is part of: Bioregistry
appears in: Gender, Sex, and Sexual Orientation Ontology
contributor: Charles Tapley Hoyt
description: Comprehensive reference information for the world's languages, especially the lesser known languages. [from homepage]
has provider formatter: https://glottolog.org/resource/languoid/id/$1
has URI prefix: https://glottolog.org/resource/languoid/id/
type: Resource
has resource example: nort3314
is deprecated: false
0000005: nort3314
has prefix: glottolog

Korean Clinical Research Information Service
has local unique identifier pattern: ^KCT\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has prefix: kcris
0000005: KCT0008394
description: The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page) Note that the web page that resolves this trial does not correspond to the semantic space
is deprecated: false

Database of human Major Histocompatibility Complex
is deprecated: true
description: Cell line databases/resources
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
appears in: Cellosaurus
type: Resource
has prefix: dbmhc
0000005: 48439

SWEET Ontology Material Microbiota
has alternative prefix: somamic
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Microbiota
is deprecated: false
keyword: microbiota
0000005: Algae
has resource example: Algae
is part of: Bioregistry
has provider formatter: http://sweetontology.net/matrMicrobiota/$1
git repository: sweet
contributor: Charles Tapley Hoyt
type: Resource
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: materials
has prefix: sweet.mamic
has URI prefix: http://sweetontology.net/matrMicrobiota/

SWEET Ontology Property Index
has prefix: sweet.propi
has alternative prefix: sopropi
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Index
has URI prefix: http://sweetontology.net/propIndex/
is deprecated: false
0000005: AdaptiveCapacity
keyword: index
has provider formatter: http://sweetontology.net/propIndex/$1
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
type: Resource
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: AdaptiveCapacity

Regulatory Elements Database for Drosophila
keyword: regulation
has URI prefix: http://redfly.ccr.buffalo.edu/
has resource example: http://redfly.ccr.buffalo.edu/
has provider formatter: http://redfly.ccr.buffalo.edu/
is part of: Bioregistry
0000005: 8
has reviewer: Charles Tapley Hoyt
type: Resource
has prefix: redfly
is deprecated: true
description: REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).

Ontology Modeling for Intelligent Domotic Environments
is deprecated: false
is part of: Bioregistry
keyword: engineering
keyword: environment
has URI prefix: http://elite.polito.it/ontologies/dogont.owl#
has provider formatter: http://elite.polito.it/ontologies/dogont.owl#$1
has prefix: dogont
keyword: nfdi4energy
has resource example: AccelerationStateValue
keyword: iot
type: Resource
keyword: nfdi4ing
description: The DogOnt ontology supports device/network independent description of houses, including both controllable and architectural elements.
0000005: AccelerationStateValue

Google Books
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: qafeQTWIWmcC
type: Resource
has URI prefix: https://books.google.com/books
description: Search the world's most comprehensive index of full-text books.
has provider formatter: https://books.google.com/books
has resource example: https://books.google.com/books
has prefix: google.book
is deprecated: false

UK Higher Education Statistics Agency
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
is part of: Bioregistry
keyword: bibliometrics
0000005: 0154
has prefix: hesa
type: Resource
description: An identifier for institutions in the United Kingdom, used in GRID and ROR.
is deprecated: false
keyword: institution

Registry of Toxic Effects of Chemical Substances
has prefix: rtecs
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
0000005: AB1925000
description: RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments.
has responsible: Vernon Putz-Anderson
has local unique identifier pattern: ^AB\d+$
is deprecated: false

DrugBank Salts
keyword: chemical
has prefix: drugbank.salt
has responsible: David Wishart
type: Resource
has resource example: DBSALT001211
0000005: DBSALT001211
is deprecated: false
has URI prefix: https://go.drugbank.com/salts/
keyword: salt
keyword: compound
has local unique identifier pattern: ^DBSALT\d{6}$
has provider formatter: https://go.drugbank.com/salts/$1
keyword: small molecule
description: DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.
is part of: Bioregistry
contributor: Charles Tapley Hoyt

SWEET Ontology Phenomena Fluid Instability
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: phenomena
0000005: AbsoluteInstability
has URI prefix: http://sweetontology.net/phenFluidInstability/
has alternative prefix: sophfi
has resource example: AbsoluteInstability
has prefix: sweet.phfi
keyword: fluid instability
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Fluid Instability
has provider formatter: http://sweetontology.net/phenFluidInstability/$1

Descriptive Ontology for Linguistic and Cognitive Engineering
keyword: knowledge and information systems
keyword: linguistics
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). The development of this library has been guided by the need of a reliable set of foundational ontologies that can serve as 1) astarting point for building other ontologies, 2) a reference point for easy and rigorous comparisons among different ontological approaches, and 3) a rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata standards (by manually mapping them into some general module(s) in the library). DOLCE is the first module of WFOL and it is not a candidate for a universal standard ontology. Rather, it is intended as a starting point for comparing and elucidating the relationships with the other modules of the library, and also for clarifying the hidden assumptions underlying existing ontologies or linguistic resources such as WordNet. As reflected by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at capturing the ontological categories underlying natural language and human commonsense. DOLCE is an ontology that focuses on particulars in the sense that its domain of discourse is restricted to them. The project is complete, though the ontology remains available for use.
keyword: computer science
keyword: subject agnostic
keyword: classification
is deprecated: true
has prefix: dolce

Mondo Disease Ontology
has responsible: https://orcid.org/0000-0002-4142-7153
has provider formatter: http://purl.obolibrary.org/obo/MONDO_$1
git repository: mondo
is part of: Bioregistry
has resource example: MONDO_0000001
type: Resource
has prefix: mondo
has download URL: mondo.owl
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
description: The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world.
keyword: medicine
keyword: infectious disease medicine
keyword: obo
keyword: ontology
has URI prefix: http://purl.obolibrary.org/obo/MONDO_
keyword: biocuration
is deprecated: false

Uberon Property
has alternative prefix: UBREL
has alternative prefix: UBPROP
is deprecated: true
has prefix: ubprop
contributor: Charles Tapley Hoyt
is part of: Bioregistry
type: Resource

ClinGen Clinical Genome Expert Panel
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: https://clinicalgenome.org/affiliation/40135/
type: Resource
has provider formatter: https://clinicalgenome.org/affiliation/$1/
has URI prefix: https://bioregistry.io/clingen.affiliation:
0000005: 40135
is deprecated: false
description: ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides identifiers for a panel of experts performing variant pathogenecity evaluation.
has prefix: clingen.affiliation

NLM Publisher Codes
appears in: National Library of Medicine Catalog
is deprecated: false
0000005: wiley
keyword: ontology
has download URL: nlm.publisher.owl
is part of: Bioregistry
has responsible: NLM Customer Service
has prefix: nlm.publisher
contributor: Charles Tapley Hoyt
description: Publisher short codes appearin in the NLM Catalog.
keyword: bibliometrics
type: Resource
keyword: publisher

Ontology Concept Identifiers
has prefix: ocid
has URI prefix: https://ocid.ontochem.com/prefname
description: 'ocid' stands for "Ontology Concept Identifiers" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology.
is deprecated: false
has local unique identifier pattern: ^[0-9]{12}$
has resource example: https://ocid.ontochem.com/prefname
0000005: 190000021540
has provider formatter: https://ocid.ontochem.com/prefname
is part of: Bioregistry
type: Resource

Asset Description Metadata Schema Vocabulary
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: http://www.w3.org/ns/adms#$1
has resource example: Asset
has prefix: adms
type: Resource
0000005: Asset
git repository: ADMS
keyword: metadata
description: A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies).
has URI prefix: http://www.w3.org/ns/adms#

SWEET Ontology Phenomena Atmosphere Sky
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: sophatmos
keyword: atmosphere sky
type: Resource
keyword: phenomena
has URI prefix: http://sweetontology.net/phenAtmoSky/
has prefix: sweet.phatmos
has provider formatter: http://sweetontology.net/phenAtmoSky/$1
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Sky
has resource example: AirPollution
0000005: AirPollution

RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting
has responsible: Ivan Herman
keyword: rdf
has resource example: PrefixOrTermMapping
description: RDFa Core is a specification for attributes to express structured data in any markup language. The embedded data already available in the markup language (e.g., HTML) can often be reused by the RDFa markup, so that publishers don't need to repeat significant data in the document content. (from https://www.w3.org/TR/rdfa-core/)
is deprecated: false
has prefix: rdfa
has URI prefix: http://www.w3.org/ns/rdfa#
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: PrefixOrTermMapping
type: Resource
has provider formatter: http://www.w3.org/ns/rdfa#$1

UR-DBMS Syndrome Finder
has resource example: http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has URI prefix: http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php
is deprecated: true
has provider formatter: http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php
appears in: Nanbyo Disease Ontology
has prefix: urdbms.syndromefinder
0000005: 3567

Scientific Evidence and Provenance Information Ontology
has local unique identifier pattern: ^\d{7}$
type: Resource
0000005: 0000048
has responsible: Matthew Brush
has URI prefix: http://purl.obolibrary.org/obo/SEPIO_
keyword: obo
has prefix: sepio
has provider formatter: http://purl.obolibrary.org/obo/SEPIO_$1
keyword: ontology
git repository: SEPIO-ontology
keyword: mathematics
has download URL: sepio.owl
is deprecated: false
description: An ontology for representing the provenance of scientific claims and the evidence that supports them.
keyword: nfdi4chem
has resource example: SEPIO_0000048
is part of: Bioregistry
keyword: nfdi4ing

GenPept
is deprecated: false
is part of: Bioregistry
description: The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.
has prefix: genpept
type: Resource
has local unique identifier pattern: ^\w{3}\d{5}(\.\d+)?$
has resource example: https://www.ncbi.nlm.nih.gov/protein/CAA71118.1
has provider formatter: https://www.ncbi.nlm.nih.gov/protein/$1
has URI prefix: https://bioregistry.io/genpept:
0000005: CAA71118.1

Prefix Commons
has provider formatter: https://bioregistry.io/metaregistry/prefixcommons/$1
0000005: ChEBI
has resource example: ChEBI
is part of: Bioregistry
has prefix: prefixcommons
contributor: Charles Tapley Hoyt
type: Resource
description: A registry of life science prefxes
is deprecated: false
has URI prefix: https://bioregistry.io/metaregistry/prefixcommons/

MINID Test
0000005: 3SBPLMKKVEVR
is deprecated: false
is part of: Bioregistry
has prefix: minid.test
has local unique identifier pattern: ^[A-Za-z0-9]+$
description: Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace.
has URI prefix: https://hdl.handle.net/hdl:20.500.12633/
type: Resource
has provider formatter: https://hdl.handle.net/hdl:20.500.12633/$1
is part of: Minimal Viable Identifier
has resource example: 3SBPLMKKVEVR

SWEET Ontology Representation Science Provenance
type: Resource
has provider formatter: http://sweetontology.net/reprSciProvenance/$1
has resource example: Agent
has URI prefix: http://sweetontology.net/reprSciProvenance/
has prefix: sweet.repsp
0000005: Agent
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Science Provenance
is part of: Bioregistry
keyword: representation science provenance
git repository: sweet
contributor: Charles Tapley Hoyt
has alternative prefix: sorepsp
is part of: Semantic Web for Earth and Environment Technology Ontology

MediaDive Solution
has URI prefix: https://mediadive.dsmz.de/solutions/
has responsible: Jörg Overmann
has local unique identifier pattern: ^S\d+$
is deprecated: false
has prefix: mediadive.solution
description: The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]
has resource example: S6
is part of: Bioregistry
contributor: Charles Tapley Hoyt
0000005: S6
type: Resource
has provider formatter: https://mediadive.dsmz.de/solutions/$1

NIF Standard Ontology: Cognitive Function
has alternative prefix: NLXFUNC
0000005: 90801
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_func_$1
has responsible: Tom Gillespie
is deprecated: false
git repository: NIF-Ontology
has local unique identifier pattern: ^\d+$
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_func_
description: NLXFUNC covers terms for cognitive function.
is part of: Bioregistry
has resource example: nlx func 90801
type: Resource
keyword: neuroscience
has prefix: nlx.func
has reviewer: Charles Tapley Hoyt
contributor: Tom Gillespie

DigitRubber Ontology
keyword: ontology
has provider formatter: https://www.tib.eu/digitrubber#DIGITRUBBER_$1
is deprecated: false
0000005: 000040
is part of: Bioregistry
has download URL: digitrubber.owl
contributor: Charles Tapley Hoyt
has URI prefix: https://www.tib.eu/digitrubber#DIGITRUBBER_
has resource example: DIGITRUBBER_000040
git repository: DIGIT-RUBBER
description: An ontology demonstrating rich ontology for rubber extrusion.
has prefix: digitrubber
type: Resource

International Classification of Diseases for Oncology
description: The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases
has URI prefix: http://codes.iarc.fr/search.php
is deprecated: false
has local unique identifier pattern: ^[8-9]\d{3}(/[0-3])?$
is part of: Bioregistry
has prefix: icdo
0000005: 9861/3
type: Resource
contributor: Charles Tapley Hoyt
has resource example: http://codes.iarc.fr/search.php
has provider formatter: http://codes.iarc.fr/search.php
has alternative prefix: ICD-O
has alternative prefix: ICDO

Bibliographic Framework Initiative Vocabulary
keyword: computer science
has responsible: Kirk Hess
keyword: subject agnostic
has alternative prefix: bf
has download URL: bibframe.rdf
has URI prefix: http://id.loc.gov/ontologies/bibframe/
0000005: DescriptionLevel
is deprecated: false
keyword: miscellaneous
has prefix: bibframe
keyword: ontology
has resource example: DescriptionLevel
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: The Bibframe vocabulary consists of RDF classes and properties used for the description of items cataloged principally by libraries, but may also be used to describe items cataloged by museums and archives. Classes include the three core classes - Work, Instance, and Item - in addition to many more classes to support description. Properties describe characteristics of the resource being described as well as relationships among resources. For example: one Work might be a "translation of" another Work; an Instance may be an "instance of" a particular Bibframe Work. Other properties describe attributes of Works and Instances. For example: the Bibframe property "subject" expresses an important attribute of a Work (what the Work is about), and the property "extent" (e.g. number of pages) expresses an attribute of an Instance.
git repository: bibframe-ontology
has provider formatter: http://id.loc.gov/ontologies/bibframe/$1
type: Resource

ExAC Variant
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$
type: Resource
has resource example: 22-46615880-T-C
0000005: 22-46615880-T-C
has URI prefix: http://exac.broadinstitute.org/variant/
has provider formatter: http://exac.broadinstitute.org/variant/$1
has prefix: exac.variant
description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.

Ali Syed

System Science of Biological Dynamics project
is deprecated: false
has provider formatter: https://ssbd.riken.jp/database/project/$1
has resource example: https://ssbd.riken.jp/database/project/1
0000005: 1
description: Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations.
has URI prefix: https://ssbd.riken.jp/database/project/
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
contributor: Charles Tapley Hoyt
has prefix: ssbd.project

Biosapiens Protein Feature Ontology
has provider formatter: https://biopragmatics.github.io/providers/bs/$1
description: SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library.
has URI prefix: https://biopragmatics.github.io/providers/bs/
type: Resource
has download URL: biosapiens.obo
keyword: ontology
has prefix: bs
is deprecated: false
has resource example: https://biopragmatics.github.io/providers/bs/00042
git repository: SO-Ontologies
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
0000005: 00042
contributor: Charles Tapley Hoyt

Rice annotation Project database
has resource example: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1
description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB.
has provider formatter: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1
has local unique identifier pattern: ^Os\S+t\d{7}-\d{2}$
is deprecated: false
is part of: Bioregistry
has prefix: rapdb.transcript
keyword: genome
keyword: dna
has URI prefix: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1
type: Resource
0000005: Os01t0883800-02

MetaNetX compartment
has provider formatter: https://www.metanetx.org/comp_info/$1
type: Resource
has prefix: metanetx.compartment
description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.
is deprecated: false
has URI prefix: https://www.metanetx.org/comp_info/
has resource example: MNXC15
0000005: MNXC15
has local unique identifier pattern: ^(MNX[CD]\d+|BOUNDARY|IN|OUT)$
is part of: Bioregistry

Influenza Virus Database
is deprecated: false
description: IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.
keyword: genome
keyword: dna
is part of: Bioregistry
0000005: E13035
has URI prefix: http://influenza.psych.ac.cn/search/detail.jsp
type: Resource
keyword: gene
has provider formatter: http://influenza.psych.ac.cn/search/detail.jsp
has prefix: ivdb
has resource example: http://influenza.psych.ac.cn/search/detail.jsp

SWEET Ontology Property Difference
is part of: Bioregistry
has alternative prefix: sopropdife
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has prefix: sweet.propdife
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Difference
has resource example: Amplitude
0000005: Amplitude
is deprecated: false
keyword: difference
has provider formatter: http://sweetontology.net/propDifference/$1
has URI prefix: http://sweetontology.net/propDifference/

NCBI Bookshelf
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
0000005: NBK331
has resource example: NBK331
has local unique identifier pattern: ^NBK\d+$
has provider formatter: https://www.ncbi.nlm.nih.gov/books/$1
description: The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover.
has prefix: ncbibook
is deprecated: false
has URI prefix: https://www.ncbi.nlm.nih.gov/books/

Veterinary Substances DataBase
type: Resource
has prefix: vsdb
has URI prefix: https://bioregistry.io/vsdb:
0000005: 1868
description: Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source.
is deprecated: false
has resource example: 1868.htm
has provider formatter: https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt

Human Chromosome Ontology
has prefix: hco
0000005: MT
has URI prefix: http://biohackathon.org/resource/hco#
has provider formatter: http://biohackathon.org/resource/hco#$1
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^.+$
type: Resource
has resource example: MT
description: The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes.

NFDI-MatWerk Collection
type: Collection
creator: Charles Tapley Hoyt
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI-MatWerk
has part: Bioregistry

LinkedIn personal profile ID
is deprecated: false
is part of: Bioregistry
has resource example: deborahlehr
has local unique identifier pattern: ^[\w0-9\-&_'’\.]+$
contributor: Charles Tapley Hoyt
keyword: person
description: identifier for a person, on the LinkedIn website
has provider formatter: https://www.linkedin.com/in/$1
has URI prefix: https://www.linkedin.com/in/
keyword: researcher
has prefix: linkedin
type: Resource
0000005: deborahlehr

SWEET Ontology State Space Scale
is deprecated: false
has provider formatter: http://sweetontology.net/stateSpaceScale/$1
is part of: Bioregistry
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has prefix: sweet.stss
keyword: state space scale
has resource example: Continental
0000005: Continental
has URI prefix: http://sweetontology.net/stateSpaceScale/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Space Scale
type: Resource
has alternative prefix: sostss

Eukaryotic Linear Motif Resource
has prefix: elm
has URI prefix: https://bioregistry.io/elm:
has resource example: CLV MEL PAP 1.html
is part of: Bioregistry
has local unique identifier pattern: ^[A-Za-z_0-9]+$
description: Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances.
type: Resource
has provider formatter: http://elm.eu.org/elms/elmPages/$1.html
0000005: CLV_MEL_PAP_1
keyword: life science
has responsible: https://orcid.org/0000-0003-0657-5166
is deprecated: false

Industrial Data Ontology
0000005: Activity
is deprecated: false
keyword: engineering
is part of: Bioregistry
has resource example: Activity
has prefix: tib.lis
type: Resource
has URI prefix: http://rds.posccaesar.org/ontology/lis14/rdl/
keyword: nfdi4ing
description: The Industrial Data Ontology is an upper ontology for industrial data, inspired by the ISO 15926-2 data model and Basic Formal Ontology.
has provider formatter: http://rds.posccaesar.org/ontology/lis14/rdl/$1

runBioSimulations
has URI prefix: https://run.biosimulations.org/simulations/
has prefix: runbiosimulations
type: Resource
has resource example: https://run.biosimulations.org/simulations/5fde96bdc5f1aa9ff0cce18a
has local unique identifier pattern: ^[0-9a-z]{24,24}$
has provider formatter: https://run.biosimulations.org/simulations/$1
description: runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive.
is deprecated: false
0000005: 5fde96bdc5f1aa9ff0cce18a
is part of: Bioregistry

MarFun
0000005: MMP3888430
has local unique identifier pattern: ^MMP\d+.\d+$
is deprecated: false
has prefix: mmp.fun
has URI prefix: https://mmp.sfb.uit.no/databases/marfun/#/records/
is part of: Bioregistry
description: MarFun is manually curated database for marine fungi which is a part of the MAR databases.
type: Resource
has resource example: records/MMP3888430
has provider formatter: https://mmp.sfb.uit.no/databases/marfun/#/records/$1

Vertebrate Breed Ontology Issue Tracker
has resource example: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126
has provider formatter: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/$1
description: An issue on the Vertebrate Breed Ontology GitHub issue tracker
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
0000005: 126
type: Resource
contributor: Charles Tapley Hoyt
has prefix: vbo.issue
has URI prefix: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/
is deprecated: false

Digital Reference
is deprecated: false
keyword: economics
has provider formatter: http://www.w3id.org/ecsel-dr-SO#$1
0000005: Application
keyword: electrical engineering
description: Holistic Ontology for semiconductor manufacturing and development, products and systems containing semiconductors and connected supply chains.
is part of: Bioregistry
type: Resource
keyword: nfdi4ing
has resource example: Application
has URI prefix: http://www.w3id.org/ecsel-dr-SO#
keyword: coypu
has prefix: tib.dr

SWEET Ontology Property Capacity
has URI prefix: http://sweetontology.net/propCapacity/
has provider formatter: http://sweetontology.net/propCapacity/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Capacity
keyword: capacity
is deprecated: false
has prefix: sweet.propcap
has alternative prefix: sopropcap
has resource example: Capacity
is part of: Bioregistry
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
0000005: Capacity

Genomes Online Database
is part of: Bioregistry
has URI prefix: https://gold.jgi.doe.gov/resolver
has responsible: TBK Reddy
keyword: metagenomics
keyword: phylogenetics
has download URL: gold.owl
has local unique identifier pattern: ^[A-Z][a-z][0-9]+$
type: Resource
0000005: Gs0000008
keyword: ontology and terminology
keyword: ontology
has provider formatter: https://gold.jgi.doe.gov/resolver
has resource example: https://gold.jgi.doe.gov/resolver
keyword: genome
keyword: genomics
is deprecated: false
keyword: metabolomics
has prefix: gold
description: The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.

Molecular Design Limited Hash
is part of: Bioregistry
appears in: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
contributor: Charles Tapley Hoyt
description: The MDL number contains a unique identification number for each reaction and variation. The format is RXXXnnnnnnnn. R indicates a reaction, XXX indicates which database contains the reaction record. The numeric portion, nnnnnnnn, is an 8-digit number. [wikipedia]
type: Resource
has prefix: mdl
is deprecated: false
0000005: MFCD00011659
has local unique identifier pattern: ^\w{4}\d{8}$

Five Stars of Online Research Articles Ontology
0000005: hasOpenAccessRating
keyword: subject agnostic
is deprecated: false
git repository: fivestars
has prefix: fivestars
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has responsible: Silvio Peroni
description: An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata.
type: Resource

SWEET Ontology Property Energy Flux
has provider formatter: http://sweetontology.net/propEnergyFlux/$1
type: Resource
git repository: sweet
has URI prefix: http://sweetontology.net/propEnergyFlux/
has resource example: AbsorbedSolarRadiation
0000005: AbsorbedSolarRadiation
keyword: energy flux
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Energy Flux
has prefix: sweet.propef
has alternative prefix: sopropef
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology

Alan Wood's Pesticides
has resource example: derivatives/thiocyclam hydrochloride.html
description: The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients.
has prefix: pesticides
has provider formatter: http://www.alanwood.net/pesticides/$1.html
is deprecated: false
has URI prefix: https://bioregistry.io/pesticides:
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

Human Plasma Membrane Receptome Families
is deprecated: false
keyword: protein
has provider formatter: http://www.receptome.org/families/Frameset_family.asp
description: The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database.
has resource example: http://www.receptome.org/families/Frameset_family.asp
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: receptome.family
type: Resource
has URI prefix: http://www.receptome.org/families/Frameset_family.asp
0000005: 5.1

Cultural Objects Names Authority
has URI prefix: http://vocab.getty.edu/page/cona/
has provider formatter: http://vocab.getty.edu/page/cona/$1
type: Resource
0000005: 700054086
is deprecated: false
description: CONA compiles titles, attributions, depicted subjects, and other metadata about works of art, architecture, and cultural heritage, both extant and historical, physical and conceptual. Metadata is gathered and linked from museum collections, special collections, archives, libraries, scholarly research, and other sources. CONA is linked to the AAT, TGN, ULAN, and the IA (Iconography Authority). Through rich metadata and links, CONA may provide a powerful conduit for research and discovery for digital art history. [from homepage]
has prefix: getty.cona
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: http://vocab.getty.edu/page/cona/700054086

Planarian Phenotype Ontology
keyword: obo
git repository: planarian-phenotype-ontology
keyword: ontology
depends on: Relation Ontology
has URI prefix: http://purl.obolibrary.org/obo/PLANP_
has prefix: planp
is deprecated: false
description: Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.
has local unique identifier pattern: ^\d+$
depends on: Phenotype And Trait Ontology
has download URL: planp.owl
depends on: Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology
has resource example: PLANP_0000001
is part of: Bioregistry
depends on: Gene Ontology
type: Resource
has responsible: https://orcid.org/0000-0002-3528-5267
has provider formatter: http://purl.obolibrary.org/obo/PLANP_$1
0000005: 0000001

Iconclass Classification
has responsible: https://orcid.org/0000-0002-0006-7542
is deprecated: false
has download URL: iconclass.owl
has prefix: iconclass
keyword: ontology
0000005: 3
is part of: Bioregistry
has URI prefix: https://iconclass.org/
contributor: Charles Tapley Hoyt
has resource example: https://iconclass.org/3
has provider formatter: https://iconclass.org/$1
description: A classification system for the subject matter of works of art, originating from work from Henri van de Waal in the 1940.
type: Resource

Crystallographic Information Framework
has resource example: space group symop.operation xyz
is deprecated: false
is part of: Bioregistry
keyword: nfdi4cat
has URI prefix: http://emmo.info/emmo/cif-core#
contributor: Charles Tapley Hoyt
has provider formatter: http://emmo.info/emmo/cif-core#$1
description: A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)
type: Resource
keyword: material science
has prefix: emmo.cif
0000005: _space_group_symop.operation_xyz
has responsible: 0000-0002-1560-809X
git repository: CIF-ontology
keyword: physics

Xenobiotics Metabolism Database
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has URI prefix: http://www.xmetdb.org/xmetdb/protocol/
contributor: Charles Tapley Hoyt
0000005: 171
has provider formatter: http://www.xmetdb.org/xmetdb/protocol/$1
type: Resource
has resource example: http://www.xmetdb.org/xmetdb/protocol/171
has prefix: xmetdb
description: Metabolites in the Xenobiotics Metabolism Database.
is deprecated: true

Zazuko Prefix Server
description: This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from <https://prefix.zazuko.com/about>)
is deprecated: false
has resource example: frbr:
has prefix: zazuko
has responsible: Adrian Gschwend
is part of: Bioregistry
has URI prefix: https://bioregistry.io/zazuko:
type: Resource
contributor: Charles Tapley Hoyt
has provider formatter: https://prefix.zazuko.com/prefix/$1:
0000005: frbr

NFDI4Earth Ontology
keyword: ess
0000005: API
is deprecated: false
is part of: Bioregistry
description: The ontology and metadata schema for the NFDI4Earth Knowledge Hub. See serializations of this schema as an OWL ontology here: - [RDF/XML](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.xml) - [RDF/Turtle](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.ttl) - [RDF/JSON-LD](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.jsonld) - [RDF/N-Triples](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.nt)
has resource example: API
keyword: earth sciences
has URI prefix: http://nfdi4earth.de/ontology/
type: Resource
has prefix: n4e
has provider formatter: http://nfdi4earth.de/ontology/$1

ZINC is not Commercial
has URI prefix: http://zinc15.docking.org/substances/
has resource example: ZINC1084
has provider formatter: http://zinc15.docking.org/substances/$1
has prefix: zinc
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^(ZINC)?\d+$
description: ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.
type: Resource
0000005: ZINC1084

EAWAG Biocatalysis/Biodegradation Database rule
0000005: bt0001
is part of: Bioregistry
has provider formatter: http://www.umbbd.ethz.ch/servlets/rule.jsp
type: Resource
has local unique identifier pattern: ^bt\d+$
has resource example: http://www.umbbd.ethz.ch/servlets/rule.jsp
has alternative prefix: UM-BBD_ruleID
has URI prefix: http://www.umbbd.ethz.ch/servlets/rule.jsp
description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules.
has prefix: umbbd.rule
is deprecated: false

VEuPathDB ontology
has provider formatter: http://purl.obolibrary.org/obo/EUPATH_$1
has URI prefix: http://purl.obolibrary.org/obo/EUPATH_
keyword: obo
keyword: ontology
keyword: population genetics
git repository: VEuPathDB-ontology
is part of: Bioregistry
keyword: microbiome
keyword: functional genomics
has download URL: eupath.owl
has responsible: Jie Zheng
has local unique identifier pattern: ^\d{7}$
has prefix: eupath
type: Resource
0000005: 0010316
keyword: epidemiology
keyword: biomedical science
is deprecated: true
description: The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.
has resource example: EUPATH_0010316
appears in: Sickle Cell Disease Ontology

MEROPS Clan
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://www.ebi.ac.uk/merops/cgi-bin/clansum
has prefix: merops.clan
has responsible: Neil D Rawlings
type: Resource
has URI prefix: https://www.ebi.ac.uk/merops/cgi-bin/clansum
has resource example: https://www.ebi.ac.uk/merops/cgi-bin/clansum
is deprecated: false
0000005: IA
description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

Library of Congress Subject Headings
has alternative prefix: lcnafid
has URI prefix: https://id.loc.gov/authorities/
has local unique identifier pattern: ^\w{1,2}\d{8,10}$
is part of: Bioregistry
has alternative prefix: lcnaf
contributor: Charles Tapley Hoyt
type: Resource
keyword: subject agnostic
has prefix: lcsh
description: Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage)
has part: Library of Congress Subject Headings - Genre Forms
has resource example: nb2018006591
is deprecated: false
0000005: nb2018006591
has provider formatter: https://id.loc.gov/authorities/$1

International Standard Classification of Education, 2011 Edition
is deprecated: false
has resource example: level1
is part of: Bioregistry
has URI prefix: https://w3id.org/kim/isced-2011/level
keyword: education level
contributor: Charles Tapley Hoyt
keyword: open educational resources
type: Resource
has provider formatter: https://w3id.org/kim/isced-2011/level$1
description: ISCED is designed to serve as a framework to classify educational activities as defined in programmes and the resulting qualifications into internationally agreed categories. The basic concepts and definitions of ISCED are therefore intended to be internationally valid and comprehensive of the full range of education systems.
has prefix: isced2011
0000005: 1

NFDI4Biodiversity Collection
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Biodiversity
has part: Bioregistry
type: Collection
creator: Charles Tapley Hoyt

MetaNetX chemical
description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.
is deprecated: false
has URI prefix: https://www.metanetx.org/chem_info/
has local unique identifier pattern: ^(MNXM\d+|BIOMASS|WATER)$
has provider formatter: https://www.metanetx.org/chem_info/$1
is part of: Bioregistry
has resource example: MNXM1723
0000005: MNXM1723
type: Resource
has prefix: metanetx.chemical

European Medicines Evaluation Agency
0000005: EMEA/H/C/000181
is deprecated: false
has prefix: emea
is part of: Bioregistry
description: Product number for the European Medicines Agency
type: Resource
contributor: Charles Tapley Hoyt

Ecological Trait-data Standard
description: The Ecological Trait-data Standard defines terms for the use in datasets containing quantitative and qualitative functional traits.
keyword: ess
is deprecated: false
keyword: fair data spaces
has provider formatter: http://terminologies.gfbio.org/terms/ETS/$1
is part of: Bioregistry
has URI prefix: http://terminologies.gfbio.org/terms/ETS/
keyword: earth sciences
keyword: life sciences, biology
has resource example: BiodiversityExploratories
0000005: BiodiversityExploratories
type: Resource
has prefix: gfbio.ets

Stress Knowledge Map
0000005: rx00408
has URI prefix: https://bioregistry.io/skm:
is part of: Bioregistry
has prefix: skm
type: Resource
has resource example: https://skm.nib.si/api/pss/reactions
has local unique identifier pattern: ^rx[0-9]{5}$
has provider formatter: https://skm.nib.si/api/pss/reactions
description: Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors.
is deprecated: false

Histopathology Ontology
0000005: 2000191
has provider formatter: http://purl.obolibrary.org/obo/MC_$1
keyword: ontology
git repository: hpath
has download URL: hpath.obo
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has responsible: Carlo Ravagli
contributor: Charles Tapley Hoyt
has alternative prefix: MC
description: An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species. The original structure of the histopathology ontology was designed ab initio when the [INHAND](http://www.goreni.org/) manuscripts were not available. However, the ontology has been repetitively reviewed and updated to align with the subsequently published INHAND manuscripts. During this process cross references to INHAND lesion identifiers were added to the ontology. [from GitHub]
has URI prefix: http://purl.obolibrary.org/obo/MC_
type: Resource
has prefix: hpath
has resource example: MC_2000191

Laboratory of Systems Pharmacology Compound
is deprecated: false
has provider formatter: https://labsyspharm.github.io/lspci/$1
keyword: metabolites
has local unique identifier pattern: ^\d+$
keyword: chemistry
0000005: 1
has prefix: lspci
has resource example: https://labsyspharm.github.io/lspci/1
is part of: Bioregistry
description: Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)
type: Resource
contributor: Charles Tapley Hoyt
has URI prefix: https://labsyspharm.github.io/lspci/
keyword: drugs

NFDIxCS Collection
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDIxCS
creator: Charles Tapley Hoyt
has part: Bioregistry
type: Collection

Plant Anatomy Ontology
is part of: Bioregistry
type: Resource
has provider formatter: http://purl.obolibrary.org/obo/PAO_$1
has prefix: pao
has responsible: Pankaj Jaiswal
has URI prefix: http://purl.obolibrary.org/obo/PAO_
is deprecated: true
keyword: obo
keyword: ontology

Human Intermediate Filament Database
has prefix: interfil
type: Resource
0000005: NM_006262
has provider formatter: http://www.interfil.org/details.php
has reviewer: Charles Tapley Hoyt
description: The Intermediate Filament Database functions as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants.
is deprecated: false
has resource example: http://www.interfil.org/details.php
has URI prefix: http://www.interfil.org/details.php
keyword: genome
is part of: Bioregistry

FaceBase Data Repository
has prefix: facebase
has responsible: Yang Chai
type: Resource
0000005: FB00000917
keyword: epigenetics
keyword: anatomy
is deprecated: false
keyword: medicine
has resource example: https://www.facebase.org/data/record/
has local unique identifier pattern: ^FB\d{8}$
has provider formatter: https://www.facebase.org/data/record/
has URI prefix: https://www.facebase.org/data/record/
keyword: genetics
description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.
is part of: Bioregistry
keyword: developmental biology

Terminology of Anatomy of Human Embryology
has prefix: tahe
is deprecated: true
keyword: obo
has URI prefix: http://purl.obolibrary.org/obo/TAHE_
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/TAHE_$1
is part of: Bioregistry
type: Resource

Resource Description Framework
has provider formatter: http://www.w3.org/1999/02/22-rdf-syntax-ns#$1
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has resource example: type
has prefix: rdf
keyword: computer science
keyword: subject agnostic
0000005: type
has URI prefix: http://www.w3.org/1999/02/22-rdf-syntax-ns#
description: This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts
is deprecated: false
keyword: w3c rec
has responsible: https://orcid.org/0000-0001-5699-0515

Data Type
description: Identifies the type of data, which has a bearing on the acceptable data values, the operations that can be performed with the data, and the ways in which the data are stored.
has URI prefix: https://vocabularies.cessda.eu/vocabulary/DataType#code_
is deprecated: false
has prefix: ddi.datatype
has provider formatter: https://vocabularies.cessda.eu/vocabulary/DataType#code_$1
0000005: String
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has resource example: code String
has identifier space owner: 015em2733

LRMI Learning Resource Type Concept Scheme
has prefix: lrmi.resourcetype
has provider formatter: http://purl.org/dcx/lrmi-vocabs/learningResourceType/$1
0000005: activityPlan
has URI prefix: http://purl.org/dcx/lrmi-vocabs/learningResourceType/
is deprecated: false
is part of: Bioregistry
keyword: learning resource
contributor: Charles Tapley Hoyt
git repository: lrmi
has resource example: activityPlan
description: A top-level concept scheme that enumerates different types of Learning Resource, designed to supplement existing more generic resource type schemes and which can support local extensions.
keyword: open educational resource
type: Resource

FAIRmat Resources
has part: NeXusOntology
type: Collection
has part: Thin-film Solar Cells Ontology
creator: Charles Tapley Hoyt
description: Prefixes for ontologies relevant for [FAIRmat](https://www.nfdi.de/consortia-fairmat).
has part: A vocabulary for the catalysis disciplines
has part: Basic Formal Ontology

Aceview Worm
has prefix: aceview.worm
has local unique identifier pattern: ^[a-z0-9-]+$
has responsible: Danielle Thierry-Mieg
is part of: Bioregistry
type: Resource
keyword: gene
has resource example: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi
description: AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression.
has provider formatter: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi
has URI prefix: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi
keyword: rna
0000005: aap-1
is deprecated: false
keyword: dna

SPAR Ontologies
description: The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF.
has part: DataCite Ontology
creator: Charles Tapley Hoyt
type: Collection
has part: Citation Counting and Context Characterisation Ontology
has part: Document Components Ontology
has part: Scholarly Contributions and Roles Ontology
has part: Publishing Workflow Ontology
has part: Bibliometric Data Ontology
has part: Discourse Elements Ontology
has part: Citation Typing Ontology
has part: FaBiO, the FRBR-aligned Bibliographic Ontology
has part: Funding, Research Administration and Projects Ontology
has part: Plant Stress Ontology
has part: Mention Typing Ontology
has part: Publishing Roles Ontology
has part: Bibliographic Reference Ontology

OpenAlex
has resource example: W2741809807
keyword: wikidata
description: OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other.
is deprecated: false
has responsible: https://orcid.org/0000-0003-1613-5981
has prefix: openalex
has URI prefix: https://openalex.org/
contributor: https://orcid.org/0000-0002-3012-7446
has local unique identifier pattern: ^[WAICV]\d{2,}$
keyword: knowledge graph
is part of: Bioregistry
type: Resource
has provider formatter: https://openalex.org/$1
0000005: W2741809807
has reviewer: Charles Tapley Hoyt

NIAID ChemDB ID
has resource example: http://chemdb.niaid.nih.gov/CompoundDetails.aspx
0000005: 059486
has provider formatter: http://chemdb.niaid.nih.gov/CompoundDetails.aspx
is deprecated: false
has prefix: niaid.chemdb
has URI prefix: http://chemdb.niaid.nih.gov/CompoundDetails.aspx
description: ID in NIAID ChemDB
is part of: Bioregistry
type: Resource

Software Licenses Ontology
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: SWL_0000013
has responsible: Ruth Duerr
git repository: swl
has local unique identifier pattern: ^\d{7}$
type: Resource
has provider formatter: http://cor.esipfed.org/ont/SWL_$1
keyword: license
is deprecated: true
0000005: 0000013
description: This mini-ontology contains classes and instances for each version of the licenses that are commonly used in software projects, particularly open source software projects. The URI's for each are the canonical URI's for that license (where they exist).
has URI prefix: http://cor.esipfed.org/ont/SWL_
has prefix: earthcube.swl

FuncBase Human
description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.
has resource example: http://func.mshri.on.ca/human/genes/list_functional_scores/119514
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has provider formatter: http://func.mshri.on.ca/human/genes/list_functional_scores/$1
has prefix: funcbase.human
type: Resource
has URI prefix: http://func.mshri.on.ca/human/genes/list_functional_scores/
is deprecated: false
0000005: 119514

Merck Index Monograph
is deprecated: false
0000005: M2871
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: https://merckindex.rsc.org/monographs/
has provider formatter: https://merckindex.rsc.org/monographs/$1
description: A semantic space of small molecules
type: Resource
has prefix: merckindex.monograph
has resource example: M2871

OECD Harmonised Templates
contributor: https://orcid.org/0000-0001-9439-5346
description: The Organisation for Economic Co-operation and Development (OECD) Harmonised Templates (OHTs) are standard data formats for reporting information used for the risk assessment of chemicals, mainly studies done on chemicals to determine their properties or effects on human health and the environment, but also for storing data on use and exposure.
is deprecated: false
is part of: Bioregistry
has prefix: oecd.template
has local unique identifier pattern: ^\d+\.\d+$
type: Resource
0000005: 74.186
has reviewer: Charles Tapley Hoyt

Access to Biological Collection Data Schema
0000005: Accession
keyword: ess
keyword: fair data spaces
is deprecated: false
is part of: Bioregistry
description: The base ontology of the ABCD Standard.
keyword: life sciences, biology
has prefix: tdwg.abcd
type: Resource

RiceNetDB Protein
type: Resource
has prefix: ricenetdb.protein
has resource example: http://bis.zju.edu.cn/ricenetdb/proteindetails.php
is deprecated: false
description: RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.
has local unique identifier pattern: ^LOC\_Os\d{1,2}g\d{5}$
has provider formatter: http://bis.zju.edu.cn/ricenetdb/proteindetails.php
is part of: Bioregistry
has URI prefix: http://bis.zju.edu.cn/ricenetdb/proteindetails.php
0000005: LOC_Os01g49190

Swiss Personalized Health Network Schema
is part of: Bioregistry
type: Resource
git repository: sphn-ontology
0000005: Allergy
contributor: https://orcid.org/0000-0002-3583-7340
has reviewer: Charles Tapley Hoyt
has provider formatter: https://biomedit.ch/rdf/sphn-ontology/sphn#$1
has URI prefix: https://biomedit.ch/rdf/sphn-ontology/sphn#
has resource example: Allergy
has prefix: sphn
has responsible: Sabine Oesterle
keyword: ontology
has local unique identifier pattern: ^\S+$
is deprecated: false
has download URL: sphn rdf schema.owl
description: The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/).

Universal Natural Products Database
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has prefix: unpd
keyword: compound
is deprecated: true
keyword: natural product
keyword: small molecule

The COnCEPT upper-level Design Ontology
is part of: Bioregistry
keyword: engineering
has prefix: condo
has resource example: AestheticFunction
description: The COnCEPT upper-level Design Ontology (COnDO).
has URI prefix: http://www.w3id.org/Concept/Ontology/COnDO#
type: Resource
keyword: nfdi4ing
has provider formatter: http://www.w3id.org/Concept/Ontology/COnDO#$1
0000005: AestheticFunction
is deprecated: false

SAREF4MARI: an extension of SAREF for the maritime domain
keyword: fid move
is part of: Bioregistry
has URI prefix: https://saref.etsi.org/saref4mari/
has prefix: saref.maritime
type: Resource
has alternative prefix: s4mari
has provider formatter: https://saref.etsi.org/saref4mari/$1
description: SAREF4MARI is an extension of SAREF for the maritime domain.
keyword: traffic engineering
0000005: AISDevice
is deprecated: false
has resource example: AISDevice

Veterinary Nomenclature
is deprecated: false
description: The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems.
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
appears in: Vertebrate Breed Ontology
has responsible: David Brodbelt
has prefix: venom
type: Resource
0000005: 12969

Union List of Artist Names
is part of: Bioregistry
has URI prefix: http://vocab.getty.edu/ulan/
contributor: Charles Tapley Hoyt
0000005: 500202846
has provider formatter: http://vocab.getty.edu/ulan/$1
type: Resource
has prefix: getty.ulan
has resource example: http://vocab.getty.edu/ulan/500202846
description: The Getty Thesaurus of Geographic Names (TGN) is a structured vocabulary, including names, descriptions, and other metadata for extant and historical cities, empires, archaeological sites, and physical features important to research of art and architecture. TGN may be linked to GIS (Geographical Information System), maps, and other geographic resources. [from https://collectionstrust.org.uk/resource/thesaurus-of-geographic-names-tgn-getty/]
is deprecated: false

Fission Yeast Experimental Conditions Ontology
contributor: Valerie Wood
is deprecated: false
is part of: Bioregistry
0000005: 0000003
description: PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase.
has responsible: Valerie Wood
has prefix: fyeco
git repository: fypo
has local unique identifier pattern: ^\d{7}$
has reviewer: Charles Tapley Hoyt
type: Resource

Person
description: A person
equivalent class: Person
type: Class

UK Provider Reference Number
has local unique identifier pattern: ^[1-9]\d*$
has provider formatter: https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: identifier for an educational organization issued by the UK Register of Learning Providers
has URI prefix: https://bioregistry.io/ukprn:
type: Resource
has resource example: https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails
has alternative prefix: ukprns
0000005: 10007835
is deprecated: false
has prefix: ukprn

Gene Wiki
has resource example: http://plugins.biogps.org/cgi-bin/wp.cgi
keyword: genetics
is deprecated: false
has prefix: genewiki
has local unique identifier pattern: ^\d+$
0000005: 1017
has URI prefix: http://plugins.biogps.org/cgi-bin/wp.cgi
is part of: Bioregistry
has provider formatter: http://plugins.biogps.org/cgi-bin/wp.cgi
description: The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI.
type: Resource
has responsible: https://orcid.org/0000-0002-9859-4104
0000011: NCBI Gene
keyword: life science

RAP-DB Locus
has resource example: https://rapdb.dna.affrc.go.jp/locus/
0000005: Os01g0883800
is deprecated: false
description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB.
has prefix: rapdb.locus
has local unique identifier pattern: ^Os\S+g\d{7}$
has URI prefix: https://rapdb.dna.affrc.go.jp/locus/
is part of: Bioregistry
has provider formatter: https://rapdb.dna.affrc.go.jp/locus/
has alternative prefix: irgsp
type: Resource

European Bank for induced pluripotent Stem Cells
is deprecated: false
0000005: ESi007-A
has resource example: ESi007-A
has local unique identifier pattern: ^E(S|D)i\d+-\w$
is part of: Bioregistry
has prefix: ebisc
description: Cell line collections (Providers)
has URI prefix: https://cells.ebisc.org/
has provider formatter: https://cells.ebisc.org/$1
type: Resource

RNA Virus Database
type: Resource
has resource example: http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php
description: The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments and contains translated genome sequences for all species.
has prefix: rnavdb
is deprecated: false
has URI prefix: http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php
keyword: rna
0000005: 164750
has provider formatter: http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php
keyword: genome
is part of: Bioregistry

PEPhub
0000005: geo
contributor: Mufaddal Naguthanawala
has responsible: https://orcid.org/0000-0001-5643-4068
is deprecated: false
has prefix: pephub
has local unique identifier pattern: ^[A-Za-z0-9_\-]+(/[A-Za-z0-9_\-]+)?$
has resource example: geo
has reviewer: https://orcid.org/0000-0001-9439-5346
description: PEPhub is a database, web interface, and API for sharing, retrieving, and validating sample metadata. PEPhub uses Portable Encapsulated Projects (PEP) biological metadata standard to store, edit, and access PEPs in one place.
is part of: Bioregistry
type: Resource
has provider formatter: https://pephub.databio.org/$1
has URI prefix: https://pephub.databio.org/

has prefix
equivalent property: prefix
equivalent property: systemCode
type: Property
description: has canonical prefix
range: string
equivalent property: preferredPrefix
domain: Resource
equivalent property: preferredNamespacePrefix

ModelDB
keyword: life science
is deprecated: false
0000005: 45539
keyword: neurobiology
keyword: computational biology
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has prefix: modeldb
has provider formatter: https://modeldb.science/$1
description: ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.
has URI prefix: https://modeldb.science/
type: Resource
has resource example: https://modeldb.science/45539
has responsible: 0000-0002-5176-943X

StoreDB File
has resource example: https://www.storedb.org/store_v3/download.jsp
has provider formatter: https://www.storedb.org/store_v3/download.jsp
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has URI prefix: https://www.storedb.org/store_v3/download.jsp
0000005: 12929
contributor: Charles Tapley Hoyt
type: Resource
has prefix: storedb.file
description: File inside StoreDB at University of Cambridge

MolBiC Compound
has responsible: https://orcid.org/0000-0001-8069-0053
has prefix: molbic.compound
has local unique identifier pattern: ^CP\d+$
contributor: Mufaddal Naguthanawala
has provider formatter: https://molbic.idrblab.net/data/compound/details/$1
is deprecated: false
description: MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for chemical compounds with experimentally validated bioactivity in cellular contexts.
has reviewer: https://orcid.org/0000-0001-9439-5346
has resource example: CP0041613
is part of: Bioregistry
has URI prefix: https://molbic.idrblab.net/data/compound/details/
type: Resource
0000005: CP0041613

Qualification Ontology
git repository: qualo
0000005: 0000001
has resource example: https://w3id.org/qualo/id/0000001
has local unique identifier pattern: ^\d{7}$
has provider formatter: https://w3id.org/qualo/id/$1
has responsible: Charles Tapley Hoyt
description: An ontology of qualifications, distinctions, and certifications that uses the Phenotype And Trait Ontology term quality (PATO:0000001) as a root term.
is deprecated: false
is part of: Bioregistry
has prefix: qualo
has URI prefix: https://w3id.org/qualo/id/
type: Resource
contributor: Charles Tapley Hoyt

KEGG Reaction
has local unique identifier pattern: ^R\d+$
has URI prefix: https://www.kegg.jp/entry/
has resource example: R00100
is part of: Bioregistry
type: Resource
has alternative prefix: KEGG_REACTION
is part of: Kyoto Encyclopedia of Genes and Genomes
has responsible: Minoru Kanehisa
has provider formatter: https://www.kegg.jp/entry/$1
0000005: R00100
keyword: enzyme
has prefix: kegg.reaction
keyword: pathway
description: KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.
is deprecated: false

Animal TFDB Family
type: Resource
description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.
0000005: CUT
has prefix: atfdb.family
has resource example: family summary/TF/CUT
has provider formatter: https://guolab.wchscu.cn/AnimalTFDB4//#/family_summary/TF/$1
has URI prefix: https://guolab.wchscu.cn/AnimalTFDB4//#/family_summary/TF/
has local unique identifier pattern: ^\w+$
is deprecated: false
is part of: Bioregistry

SWEET Ontology Material Particle
keyword: particle
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has alternative prefix: somapa
has prefix: sweet.mapa
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Particle
has resource example: AnomalousEnergeticParticle
type: Resource
keyword: materials
is deprecated: false
has URI prefix: http://sweetontology.net/matrParticle/
0000005: AnomalousEnergeticParticle
has provider formatter: http://sweetontology.net/matrParticle/$1

MGnify Project
type: Resource
has prefix: mgnify.proj
0000005: ERP004492
has provider formatter: https://www.ebi.ac.uk/metagenomics/projects/$1
is deprecated: false
is part of: Bioregistry
description: MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.
has resource example: ERP004492
has local unique identifier pattern: ^[A-Z]+[0-9]+$
has URI prefix: https://www.ebi.ac.uk/metagenomics/projects/

Open Citation Identifier
type: Resource
has URI prefix: https://opencitations.net/index/ci/
0000005: 01027931310-01022252312
has prefix: oci
has local unique identifier pattern: ^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$
is deprecated: false
is part of: Bioregistry
description: Each OCI (Open Citation Identifier) has a simple structure: oci:<identifier>-<identifier>, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entity - see https://doi.org/10.6084/m9.figshare.7127816.v2 for additional information. In each OCI, the first <identifier> is the identifier for the citing bibliographic resource, while the second <identifier> is the identifier for the cited bibliographic resource.
has provider formatter: https://opencitations.net/index/ci/$1
has resource example: https://opencitations.net/index/ci/01027931310-01022252312

SWEET Ontology Process State Change
has URI prefix: http://sweetontology.net/procStateChange/
is part of: Bioregistry
has resource example: Boiling
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: state change
has alternative prefix: soprocsc
0000005: Boiling
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process State Change
is deprecated: false
has provider formatter: http://sweetontology.net/procStateChange/$1
has prefix: sweet.procsc

HoloFood animal
type: Resource
has URI prefix: https://www.holofooddata.org/animal/
is deprecated: false
contributor: 0009-0008-8406-631X
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: holofood.animal
has resource example: SAMEA112904733
is part of: Bioregistry
0000005: SAMEA112904733
has local unique identifier pattern: ^SAMEA\d{9}$
description: The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the animal semantic space correspond to animals that samples in the database are obtained from.
has provider formatter: https://www.holofooddata.org/animal/$1
has responsible: https://orcid.org/0000-0002-5805-7195

International Medical Device Regulators Forum
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: imdrf
description: The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence.
type: Resource
is deprecated: false

Vertebrate Taxonomy Ontology
has local unique identifier pattern: ^\d{7}$
0000005: 9008500
type: Resource
has resource example: VTO_9008500
has provider formatter: http://purl.obolibrary.org/obo/VTO_$1
keyword: taxonomy
description: Comprehensive hierarchy of extinct and extant vertebrate taxa.
keyword: obo
keyword: ontology
keyword: bone element
is deprecated: false
git repository: vertebrate-taxonomy-ontology
is part of: Bioregistry
has download URL: vto.owl
has URI prefix: http://purl.obolibrary.org/obo/VTO_
has responsible: https://orcid.org/0000-0002-8688-6599
has prefix: vto

International Nonproprietary Names
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://mednet-communities.net/inn/db/ViewINN.aspx
has prefix: inn
type: Resource
has alternative prefix: INN_ID
description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.
has resource example: https://mednet-communities.net/inn/db/ViewINN.aspx
0000005: fluticasone
has URI prefix: https://mednet-communities.net/inn/db/ViewINN.aspx
is deprecated: false

iNaturalist Place
description: Identifier for a place in iNaturalist
has provider formatter: https://www.inaturalist.org/places/$1
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has resource example: https://www.inaturalist.org/places/7207
0000005: 7207
has URI prefix: https://www.inaturalist.org/places/
has prefix: inaturalist.place
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false

SWEET Ontology State Space Configuration
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Space Configuration
has alternative prefix: sostsc
is deprecated: false
is part of: Bioregistry
has resource example: Antumbra
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/stateSpaceConfiguration/$1
keyword: state space configuration
0000005: Antumbra
has URI prefix: http://sweetontology.net/stateSpaceConfiguration/
has prefix: sweet.stsc
type: Resource

Thing Description Ontology
type: Resource
has prefix: wot.td
keyword: nfdi4ing
description: This ontology aims to model the Web of Things domain according to the W3C Interest Group (http://w3c.github.io/wot/)
is deprecated: false
0000005: description
has provider formatter: https://www.w3.org/2019/wot/td#$1
is part of: Bioregistry
keyword: engineering
has URI prefix: https://www.w3.org/2019/wot/td#
has resource example: description

European Language Social Science Thesaurus
has prefix: elsst
description: The European Language Social Science Thesaurus (ELSST) is a broad-based, multilingual thesaurus for the social sciences. It is owned and published by the Consortium of European Social Science Data Archives (CESSDA) and its national Service Providers. The thesaurus consists of over 3,000 concepts and covers the core social science disciplines: politics, sociology, economics, education, law, crime, demography, health, employment, information and communication technology and, increasingly, environmental science. [from homepage]
keyword: economics
has provider formatter: https://elsst.cessda.eu/id/3/$1
has responsible: Alen Vodopijevec
is part of: Bioregistry
keyword: social science
has URI prefix: https://elsst.cessda.eu/id/3/
contributor: Charles Tapley Hoyt
type: Resource
is deprecated: false

David Wishart
label: David S. Wishart

The RNA Modification Database
is part of: Bioregistry
has provider formatter: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl
0000005: 051
contributor: Charles Tapley Hoyt
type: Resource
has local unique identifier pattern: ^\d{3}$
description: A comprehensive listing of post-transcriptionally modified nucleosides from RNA -
has resource example: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl
has URI prefix: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl
has prefix: rnamod
keyword: rna
is deprecated: false
keyword: post-transcriptional modification
keyword: structural bioinformatcs

SWEET Ontology Phenomena Hydrosphere
has provider formatter: http://sweetontology.net/phenHydro/$1
has URI prefix: http://sweetontology.net/phenHydro/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Hydrosphere
is deprecated: false
keyword: hydrosphere
0000005: BaseFlow
has resource example: BaseFlow
has alternative prefix: sophhy
has prefix: sweet.phhy
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: phenomena

Material properties ontology
is part of: Bioregistry
has provider formatter: http://bimerr.iot.linkeddata.es/def/material-properties#$1
type: Resource
keyword: nfdi4ing
description: The material properties ontology provides the vocabulary to describe the composition of building elements.
has resource example: Accesories
has URI prefix: http://bimerr.iot.linkeddata.es/def/material-properties#
has prefix: tib.mat
is deprecated: false
keyword: digital planning and construction
keyword: engineering
keyword: fid baudigital
0000005: Accesories

ShareLoc
has resource example: ontology/vocabulary/SHARELOC 000004
description: ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc.
keyword: ontology
has prefix: shareloc
is deprecated: false
has URI prefix: https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_
has download URL: shareloc.owl
is part of: Bioregistry
has local unique identifier pattern: ^\d{6}$
type: Resource
0000005: 000004
has provider formatter: https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1

Degradome Database
has URI prefix: http://degradome.uniovi.es/cgi-bin/protease/
has local unique identifier pattern: ^[AMCST][0-9x][0-9]$
has prefix: degradome
is deprecated: false
0000005: Ax1
is part of: Bioregistry
type: Resource
description: The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced.
has resource example: Ax1
has provider formatter: http://degradome.uniovi.es/cgi-bin/protease/$1

Software Functions Ontology
is deprecated: false
keyword: software
git repository: sfo
has responsible: Ruth Duerr
is part of: Bioregistry
has local unique identifier pattern: ^\d{7}$
type: Resource
contributor: Charles Tapley Hoyt
description: This ontology defines a taxonomy of software functions based on the work of the NSF-funded EarthCube Resource Registry working group. The functions are generally organized by their role in the research process.
has URI prefix: http://cor.esipfed.org/ont/earthcube/SFO_
0000005: 0000001
has resource example: SFO_0000001
has prefix: earthcube.sfo
keyword: software function
has provider formatter: http://cor.esipfed.org/ont/earthcube/SFO_$1

PhosphoPoint Kinase
type: Resource
0000005: AURKA
has prefix: phosphopoint.kinase
is deprecated: false
has resource example: http://kinase.bioinformatics.tw/showall.jsp
description: PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information.
has URI prefix: https://bioregistry.io/phosphopoint.kinase:
has local unique identifier pattern: ^\w+$
has provider formatter: http://kinase.bioinformatics.tw/showall.jsp
is part of: Bioregistry

Dynamic Ecological Information Management System - Site and Dataset Registry - Locations
has local unique identifier pattern: ^[0-9a-f\-]+$
is part of: Bioregistry
description: Locations in DEIMS SDR
has provider formatter: https://deims.org/locations/$1
contributor: Charles Tapley Hoyt
has URI prefix: https://deims.org/locations/
has prefix: deims.location
has responsible: Christoph Wohner
type: Resource
is deprecated: false

CIViC Evidence
has resource example: https://civicdb.org/links/evidence/1199
is part of: Bioregistry
has provider formatter: https://civicdb.org/links/evidence/$1
type: Resource
has responsible: Malachi Griffith
description: Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract).
has prefix: civic.eid
has URI prefix: https://civicdb.org/links/evidence/
has local unique identifier pattern: ^[0-9]+$
has alternative prefix: civic.evidence
is deprecated: false
0000005: 1199

Vitro Application Ontology
0000005: descriptionAnnot
has resource example: descriptionAnnot
keyword: ontology
is deprecated: false
has download URL: vitro-0.7.owl
is part of: Bioregistry
appears in: FaBiO, the FRBR-aligned Bibliographic Ontology
has provider formatter: http://vitro.mannlib.cornell.edu/ns/vitro/0.7#$1
contributor: Charles Tapley Hoyt
git repository: Vitro
has URI prefix: http://vitro.mannlib.cornell.edu/ns/vitro/0.7#
appears in: Friend of a Friend
type: Resource
description: Vitro is a full stack framework for building semantic web applications. It is not domain specific.
has prefix: vitro

Global Proteome Machine Database
0000005: GPM32310002988
has URI prefix: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=
has resource example: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002988
has provider formatter: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1
is deprecated: false
has local unique identifier pattern: ^GPM\d+$
keyword: bioinformatics
has prefix: gpmdb
keyword: proteomics
is part of: Bioregistry
has responsible: https://orcid.org/0000-0001-5782-1000
type: Resource
description: The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.

Simplified Upper Level Ontology
keyword: health
is deprecated: false
has responsible: https://orcid.org/0000-0003-4727-9435
has URI prefix: https://w3id.org/sulo/
has prefix: sulo
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: The Simplified Upper Level Ontology (SULO) is ontology with a minimal set of classes and relations to guide the development of a personal health knowledge graph. [from homepage]
has provider formatter: https://w3id.org/sulo/$1
0000005: Capability
type: Resource
has resource example: Capability
git repository: sulo

International Standard for Intelligent Information Request and Delivery Core Ontology
is part of: Bioregistry
git repository: models
description: An ontology encoding the core metadata based on the Intelligent Information Request and Delivery (iiRDS) standard
has prefix: iirds.core
has provider formatter: http://iirds.tekom.de/iirds#$1
has URI prefix: http://iirds.tekom.de/iirds#
type: Resource
keyword: nfdi4ing
keyword: computer science
0000005: Action
has resource example: Action
is deprecated: false

National Repository of Fish Cell Lines
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has local unique identifier pattern: ^NRFC\d+$
type: Resource
has prefix: nrfc
description: The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)
0000005: NRFC051
is deprecated: false

Internet Standard -- IETF Request for Comments
0000005: 5013
is deprecated: false
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has URI prefix: https://tools.ietf.org/rfc/rfc
has prefix: rfc
type: Resource
description: Legacy site for IETF RFC proposals
has resource example: rfc5013
has provider formatter: https://tools.ietf.org/rfc/rfc$1

European Paediatric Cardiac Codes
description: Collection of European paediatric cardiac coding files
is deprecated: false
has prefix: epcc
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

NCI Drug Dictionary ID
has URI prefix: https://www.cancer.gov/publications/dictionaries/cancer-drug/def/
has prefix: nci.drug
has resource example: beta-carotene
description: identifier of an entry in the NCI Drug Dictionary
is deprecated: false
is part of: Bioregistry
type: Resource
0000005: beta-carotene
has provider formatter: https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1

ODAM Data explorer
is deprecated: false
0000005: frim1
description: ODAM (Open Data for Access and Mining) is an Experimental data table management software (EDTMS) to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines. ODAM allows datasets to be explored and then extracted in whole or in part as needed. For more information/explanation, see ODAM User's Guide : https://inrae.github.io/ODAM/
has resource example: https://pmb-bordeaux.fr/dataexplorer/
has prefix: odamexplorer
is part of: Bioregistry
has local unique identifier pattern: ^[A-Za-z][A-Za-z0-9]+$
type: Resource
has provider formatter: https://pmb-bordeaux.fr/dataexplorer/
has URI prefix: https://pmb-bordeaux.fr/dataexplorer/

NEPOMUK Contact Ontology
description: NEPOMUK Contact Ontology describes contact information, common in many places on the desktop. It evolved from the VCARD specification (RFC 2426) and has been inspired by the Vcard Ontology by Renato Ianella. The scope of NCO is much broader though. This document gives an overview of the classes, properties and intended use cases of the NCO ontology. (from homepage)
is deprecated: false
has URI prefix: http://www.semanticdesktop.org/ontologies/2007/03/22/nco#
has resource example: fullname
has prefix: nepomuk.nco
has provider formatter: http://www.semanticdesktop.org/ontologies/2007/03/22/nco#$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
0000005: fullname

SWEET Ontology Phenomena Geologic
has URI prefix: http://sweetontology.net/phenGeol/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic
type: Resource
keyword: phenomena
keyword: geologic
has prefix: sweet.phg
0000005: CompositeProcess
is deprecated: false
is part of: Bioregistry
has alternative prefix: sophg
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/phenGeol/$1
has resource example: CompositeProcess

Proteomic Data Commons
has resource example: PDC000351
is part of: Bioregistry
type: Resource
has prefix: pdc.study
has reviewer: Charles Tapley Hoyt
0000005: PDC000351
description: The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public.
has URI prefix: https://pdc.cancer.gov/pdc/study/
has local unique identifier pattern: ^PDC\d+$
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has provider formatter: https://pdc.cancer.gov/pdc/study/$1

has local unique identifier pattern
equivalent property: hasRegexPattern
description: The pattern for identifiers in the given resource
domain: Resource
equivalent property: P1793
type: Property
equivalent property: identifierPattern
range: string

PepBank Peptide Database
is part of: Bioregistry
keyword: protein
0000005: 21877
has prefix: pepbank
has provider formatter: http://pepbank.mgh.harvard.edu/interactions/details/$1
description: PepBank is a database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored.
type: Resource
keyword: structure
has reviewer: Charles Tapley Hoyt
has URI prefix: http://pepbank.mgh.harvard.edu/interactions/details/
has resource example: http://pepbank.mgh.harvard.edu/interactions/details/21877
is deprecated: true

Korean Cell Line Bank
has prefix: kclb
has provider formatter: https://cellbank.snu.ac.kr/english/sub/catalog.php
is deprecated: false
description: Cell line collections (Providers)
has resource example: https://cellbank.snu.ac.kr/english/sub/catalog.php
is part of: Bioregistry
has URI prefix: https://cellbank.snu.ac.kr/english/sub/catalog.php
contributor: Charles Tapley Hoyt
type: Resource
0000005: 10020.2

SPARQL 1.1 Service Description
is deprecated: false
keyword: w3c rec
description: Un vocabulaire pour décrire des services SPARQL publiés via le protocole SPARQL 1.1 pour RDF. Ces descriptions fournissent un mécanisme par lequel un client ou un utilisateur final peuvent obtenir des informations sur le service SPARQL, telles que les extensions de fonctions supportées ou les détails à propos des jeux de données disponibles.
0000005: endpoint
is part of: Bioregistry
has prefix: sd
type: Resource

Wikipedia
has local unique identifier pattern: ^\S+$
0000005: SM_UB-81
has alternative prefix: wikipedia
has provider formatter: http://en.wikipedia.org/wiki/$1
is deprecated: false
has URI prefix: http://en.wikipedia.org/wiki/
description: Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.
is part of: Bioregistry
has prefix: wikipedia.en
contributor: https://orcid.org/0000-0002-6601-2165
has alternative prefix: Wikipedia
has resource example: SM UB-81
type: Resource

has canonical
type: Property
domain: Resource
description: A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix. See examples [here](https://bioregistry.io/highlights/relations#canonical).
range: Resource

Thai Clinical Trials Registry
has local unique identifier pattern: ^TCTR\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
0000005: TCTR20230429001
has resource example: TCTR20230429001
description: The TCTR was estabished in 2009 and has been operated by Clinical Research Collaboration Network (CRCN), an organization under the Medical Research Foundation, which is a non-profit organization, and financially supported by Thailand Center of Excellence for Life Sciences (TCELS). CRCN has been retitled the Medical Research Network (MedResNet) since June 15, 2012. (from homepage)
has prefix: tctr
has provider formatter: https://www.thaiclinicaltrials.org/show/$1
has URI prefix: https://www.thaiclinicaltrials.org/show/
is deprecated: false

General Multilingual Environmental Thesaurus Concept
keyword: environmental science
keyword: ess
has resource example: https://www.eionet.europa.eu/gemet/en/concept/627
has URI prefix: https://www.eionet.europa.eu/gemet/en/concept/
is deprecated: false
0000005: 627
keyword: biodiversity
keyword: ecology
description: The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.
has provider formatter: https://www.eionet.europa.eu/gemet/en/concept/$1
keyword: earth sciences
has prefix: gemet.concept
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has responsible: Eionet Helpdesk
type: Resource
contributor: Charles Tapley Hoyt

International Traditional Medicine Clinical Trial Registry
has local unique identifier pattern: ^ITMCTR\d+$
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: itmctr
0000005: ITMCTR2023000002
description: The International Traditional Medicine Clinical Trial Registry (ITMCTR) is a non-profit online register of clinical trials being conducted in the field of traditional medicine. It isoperated by the China Academy of Chinese Medical Sciences and The China Center For Evidence Based Traditional Chinese Medicine. It is recognized as a Primary Registry of WHO, and contributes data to the WHO ICTRP. (from website)
type: Resource

SWEET Ontology Phenomena Star
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Star
has provider formatter: http://sweetontology.net/phenStar/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: sweet.phst
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: Asteroseismology
keyword: phenomena
has URI prefix: http://sweetontology.net/phenStar/
keyword: star
has alternative prefix: sophst
is deprecated: false
0000005: Asteroseismology

Simple Knowledge Organization System (SKOS) version of Materials Data Vocabulary
has URI prefix: https://data.nist.gov/od/dm/nmrr/vocab/
has prefix: tib.mdv
is deprecated: false
has resource example: https://data.nist.gov/od/dm/nmrr/vocab/
has provider formatter: https://data.nist.gov/od/dm/nmrr/vocab/
is part of: Bioregistry
description: A version of the Materials Data Vocabulary structured as Simple Knowledge Organization System (SKOS). The XML was originally created by the TemaTres software. This vocabulary describes the applicability to material science of records in the NIST Materials Resource Registry (NMRR - https://materials.registry.nist.gov/). The NMRR allows for the registration of materials resources, bridging the gap between existing resources and the end users. The NMRR functions as a node in a federated system, making the registered information available for research to the materials community. This is being developed at the National Institute of Standards and Technology and is made available to solicit comments from the Material Science community. (An Excel version of the file is also included in the distributions for ease of use.) Please cite this resource as: Medina-Smith, Andrea; Becker, Chandler (2017), Simple Knowledge Organization System (SKOS) version of Materials Data Vocabulary , National Institute of Standards and Technology, https://doi.org/10.18434/T4/1435037
type: Resource
keyword: material science
keyword: nfdi4ing
0000005: 953

SWEET Ontology Human Environmental Standards
keyword: environmental standards
has resource example: AAQS
is deprecated: false
0000005: AAQS
has prefix: sweet.hues
is part of: Bioregistry
has provider formatter: http://sweetontology.net/humanEnvirStandards/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Environmental Standards
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has URI prefix: http://sweetontology.net/humanEnvirStandards/
has alternative prefix: sohues

COG Categories
has prefix: cog.category
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/K
has provider formatter: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1
keyword: pathways
type: Resource
description: Higher-level classifications of COG Pathways
0000005: K
has URI prefix: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/
has responsible: Michael Y Galperin
is deprecated: false

SWEET Ontology Property Rotation
has alternative prefix: sopropr
has prefix: sweet.propr
has resource example: AbsoluteVorticity
keyword: rotation
is deprecated: false
0000005: AbsoluteVorticity
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/propRotation/$1
has URI prefix: http://sweetontology.net/propRotation/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Rotation

Long Term Ecological Research Controlled Vocabulary
description: Ecological terms
has resource example: https://vocab.lternet.edu/vocab/vocab/index.php
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
0000005: 182
type: Resource
contributor: Charles Tapley Hoyt
has prefix: lter
has URI prefix: https://vocab.lternet.edu/vocab/vocab/index.php
has provider formatter: https://vocab.lternet.edu/vocab/vocab/index.php
is deprecated: false

Codon Usage Tabulated from GenBank
0000011: NCBI Taxonomy
has provider formatter: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi
description: Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank.
has resource example: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi
is deprecated: false
keyword: dna
has prefix: cutg
is part of: Bioregistry
has URI prefix: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi
type: Resource
keyword: gene
0000005: 9606
has reviewer: Charles Tapley Hoyt

Aspergillus Genome Database
type: Resource
0000005: ASPL0000349247
has provider formatter: http://www.aspergillusgenome.org/cgi-bin/locus.pl
is deprecated: true
has resource example: http://www.aspergillusgenome.org/cgi-bin/locus.pl
has URI prefix: http://www.aspergillusgenome.org/cgi-bin/locus.pl
has prefix: aspgd.locus
description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information.
is part of: Bioregistry
has local unique identifier pattern: ^[A-Za-z_0-9]+$

SWEET Ontology Phenomena Ocean Coastal
is part of: Bioregistry
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Ocean Coastal
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
keyword: ocean coastal
has URI prefix: http://sweetontology.net/phenOceanCoastal/
has alternative prefix: sophoc
has resource example: Attrition
has provider formatter: http://sweetontology.net/phenOceanCoastal/$1
keyword: phenomena
has prefix: sweet.phoc
0000005: Attrition
is deprecated: false

Pointer Methods in RDF
type: Resource
has provider formatter: https://www.w3.org/2009/pointers#$1
description: This specification contains a framework for representing pointers - entities that permit identifying a portion or segment of a piece of content - making use of the Resource Description Framework (RDF). It also describes a number of specific types of pointers that permit portions of a document to be referred to in different ways. When referring to a specific part of, say, a piece of web content, it is useful to be able to have a consistent manner by which to refer to a particular segment of a web document, to have a variety of ways by which to refer to that same segment, and to make the reference robust in the face of changes to that document. This specification is part of the Evaluation And Report Language (EARL) but can be reused in other contexts too. [from homepage]
has resource example: Pointer
0000005: Pointer
has URI prefix: https://www.w3.org/2009/pointers#
has prefix: ptr
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt

SWEET Ontology Property Space Distance
keyword: space distance
has alternative prefix: sopropsdis
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has URI prefix: http://sweetontology.net/propSpaceDistance/
has provider formatter: http://sweetontology.net/propSpaceDistance/$1
has resource example: AttenuationCoefficient
has prefix: sweet.propsdis
0000005: AttenuationCoefficient
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Distance
is deprecated: false

Flavor and Extract Manufacturers Association
is deprecated: false
0000005: 4667
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: fema
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
description: FEMA provides identifiers for flavor ingredients deemed safe for food use. These entities include chemical compounds and natural substances used as flavoring agents, each reviewed by the FEMA Expert Panel for GRAS (Generally Recognized As Safe) status. The identifiers link to safety data and regulatory assessments, including evaluations by the U.S. FDA and, where applicable, the Joint FAO/WHO Expert Committee on Food Additives (JECFA).
has responsible: https://orcid.org/0000-0002-7806-4173
contributor: Mufaddal Naguthanawala

Gene Ontology Database references
0000005: 0000041
is deprecated: false
is part of: Bioregistry
has provider formatter: https://geneontology.org/GO_REF/$1
has resource example: https://geneontology.org/GO_REF/0000041
has local unique identifier pattern: ^\d{7}$
type: Resource
description: The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of "GO content" meetings at which substantial changes in the ontologies are discussed and made.
has prefix: go.ref
has URI prefix: https://geneontology.org/GO_REF/

SWEET Ontology Representation Space Coordinate
has prefix: sweet.repscd
has provider formatter: http://sweetontology.net/reprSpaceCoordinate/$1
keyword: representation space coordinate
0000005: AngularCoordinate
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space Coordinate
has alternative prefix: sorepscd
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: http://sweetontology.net/reprSpaceCoordinate/
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: AngularCoordinate

Physiome Model Repository workspace
type: Resource
has URI prefix: https://models.physiomeproject.org/workspace/
has provider formatter: https://models.physiomeproject.org/workspace/$1
has resource example: modularmassactionprimer
is deprecated: false
0000005: modularmassactionprimer
has local unique identifier pattern: ^[a-zA-Z0-9_\-]+(/.*?)?$
description: Workspace (Git repository) for modeling projects managed by the Physiome Model Repository
is part of: Bioregistry
has prefix: pmr.workspace

Healthcare metadata - DICOM ontology
description: DICOM — Digital Imaging and Communications in Medicine — is the international standard for medical images and related information (ISO 12052). It defines the formats for medical images that can be exchanged with the data and quality necessary for clinical use. DICOM is implemented in almost every radiology, cardiology imaging, and radiotherapy device (X-ray, CT, MRI, ultrasound, etc.), and increasingly in devices in other medical domains such as ophthalmology and dentistry. With tens of thousands of imaging devices in use, DICOM is one of the most widely deployed healthcare messaging standards in the world. There are literally billions of DICOM images currently in use for clinical care. Since its first publication in 1993, DICOM has revolutionized the practice of radiology, allowing the replacement of X-ray film with a fully digital workflow. Much as the Internet has become the platform for new consumer information applications, DICOM has enabled advanced medical imaging applications that have “changed the face of clinical medicine”. From the emergency department, to cardiac stress testing, to breast cancer detection, DICOM is the standard that makes medical imaging work — for doctors and for patients.
has responsible: https://orcid.org/0000-0002-2406-1145
type: Resource
has download URL: dicom.owl
keyword: biomedical science
0000005: 109082
has resource example: http://dicom.nema.org/resources/ontology/DCM/109082
keyword: anatomy
is deprecated: false
keyword: medicine
has URI prefix: http://dicom.nema.org/resources/ontology/DCM/
has prefix: dicom
has provider formatter: http://dicom.nema.org/resources/ontology/DCM/$1
keyword: ontology
is part of: Bioregistry
has local unique identifier pattern: ^\d+$

Indian Crop Phenome Database Study
contributor: Sonia Balyan
has provider formatter: https://ibdc.dbtindia.gov.in/icpd/study-view-home/$1
type: Resource
has reviewer: Charles Tapley Hoyt
0000005: PST_100013
is deprecated: false
has URI prefix: https://ibdc.dbtindia.gov.in/icpd/study-view-home/
description: This resource is about studies in the Indian Crop Phenome Database (ICPD). The ICPD is a domain of the Indian Biological Data Center (IBDC), Regional Centre for Biotechnology, Faridabad, developed for the digitization of crop phenome data. Being the global agricultural powerhouse, the bulk of biological data generated in India is associated with agricultural trials. Ironically most of the trial data has been inaccessible to other researchers, and remains unpublished, and is lost as time passes. Therefore, ICPD would act as single-stop user-friendly platform for freely archiving, organizing, analyzing, and sharing the multi-crop phenome data following FAIR (Findable, Accessible, Interoperable and Re-usable) data principles. [from homepage]
has responsible: Sonia Balyan
has prefix: icpd.study
has resource example: PST_100013
has local unique identifier pattern: ^PST_\d+$
is part of: Bioregistry

Classification of Transcription Factors in Mammalia
keyword: binding
keyword: expression data
is deprecated: false
keyword: bioinformatics
keyword: transcription factor
has prefix: tfclass
description: TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here..
0000005: 2.1.1
is part of: Bioregistry
keyword: transcriptomics
type: Resource
has responsible: https://orcid.org/0000-0002-7729-8453
has resource example: http://tfclass.bioinf.med.uni-goettingen.de/
has provider formatter: http://tfclass.bioinf.med.uni-goettingen.de/
contributor: Charles Tapley Hoyt
has URI prefix: http://tfclass.bioinf.med.uni-goettingen.de/
keyword: binding site
keyword: transcription factor binding site prediction
keyword: phylogenetics

Biological Magnetic Resonance Data Bank
is deprecated: false
has prefix: bmrb.entry
has provider formatter: https://bmrb.io/data_library/summary/index.php
description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.
has URI prefix: https://bmrb.io/data_library/summary/index.php
is part of: Bioregistry
type: Resource
has resource example: https://bmrb.io/data_library/summary/index.php
keyword: structural biology
has responsible: https://orcid.org/0000-0003-1799-6134
has alternative prefix: bmrb
has local unique identifier pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$
0000005: 15000

LRMI Alignment Type Vocabulary
has URI prefix: http://purl.org/dcx/lrmi-vocabs/alignmentType/
is deprecated: false
has provider formatter: http://purl.org/dcx/lrmi-vocabs/alignmentType/$1
has prefix: lrmi.alignmenttype
is part of: Bioregistry
keyword: learning resource
contributor: Charles Tapley Hoyt
git repository: lrmi
has resource example: assesses
keyword: open educational resource
0000005: assesses
description: A concept scheme that defines the types of relationships between a learning resource and a node in an educational framework.
type: Resource

NFDI4Memory Collection
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Memory
creator: Charles Tapley Hoyt
type: Collection
has part: Bioregistry

Semantically-Interlinked Online Communities Services Ontology - Quote Ontology
description: Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining basic information on community-related web services.
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: http://rdfs.org/sioc/services#$1
has prefix: sioc.quote
0000005: has_service
has resource example: has service
is deprecated: false
has URI prefix: http://rdfs.org/sioc/services#

ChemBioSys Institution
has prefix: chembiosys.institution
has provider formatter: https://data.chembiosys.de/institutions/$1
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has URI prefix: https://data.chembiosys.de/institutions/
has resource example: https://data.chembiosys.de/institutions/13
type: Resource
0000005: 13
description: An institution in the ChemBioSys data platform

SWEET Ontology Realm Geologic Orogen
has provider formatter: http://sweetontology.net/realmGeolOrogen/$1
is deprecated: false
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Orogen
has resource example: Arc
keyword: geologic orogen
0000005: Arc
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
keyword: realm
is part of: Semantic Web for Earth and Environment Technology Ontology
has URI prefix: http://sweetontology.net/realmGeolOrogen/
has prefix: sweet.reagor
has alternative prefix: soreagor
type: Resource

SWEET Ontology Relationships
has URI prefix: http://sweetontology.net/rela/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships
has alternative prefix: sorel
has prefix: sweet.rel
is part of: Bioregistry
keyword: relationships
has resource example: hasPhenomena
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/rela/$1
type: Resource
0000005: hasPhenomena
is deprecated: false

SWEET Ontology Realm Geologic
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic
is deprecated: false
has provider formatter: http://sweetontology.net/realmGeol/$1
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
0000005: Asthenosphere
has alternative prefix: soreag
has resource example: Asthenosphere
type: Resource
has prefix: sweet.reag
keyword: realm
has URI prefix: http://sweetontology.net/realmGeol/
keyword: geologic

Primate Brain Atlas
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
has prefix: pba
contributor: Charles Tapley Hoyt
0000005: 128011350
has download URL: allen-pba.obo
has URI prefix: https://biopragmatics.github.io/providers/pba/
git repository: primate brain atlas ontology
has resource example: https://biopragmatics.github.io/providers/pba/128011350
has provider formatter: https://biopragmatics.github.io/providers/pba/$1
keyword: ontology
is deprecated: false
description: A controlled vocabulary to support the study of transcription in the primate brain

miRBase Families
type: Resource
has prefix: mirbase.family
has URI prefix: http://www.mirbase.org/cgi-bin/mirna_summary.pl
keyword: gene
has responsible: Sam Griffiths-Jones
has alternative prefix: MIRBASE_FAMILY
keyword: mirna
keyword: ontology
is deprecated: false
description: The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.
is part of: Bioregistry
has resource example: http://www.mirbase.org/cgi-bin/mirna_summary.pl
has download URL: mirbase.family.owl
contributor: Charles Tapley Hoyt
has provider formatter: http://www.mirbase.org/cgi-bin/mirna_summary.pl
0000005: MIPF0000002

Google Scholar Researcher
has URI prefix: https://scholar.google.com/citations
has provider formatter: https://scholar.google.com/citations
has resource example: https://scholar.google.com/citations
is deprecated: false
0000005: PjrpzUIAAAAJ
has local unique identifier pattern: ^[-_0-9A-Za-z]{12}$
description: Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.
is part of: Bioregistry
has prefix: google.scholar
type: Resource
contributor: Charles Tapley Hoyt

GND-Ontologie
has resource example: AdministrativeUnit
has URI prefix: https://d-nb.info/standards/elementset/gnd#
description: GND stands for "Gemeinsame Normdatei" (Integrated Authority File) and offers a broad range of elements to describe authorities. The GND originates from the German library community and aims to solve the name ambiguity problem in the library world.
keyword: catalogs
type: Resource
0000005: AdministrativeUnit
keyword: computer science
keyword: ess
is deprecated: false
has prefix: gndo
has provider formatter: https://d-nb.info/standards/elementset/gnd#$1
is part of: Bioregistry

BioProject
is deprecated: false
keyword: life science
has provider formatter: https://www.ncbi.nlm.nih.gov/bioproject/
has URI prefix: https://www.ncbi.nlm.nih.gov/bioproject/
has prefix: bioproject
is part of: Bioregistry
description: BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories.
0000005: PRJDB3
has resource example: https://www.ncbi.nlm.nih.gov/bioproject/
type: Resource
has local unique identifier pattern: ^PRJ[DEN][A-Z]\d+$
has responsible: Ilene Karsch-Mizrachi

Vir-Mir db
has provider formatter: http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi
is part of: Bioregistry
keyword: structure
has URI prefix: http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi
has resource example: http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi
has reviewer: Charles Tapley Hoyt
type: Resource
description: A database containing predicted viral miRNA candidate hairpins.
has prefix: virmirdb
0000011: NCBI Taxonomy
keyword: rna
0000005: 11002
is deprecated: false

Hathi Trust Digital Library
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: https://catalog.hathitrust.org/Record/008893080
0000005: 008893080
contributor: Charles Tapley Hoyt
type: Resource
has prefix: hathitrust
description: Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world.
has URI prefix: https://catalog.hathitrust.org/Record/
has provider formatter: https://catalog.hathitrust.org/Record/$1

Homologous Organ Groups
has resource example: https://biopragmatics.github.io/providers/hog/0000255
is part of: Bioregistry
0000005: 0000255
contributor: Charles Tapley Hoyt
type: Resource
has local unique identifier pattern: ^\d{7}$
has download URL: HOG.obo
keyword: ontology
has URI prefix: https://biopragmatics.github.io/providers/hog/
is deprecated: false
has prefix: hog
has provider formatter: https://biopragmatics.github.io/providers/hog/$1
description: Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc.

GeneTree
is part of: Bioregistry
type: Resource
has provider formatter: http://www.ensembl.org/Multi/GeneTree/Image
keyword: gene
has prefix: genetree
0000005: ENSGT00550000074763
has URI prefix: http://www.ensembl.org/Multi/GeneTree/Image
has resource example: http://www.ensembl.org/Multi/GeneTree/Image
keyword: classification
has responsible: Paul Flicek
has local unique identifier pattern: ^ENSGT\d+$
description: Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl.
is deprecated: false
keyword: protein

GlycoPOST
is part of: Bioregistry
type: Resource
has resource example: GPST000024
keyword: life science
has URI prefix: https://glycopost.glycosmos.org/entry/
0000005: GPST000024
has provider formatter: https://glycopost.glycosmos.org/entry/$1
has prefix: glycopost
keyword: glycomics
has local unique identifier pattern: ^GPST[0-9]{6}$
is deprecated: false
description: GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their "raw/processed" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.

ToxoDB
type: Resource
has resource example: http://toxodb.org/toxo/showRecord.do
description: ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
has provider formatter: http://toxodb.org/toxo/showRecord.do
has prefix: toxoplasma
has URI prefix: http://toxodb.org/toxo/showRecord.do
has local unique identifier pattern: ^\w+$
0000005: TGME49_053730
is deprecated: false
is part of: Bioregistry

E-cyanobacterium rule
has prefix: ecyano.rule
has resource example: https://e-cyanobacterium.org/bcs/rule/56
has URI prefix: https://e-cyanobacterium.org/bcs/rule/
has provider formatter: https://e-cyanobacterium.org/bcs/rule/$1
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.
type: Resource
0000005: 56

SWEET Ontology Representation Mathematics
is deprecated: false
has alternative prefix: sorepm
has URI prefix: http://sweetontology.net/reprMath/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has resource example: Array
has prefix: sweet.repm
has provider formatter: http://sweetontology.net/reprMath/$1
type: Resource
0000005: Array
keyword: representation mathematics

Code Ontology
is deprecated: false
keyword: engineering
has resource example: AccessModifier
has prefix: woc.ontology
has URI prefix: http://rdf.webofcode.org/woc/
is part of: Bioregistry
keyword: nfdi4ing
has provider formatter: http://rdf.webofcode.org/woc/$1
git repository: parser
type: Resource
0000005: AccessModifier
description: An ontology that represents object-oriented programming languages

Vocabulary of Materials Tribology Lab at KIT
has URI prefix: https://purls.helmholtz-metadaten.de/vp/kitmtxx-41732562-vp/
has prefix: kit.mtxx
is deprecated: false
has provider formatter: https://purls.helmholtz-metadaten.de/vp/kitmtxx-41732562-vp/$1
is part of: Bioregistry
type: Resource
keyword: material science
keyword: nfdi4ing
description: Objects of this class contain a self-bound collection of mass bearing particles.

Allotrope role
description: The role component of the Allotrope ontology suite
has provider formatter: http://purl.allotrope.org/ontologies/role#AFRL_$1
has URI prefix: http://purl.allotrope.org/ontologies/role#AFRL_
0000005: 0000248
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
is part of: Allotrope Merged Ontology Suite
has resource example: AFRL_0000248
has prefix: allotrope.role
type: Resource

PREMIS 3 Ontology
keyword: catalogs
type: Resource
keyword: nfdi4culture
is deprecated: false
0000005: Agent
has URI prefix: http://www.loc.gov/premis/rdf/v3/
has provider formatter: http://www.loc.gov/premis/rdf/v3/$1
description: Ontology for PREMIS 3, the international standard for metadata to support the preservation of digital objects and ensure their long-term usability.
has prefix: premis
has alternative prefix: premis3
is part of: Bioregistry
has resource example: Agent
contributor: Charles Tapley Hoyt

NIF Standard Ontology: Organisms
has responsible: Tom Gillespie
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_organ_
has local unique identifier pattern: ^\d+$
description: NLXORG covers organisms.
is part of: Bioregistry
0000005: 090701
has alternative prefix: NLXORG
has reviewer: Charles Tapley Hoyt
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1
has prefix: nlx.org
contributor: Tom Gillespie
type: Resource
keyword: taxonomy
git repository: NIF-Ontology
has resource example: nlx organ 090701
is deprecated: false

SWEET Ontology State Spectral Band
is deprecated: false
has prefix: sweet.stsb
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Spectral Band
0000005: BandLimited
has alternative prefix: sostsb
has URI prefix: http://sweetontology.net/stateSpectralBand/
has provider formatter: http://sweetontology.net/stateSpectralBand/$1
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: state spectral band
has resource example: BandLimited
type: Resource

NFDI Core Ontology
type: Resource
git repository: nfdicore
has responsible: Jörg Waitelonis
description: A mid-level ontology for representing metadata related to NFDI resources, including individuals, organizations, projects, data portals, and more
is deprecated: false
0000005: 0000106
has prefix: nfdi.core
keyword: ontology
has URI prefix: https://nfdi.fiz-karlsruhe.de/ontology/NFDI_
has resource example: NFDI_0000106
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has download URL: nfdicore.owl
has provider formatter: https://nfdi.fiz-karlsruhe.de/ontology/NFDI_$1

Probes and Drugs
is part of: Bioregistry
0000005: PD000596
contributor: Charles Tapley Hoyt
has resource example: PD000596
description: The Probes & Drugs portal (P&D) is a hub for the integration of high-quality bioactive compound sets enabling their analysis and comparison. Its main focus is on chemical probes and drugs but it also includes additional relevant sets from specialist databases/scientific publications, and vendor sets. Upon these, established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology, DrugCentral or DrugBank) are utilized for compounds' biological annotation.
type: Resource
has provider formatter: https://www.probes-drugs.org/compound/$1
has URI prefix: https://www.probes-drugs.org/compound/
is deprecated: false
has responsible: https://orcid.org/0000-0001-5325-4934
has local unique identifier pattern: ^PD\d{6}$
has prefix: probesanddrugs

PharmGKB Variant
keyword: snp
has URI prefix: https://www.pharmgkb.org/variant/
type: Resource
0000005: PA166156302
has provider formatter: https://www.pharmgkb.org/variant/$1
has resource example: PA166156302
keyword: genetic variation
description: SNPs and other variants that can be mapped to dbSNP.
is deprecated: false
has prefix: pharmgkb.variant
has download URL: pharmgkb.variant.owl
keyword: ontology
keyword: genetic variant
has local unique identifier pattern: ^PA\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has responsible: Teri E Klein

SWEET Ontology Realm Land Aeolian
keyword: aeolianland
has prefix: sweet.reala
has alternative prefix: soreala
has resource example: Aeolian
is deprecated: false
is part of: Bioregistry
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
0000005: Aeolian
has provider formatter: http://sweetontology.net/realmLandAeolian/$1
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Aeolian
type: Resource
has URI prefix: http://sweetontology.net/realmLandAeolian/

ASKEM Epidemiology Prefixes
creator: Charles Tapley Hoyt
type: Collection
has part: Human Phenotype Ontology
has part: RDF Schema
has part: Symptom Ontology
has part: Data Science Ontology
has part: Digital Object Identifier
has part: Ontology of Adverse Events
has part: Ontology of Vaccine Adverse Events
has part: Basic Formal Ontology
has part: Human Disease Ontology
has part: OBO in OWL
has part: PubMed
has part: Vaccine Ontology
description: Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project.
has part: Common Anatomy Reference Ontology
has part: PubMed Central
has part: Infectious Disease Ontology
has part: Web Ontology Language
has part: Relation Ontology
has part: Pathogen Transmission Ontology

dictyBase
has provider formatter: http://dictybase.org/gene/$1
has part: Dictybase Gene
has prefix: dictybase
has URI prefix: http://dictybase.org/gene/
type: Resource
has responsible: https://orcid.org/0000-0002-4532-2703
keyword: comparative genomics
has alternative prefix: dictyBase
keyword: anatomy
keyword: life science
has resource example: http://dictybase.org/gene/DDB0191090
0000005: DDB0191090
description: A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics
is deprecated: false
is part of: Bioregistry
keyword: genome

RGD Disease Ontology
has prefix: rdo
keyword: ontology
is deprecated: false
has download URL: RDO.owl
has provider formatter: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1
0000005: 9002859
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#
has resource example: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#9002859
description: Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms.
has local unique identifier pattern: ^\d{7}$

MGnify Analysis
has provider formatter: https://www.ebi.ac.uk/metagenomics/analyses/$1
has URI prefix: https://www.ebi.ac.uk/metagenomics/analyses/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: MGYA00002270
has local unique identifier pattern: ^MGYA\d+$
type: Resource
0000005: MGYA00002270
description: Analyses of microbiome data within MGnify
is deprecated: false
has prefix: mgnify.analysis

Richard Scheuermann
label: Richard H. Scheuermann

SWEET Ontology Human Agriculture
is part of: Bioregistry
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has provider formatter: http://sweetontology.net/humanAgriculture/$1
keyword: agriculture
0000005: AnimalProduction
type: Resource
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Agriculture
has alternative prefix: sohua
has prefix: sweet.hua
has URI prefix: http://sweetontology.net/humanAgriculture/
is deprecated: false
has resource example: AnimalProduction

Fetal Calf Serum-Free Database
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://fcs-free.org/fcs-database
type: Resource
0000005: 240-17-488-3-4-12
has prefix: fcsfree
has resource example: https://fcs-free.org/fcs-database
has URI prefix: https://fcs-free.org/fcs-database
is deprecated: false
description: Cell line databases/resources

European Searchable Tumour Line Database
is part of: Bioregistry
has resource example: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi
has prefix: estdab
has provider formatter: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi
type: Resource
has local unique identifier pattern: ^\d{3}$
is deprecated: true
has identifier space owner: 02catss52
0000005: 046
has URI prefix: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi
description: Cell line databases/resources

Henriette Harmse

Identifiers.org Terms
is deprecated: false
has provider formatter: https://biomodels.net/vocab/idot.rdf#$1
0000005: Namespace
has local unique identifier pattern: ^[A-Za-z]+$
description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.
has resource example: Namespace
is part of: Bioregistry
type: Resource
has prefix: idot
has URI prefix: https://biomodels.net/vocab/idot.rdf#

SpliceNest
is part of: Bioregistry
keyword: gene
has URI prefix: http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi
has reviewer: Charles Tapley Hoyt
has provider formatter: http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi
type: Resource
description: SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome.
is deprecated: true
has resource example: http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi
0000005: Hs635
has prefix: splicenest
keyword: genome
keyword: dna

Europeana Data Model vocabulary
0000005: Event
keyword: catalogs
has resource example: Event
type: Resource
has prefix: edm
has download URL: edm.owl
is deprecated: false
has provider formatter: http://www.europeana.eu/schemas/edm/$1
keyword: ontology
has URI prefix: http://www.europeana.eu/schemas/edm/
git repository: metis-schema
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: The Europeana Data Model (EDM) is aimed at being an integration medium for collecting, connecting and enriching the descriptions provided by Europeana data providers. The RDF vocabulary for http://www.europeana.eu/schemas/edm/ defines the elements introduced by EDM (as opposed to the ones EDM re-uses from other namespaces).

Antibody-Antigen Complex Database
description: Identifiers represent antibody-antigen complexes in the Antigen-Antibody Complex Database (AACDB), which provides comprehensive structural and functional annotations including paratope and epitope information, antibody developability data, and antigen-drug target relationships to support immunoinformatics research and therapeutic antibody development.
has URI prefix: https://i.uestc.edu.cn/AACDB/details.php
has resource example: https://i.uestc.edu.cn/AACDB/details.php
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has provider formatter: https://i.uestc.edu.cn/AACDB/details.php
has reviewer: https://orcid.org/0000-0001-9439-5346
keyword: antigen
type: Resource
keyword: molecular biophysics
0000005: 61
keyword: antibody
keyword: structural biology
has responsible: https://orcid.org/0000-0003-3282-8892
is deprecated: false
contributor: Kangho Ji
has prefix: aacdb

tRNA Gene Database
description: The tRNA Gene DataBase Curated by Experts "tRNADB-CE" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones.
is part of: Bioregistry
0000005: 265912
type: Resource
has provider formatter: http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi
keyword: gene
has reviewer: Charles Tapley Hoyt
has prefix: trnadbce
keyword: rna
has resource example: http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi
has URI prefix: http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi
is deprecated: false
keyword: genome
keyword: dna

Genetic Testing Registry Labs
is deprecated: false
has prefix: gtr.lab
has URI prefix: https://www.ncbi.nlm.nih.gov/gtr/labs/
has resource example: https://www.ncbi.nlm.nih.gov/gtr/labs/000320401
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
description: The Genetic Testing Registry provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease.
type: Resource
0000005: 000320401
has provider formatter: https://www.ncbi.nlm.nih.gov/gtr/labs/$1

Mode Of Collection
description: The procedure, technique, or mode of inquiry used to attain the data.
has provider formatter: https://vocabularies.cessda.eu/vocabulary/ModeOfCollection#code_$1
has resource example: code Interview
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/ModeOfCollection#code_
is part of: Bioregistry
0000005: Interview
has prefix: ddi.modeofcollection
type: Resource
contributor: Charles Tapley Hoyt
has identifier space owner: 015em2733

Product Types Ontology
0000005: Atlas
has prefix: pto
has URI prefix: http://www.productontology.org/id/
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has provider formatter: http://www.productontology.org/id/$1
has resource example: Atlas
description: Identifiers for product types (product, price, and company data) based on Wikipedia
is deprecated: false

General Process Ontology
description: Ontology to model processes
has URI prefix: https://gpo.ontology.link/GPO_
is deprecated: false
keyword: engineering
is part of: Bioregistry
has provider formatter: https://gpo.ontology.link/GPO_$1
type: Resource
git repository: ontology
has prefix: tib.gpo
keyword: nfdi4ing

Oryzabase Reference
has prefix: oryzabase.reference
has resource example: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/42840
has provider formatter: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1
is deprecated: false
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
description: The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan.
has URI prefix: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/
0000005: 42840

has responsible
domain: Registry
description: The main contact person for a registry
range: Person
type: Property

Genotype-Tissue Expression
has local unique identifier pattern: ^\w.+$
is deprecated: false
is part of: Bioregistry
type: Resource
description: The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation.
0000005: BRIP1
has URI prefix: https://www.gtexportal.org/home/gene/
has resource example: BRIP1
has prefix: gtex
has provider formatter: https://www.gtexportal.org/home/gene/$1

Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
is deprecated: true
has prefix: sael

Gemina Symptom Ontology
is deprecated: true
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has prefix: syoid
type: Resource

Analytical methods for geochemistry
keyword: earth sciences
has URI prefix: https://w3id.org/geochem/1.0/analyticalmethod/
type: Resource
has resource example: acceleratormassspectrometry
description: This concept scheme contains skos concepts for analysis methods used to produce observation results with information about the physical properties, chemical or isotopic composition, crystallography, or molecular structure of material samples. Based on spreadsheet compilation of method vocabularies from Geo.X, GEOROC, PetDB and OSIRIS-REx. Definitions added and updated based on web research, and SKOS serialization by S.M. Richard. Note that although there are high-level method categories for 'Physical property measurements' and the 'Bioanalytical method', these are placeholders and only include a few examples that are relevant to analytical methods in geo- or cosmochemistry.
has provider formatter: https://w3id.org/geochem/1.0/analyticalmethod/$1
keyword: ess
0000005: acceleratormassspectrometry
is deprecated: false
is part of: Bioregistry
has prefix: tib.meth

Semantically-Interlinked Online Communities Types Ontology
has prefix: sioc.types
has URI prefix: http://rdfs.org/sioc/types#
is deprecated: false
has resource example: AddressBook
0000005: AddressBook
has provider formatter: http://rdfs.org/sioc/types#$1
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
description: Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining subclasses and subproperties of SIOC terms.

Kinetic Data of RNA-Protein Interactions Database
keyword: kinetics
keyword: rna-protein interactions
has provider formatter: http://www.kdbirp.aiddlab.com/detail/$1
0000005: 183
is deprecated: false
keyword: binding affinity
description: Identifiers represent RNA-protein interaction entries with quantitative kinetic data in the Kinetic Data of Biomolecular Interactions for RNA-Protein database (KDBI-RP), which is an open-access database cataloging association rates, dissociation rates, and equilibrium dissociation constants for RNA-protein interactions.
contributor: Kangho Ji
has resource example: http://www.kdbirp.aiddlab.com/detail/183
has URI prefix: http://www.kdbirp.aiddlab.com/detail/
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: kdbirp
type: Resource
has reviewer: Charles Tapley Hoyt
has responsible: Xian Zeng

ESCO Skill
has provider formatter: http://data.europa.eu/esco/skill/$1
is deprecated: false
description: A vocabulary of knowledge, skills and competences relevant to the European labour market. In ESCO v1.2.0, the skills pillar is structured in a hierarchy which contains the following four sub-classifications: 1) Knowledge, 2) Language skills and knowledge, 3) Skills, and 4) Transversal skills. [adapted from homepage]
is part of: Bioregistry
has URI prefix: http://data.europa.eu/esco/skill/
type: Resource
contributor: Charles Tapley Hoyt
has prefix: esco.skill

Linguist
is deprecated: false
git repository: linguist
has resource example: Python
0000005: Python
has local unique identifier pattern: ^[a-zA-Z0-9 +#'*]+$
is part of: Bioregistry
type: Resource
description: Registry of programming languages for the Linguist program for detecting and highlighting programming languages.
has prefix: linguist
has provider formatter: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1
has URI prefix: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#

KEGG Enzyme
type: Resource
has provider formatter: http://www.genome.jp/dbget-bin/www_bget
has URI prefix: http://www.genome.jp/dbget-bin/www_bget
description: KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links.
has prefix: kegg.enzyme
is deprecated: false
0000011: Enzyme Nomenclature
is part of: Bioregistry
is part of: Kyoto Encyclopedia of Genes and Genomes

is deprecated
domain: Resource
type: Property
description: A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc.
range: boolean

SWEET Ontology Property Function
has provider formatter: http://sweetontology.net/propFunction/$1
is deprecated: false
has URI prefix: http://sweetontology.net/propFunction/
has prefix: sweet.propfu
is part of: Bioregistry
keyword: function
has resource example: AnnualAverage
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
has alternative prefix: sopropfu
0000005: AnnualAverage
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Function
type: Resource

Gmelin's Handbook of Inorganic Chemistry
has local unique identifier pattern: ^[1-9][0-9]{1,6}$
type: Resource
has prefix: gmelin
description: The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s.
0000005: 1466
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt

Cotton Ontology
has URI prefix: https://cropontology.org/rdf/CO_358:
has provider formatter: https://cropontology.org/rdf/CO_358:$1
has resource example: CO 358:0000139
has download URL: CO 358.owl
0000005: 0000139
keyword: ontology
description: This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.
has responsible: Elizabeth Arnaud
is deprecated: false
is part of: Bioregistry
has prefix: co_358
has local unique identifier pattern: ^\d{7}$
type: Resource
git repository: Crop-Ontology

Semion author ID (archived)
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has prefix: semion
type: Resource
0000005: 22132778
has URI prefix: https://web.archive.org/web/1/https://www.semion.io/Author/
has resource example: https://web.archive.org/web/1/https://www.semion.io/Author/22132778
is deprecated: false
description: identifier of an author or reviewer, in Semion
has provider formatter: https://web.archive.org/web/1/https://www.semion.io/Author/$1

Alpha Tom Kodamullil
label: Dr. Alpha Tom Kodamullil

MycoBrowser marinum
type: Resource
has local unique identifier pattern: ^MMAR\_\d+$
0000005: MMAR_2462
has provider formatter: https://mycobrowser.epfl.ch/genes/$1
is part of: MycoBrowser
is deprecated: false
has prefix: myco.marinum
description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.
has resource example: MMAR 2462
has URI prefix: https://mycobrowser.epfl.ch/genes/
keyword: sequence
is part of: Bioregistry
keyword: genome

SWEET Ontology Realm Hydrosphere Body
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Hydrosphere Body
is deprecated: false
has URI prefix: http://sweetontology.net/realmHydroBody/
0000005: Aqueduct
has alternative prefix: soreahb
has resource example: Aqueduct
is part of: Bioregistry
has provider formatter: http://sweetontology.net/realmHydroBody/$1
has prefix: sweet.reahb
contributor: Charles Tapley Hoyt
keyword: hydrosphere body
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
type: Resource
keyword: realm

LG Chemical Entity Detection Dataset (LGCEDe)
has provider formatter: https://s3.us-east-2.amazonaws.com/lg.cede/$1
0000005: LGCEDe-S-000002244
is deprecated: false
has resource example: LGCEDe-S-000002244
has prefix: lgai.cede
description: LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR).
has local unique identifier pattern: ^LGCEDe-S-\d{9}$
is part of: Bioregistry
type: Resource
has URI prefix: https://s3.us-east-2.amazonaws.com/lg.cede/

SWEET Ontology State Realm
is deprecated: false
has alternative prefix: sostre
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Realm
has prefix: sweet.stre
is part of: Bioregistry
type: Resource
git repository: sweet
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
has URI prefix: http://sweetontology.net/stateRealm/
keyword: state realm
0000005: RealmConfiguration
has provider formatter: http://sweetontology.net/stateRealm/$1
has resource example: RealmConfiguration

Food Classification and Description System (from FSA Food Type identifiers)
is deprecated: false
has URI prefix: http://data.food.gov.uk/codes/foodtype/id/
has provider formatter: http://data.food.gov.uk/codes/foodtype/id/$1
has prefix: foodex2
0000005: A0TMC
has resource example: A0TMC
is part of: Bioregistry
type: Resource
description: Food Type identifiers, supporting codes and vocabularies based on the EFSA FoodEx2 (https://www.efsa.europa.eu/en/data/data-standardisation) that are being tested in the development of the FSA's code and data standards repository. These codes may be used within FSA data.

CATH superfamily
is part of: Bioregistry
has prefix: cath.superfamily
type: Resource
has resource example: http://www.cathdb.info/cathnode/1.10.10.200
has local unique identifier pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$
has provider formatter: http://www.cathdb.info/cathnode/$1
is part of: CATH Protein Structural Domain Superfamily
0000005: 1.10.10.200
has URI prefix: http://www.cathdb.info/cathnode/
is deprecated: false
description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification.

SWEET Ontology Phenomena Fluid Transport
keyword: fluid transport
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
is part of: Semantic Web for Earth and Environment Technology Ontology
type: Resource
git repository: sweet
has prefix: sweet.phft
0000005: Advection
keyword: phenomena
has URI prefix: http://sweetontology.net/phenFluidTransport/
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Fluid Transport
has provider formatter: http://sweetontology.net/phenFluidTransport/$1
has alternative prefix: sophft
has resource example: Advection

ChemBioSys Study
is part of: Bioregistry
description: A study in the ChemBioSys data platform
has local unique identifier pattern: ^\d+$
contributor: Charles Tapley Hoyt
has URI prefix: https://data.chembiosys.de/studies/
type: Resource
has resource example: https://data.chembiosys.de/studies/20
0000005: 20
has provider formatter: https://data.chembiosys.de/studies/$1
has prefix: chembiosys.study
is deprecated: false

HemOnc Terminology
is deprecated: false
contributor: https://orcid.org/0000-0001-9439-5346
has prefix: hemonc
has local unique identifier pattern: ^\d+$
has reviewer: https://orcid.org/0000-0002-8169-9049
is part of: Bioregistry
0000005: 15543
description: HemOnc.org is the largest freely available medical wiki of interventions, regimens, and general information relevant to the fields of hematology and oncology.
type: Resource

has URI prefix
description: The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved.
type: Property
equivalent property: namespace
equivalent property: preferredNamespaceUri
range: string
equivalent property: uriSpace
domain: Resource

Developing Mouse Brain Atlas
has prefix: dmba
type: Resource
has resource example: DMBA_15567
has download URL: dmbao.owl
keyword: ontology
description: A controlled vocabulary to support the study of transcription in the developing mouse brain
is deprecated: false
git repository: developing mouse brain atlas ontology
has provider formatter: https://purl.brain-bican.org/ontology/dmbao/DMBA_$1
0000005: 15567
has URI prefix: https://purl.brain-bican.org/ontology/dmbao/DMBA_
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt

SWEET Ontology State Biological
0000005: BiologicalState
has prefix: sweet.stb
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Biological
has URI prefix: http://sweetontology.net/stateBiological/
is deprecated: false
is part of: Bioregistry
has provider formatter: http://sweetontology.net/stateBiological/$1
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
contributor: Charles Tapley Hoyt
keyword: state biological
type: Resource
has alternative prefix: sostb
has resource example: BiologicalState

SustainGraph Ontology
has prefix: sustaingraph
type: Resource
has URI prefix: https://netmode.gitlab.io/sustaingraph/
has provider formatter: https://netmode.gitlab.io/sustaingraph/$1
description: The SustainGraph ontology is developed to track the United Nations Sustainable Development Goals(SDGs) at national and regional level, their evolution accross time and inter-connectedness with existing and emerging policies and directives at European Union (EU) and global level. It is described using W3C RDF Schema and the Web Ontology Language.
keyword: miscellaneous
0000005: 6T
is deprecated: false
has resource example: 6T
is part of: Bioregistry

General Multilingual Environmental Thesaurus Theme
0000005: 4
has resource example: https://www.eionet.europa.eu/gemet/en/theme/4
has URI prefix: https://www.eionet.europa.eu/gemet/en/theme/
is deprecated: false
description: Themes listed in GEMET
has local unique identifier pattern: ^\d+$
has prefix: gemet.theme
has provider formatter: https://www.eionet.europa.eu/gemet/en/theme/$1
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt

Conference Ontology
has provider formatter: https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1
keyword: ontology
is deprecated: false
0000005: isDocumentRelatedTo
has URI prefix: https://w3id.org/scholarlydata/ontology/conference-ontology.owl#
has resource example: isDocumentRelatedTo
description: The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. The conference-ontology adopts best ontology design practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and guarantees interoperability with SWC ontology and all other pertinent vocabularies. (from homepage)
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has prefix: conference
has download URL: conference-ontology.owl

Dialnet author ID
is deprecated: false
has prefix: dialnet.author
has provider formatter: https://dialnet.unirioja.es/servlet/autor
0000005: 241889
has local unique identifier pattern: ^[1-9]\d*$
keyword: person
is part of: Bioregistry
keyword: researcher
has resource example: https://dialnet.unirioja.es/servlet/autor
type: Resource
contributor: Charles Tapley Hoyt
has URI prefix: https://dialnet.unirioja.es/servlet/autor
description: identifier of an author in Dialnet

HMS LINCS Cell
0000005: 50583
description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.
is deprecated: false
has local unique identifier pattern: ^5\d{4}$
has provider formatter: https://lincs.hms.harvard.edu/db/cells/$1
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has prefix: hms.lincs.cell
has URI prefix: https://lincs.hms.harvard.edu/db/cells/
has resource example: https://lincs.hms.harvard.edu/db/cells/50583

EndlessForms Studio Image
description: Images used as reference
is deprecated: false
0000005: 3
is part of: Bioregistry
has provider formatter: https://images.endlessforms.info/image/$1
has local unique identifier pattern: ^\d+$
type: Resource
has URI prefix: https://images.endlessforms.info/image/
contributor: Charles Tapley Hoyt
has prefix: endlessforms.image
has responsible: Melissa D Clarkson
has resource example: https://images.endlessforms.info/image/3

Educational Sectors Vocabulary
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
git repository: vocabs-edu
has resource example: earlyChildhood
0000005: earlyChildhood
has prefix: kim.esv
type: Resource
description: This is a vocabulary for educational sectors as used in the OER World Map (https://oerworldmap.org)
has provider formatter: https://w3id.org/class/sectors/$1
has URI prefix: https://w3id.org/class/sectors/

Span
has prefix: span
keyword: ontology
is deprecated: false
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has alternative prefix: bfo11span
description: Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality.
keyword: upper-level ontology

SWEET Ontology Material Element
has provider formatter: http://sweetontology.net/matrElement/$1
has alternative prefix: somael
has resource example: Actinoid
is part of: Bioregistry
has prefix: sweet.mael
contributor: Charles Tapley Hoyt
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: element
type: Resource
has URI prefix: http://sweetontology.net/matrElement/
keyword: materials
is deprecated: false
0000005: Actinoid
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Element

Diseases Database
has resource example: ddb1784.htm
is deprecated: false
has local unique identifier pattern: ^\d+$
description: The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities.
0000005: 1784
has URI prefix: https://bioregistry.io/diseasesdb:
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
has prefix: diseasesdb
has provider formatter: https://www.diseasesdatabase.com/ddb$1.htm

Open Geospatial Consortium Simple Features Vocabulary
has provider formatter: http://www.opengis.net/ont/sf#$1
has prefix: ogc.sf
is deprecated: false
has resource example: Triangle
0000005: Triangle
is part of: Bioregistry
type: Resource
has URI prefix: http://www.opengis.net/ont/sf#
description: An RDF/OWL vocabulary for defining SimpleFeature geometry types

Vienna Drosophila Resource Center
is deprecated: false
has URI prefix: https://bioregistry.io/vdrc:
has provider formatter: https://shop.vbc.ac.at/vdrc_store/$1.html
has local unique identifier pattern: ^\d+$
keyword: fly lines
description: Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID]
is part of: Bioregistry
type: Resource
0000005: 100291
keyword: drosophila
has prefix: vdrc
keyword: biomaterial supply resource
has resource example: 100291.html

European Union Publications Office dataset
is part of: Bioregistry
has prefix: eu.publication
contributor: Charles Tapley Hoyt
has provider formatter: http://publications.europa.eu/resource/dataset/$1
0000005: euvoc
description: Datasets published by the Publications Office of the European Union
type: Resource
has resource example: euvoc
has URI prefix: http://publications.europa.eu/resource/dataset/
is deprecated: false

Uniprot Core Ontology
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource
has URI prefix: http://purl.uniprot.org/core/
has download URL: core.owl
keyword: biology
has responsible: Alex Bateman
has provider formatter: http://purl.uniprot.org/core/$1
keyword: ontology
has resource example: certain
description: Properties and classes used for protein annotation
has prefix: uniprot.core
is deprecated: false
0000005: certain

Rice Metabolic Pathways
0000005: PWY-1042
keyword: pathway
is deprecated: false
is part of: Bioregistry
has prefix: ricecyc
description: RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project
type: Resource
has URI prefix: http://pathway.gramene.org/RICE/NEW-IMAGE
has resource example: http://pathway.gramene.org/RICE/NEW-IMAGE
keyword: gene
has provider formatter: http://pathway.gramene.org/RICE/NEW-IMAGE
has reviewer: Charles Tapley Hoyt

has resource example
type: Property
range: string
domain: Resource
equivalent property: exampleResource
description: An expanded example URL for a resource or metaresource.

Carnegie Stage
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has provider formatter: https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages#Stage_$1
type: Resource
0000005: 20
has prefix: carnegie.stage
has resource example: Stage 20
description: One of the 23 stages of embryo development
is deprecated: false
has URI prefix: https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages#Stage_

has URI pattern
type: Property
equivalent property: uriRegexPattern
range: string
description: The pattern for expanded URIs in the given resource
equivalent property: accessIdentifierPattern
equivalent property: P8966
domain: Resource

Allotrope quality
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
description: The quality component of the Allotrope ontology suite
contributor: Charles Tapley Hoyt
has resource example: AFQ_0000236
is part of: Allotrope Merged Ontology Suite
has URI prefix: http://purl.allotrope.org/ontologies/quality#AFQ_
type: Resource
has provider formatter: http://purl.allotrope.org/ontologies/quality#AFQ_$1
is deprecated: false
has prefix: allotrope.quality
0000005: 0000236

International Classification of Functioning, Disability and Health
keyword: primary health care
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
has resource example: http://id.who.int/icd/entity/326705068
contributor: Charles Tapley Hoyt
has download URL: icf.owl
type: Resource
keyword: biomedical science
has prefix: icf
keyword: health science
keyword: medicine
0000005: 326705068
has URI prefix: https://icd.who.int/dev11/l-icf/en#/http://id.who.int/icd/entity/
keyword: ontology
has provider formatter: https://icd.who.int/dev11/l-icf/en#/http://id.who.int/icd/entity/$1
is deprecated: false
description: The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels.
keyword: electronic health record

microRNA Gene Database
description: mircoRNA Gene Database is a collection of animal microRNA genes. This database allows researchers to analyze mircoRNA properties like secondary structure and features in a phylogenetic context.
has local unique identifier pattern: ^[a-zA-Z0-9]+(-[a-zA-Z0-9]+)+$
has URI prefix: https://mirgenedb.org/browse
contributor: 0009-0008-8406-631X
has resource example: https://mirgenedb.org/browse
is deprecated: false
has prefix: mirgenedb
is part of: Bioregistry
has provider formatter: https://mirgenedb.org/browse
has reviewer: https://orcid.org/0000-0001-9439-5346
0000005: Hsa-Let-7-P2a3
has responsible: https://orcid.org/0000-0003-0352-3037
type: Resource

IUPAC Compendium of Analytical Nomenclature (Orange Book)
has prefix: orangebook
is deprecated: false
description: The first number is the chapter then the remainder are subsections.
0000005: 10.2.1.1.3
is part of: Bioregistry
contributor: Charles Tapley Hoyt
type: Resource

SWEET Ontology Phenomena Environmental Impact
has provider formatter: http://sweetontology.net/phenEnvirImpact/$1
is deprecated: false
has alternative prefix: sophei
0000005: AirPollution
has prefix: sweet.phei
keyword: environmental impact
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: AirPollution
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
keyword: phenomena
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Environmental Impact
has URI prefix: http://sweetontology.net/phenEnvirImpact/

Gene Ontology Causal Activity Model
is deprecated: false
description: GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.
is part of: Bioregistry
has URI prefix: https://model.geneontology.org/
has prefix: go.model
has resource example: https://model.geneontology.org/5fce9b7300001250
0000005: 5fce9b7300001250
has provider formatter: https://model.geneontology.org/$1
type: Resource

Frédéric Bastian
label: Frederic Bastian

ClassyFire
keyword: ontology
has provider formatter: http://classyfire.wishartlab.com/tax_nodes/C$1
is deprecated: false
has resource example: http://classyfire.wishartlab.com/tax_nodes/C0004828
has alternative prefix: chemont
has download URL: ChemOnt 2 1.obo.zip
is part of: Bioregistry
0000005: 0004828
has URI prefix: http://classyfire.wishartlab.com/tax_nodes/C
has prefix: classyfire
type: Resource
description: ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API.
has alternative prefix: CHEMONTID
has local unique identifier pattern: ^\d{7}$

Bgee family
has prefix: bgee.family
has local unique identifier pattern: ^(ENSFM|ENSGTV:)\d+$
contributor: 0000-0003-3947-488X
type: Resource
is deprecated: true
description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species.
has URI prefix: http://bgee.unil.ch/bgee/bgee
has resource example: http://bgee.unil.ch/bgee/bgee
0000005: ENSFM00500000270089
has provider formatter: http://bgee.unil.ch/bgee/bgee
is part of: Bioregistry

AnVIL DRS
has provider formatter: https://data.terra.bio/ga4gh/drs/v1/objects/$1
has URI prefix: https://data.terra.bio/ga4gh/drs/v1/objects/
is deprecated: false
is part of: Bioregistry
description: This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research.
has local unique identifier pattern: ^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$
has prefix: drsanv0
type: Resource

NASA GeneLab
has provider formatter: https://genelab-data.ndc.nasa.gov/genelab/accession/$1
is deprecated: false
is part of: Bioregistry
has URI prefix: https://genelab-data.ndc.nasa.gov/genelab/accession/
has prefix: ngl
0000005: GLDS-141
type: Resource
has resource example: GLDS-141
description: NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.
has local unique identifier pattern: ^GLDS-\d+$

FHIR United States Implementation Guides
has URI prefix: https://hl7.org/fhir/us/
has provider formatter: https://hl7.org/fhir/us/$1
is deprecated: false
0000005: immds
has resource example: immds
has prefix: fhir.implementation
is part of: Bioregistry
description: A set of guides on implementing various processes within hospitals or healthcare systems.
contributor: Charles Tapley Hoyt
type: Resource

EasyChair Call for Paper
has prefix: easychair.cfp
keyword: conferences
keyword: metascience
has URI prefix: https://easychair.org/cfp/
is deprecated: false
description: Conferences in EasyChair
is part of: Bioregistry
type: Resource
0000005: SysBioCancer2022
contributor: Charles Tapley Hoyt
has provider formatter: https://easychair.org/cfp/$1
has resource example: SysBioCancer2022

Diversification criteria of R|EX research
has URI prefix: https://vocabularies.cessda.eu/vocabulary/rexgroups#code_
has provider formatter: https://vocabularies.cessda.eu/vocabulary/rexgroups#code_$1
description: This CV, developed within the framework of the DP-R|EX joint project, involving the partner institutions DeZIM, Qualiservice and GESIS, maps the dimensions of discrimination and racialised characteristics relevant to the research area. The compilation is based on a systematic evaluation of the relevant national and international empirical research literature. These include self-attributed characteristics as well as anticipated attributions by others. The characteristics do not necessarily correspond to the studied units in the data set, but can also be the subject of studied concepts or theories in the surveys, such as on specific prejudices and attitudes.
is deprecated: false
is part of: Bioregistry
has prefix: gesis.rexgroups
has identifier space owner: 018afyw53
0000005: v1
type: Resource
contributor: Charles Tapley Hoyt
has resource example: code v1

Scopus Publication
is deprecated: false
description: identifier for a source/publication venue (journal, conference, etc) in Scopus
has resource example: https://www.scopus.com/sourceid/16129
has URI prefix: https://www.scopus.com/sourceid/
0000005: 16129
is part of: Bioregistry
has provider formatter: https://www.scopus.com/sourceid/$1
type: Resource
has prefix: scopus.publication
has local unique identifier pattern: ^[1-9]\d{0,11}$

Allotrope process
description: The process component of the Allotrope ontology suite
has prefix: allotrope.process
has URI prefix: http://purl.allotrope.org/ontologies/process#AFP_
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
type: Resource
contributor: Charles Tapley Hoyt
is part of: Allotrope Merged Ontology Suite
has provider formatter: http://purl.allotrope.org/ontologies/process#AFP_$1
0000005: 0001263
has resource example: AFP_0001263
is deprecated: false

FlyMine Chromosome Band
keyword: gene expression
has prefix: flymine.chromosome
type: Resource
has resource example: https://www.flymine.org/flymine/report/ChromosomeBand/1047874
description: FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge.
has reviewer: Charles Tapley Hoyt
has provider formatter: https://www.flymine.org/flymine/report/ChromosomeBand/$1
0000005: 1047874
is deprecated: false
has URI prefix: https://www.flymine.org/flymine/report/ChromosomeBand/
is part of: Bioregistry
keyword: protein
keyword: genome

Brain Architecture Knowledge Management System Neuroanatomical Ontology
is part of: Bioregistry
contributor: Charles Tapley Hoyt
description: BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.
type: Resource
has prefix: bams
is deprecated: true

FlyBase Qualifiers
0000005: 00005254
is part of: Bioregistry
has local unique identifier pattern: ^\d+$
type: Resource
contributor: Charles Tapley Hoyt
is deprecated: true
has prefix: fbql

Type of Address
is part of: Bioregistry
contributor: Charles Tapley Hoyt
has resource example: code Mailing
type: Resource
0000005: Mailing
has prefix: ddi.typeofaddress
description: Identifies the type of address entered as contact information for an individual or an organization.
has provider formatter: https://vocabularies.cessda.eu/vocabulary/TypeOfAddress#code_$1
has URI prefix: https://vocabularies.cessda.eu/vocabulary/TypeOfAddress#code_
has identifier space owner: 015em2733
is deprecated: false

Unimod protein modification database for mass spectrometry
keyword: ontology
description: Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).
is deprecated: false
keyword: bioinformatics
0000005: 1200
has local unique identifier pattern: ^\d+$
is part of: Bioregistry
has resource example: http://www.unimod.org/modifications_view.php
has prefix: unimod
type: Resource
has responsible: John Cottrell
has provider formatter: http://www.unimod.org/modifications_view.php
has download URL: unimod.owl
has URI prefix: http://www.unimod.org/modifications_view.php

CSV on the Web Vocabulary
type: Resource
description: This document describes the RDFS vocabulary description used in the Metadata Vocabulary for Tabular Data along with the default JSON-LD Context.
has prefix: csvw
keyword: vocabularies
is deprecated: false
0000005: uriTemplate
is part of: Bioregistry
keyword: w3c rec

British Oceanographic Data Centre data storage units
has alternative prefix: nvs.P06
has provider formatter: http://vocab.nerc.ac.uk/collection/P06/current/$1
keyword: units
has resource example: UMKS
has prefix: bodc.unit
is deprecated: false
is part of: Bioregistry
0000005: UMKS
description: terms approved for use by BODC to describe the measurement units for data held in its repositories.
contributor: Charles Tapley Hoyt
keyword: unit
has URI prefix: http://vocab.nerc.ac.uk/collection/P06/current/
type: Resource

SWEET Ontology Phenomena Geologic Volcano
is part of: Bioregistry
keyword: geologic volcano
has URI prefix: http://sweetontology.net/phenGeolVolcano/
contributor: Charles Tapley Hoyt
has alternative prefix: sophgv
type: Resource
git repository: sweet
is part of: Semantic Web for Earth and Environment Technology Ontology
has provider formatter: http://sweetontology.net/phenGeolVolcano/$1
0000005: EruptionCloud
keyword: phenomena
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Volcano
has resource example: EruptionCloud
is deprecated: false
has prefix: sweet.phgv

European Science Vocabulary Ontology
0000005: isTextual
is deprecated: false
is part of: Bioregistry
description: The Euvoc ontology, published by the Publications Office of the European Union, supports the development of authority tables (Name Authority Lists or NALs), Eurovoc and EU corporate datasets. It contains a set of classes and properties enabling all the information to be expressed in multilingual format. It helps define relationships between terms and concepts across multiple domains, supporting interoperability and standardization across European Union documentation and databases. It also defines a set a commonly use properties (i.e: start date, end dates, status), and supports the reusability on common data (currencies, languages, countries). The Euvoc ontology is maintained by the Publications Office of the European Union and disseminated on the EU Vocabularies website.
type: Resource
contributor: Charles Tapley Hoyt
has prefix: euroscivoc.schema

NFDI4Objects Collection
has part: Bioregistry
type: Collection
creator: Charles Tapley Hoyt
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Objects

CGH Data Base
description: Cell line databases/resources
is deprecated: false
0000005: 300165/p13898_2106T
is part of: Bioregistry
type: Resource
has prefix: cghdb

Battery Interface Ontology
has prefix: battinfo
is deprecated: false
is part of: Bioregistry
has provider formatter: https://w3id.org/emmo/domain/battery#battery_$1
keyword: engineering
description: A battery interface domain ontology based on EMMO.
keyword: electrical engineering
git repository: BattINFO
type: Resource
has URI prefix: https://w3id.org/emmo/domain/battery#battery_
keyword: nfdi4ing