Diversification criteria of R|EX research
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
0000005: v1
has provider formatter: https://vocabularies.cessda.eu/vocabulary/rexgroups#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/rexgroups#code_
0000026: 018afyw53
0000027: code v1
0000029: gesis.rexgroups

Analysis Unit
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: Individual
has provider formatter: https://vocabularies.cessda.eu/vocabulary/AnalysisUnit#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/AnalysisUnit#code_
0000026: 015em2733
0000027: code Individual
0000029: ddi.analysisunit

Long Term Ecological Research Controlled Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Ecological terms
is part of: bioregistry
0000005: 182
has provider formatter: https://vocab.lternet.edu/vocab/vocab/index.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://vocab.lternet.edu/vocab/vocab/index.php
0000027: https://vocab.lternet.edu/vocab/vocab/index.php
0000029: lter

SWEET Ontology State Space
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Space
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state space
0000005: Big
has provider formatter: http://sweetontology.net/stateSpace/$1
is deprecated: false
has alternative prefix: sostsp
has URI prefix: http://sweetontology.net/stateSpace/
0000027: Big
0000029: sweet.stsp

Ontology of Genetic Susceptibility Factor
type: Resource
description: An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.
is part of: bioregistry
git repository: OGSF
keyword: ontology
keyword: adverse reaction
keyword: genetics
keyword: disease
keyword: genetic disorder
keyword: epidemiology
keyword: biomedical science
keyword: obo
0000005: 0000025
has provider formatter: http://purl.obolibrary.org/obo/OGSF_$1
has local unique identifier pattern: ^\d{7}$
0000010: ogsf.owl
is deprecated: true
has responsible: Asiyah Yu Lin
has URI prefix: http://purl.obolibrary.org/obo/OGSF_
0000027: OGSF_0000025
0000029: ogsf

International Classification of Diseases, 11th Revision (Foundation Component)
type: Resource
contributor: https://orcid.org/0000-0002-7356-1779
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: ontology
keyword: morbidity
keyword: disease
keyword: electronic health record
keyword: diagnosis
keyword: global health
keyword: epidemiology
keyword: biomedical science
keyword: health science
0000005: 402558626
has provider formatter: https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1
has local unique identifier pattern: ^[1-9]\d*$
0000010: icd11.owl
is deprecated: false
has responsible: ICD Helpdesk
has alternative prefix: ICD-11
has alternative prefix: icd11.foundation
has alternative prefix: ICD11
has URI prefix: https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/
0000027: http://id.who.int/icd/entity/402558626
0000029: icd11

Pol Castellano Escuder

Web of Science work ID
type: Resource
description: unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix)
is part of: bioregistry
0000005: 000177759000002
has provider formatter: https://www.webofscience.com/wos/woscc/full-record/WOS:$1
is deprecated: false
has alternative prefix: wos
has alternative prefix: wosuid
has alternative prefix: wosid
has URI prefix: https://www.webofscience.com/wos/woscc/full-record/WOS:
0000027: WOS:000177759000002
0000029: wos.work

microRNA Ontology
type: Resource
description: An application ontology for use with miRNA databases.
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/MIRNAO_$1
0000010: mirnao.owl
is deprecated: true
has responsible: Pantelis Topalis
has URI prefix: http://purl.obolibrary.org/obo/MIRNAO_
0000029: mirnao

SWEET Ontology Representation Data Service
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Service
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation data service
0000005: Access
has provider formatter: http://sweetontology.net/reprDataService/$1
is deprecated: false
has alternative prefix: sorepds
has URI prefix: http://sweetontology.net/reprDataService/
0000027: Access
0000029: sweet.repds

Martin Pospíšek

Cube db
type: Resource
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.
is part of: bioregistry
0000005: AKR
has provider formatter: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/
has local unique identifier pattern: ^[A-Za-z_0-9]+$
is deprecated: true
has URI prefix: https://bioregistry.io/cubedb:
0000027: AKR
0000029: cubedb

Tudor Oprea

Etsuko Yasugi

ClinGen Allele Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: https://orcid.org/0000-0002-8719-7760
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.
is part of: bioregistry
keyword: mutations
keyword: alleles
keyword: genetics
0000005: CA981206459
has provider formatter: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid
has local unique identifier pattern: ^CA\d+$
is deprecated: false
has alternative prefix: CAID
has alternative prefix: clingene
has URI prefix: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid
0000027: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid
0000029: clingen.allele

SubtiWiki
type: Resource
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.
is part of: bioregistry
keyword: life science
keyword: rna
keyword: dna
keyword: protein
keyword: gene
0000005: BSU29180
has provider formatter: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1
has local unique identifier pattern: ^BSU\d{5}$
is deprecated: false
has responsible: https://orcid.org/0000-0001-5881-5390
has URI prefix: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/
0000027: BSU29180
0000029: subtiwiki

Developing Mouse Brain Atlas
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the developing mouse brain
is part of: bioregistry
git repository: developing mouse brain atlas ontology
keyword: ontology
0000005: 15567
has provider formatter: https://purl.brain-bican.org/ontology/dmbao/DMBA_$1
has local unique identifier pattern: ^\d+$
0000010: dmbao.owl
is deprecated: false
has URI prefix: https://purl.brain-bican.org/ontology/dmbao/DMBA_
0000027: DMBA_15567
0000029: dmba

National Library of Medicine Catalog
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
keyword: ontology
keyword: journal
0000005: 101775319
has provider formatter: https://www.ncbi.nlm.nih.gov/nlmcatalog/$1
has local unique identifier pattern: ^\d+$
0000010: nlm.owl
is deprecated: false
has responsible: NLM Customer Service
has URI prefix: https://www.ncbi.nlm.nih.gov/nlmcatalog/
0000027: https://www.ncbi.nlm.nih.gov/nlmcatalog/101775319
0000029: nlm

TreeBASE
type: Resource
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.
is part of: bioregistry
git repository: issues
keyword: phylogenetics
keyword: classification
keyword: phylogenomics
0000005: TB2:S1000
has provider formatter: http://purl.org/phylo/treebase/phylows/study/$1
has local unique identifier pattern: ^TB[1,2]?:[A-Z][a-z]?\d+$
is deprecated: true
has responsible: https://orcid.org/0000-0001-9254-7318
has URI prefix: https://bioregistry.io/treebase:
0000027: http://purl.org/phylo/treebase/phylows/study/TB2:S1000
0000029: treebase

NFDI MatWerk Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
git repository: mwo
keyword: ontology
0000005: 0001109
has provider formatter: http://purls.helmholtz-metadaten.de/mwo/mwo_$1
has local unique identifier pattern: ^\d{7}$
0000010: mwo.owl
is deprecated: false
has responsible: Hossein Beygi Nasrabadi
has URI prefix: http://purls.helmholtz-metadaten.de/mwo/mwo_
0000027: mwo_0001109
0000029: mwo

ViralZone
type: Resource
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.
is part of: bioregistry
keyword: molecular biology
keyword: virology
keyword: epidemiology
keyword: virus
keyword: life science
0000005: 992
has provider formatter: https://viralzone.expasy.org/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Philippe Le Mercier
has alternative prefix: vz
has URI prefix: https://viralzone.expasy.org/
0000027: https://viralzone.expasy.org/992
0000029: viralzone

snoDB
type: Resource
contributor: https://orcid.org/0009-0000-6974-6386
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 part of: bioregistry
keyword: rna
keyword: snorna-protein
keyword: human nucleolar rna
0000005: snoDB0001
has provider formatter: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/detailed_view/$1
has local unique identifier pattern: ^snoDB\d{4}$
is deprecated: false
has responsible: Michelle S Scott
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/detailed_view/
0000027: snoDB0001
0000029: snodb

MycoBrowser leprae
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 leprae information.
is part of: bioregistry
is part of: myco
keyword: genome
keyword: sequence
0000005: ML0224
has provider formatter: https://mycobrowser.epfl.ch/genes/$1
has local unique identifier pattern: ^ML\w+$
is deprecated: false
has URI prefix: https://mycobrowser.epfl.ch/genes/
0000027: ML0224
0000029: myco.lepra

ClinGen Curation
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
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
is part of: bioregistry
0000005: 004126
has provider formatter: https://search.clinicalgenome.org/CCID:$1
has local unique identifier pattern: ^\d{6}$
is deprecated: false
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://search.clinicalgenome.org/CCID:
0000027: CCID:004126
0000029: clingen.curation

Lifestyle Factors Ontology
type: Resource
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.
is part of: bioregistry
keyword: ontology
0000005: 0000015
has provider formatter: http://purl.obolibrary.org/obo/LFID_$1
0000010: LSFO.owl
is deprecated: false
has responsible: Lars Juhl Jensen
has URI prefix: http://purl.obolibrary.org/obo/LFID_
0000027: LFID_0000015
0000029: lifestylefactors

SWEET Ontology Phenomena Atmosphere Lightning
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Lightning
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
keyword: atmosphere lightning
0000005: BallLightning
has provider formatter: http://sweetontology.net/phenAtmoLightning/$1
is deprecated: false
has alternative prefix: sophatmol
has URI prefix: http://sweetontology.net/phenAtmoLightning/
0000027: BallLightning
0000029: sweet.phatmol

Human Gene Mutation Database
type: Resource
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.
is part of: bioregistry
0000005: CALM1
has provider formatter: http://www.hgmd.cf.ac.uk/ac/gene.php
has local unique identifier pattern: ^[A-Z_0-9]+$
is deprecated: false
has URI prefix: http://www.hgmd.cf.ac.uk/ac/gene.php
0000027: http://www.hgmd.cf.ac.uk/ac/gene.php
0000029: hgmd

Open Energy Ontology
type: Resource
contributor: https://orcid.org/0000-0003-3722-5564
description: OEO is a domain reference ontology for energy system modeling.
is part of: bioregistry
git repository: ontology
keyword: nfdi4energy
keyword: nfdi4ing
keyword: ontology
keyword: energy
keyword: engineering
keyword: mechanical engineering, energy technology
keyword: energy engineering
0000005: 00030015
has provider formatter: https://openenergyplatform.org/ontology/oeo/OEO_$1
has local unique identifier pattern: ^\d+$
0000010: oeo-full.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-3722-5564
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://openenergyplatform.org/ontology/oeo/OEO_
0000027: OEO_00030015
0000029: oeo

Human Protein Reference Database
type: Resource
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
keyword: protein
keyword: structure
0000005: 00001
has provider formatter: http://www.hprd.org/protein/$1
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: https://orcid.org/0000-0001-9943-6127
has URI prefix: http://www.hprd.org/protein/
0000027: http://www.hprd.org/protein/00001
0000029: hprd

International Nucleotide Sequence Database Collaboration (INSDC) Run
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
description: An experimental run, served thrugh the ENA
is part of: bioregistry
0000005: ERR436051
has provider formatter: https://www.ebi.ac.uk/ena/browser/view/$1
has local unique identifier pattern: ^(E|D|S)RR[0-9]{6,}$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.ebi.ac.uk/ena/browser/view/
0000027: ERR436051
0000029: insdc.run

TubercuList knowledge base
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.
is part of: myco
is part of: bioregistry
keyword: dna
keyword: protein
keyword: genome
0000005: Rv1908c
has provider formatter: https://mycobrowser.epfl.ch/genes/$1
has local unique identifier pattern: ^Rv\d{4}(A|B|c)?$
is deprecated: false
has responsible: https://orcid.org/0000-0003-1400-5585
has alternative prefix: TubercuList
has URI prefix: https://mycobrowser.epfl.ch/genes/
0000027: Rv1908c
0000029: myco.tuber

Open Biomedical Annotations
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
git repository: OBAN
keyword: ontology
0000005: provenance
has provider formatter: http://purl.org/oban/$1
has local unique identifier pattern: ^\w+$
0000010: oban core.owl
is deprecated: false
has URI prefix: http://purl.org/oban/
0000027: provenance
0000029: oban

SWEET Ontology Material Natural Resource
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Natural Resource
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: natural resource
keyword: materials
0000005: Anthracite
has provider formatter: http://sweetontology.net/matrNaturalResource/$1
is deprecated: false
has alternative prefix: somanr
has URI prefix: http://sweetontology.net/matrNaturalResource/
0000027: Anthracite
0000029: sweet.manr

Open Science Framework ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: ID in osf.io
is part of: bioregistry
keyword: work
keyword: paper
keyword: author
keyword: person
keyword: researcher
0000005: 2u4tf
has provider formatter: https://osf.io/$1
has local unique identifier pattern: ^[a-z0-9]{5}$
is deprecated: false
has URI prefix: https://osf.io/
0000027: 2u4tf
0000029: osf

XHTML Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
keyword: api
0000005: alternate
has provider formatter: http://www.w3.org/1999/xhtml/vocab#$1
is deprecated: false
has URI prefix: http://www.w3.org/1999/xhtml/vocab#
0000027: alternate
0000029: xhv

KEGG genome
type: Resource
description: KEGG Genome is a collection of organisms whose genomes have been completely sequenced.
is part of: bioregistry
is part of: kegg
keyword: ontology
keyword: genome
0000005: T06648
has provider formatter: http://www.kegg.jp/entry/$1
has local unique identifier pattern: ^(T0\d+|\w{3,5})$
0000010: kegg.genome.owl
is deprecated: false
has responsible: 0000-0001-6123-540X
has alternative prefix: kegg_genomes
has alternative prefix: kegg_genome
has URI prefix: http://www.kegg.jp/entry/
0000027: T06648
0000029: kegg.genome

Experimental Measurements Purposes and Treatments ontologY
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
git repository: empty-ontology
keyword: ontology
0000005: 00000085
has provider formatter: http://purl.obolibrary.org/obo/EMPTY_$1
has local unique identifier pattern: ^\d+$
0000010: empty.owl
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/EMPTY_
0000027: EMPTY_00000085
0000029: empty

Oral Health and Disease Ontology
type: Resource
description: The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.
is part of: bioregistry
git repository: ohd-ontology
keyword: dentistry
keyword: medicine
keyword: obo
keyword: oral surgery
keyword: ontology
0000005: 0000006
has provider formatter: http://purl.obolibrary.org/obo/OHD_$1
has local unique identifier pattern: ^\d{7}$
0000010: ohd.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9625-1899
has URI prefix: http://purl.obolibrary.org/obo/OHD_
0000027: OHD_0000006
0000029: ohd

ChemFOnt Chemical
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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.
is part of: bioregistry
keyword: ontology
keyword: chemical
0000005: CFc000239295
has provider formatter: https://www.chemfont.ca/chemicals/$1
has local unique identifier pattern: ^CFc\d{9}$
is deprecated: false
has responsible: David Wishart
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.chemfont.ca/chemicals/
0000027: https://www.chemfont.ca/chemicals/CFc000239295
0000029: chemfont.chemical

Yeast Intron Database v3
type: Resource
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 part of: bioregistry
0000005: SNR17A
has provider formatter: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb
has local unique identifier pattern: ^[A-Z0-9]+$
is deprecated: true
has URI prefix: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb
0000027: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb
0000029: yid

Thesaurus for long-term ecological research, monitoring, experiments
type: Resource
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.
is part of: bioregistry
git repository: issues
keyword: ontology
keyword: ecology
keyword: geochemistry
keyword: monitoring
keyword: earth sciences
keyword: geographic location
keyword: environmental science
keyword: observations
keyword: ess
keyword: natural science
has provider formatter: http://vocabs.lter-europe.net/EnvThes/$1
is deprecated: false
has responsible: Barbara Magagna
has URI prefix: http://vocabs.lter-europe.net/EnvThes/
0000029: envthes

Nonribosomal Peptides Database
type: Resource
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.
is part of: bioregistry
keyword: life science
keyword: protein
0000005: NOR00681
has provider formatter: https://bioinfo.cristal.univ-lille.fr/norine/result.jsp
has local unique identifier pattern: ^NOR\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-3197-0715
has URI prefix: https://bioinfo.cristal.univ-lille.fr/norine/result.jsp
0000027: https://bioinfo.cristal.univ-lille.fr/norine/result.jsp
0000029: norine

Building Ontology
type: Resource
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.
is part of: bioregistry
keyword: nfdi4ing
keyword: architecture
keyword: civil engineering
keyword: ontology
keyword: digital planning and construction
keyword: fid baudigital
0000005: AirConditioningUnit
has provider formatter: http://bimerr.iot.linkeddata.es/def/building#$1
0000010: building.owl
is deprecated: false
has URI prefix: http://bimerr.iot.linkeddata.es/def/building#
0000027: AirConditioningUnit
0000029: building

The Statistical Methods Ontology
type: Resource
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.
is part of: bioregistry
git repository: stato
keyword: data analysis
keyword: graph
keyword: experimental measurement
keyword: ess
keyword: study design
keyword: obo
keyword: ontology
keyword: data visualization
keyword: dataplant
keyword: statistics
keyword: omics
0000005: 0000288
has provider formatter: http://purl.obolibrary.org/obo/STATO_$1
has local unique identifier pattern: ^\d{7}$
0000010: stato.owl
is deprecated: false
0000018: Ontology for Avida digital evolution platform
0000018: scdo
0000018: Performance Summary Display Ontology
has responsible: Philippe Rocca-Serra
has URI prefix: http://purl.obolibrary.org/obo/STATO_
0000027: STATO_0000288
0000029: stato

GESAH Graphic Arts Ontology
type: Resource
description: The GESAH Graphic Arts Ontology is designed for the inventory, classification and structured description of works on paper.
is part of: bioregistry
keyword: architecture
keyword: nfdi4culture
keyword: history
0000005: applies_to
has provider formatter: http://ontology.tib.eu/gesah/$1
is deprecated: false
has URI prefix: http://ontology.tib.eu/gesah/
0000027: applies to
0000029: gesah

Unipathway
type: Resource
description: A manually curated resource for the representation and annotation of metabolic pathways
is part of: bioregistry
git repository: unipathway
keyword: pathway
keyword: obo
keyword: ontology
0000005: UCR00513
has provider formatter: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa
has local unique identifier pattern: ^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$
0000010: upa.owl
is deprecated: true
depends on: ro
has responsible: https://orcid.org/0000-0002-1216-2969
has alternative prefix: unipathway
has alternative prefix: UPa
has alternative prefix: unipathway.pathway
has URI prefix: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa
0000027: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa
0000029: upa

SWEET Ontology Realm Atmospheric
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Atmospheric
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: realm
keyword: atmospheric
0000005: AtmosphereLayer
has provider formatter: http://sweetontology.net/realmAtmo/$1
is deprecated: false
has alternative prefix: soreaa
has URI prefix: http://sweetontology.net/realmAtmo/
0000027: AtmosphereLayer
0000029: sweet.reaa

Zazuko Prefix Server
type: https://bioregistry.io/schema/#0000002
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: 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
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
has part: vso
has part: vs
has part: sd
has part: skosxl
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
has part: sh
has part: gs1
has part: hydra
has part: wdrs
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
0000005: frbr
has provider formatter: https://prefix.zazuko.com/prefix/$1:
has resolver formatter: https://prefix.zazuko.com/$1:$2
has responsible: Adrian Gschwend

Yeast Intron Database v4.3
type: Resource
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].
is part of: bioregistry
0000005: SNR17A
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 URI prefix: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl
0000027: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl
0000029: yeastintron

Shoshana J. Wodak

Text+ Collection
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for Text+
has part: bioregistry

nmrXiv project
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A project in the nmrXiv
is part of: bioregistry
keyword: project
keyword: datasets
0000005: P136
has provider formatter: https://nmrxiv.org/project/$1
has local unique identifier pattern: ^P\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-2564-3243
has URI prefix: https://nmrxiv.org/project/
0000027: P136
0000029: nmrxiv.project

Guide to Pharmacology Ligand
type: Resource
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 part of: bioregistry
0000005: 1755
has provider formatter: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: IUPHAR_LIGAND_ID
has alternative prefix: IUPHAR_LIGAND
has URI prefix: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward
0000027: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward
0000029: iuphar.ligand

KIM School Subjects
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary describing subjects taught in German primary and secondary school (not university/hochschulen), such as German, math, and art.
is part of: bioregistry
git repository: schulfaecher
keyword: subject
keyword: school subject
keyword: discipline
0000005: s1000
has provider formatter: http://w3id.org/kim/schulfaecher/$1
is deprecated: false
has URI prefix: http://w3id.org/kim/schulfaecher/
0000027: s1000
0000029: kim.schulfaecher

Sergio José Rodríguez Méndez

The Bioinorganic Motif Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
keyword: protein
0000005: MOL000160
has provider formatter: https://www.flymine.org/come/entry
is deprecated: false
has alternative prefix: COMe
has URI prefix: https://www.flymine.org/come/entry
0000027: https://www.flymine.org/come/entry
0000029: come

Homeodomain Research
type: Resource
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.
is part of: bioregistry
keyword: genome
0000005: 63
has provider formatter: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi
0000027: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi
0000029: hdr

GlycoNAVI
type: Resource
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.
is part of: bioregistry
git repository: doc
keyword: life science
keyword: glycomics
keyword: chemistry
keyword: organic chemistry
0000005: GN_G03681DA
has provider formatter: https://glyconavi.org/hub/
has local unique identifier pattern: ^GN_[A-Za-z0-9_:]+$
is deprecated: false
has responsible: 0000-0001-9504-189X
has URI prefix: https://glyconavi.org/hub/
0000027: https://glyconavi.org/hub/
0000029: glyconavi

European Registry of Materials
type: Resource
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.
is part of: bioregistry
keyword: materials science
keyword: chemical entity
keyword: nanotechnology
keyword: materials informatics
0000005: ERM00000044
has provider formatter: https://nanocommons.github.io/identifiers/registry#$1
has local unique identifier pattern: ^ERM[0-9]{8}$
is deprecated: false
has responsible: Tim Vandermeersch
has URI prefix: https://nanocommons.github.io/identifiers/registry#
0000027: ERM00000044
0000029: erm

Japan Collection of Microorganisms
type: Resource
description: The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.
is part of: bioregistry
keyword: microbial
keyword: taxonomy
keyword: life science
0000005: 17254
has provider formatter: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number
0000027: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number
0000029: jcm

Ontology for Chemical Kinetic Reaction Mechanisms
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Represents chemical kinetic reaction mechanisms.
is part of: bioregistry
keyword: ontology
keyword: chemical and environmental engineering
keyword: chemistry
keyword: nfdi4cat
keyword: nfdi4chem
0000005: ElementNumber
has provider formatter: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1
0000010: OntoKin.owl
is deprecated: false
has URI prefix: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#
0000027: ElementNumber
0000029: worldavatar.kin

Contextual Ontology-based Repository Analysis Library - Context and Measurement Ontology
type: Resource
contributor: John-Marc Chandonia
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.
is part of: bioregistry
git repository: CORAL
keyword: ontology
0000005: 0000001
has local unique identifier pattern: ^\d+$
0000010: context measurement ontology.obo
is deprecated: false
has responsible: John-Marc Chandonia
has reviewer: https://orcid.org/0000-0003-4423-4370
0000029: coral.como

TogoID
type: https://bioregistry.io/schema/#0000002
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: 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
has part: Prosite
has part: Hgnc
has part: Atc
has part: Lipidmaps
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
has part: Interpro
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 part: Togovar
has part: Insdc
has part: UniprotMnemonic
0000005: AffyProbeset
has provider formatter: https://togoid.dbcls.jp/#$1
has responsible: https://orcid.org/0000-0003-2391-0384

SemWeb Vocab Status ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
keyword: ontology
keyword: semantic web
keyword: metadata
0000005: term_status
has provider formatter: http://www.w3.org/2003/06/sw-vocab-status/ns#$1
0000010: ns
is deprecated: false
has URI prefix: http://www.w3.org/2003/06/sw-vocab-status/ns#
0000027: term status
0000029: vs

DepMap Cell Lines
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells.
is part of: bioregistry
keyword: cancer cell line
keyword: cell
keyword: cell line
keyword: ontology
0000005: ACH-000001
has provider formatter: https://depmap.org/portal/cell_line/$1
has local unique identifier pattern: ^ACH-\d+$
0000010: depmap.owl
is deprecated: false
has responsible: Francisca Vazquez
has URI prefix: https://depmap.org/portal/cell_line/
0000027: ACH-000001
0000029: depmap

EndlessForms Studio Image Collections
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Collections of images, based on topics, such as the human skull collection
is part of: bioregistry
0000005: 2
has provider formatter: https://images.endlessforms.info/collection/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: 0000-0001-9979-176X
has URI prefix: https://images.endlessforms.info/collection/
0000027: https://images.endlessforms.info/collection/2
0000029: endlessforms.collection

SWEET Ontology Representation Data Service Validation
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Service Validation
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation data service validation
0000005: Acceptance
has provider formatter: http://sweetontology.net/reprDataServiceValidation/$1
is deprecated: false
has alternative prefix: sorepdsv
has URI prefix: http://sweetontology.net/reprDataServiceValidation/
0000027: Acceptance
0000029: sweet.repdsv

FuncBase Fly
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.
is part of: bioregistry
0000005: 10194
has provider formatter: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://func.mshri.on.ca/fly/genes/list_functional_scores/
0000027: http://func.mshri.on.ca/fly/genes/list_functional_scores/10194
0000029: funcbase.fly

Kristian Axelsen

miRBase Families
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
keyword: gene
keyword: mirna
keyword: ontology
0000005: MIPF0000002
has provider formatter: http://www.mirbase.org/cgi-bin/mirna_summary.pl
0000010: mirbase.family.owl
is deprecated: false
has responsible: 0000-0001-6043-807X
has alternative prefix: MIRBASE_FAMILY
has URI prefix: http://www.mirbase.org/cgi-bin/mirna_summary.pl
0000027: http://www.mirbase.org/cgi-bin/mirna_summary.pl
0000029: mirbase.family

RDF Schema
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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: life science
keyword: ontology and terminology
keyword: ontology
keyword: bioinformatics
keyword: w3c rec
keyword: linguistics
0000005: label
has provider formatter: http://www.w3.org/2000/01/rdf-schema#$1
0000010: download.trig.gz
is deprecated: false
has responsible: https://orcid.org/0000-0002-6450-7041
has URI prefix: http://www.w3.org/2000/01/rdf-schema#
0000027: label
0000029: rdfs

SWEET Ontology State Spectral Band
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Spectral Band
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state spectral band
0000005: BandLimited
has provider formatter: http://sweetontology.net/stateSpectralBand/$1
is deprecated: false
has alternative prefix: sostsb
has URI prefix: http://sweetontology.net/stateSpectralBand/
0000027: BandLimited
0000029: sweet.stsb

ChecklistBank
type: Resource
description: ChecklistBank is an index and repository for taxonomic and nomenclatural datasets
is part of: bioregistry
0000005: 1010
has provider formatter: https://www.checklistbank.org/dataset/$1
has local unique identifier pattern: ^[0-9]+(LR)?$
is deprecated: false
has URI prefix: https://www.checklistbank.org/dataset/
0000027: https://www.checklistbank.org/dataset/1010
0000029: clb

Xenopus Anatomy Ontology
type: Resource
description: XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.
is part of: bioregistry
git repository: xao
keyword: developmental biology
keyword: life cycle
keyword: structure
keyword: anatomy
keyword: morphology
keyword: life science
keyword: obo
keyword: ontology
keyword: life cycle stage
0000005: 0004486
has provider formatter: http://purl.obolibrary.org/obo/XAO_$1
has local unique identifier pattern: ^\d{7}$
0000010: xao.owl
is deprecated: false
0000018: xpo
has responsible: https://orcid.org/0000-0002-9611-1279
has URI prefix: http://purl.obolibrary.org/obo/XAO_
0000027: XAO_0004486
0000029: xao

SWEET Ontology Representation Scientific Law
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Law
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation scientific law
0000005: BernoulliTheorem
has provider formatter: http://sweetontology.net/reprSciLaw/$1
is deprecated: false
has alternative prefix: sorepsl
has URI prefix: http://sweetontology.net/reprSciLaw/
0000027: BernoulliTheorem
0000029: sweet.repsl

J. Michael Cherry
label: Mike Cherry

Sampling Procedure
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A typology of sampling methods.
is part of: bioregistry
0000005: TotalUniverseCompleteEnumeration
has provider formatter: https://vocabularies.cessda.eu/vocabulary/SamplingProcedure#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/SamplingProcedure#code_
0000026: 015em2733
0000027: code TotalUniverseCompleteEnumeration
0000029: ddi.samplingprocedure

WGS84 Geo Positioning
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum
is part of: bioregistry
keyword: geography
0000005: latitude
has provider formatter: http://www.w3.org/2003/01/geo/wgs84_pos#$1
is deprecated: false
has URI prefix: http://www.w3.org/2003/01/geo/wgs84_pos#
0000027: latitude
0000029: wgs84

Tomohiro Oga

Protein Affinity Reagents
type: Resource
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
0000005: 0116
has provider formatter: https://www.ebi.ac.uk/ontology-lookup/
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: https://www.ebi.ac.uk/ontology-lookup/
0000027: https://www.ebi.ac.uk/ontology-lookup/
0000029: psipar

Disease Class
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Legacy disease classes that later became MONDO
is part of: bioregistry
keyword: ontology
0000005: 0000598
has provider formatter: https://biopragmatics.github.io/providers/diseaseclass/$1
has local unique identifier pattern: ^\d{7}$
0000010: missing-omc.obo
is deprecated: true
0000018: Experimental Factor Ontology
has URI prefix: https://biopragmatics.github.io/providers/diseaseclass/
0000027: https://biopragmatics.github.io/providers/diseaseclass/0000598
0000029: diseaseclass

AmphibiaWeb Species ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for a species, in the AmphibiaWeb database
is part of: bioregistry
0000005: 149
has provider formatter: https://amphibiaweb.org/species/$1
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has URI prefix: https://amphibiaweb.org/species/
0000027: https://amphibiaweb.org/species/149
0000029: amphibiaweb.species

Environmental conditions, treatments and exposures ontology
type: Resource
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).
is part of: bioregistry
git repository: environmental-exposure-ontology
keyword: exposure
keyword: environmental science
keyword: obo
keyword: ontology
0000005: 0000001
has provider formatter: http://purl.obolibrary.org/obo/ECTO_$1
has local unique identifier pattern: ^\d{7}$
0000010: ecto.owl
is deprecated: false
depends on: go
depends on: Chemical Entities of Biological Interest
depends on: maxo
depends on: xco
depends on: NCBI Taxonomy
depends on: ncit
depends on: Environment Ontology
depends on: exo
depends on: ro
depends on: Information Artifact Ontology
depends on: nbo
depends on: pato
depends on: Uber Anatomy Ontology
has responsible: Anne Thessen
has URI prefix: http://purl.obolibrary.org/obo/ECTO_
0000027: ECTO_0000001
0000029: ecto

Dominik Martinat

Chemical Information Ontology
type: https://bioregistry.io/schema/#0000002
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 part: CHEMINF_000141
has part: CHEMINF_000409
has part: CHEMINF_000304
has part: CHEMINF_000411
has part: CHEMINF_000408
has part: CHEMINF_000563
has part: CHEMINF_000569
has part: CHEMINF_000564
0000005: 000140
has provider formatter: https://semanticscience.org/resource/CHEMINF_$1
has responsible: Tim Vandermeersch

Hannah Dörpholz

NFDI4Energy Resources
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes for ontologies relevant for the NFDI4Energy
has part: Energy Market Roles ontology
has part: bonsai
has part: dogont
has part: Functional Mock-up Interface Ontology
has part: zbw.stw
has part: sargon
has part: Open Energy Ontology
has part: SAREF4EE: the EEbus/Energy@home extension of SAREF
has part: Brick Ontology
has part: Retail Energy Market of Great Britain
has part: digitalconstruction.energy
has part: SAREF4GRID: an extension of SAREF for the Smart Grid domain
has part: openadr
has part: udsaes.sms
has part: Mid-level Energy Ontology

Chan Zuckerberg CELLxGENE Dataset
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Assigns identifiers to datasets indexed by CELLxGENE, such those resulting from scRNA-seq experiments
is part of: bioregistry
has provider formatter: https://cellxgene.cziscience.com/e/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-8457-2836
has URI prefix: https://cellxgene.cziscience.com/e/
0000029: cellxgene.dataset

David N. Orloff

Country Names and Codes
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: ISO 3166-1 alpha-2 country codes and names.
is part of: bioregistry
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_
0000026: 02wg9xc72
0000027: code AF
0000029: cessda.countrynamesandcodes

SpliceNest
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 part of: bioregistry
keyword: gene
keyword: genome
keyword: dna
0000005: Hs635
has provider formatter: http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi
0000027: http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi
0000029: splicenest

Degradome Database
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.
is part of: bioregistry
0000005: Ax1
has provider formatter: http://degradome.uniovi.es/cgi-bin/protease/$1
has local unique identifier pattern: ^[AMCST][0-9x][0-9]$
is deprecated: false
has URI prefix: http://degradome.uniovi.es/cgi-bin/protease/
0000027: Ax1
0000029: degradome

SWEET Ontology Materials
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Materials
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: materials
0000005: Air
has provider formatter: http://sweetontology.net/matr/$1
is deprecated: false
has alternative prefix: soma
has URI prefix: http://sweetontology.net/matr/
0000027: Air
0000029: sweet.ma

NCBI Taxonomy
type: Resource
description: The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.
is part of: bioregistry
git repository: ncbitaxon
keyword: obo
keyword: ontology
keyword: dna
keyword: protein
keyword: genomics
keyword: taxonomic classification
keyword: omics
keyword: knowledge and information systems
keyword: proteomics
keyword: evolutionary biology
keyword: structure
keyword: biology
keyword: phylogenetics
keyword: taxonomy
keyword: life science
keyword: classification
0000005: 2170610
has provider formatter: http://purl.obolibrary.org/obo/NCBITaxon_$1
has local unique identifier pattern: ^(\d+)|([a-zA-Z_]+)$
0000010: ncbitaxon.owl
is deprecated: false
0000018: gallont
0000018: Agronomy Ontology
0000018: pco
0000018: Cell Line Ontology
0000018: foodon
0000018: chiro
0000018: Environment Ontology
0000018: cl
0000018: Environmental conditions, treatments and exposures ontology
0000018: Microbial Conditions Ontology
0000018: vbo
0000018: Health Surveillance Ontology
0000018: Uber Anatomy Ontology
0000018: Genomic Epidemiology Ontology
0000018: Ontology for Nutritional Studies
0000018: Provisional Cell Ontology
0000018: go
has responsible: https://orcid.org/0000-0003-1839-5322
has alternative prefix: taxid
has alternative prefix: uniprot.taxonomy
has alternative prefix: NCBI_taxid
has alternative prefix: TaxonomyID
has alternative prefix: ncbiTaxUID
has alternative prefix: NCBITaxonomyID
has alternative prefix: NCBI Taxonomy
has alternative prefix: TAX
has alternative prefix: NCBITaxon
has alternative prefix: taxon
has alternative prefix: taxonomy
has alternative prefix: NCBI_Taxon_ID
has URI prefix: http://purl.obolibrary.org/obo/NCBITaxon_
0000026: 02meqm098
0000027: NCBITaxon_2170610
0000029: ncbitaxon

Metathesaurus Names
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
0000005: U001388
has provider formatter: https://uts.nlm.nih.gov/uts/umls/vocabulary/MTH/$1
has local unique identifier pattern: ^U\d+$
is deprecated: false
0000018: umls
0000018: Mondo Disease Ontology
has alternative prefix: umls.mth
has URI prefix: https://uts.nlm.nih.gov/uts/umls/vocabulary/MTH/
0000027: U001388
0000029: mth

miRBase pre-miRNA
type: Resource
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 part of: bioregistry
keyword: biology
keyword: rna
keyword: ontology
keyword: gene
0000005: MI0026471
has provider formatter: http://www.mirbase.org/cgi-bin/mirna_entry.pl
has local unique identifier pattern: ^MI\d{7}$
0000010: mirbase.owl
is deprecated: false
has responsible: 0000-0001-6043-807X
has URI prefix: http://www.mirbase.org/cgi-bin/mirna_entry.pl
0000027: http://www.mirbase.org/cgi-bin/mirna_entry.pl
0000029: mirbase

UMLS Semantic Types Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: https://orcid.org/0000-0003-2473-2313
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.
is part of: bioregistry
keyword: ontology
0000005: T039
has provider formatter: https://uts.nlm.nih.gov/uts/umls/semantic-network/$1
has local unique identifier pattern: ^T\d{3}$
0000010: sty.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-4769-4217
has alternative prefix: umls.st
has alternative prefix: UMLSSG
has alternative prefix: umls.sty
has URI prefix: https://uts.nlm.nih.gov/uts/umls/semantic-network/
0000027: T039
0000029: sty

ArrayExpress Platform
type: Resource
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.
is part of: bioregistry
0000005: A-GEOD-50
has provider formatter: https://www.ebi.ac.uk/arrayexpress/arrays/$1
has local unique identifier pattern: ^[AEP]-\w{4}-\d+$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/arrayexpress/arrays/
0000027: A-GEOD-50
0000029: arrayexpress.platform

Ioannis Xenarios

KEGG Environ
type: Resource
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.
is part of: bioregistry
is part of: kegg
0000005: ev:E00032
has provider formatter: http://www.kegg.jp/entry/$1
has local unique identifier pattern: ^(ev\:)?E\d+$
is deprecated: true
has alternative prefix: KEGG.EDRUG
has URI prefix: http://www.kegg.jp/entry/
0000027: ev:E00032
0000029: kegg.environ

has URI prefix
type: Property
description: The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved.
domain: Resource
range: string
equivalent property: namespace
equivalent property: preferredNamespaceUri
equivalent property: uriSpace

Audubon Core Subtype Controlled Vocabulary
type: Resource
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 part of: bioregistry
keyword: fair data spaces
keyword: life sciences, biology
0000005: Animation
has provider formatter: http://rs.tdwg.org/acsubtype/$1
is deprecated: false
has responsible: Steve Baskauf
has URI prefix: http://rs.tdwg.org/acsubtype/
0000027: Animation
0000029: ac.subtype

Vaccine Ontology
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.
is part of: bioregistry
git repository: VO
keyword: pathogen
keyword: biological_process
keyword: infectious disease medicine
keyword: obo
keyword: ontology
keyword: infection process
keyword: immunology
keyword: small molecule
keyword: vaccination
keyword: pathobiochemistry
keyword: preclinical studies
keyword: vaccine
keyword: clinical studies
keyword: biomedical science
0000005: 0000093
has provider formatter: http://purl.obolibrary.org/obo/VO_$1
has local unique identifier pattern: ^\d{7}$
0000010: vo.owl
is deprecated: false
0000018: scdo
has responsible: https://orcid.org/0000-0001-9189-9661
has URI prefix: http://purl.obolibrary.org/obo/VO_
0000027: VO_0000093
0000029: vo

Zenodo
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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.
is part of: bioregistry
keyword: subject agnostic
keyword: data management
0000005: 4390079
has provider formatter: https://zenodo.org/record/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Lars Holm Nielsen
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: zenodo
has URI prefix: https://zenodo.org/record/
0000027: https://zenodo.org/record/4390079
0000029: zenodo.record

General Standard for Food Additives Online Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: 174
has provider formatter: http://www.fao.org/gsfaonline/additives/details.html
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: FAO/WHO_standards
has URI prefix: http://www.fao.org/gsfaonline/additives/details.html
0000027: http://www.fao.org/gsfaonline/additives/details.html
0000029: gsfa

SWEET Ontology Phenomena Ocean Coastal
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Ocean Coastal
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: ocean coastal
keyword: phenomena
0000005: Attrition
has provider formatter: http://sweetontology.net/phenOceanCoastal/$1
is deprecated: false
has alternative prefix: sophoc
has URI prefix: http://sweetontology.net/phenOceanCoastal/
0000027: Attrition
0000029: sweet.phoc

miRNEST
type: Resource
description: miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.
is part of: bioregistry
keyword: expression
keyword: life science
keyword: genomics
keyword: prediction
0000005: MNEST029358
has provider formatter: http://rhesus.amu.edu.pl/mirnest/copy/details.php
has local unique identifier pattern: ^MNEST\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6050-9525
has URI prefix: http://rhesus.amu.edu.pl/mirnest/copy/details.php
0000027: http://rhesus.amu.edu.pl/mirnest/copy/details.php
0000029: mirnest

Software Functions Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: sfo
keyword: software
keyword: software function
0000005: 0000001
has provider formatter: http://cor.esipfed.org/ont/earthcube/SFO_$1
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4808-4736
has URI prefix: http://cor.esipfed.org/ont/earthcube/SFO_
0000027: SFO_0000001
0000029: earthcube.sfo

Nematode Expression Pattern DataBase
type: Resource
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.
is part of: bioregistry
keyword: gene expression
keyword: life science
keyword: genome
keyword: dna
0000005: 6b1
has provider formatter: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php
has local unique identifier pattern: ^[A-Za-z0-9]+$
is deprecated: false
has URI prefix: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php
0000027: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php
0000029: nextdb

LINCS Cell
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.
is part of: bioregistry
0000005: LCL-2085
has provider formatter: http://lincsportal.ccs.miami.edu/cells/#/view/$1
has local unique identifier pattern: ^(LCL|LDC|ES|LSC|LPC)-\d+$
is deprecated: false
has alternative prefix: LINCS_LDP
has URI prefix: http://lincsportal.ccs.miami.edu/cells/#/view/
0000027: view/LCL-2085
0000029: lincs.cell

WikiPathways Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology supporting data modeling in WikiPathways
is part of: bioregistry
git repository: WpVocabularies
keyword: ontology
0000005: DataNode
has provider formatter: https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/
0000010: wp.owl
is deprecated: false
has responsible: Tim Vandermeersch
has URI prefix: https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/
0000027: https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/
0000029: wikipathways.vocab

Beta Cell Biology Consortium
type: Resource
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]
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
keyword: gene
keyword: pancreatic islet
keyword: beta cell
keyword: antibody
keyword: pancreatic islet function
keyword: mouse embryonic stem cell line
keyword: basic science
keyword: cell regeneration
keyword: cell reprogramming
keyword: cell line
keyword: data sharing
keyword: data set
keyword: adenovirus
keyword: basic research
keyword: mouse
keyword: pancreas
keyword: embryonic stem cell line
keyword: genomics
0000005: 4623
has provider formatter: https://scicrunch.org/resolver/RRID:BCBC_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://scicrunch.org/resolver/RRID:BCBC_
0000027: RRID:BCBC 4623
0000029: bcbc

ProtClustDB
type: Resource
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.
is part of: bioregistry
keyword: genetics
keyword: genomics
keyword: protein
keyword: structure
keyword: life science
0000005: O80725
has provider formatter: https://www.ncbi.nlm.nih.gov/sites/entrez
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: William Klimke
has URI prefix: https://www.ncbi.nlm.nih.gov/sites/entrez
0000027: https://www.ncbi.nlm.nih.gov/sites/entrez
0000029: protclustdb

Yeast Phenotype Ontology
type: Resource
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/YPO_$1
is deprecated: true
has responsible: J. Michael Cherry
has URI prefix: http://purl.obolibrary.org/obo/YPO_
0000029: ypo

Open Data Commons for Spinal Cord Injury
type: Resource
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.
is part of: bioregistry
keyword: neuroscience
keyword: biomedical science
keyword: neurology
keyword: neurobiology
0000005: 602
has provider formatter: https://odc-sci.org/data/$1
has local unique identifier pattern: ^[0-9]*$
is deprecated: false
has responsible: Jeffrey Grethe
has URI prefix: https://odc-sci.org/data/
0000027: https://odc-sci.org/data/602
0000029: odc.sci

Human Endogenous Retrovirus Database
type: Resource
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.
is part of: bioregistry
0000005: THE1B
has provider formatter: https://herv.img.cas.cz/s/$1
has local unique identifier pattern: ^[A-Za-z0-9\-\_]+$
is deprecated: false
has URI prefix: https://herv.img.cas.cz/s/
0000027: THE1B
0000029: erv

Zebrafish Information Network Gene
type: Resource
description: ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.
is part of: bioregistry
keyword: fish
keyword: zebrafish line
keyword: gene
keyword: antibody
keyword: zebrafish
keyword: research
keyword: expressed sequence tag
keyword: pathology
keyword: cdna
keyword: adult
keyword: embryo
keyword: ontology
keyword: animal physiology
keyword: genetics
keyword: genome
keyword: genomics
keyword: developmental biology
0000005: ZDB-GENE-041118-11
has provider formatter: http://zfin.org/$1
has local unique identifier pattern: ^ZDB\-\w+\-\d+\-\d+$
0000010: zfin.owl.gz
is deprecated: false
has responsible: https://orcid.org/0000-0001-5831-7439
has alternative prefix: ZFIN
has URI prefix: http://zfin.org/
0000027: ZDB-GENE-041118-11
0000029: zfin

Interaction Network Ontology
type: Resource
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.
is part of: bioregistry
git repository: ino
keyword: obo
keyword: ontology
keyword: molecular interaction
keyword: life science
0000005: 0000003
has provider formatter: http://purl.obolibrary.org/obo/INO_$1
has local unique identifier pattern: ^\d{7}$
0000010: ino.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9189-9661
has URI prefix: http://purl.obolibrary.org/obo/INO_
0000027: INO_0000003
0000029: ino

GlycoEpitope
type: Resource
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.
is part of: bioregistry
0000005: EP0311
has provider formatter: https://www.glycoepitope.jp/epitopes/$1
has local unique identifier pattern: ^EP\d{4}$
is deprecated: false
has URI prefix: https://www.glycoepitope.jp/epitopes/
0000027: EP0311
0000029: glycoepitope

The Prescription of Drugs Ontology
type: Resource
description: An ontology to describe entities related to prescription of drugs
is part of: bioregistry
git repository: PDRO
keyword: drug
keyword: obo
keyword: ontology
keyword: primary health care
0000005: 0010039
has provider formatter: http://purl.obolibrary.org/obo/PDRO_$1
has local unique identifier pattern: ^\d{7}$
0000010: pdro.owl
is deprecated: false
has responsible: Paul Fabry
has URI prefix: http://purl.obolibrary.org/obo/PDRO_
0000027: PDRO_0010039
0000029: pdro

Insertion sequence elements database
type: Resource
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
keyword: gene
keyword: life science
keyword: sequence
0000005: ISA1083-2
has provider formatter: https://www-is.biotoul.fr/scripts/ficheIS.php
has local unique identifier pattern: ^IS\w+(\-\d)?$
is deprecated: true
has responsible: Patricia Siguier
has URI prefix: https://www-is.biotoul.fr/scripts/ficheIS.php
0000027: https://www-is.biotoul.fr/scripts/ficheIS.php
0000029: isfinder

The Software Description Ontology
type: Resource
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.
is part of: bioregistry
git repository: SoftwareDescriptionOntology
keyword: nfdi4ing
keyword: computer science
0000005: CatalogIdentifier
has provider formatter: https://w3id.org/okn/o/sd#$1
is deprecated: false
has responsible: https://orcid.org/0000-0003-0454-7145
has URI prefix: https://w3id.org/okn/o/sd#
0000027: CatalogIdentifier
0000029: okn.sd

Individual Organism Information Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology of information entities about an individual
is part of: bioregistry
git repository: IOIO
keyword: ontology
0000005: 0000001
has provider formatter: http://purl.obolibrary.org/obo/IOIO_$1
has local unique identifier pattern: ^\d{7}$
0000010: IOIO.owl
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/IOIO_
0000027: IOIO_0000001
0000029: ioio

KEGG pathway
type: Resource
description: KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
is part of: bioregistry
keyword: pathway
0000005: rsk00410
has provider formatter: https://www.kegg.jp/pathway/$1
has local unique identifier pattern: ^\w{2,4}\d{5}$
is deprecated: false
has responsible: 0000-0001-6123-540X
has alternative prefix: KEGG-path
has alternative prefix: KEGG_PATHWAY
has URI prefix: https://www.kegg.jp/pathway/
0000027: rsk00410
0000029: kegg.pathway

Dublin Core Metadata Initiative Abstract Model
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A metadata model for Dublin Core metadata
is part of: bioregistry
keyword: general & upper
keyword: metadata model
keyword: schema
keyword: semantic web
0000005: domainIncludes
has provider formatter: http://purl.org/dc/dcam/$1
is deprecated: false
has URI prefix: http://purl.org/dc/dcam/
0000027: domainIncludes
0000029: dcam

Sharkipedia Trend
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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.
is part of: bioregistry
git repository: sharkipedia
0000005: 3447
has provider formatter: https://www.sharkipedia.org/trends/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-1710-8256
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.sharkipedia.org/trends/
0000027: https://www.sharkipedia.org/trends/3447
0000029: sharkipedia.trend

EDCC Taxonomy
type: Resource
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
keyword: educational resources
0000005: 00098e55
has provider formatter: http://data.europa.eu/ett/kos/c_$1
is deprecated: false
has URI prefix: http://data.europa.eu/ett/kos/c_
0000027: c 00098e55
0000029: edcc

MycoBrowser marinum
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 marinum information.
is part of: myco
is part of: bioregistry
keyword: sequence
keyword: genome
0000005: MMAR_2462
has provider formatter: https://mycobrowser.epfl.ch/genes/$1
has local unique identifier pattern: ^MMAR\_\d+$
is deprecated: false
has URI prefix: https://mycobrowser.epfl.ch/genes/
0000027: MMAR 2462
0000029: myco.marinum

CALIPHO Group Ontology of Human Anatomy
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: controlled-vocabulary
keyword: anatomy
keyword: ontology
keyword: human
keyword: physiology
0000005: TS-0001
has provider formatter: https://www.nextprot.org/term/$1
has local unique identifier pattern: ^TS-\d+$
0000010: caloha.obo
is deprecated: false
has responsible: https://orcid.org/0000-0002-0819-0473
has URI prefix: https://www.nextprot.org/term/
0000027: TS-0001
0000029: caloha

Genotype Ontology
type: Resource
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
is part of: bioregistry
git repository: GENO-ontology
keyword: disease phenotype
keyword: genotype
keyword: obo
keyword: ontology
keyword: genomics
0000005: 0000632
has provider formatter: http://purl.obolibrary.org/obo/GENO_$1
has local unique identifier pattern: ^\d{7}$
0000010: geno.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1048-5019
has URI prefix: http://purl.obolibrary.org/obo/GENO_
0000027: GENO_0000632
0000029: geno

SWEET Ontology Human Research
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Research
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: research
0000005: Analysis
has provider formatter: http://sweetontology.net/humanResearch/$1
is deprecated: false
has alternative prefix: sohur
has URI prefix: http://sweetontology.net/humanResearch/
0000027: Analysis
0000029: sweet.hur

Genomic Epidemiology Ontology
type: Resource
description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.
is part of: bioregistry
git repository: genepio
keyword: pathogen
keyword: obo
keyword: food
keyword: ontology
keyword: genome
keyword: genomics
keyword: epidemiology
0000005: 0001885
has provider formatter: http://purl.obolibrary.org/obo/GENEPIO_$1
has local unique identifier pattern: ^\d{7}$
0000010: genepio.owl
is deprecated: false
depends on: ro
depends on: Uber Anatomy Ontology
depends on: Chemical Entities of Biological Interest
depends on: NCBI Taxonomy
depends on: Plant Ontology
has responsible: https://orcid.org/0000-0002-8844-9165
has URI prefix: http://purl.obolibrary.org/obo/GENEPIO_
0000027: GENEPIO_0001885
0000029: genepio

Protein Model Portal
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.
is part of: bioregistry
keyword: protein
keyword: prediction
keyword: structure
0000005: Q0VCA6
has provider formatter: http://www.proteinmodelportal.org/query/uniprot/$1
has local unique identifier pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$
0000011: uniprot
is deprecated: true
has responsible: Torsten Schwede
has URI prefix: http://www.proteinmodelportal.org/query/uniprot/
0000027: Q0VCA6
0000029: pmp

ChemPro Target
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for human proteins that interact with chemoproteomic probes.
is part of: bioregistry
0000005: LDTP03903
has provider formatter: https://chemprosquare.idrblab.net/data/target/details/$1
has local unique identifier pattern: ^LDTP\d+$
is deprecated: false
has responsible: Feng Zhu
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://chemprosquare.idrblab.net/data/target/details/
0000027: LDTP03903
0000029: chempro.target

Database of Anti-Microbial Peptides
type: Resource
contributor: https://orcid.org/0009-0009-3402-8013
description: Identifiers represent antimicrobial peptides in the Database of Antimicrobial Peptides (dbAMP) which is an open-access, manually curated database of antimicrobial peptides (AMPs).
is part of: bioregistry
keyword: antimicrobial peptides
0000005: 28463
has provider formatter: https://awi.cuhk.edu.cn/dbAMP/information.php
has local unique identifier pattern: ^\d{5}$
is deprecated: false
has responsible: https://orcid.org/0000-0001-8475-7868
has reviewer: https://orcid.org/0000-0001-9439-5346
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://awi.cuhk.edu.cn/dbAMP/information.php
0000027: https://awi.cuhk.edu.cn/dbAMP/information.php
0000029: dbamp

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.
is part of: bioregistry
keyword: classification
keyword: small molecule
keyword: protein
keyword: structure
0000005: f665230-5267
has provider formatter: http://www.molmovdb.org/cgi-bin/morph.cgi
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.molmovdb.org/cgi-bin/morph.cgi
0000027: http://www.molmovdb.org/cgi-bin/morph.cgi
0000029: molmovdb

UniProt Archive
type: Resource
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.
is part of: bioregistry
keyword: protein
keyword: structure
0000005: UPI000000000A
has provider formatter: https://www.uniprot.org/uniparc/$1
has local unique identifier pattern: ^UPI[A-F0-9]{10}$
is deprecated: false
has responsible: Alex Bateman
has URI prefix: https://www.uniprot.org/uniparc/
0000027: UPI000000000A
0000029: uniparc

Chemical Component Dictionary
type: Resource
contributor: https://orcid.org/0000-0003-4062-6158
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
keyword: classification
keyword: chemical
0000005: AB0
has provider formatter: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1
has local unique identifier pattern: ^\w{1,3}$
is deprecated: false
has canonical: PDB ligand
has responsible: Helen Berman
has alternative prefix: pdbechem
has alternative prefix: PDBeChem
has URI prefix: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/
0000027: AB0
0000029: pdb-ccd

Chemical Entities of Biological Interest
type: Resource
contributor: https://orcid.org/0009-0005-4625-8212
description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.
is part of: bioregistry
git repository: ChEBI
keyword: natural product
keyword: ontology
keyword: small molecule
keyword: dataplant
keyword: chemistry
keyword: taxonomic classification
keyword: nfdi4cat
keyword: metabolomics
keyword: nfdi4chem
keyword: proteomics
keyword: molecular entity
keyword: chemical
keyword: earth sciences
keyword: lipidomics
keyword: structure
keyword: biochemistry
keyword: ess
keyword: obo
0000005: 138488
has provider formatter: http://purl.obolibrary.org/obo/CHEBI_$1
has local unique identifier pattern: ^\d+$
0000010: chebi.owl
is deprecated: false
0000018: An ontology of core ecological entities
0000018: scdo
0000018: Process Chemistry Ontology
0000018: cdno
0000018: foodon
0000018: chiro
0000018: xpo
0000018: Environment Ontology
0000018: Environmental conditions, treatments and exposures ontology
0000018: Microbial Conditions Ontology
0000018: Uber Anatomy Ontology
0000018: Genomic Epidemiology Ontology
0000018: fobi
0000018: Provisional Cell Ontology
0000018: Ontology for Nutritional Studies
0000018: maxo
has responsible: https://orcid.org/0000-0001-8123-5351
has alternative prefix: ChEBI
has alternative prefix: CHEBIID
has alternative prefix: CHEBI
has URI prefix: http://purl.obolibrary.org/obo/CHEBI_
0000027: CHEBI_138488
0000029: chebi

PharmGKB pathway
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. 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.
is part of: bioregistry
keyword: ontology
keyword: pathway
keyword: pharmacogenomics
0000005: PA146123006
has provider formatter: http://www.pharmgkb.org/pathway/$1
has local unique identifier pattern: ^PA\d+$
0000010: pharmgkb.pathways.owl
is deprecated: false
has responsible: Teri E Klein
has URI prefix: http://www.pharmgkb.org/pathway/
0000027: PA146123006
0000029: pharmgkb.pathways

GrainGenes reference
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A database for Triticeae and Avena references.
is part of: bioregistry
0000005: WGS-95-1333
has provider formatter: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi
is deprecated: false
has URI prefix: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi
0000027: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi
0000029: graingenes.reference

Pigeon Pea Ontology
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 Pigeon Pea Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
is part of: bioregistry
git repository: Crop-Ontology
keyword: food
keyword: ontology
keyword: plant phenotypes and traits
keyword: phenotype
keyword: botany
keyword: agriculture
keyword: life science
0000005: 0000140
has provider formatter: https://cropontology.org/rdf/CO_341:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 341.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_341:
0000027: CO 341:0000140
0000029: co_341

Stephen Fisher

Human Brain Atlas
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the human brain
is part of: bioregistry
git repository: human brain atlas ontology
keyword: ontology
0000005: 4005
has provider formatter: https://purl.brain-bican.org/ontology/hbao/HBA_$1
has local unique identifier pattern: ^\d+$
0000010: hbao.owl
is deprecated: false
has URI prefix: https://purl.brain-bican.org/ontology/hbao/HBA_
0000027: HBA 4005
0000029: hba

Evidence and Conclusion Ontology
type: Resource
contributor: https://orcid.org/0000-0003-3035-6940
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.
is part of: bioregistry
git repository: evidenceontology
keyword: assay
keyword: sample annotation
keyword: evidence
keyword: literature curation
keyword: text mining
keyword: life science
keyword: study design
keyword: obo
keyword: ontology
keyword: biocuration
keyword: curated information
keyword: computational biology
keyword: digital curation
keyword: resource metadata
0000005: 0007807
has provider formatter: http://purl.obolibrary.org/obo/ECO_$1
has local unique identifier pattern: ^\d{7}$
0000010: eco.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-7628-5565
has URI prefix: http://purl.obolibrary.org/obo/ECO_
0000027: ECO_0007807
0000029: eco

Database of Quantitative Cellular Signaling: Pathway
type: Resource
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.
is part of: bioregistry
keyword: pathway
0000005: 131
has provider formatter: http://doqcs.ncbs.res.in/template.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Upinder S. Bhalla
has URI prefix: http://doqcs.ncbs.res.in/template.php
0000027: http://doqcs.ncbs.res.in/template.php
0000029: doqcs.pathway

Dialnet author ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier of an author in Dialnet
is part of: bioregistry
keyword: person
keyword: researcher
0000005: 241889
has provider formatter: https://dialnet.unirioja.es/servlet/autor
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has URI prefix: https://dialnet.unirioja.es/servlet/autor
0000027: https://dialnet.unirioja.es/servlet/autor
0000029: dialnet.author

PROV Namespace
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: ontology
keyword: w3c rec
keyword: nfdi4chem
keyword: nfdi4ing
keyword: ess
0000005: Activity
has provider formatter: http://www.w3.org/ns/prov#$1
0000010: prov.owl
is deprecated: false
has URI prefix: http://www.w3.org/ns/prov#
0000027: Activity
0000029: prov

System Science of Biological Dynamics project
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: 1
has provider formatter: https://ssbd.riken.jp/database/project/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://ssbd.riken.jp/database/project/
0000027: https://ssbd.riken.jp/database/project/1
0000029: ssbd.project

Financial Industry Business Ontology
type: Resource
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
is part of: bioregistry
git repository: fibo
keyword: economics
keyword: coypu
0000005: BE/MetadataBE/BEDomain
has provider formatter: https://spec.edmcouncil.org/fibo/ontology/$1
is deprecated: false
has URI prefix: https://spec.edmcouncil.org/fibo/ontology/
0000027: BEDomain
0000029: edm.fibo

SWEET Ontology Realm Hydrosphere Body
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Hydrosphere Body
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: hydrosphere body
keyword: realm
0000005: Aqueduct
has provider formatter: http://sweetontology.net/realmHydroBody/$1
is deprecated: false
has alternative prefix: soreahb
has URI prefix: http://sweetontology.net/realmHydroBody/
0000027: Aqueduct
0000029: sweet.reahb

Protein modification
type: Resource
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.
is part of: bioregistry
git repository: psi-mod-CV
keyword: protein
keyword: dataplant
keyword: chemistry
keyword: nfdi4chem
keyword: proteomics
keyword: life sciences, biology
keyword: post-translational protein modification
keyword: enzymatic reaction
keyword: structure
keyword: molecule
keyword: life science
keyword: obo
keyword: ontology
keyword: chemical biology
0000005: 01467
has provider formatter: http://purl.obolibrary.org/obo/MOD_$1
has local unique identifier pattern: ^\d{5}$
0000010: mod.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-0045-7698
has alternative prefix: PSI-MOD
has URI prefix: http://purl.obolibrary.org/obo/MOD_
0000027: MOD_01467
0000029: mod

HOMD Sequence Metainformation
type: Resource
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.
is part of: bioregistry
keyword: microbial
keyword: genome
0000005: SEQF1003.1
has provider formatter: https://v31.homd.org/genome/genome_description
has local unique identifier pattern: ^SEQF\d+(?:\.\d+)?$
is deprecated: false
has responsible: 0000-0001-6689-317X
has URI prefix: https://v31.homd.org/genome/genome_description
0000027: https://v31.homd.org/genome/genome_description
0000029: homd.seq

Secondary Metabolism Collaboratory - taxon
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
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).
is part of: bioregistry
0000005: 1
has provider formatter: https://smc.jgi.doe.gov/sources/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3491-0198
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://smc.jgi.doe.gov/sources/
0000027: https://smc.jgi.doe.gov/sources/1
0000029: smc.source

Ensembl Protists
type: Resource
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.
is part of: bioregistry
keyword: genome
0000005: PF3D7_1328700
has provider formatter: https://protists.ensembl.org/id/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has URI prefix: https://protists.ensembl.org/id/
0000027: PF3D7_1328700
0000029: ensembl.protist

Plant Phenology Ontology
type: Resource
description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.
is part of: bioregistry
git repository: PPO
keyword: life cycle
keyword: phenology
keyword: obo
keyword: ontology
keyword: dataplant
keyword: phenotype
keyword: botany
keyword: life sciences, biology
0000005: 0002058
has provider formatter: http://purl.obolibrary.org/obo/PPO_$1
has local unique identifier pattern: ^\d{7}$
0000010: ppo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-8815-0078
has URI prefix: http://purl.obolibrary.org/obo/PPO_
0000027: PPO_0002058
0000029: ppo

Pearl Millet Ontology
type: Resource
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.
is part of: bioregistry
git repository: Crop-Ontology
keyword: ontology
keyword: plant phenotypes and traits
keyword: phenotype
keyword: botany
keyword: agriculture
0000005: 0000095
has provider formatter: https://cropontology.org/rdf/CO_327:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 327.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_327:
0000027: CO 327:0000095
0000029: co_327

Rat Genome Database qTL
type: Resource
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.
is part of: bioregistry
0000005: 1354581
has provider formatter: http://rgd.mcw.edu/rgdweb/report/qtl/main.html
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://rgd.mcw.edu/rgdweb/report/qtl/main.html
0000027: http://rgd.mcw.edu/rgdweb/report/qtl/main.html
0000029: rgd.qtl

Cell Line Database
type: Resource
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.
is part of: bioregistry
0000005: cl3603
has provider formatter: http://bioinformatics.hsanmartino.it/hypercldb/$1.html
has local unique identifier pattern: ^(cl|tum)\d+$
is deprecated: false
has alternative prefix: hypercldb
has URI prefix: https://bioregistry.io/cldb:
0000027: cl3603.html
0000029: cldb

Giacomo Lanza

Cancer Data Standards Registry and Repository
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.
is part of: bioregistry
0000005: 3771992
has provider formatter: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML
has local unique identifier pattern: ^[0-9]*$
is deprecated: false
has URI prefix: https://bioregistry.io/cadsr:
0000027: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML
0000029: cadsr

Virus-HostDB
type: Resource
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.
is part of: bioregistry
keyword: virus
0000005: 438782
has provider formatter: https://www.genome.jp/virushostdb/$1
0000011: NCBI Taxonomy
is deprecated: false
has responsible: 0000-0001-6594-377X
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.genome.jp/virushostdb/
0000027: https://www.genome.jp/virushostdb/438782
0000029: virushostdb

Iconclass Classification
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A classification system for the subject matter of works of art, originating from work from Henri van de Waal in the 1940.
is part of: bioregistry
keyword: ontology
0000005: 3
has provider formatter: https://iconclass.org/$1
0000010: iconclass.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-0006-7542
has URI prefix: https://iconclass.org/
0000027: https://iconclass.org/3
0000029: iconclass

BugBase Expt
type: Resource
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
0000005: 288
has provider formatter: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php
0000027: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php
0000029: bugbase.expt

NDFI4Cat Collection
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
creator: https://orcid.org/0000-0001-5886-7860
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: chmo
has part: A vocabulary for the catalysis disciplines
has part: bfo
has part: rex
has part: edam
has part: cheminf
has part: nfdi4chem.ontocape
has part: Descriptive Ontology for Linguistic and Cognitive Engineering
has part: Environment Ontology
has part: cao
has part: afo
has part: worldavatar.compchem
has part: bao
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: iso15926
has part: mop
has part: Systems Biology Ontology
has part: Ontology for Biomedical Investigations
has part: Ontology for Chemical Kinetic Reaction Mechanisms
has part: emmo.cif
has part: Chemical Entities of Biological Interest
has part: Ontology of units of Measure
has part: m4i

Molecular Design Limited Hash
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
0000005: MFCD00011659
has local unique identifier pattern: ^\w{4}\d{8}$
is deprecated: false
0000018: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
0000029: mdl

GeoNames
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.
is part of: bioregistry
keyword: geographic location
keyword: ontology
keyword: geography
keyword: geoinformatics
0000005: 3532759
has provider formatter: https://www.geonames.org/$1
has local unique identifier pattern: ^\d+$
0000010: geonames.owl
is deprecated: false
has responsible: Marc Wick
has alternative prefix: Geomames
has alternative prefix: Geonamaes
has URI prefix: https://www.geonames.org/
0000027: https://www.geonames.org/3532759
0000029: geonames

University hospital Medical Information Network Clinical Trial Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An additional Japanese clinical trial registry
is part of: bioregistry
0000005: UMIN000049383
has local unique identifier pattern: ^UMIN\d+$|^C\d+$
is deprecated: false
0000029: uminctr

International Standard for Intelligent Information Request and Delivery Core Ontology
type: Resource
description: An ontology encoding the core metadata based on the Intelligent Information Request and Delivery (iiRDS) standard
is part of: bioregistry
git repository: models
keyword: nfdi4ing
keyword: computer science
0000005: Action
has provider formatter: http://iirds.tekom.de/iirds#$1
is deprecated: false
has URI prefix: http://iirds.tekom.de/iirds#
0000027: Action
0000029: iirds.core

Electron Microscopy Data Bank
type: Resource
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 part of: bioregistry
keyword: virology
keyword: epidemiology
keyword: structural biology
0000005: EMD-1001
has provider formatter: https://www.ebi.ac.uk/pdbe/entry/emdb/$1
has local unique identifier pattern: ^EMD-\d{4,5}$
is deprecated: false
has responsible: https://orcid.org/0000-0001-7663-9028
has URI prefix: https://www.ebi.ac.uk/pdbe/entry/emdb/
0000026: 02catss52
0000027: EMD-1001
0000029: emdb

Angela Kranz

SWEET Ontology State Role Impact
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Impact
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state role impact
0000005: Catastrophic
has provider formatter: http://sweetontology.net/stateRoleImpact/$1
is deprecated: false
has alternative prefix: sostri
has URI prefix: http://sweetontology.net/stateRoleImpact/
0000027: Catastrophic
0000029: sweet.stri

International Committee on Taxonomy of Viruses Ontology
type: Resource
description: Ontology representation of the [International Committee on Taxonomy of Viruses (ICTV)](https://ictv.global/) for the [EVORA project](https://evora-project.eu/)
is part of: bioregistry
git repository: ictv-ontology
0000005: ICTV19990991
has provider formatter: http://ictv.global/id/MSL40/$1
is deprecated: false
has URI prefix: http://ictv.global/id/MSL40/
0000027: ICTV19990991
0000029: ictv

SWEET Ontology State Storm
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Storm
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state storm
0000005: BeaufortScale
has provider formatter: http://sweetontology.net/stateStorm/$1
is deprecated: false
has alternative prefix: sostst
has URI prefix: http://sweetontology.net/stateStorm/
0000027: BeaufortScale
0000029: sweet.stst

Publishing Workflow Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity.
is part of: bioregistry
git repository: pwo
keyword: spar
keyword: subject agnostic
0000005: Workflow
has provider formatter: http://purl.org/spar/pwo/$1
is deprecated: false
has responsible: Silvio Peroni
has URI prefix: http://purl.org/spar/pwo/
0000027: Workflow
0000029: pwo

Adam Godzik

SWEET Ontology Material Instrument
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Instrument
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: instrument
keyword: materials
0000005: Anemometer
has provider formatter: http://sweetontology.net/matrInstrument/$1
is deprecated: false
has alternative prefix: somains
has URI prefix: http://sweetontology.net/matrInstrument/
0000027: Anemometer
0000029: sweet.mains

Ensembl Glossary
type: Resource
description: The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used.
is part of: bioregistry
keyword: ontology
0000005: 0000198
has provider formatter: http://ensembl.org/glossary/ENSGLOSSARY_$1
has local unique identifier pattern: ^\d{7}$
0000010: ensembl-glossary.owl
is deprecated: false
has URI prefix: http://ensembl.org/glossary/ENSGLOSSARY_
0000027: ENSGLOSSARY_0000198
0000029: ensemblglossary

MobiVoc Open Mobility Vocabulary 1.1.4
type: Resource
description: MobiVoc is an open vocabulary for future-oriented mobility solutions.
is part of: bioregistry
keyword: fid move
keyword: nfdi4ing
keyword: traffic engineering
0000005: AccessCondition
has provider formatter: http://schema.mobivoc.org/#$1
is deprecated: false
has URI prefix: http://schema.mobivoc.org/#
0000027: AccessCondition
0000029: mobivoc

Immune Epitope Database References
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for references, typically linking to sources of evidence such as publications that support data within IEDB.
is part of: bioregistry
keyword: immunology
keyword: bioinformatics
keyword: life science
0000005: 1038233
has provider formatter: https://www.iedb.org/reference/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-8957-7612
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.iedb.org/reference/
0000027: https://www.iedb.org/reference/1038233
0000029: iedb.reference

Sue Bello

IntAct Molecule
type: Resource
description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.
is part of: bioregistry
0000005: EBI-366083
has provider formatter: https://www.ebi.ac.uk/intact/search
has local unique identifier pattern: ^EBI\-[0-9]+$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/intact/search
0000027: https://www.ebi.ac.uk/intact/search
0000029: intact.molecule

Association-Rule-Based Annotator
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
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.
is part of: bioregistry
0000005: ARBA00000001
has provider formatter: https://www.uniprot.org/arba/$1
has local unique identifier pattern: ^ARBA\d+$
is deprecated: false
has responsible: Alex Bateman
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: arba
has URI prefix: https://www.uniprot.org/arba/
0000027: ARBA00000001
0000029: uniprot.arba

BioCyc collection of metabolic pathway databases
type: Resource
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.
is part of: bioregistry
keyword: pathway
keyword: sequence
keyword: genome
0000005: ECOLI:CYT-D-UBIOX-CPLX
has provider formatter: http://biocyc.org/getid
has local unique identifier pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$
is deprecated: false
has responsible: Peter D. Karp
has URI prefix: http://biocyc.org/getid
0000027: http://biocyc.org/getid
0000029: biocyc

Database of structurally defined protein interfaces
type: Resource
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.
is part of: bioregistry
keyword: structure
keyword: protein
0000005: 21692
has provider formatter: http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl
0000027: http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl
0000029: pibase

Colin Groom

Dictyostelium discoideum anatomy
type: Resource
description: A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum.
is part of: bioregistry
git repository: migration-data
keyword: cell
keyword: anatomy
keyword: life science
keyword: obo
keyword: ontology
keyword: slime-mould
0000005: 0000006
has provider formatter: http://purl.obolibrary.org/obo/DDANAT_$1
has local unique identifier pattern: ^\d{7}$
0000010: ddanat.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-4532-2703
has URI prefix: http://purl.obolibrary.org/obo/DDANAT_
0000027: DDANAT_0000006
0000029: ddanat

Mouse Brain Atlas
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the mouse brain
is part of: bioregistry
git repository: mouse brain atlas ontology
keyword: ontology
0000005: 688
has provider formatter: https://purl.brain-bican.org/ontology/mbao/MBA_$1
has local unique identifier pattern: ^\d+$
0000010: mbao.owl
is deprecated: false
has responsible: Allen Institute for Brain Science
has URI prefix: https://purl.brain-bican.org/ontology/mbao/MBA_
0000027: MBA 688
0000029: mba

VegBank
type: Resource
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.
is part of: bioregistry
0000005: VB.Ob.3736.GRSM125
has provider formatter: http://vegbank.org/cite/$1
has local unique identifier pattern: ^VB\.[A-Za-z][A-Za-z]\..*$
is deprecated: false
has URI prefix: http://vegbank.org/cite/
0000027: VB.Ob.3736.GRSM125
0000029: vegbank

NeuronDB
type: Resource
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.
is part of: bioregistry
keyword: anatomy
keyword: neurobiology
keyword: molecular neuroscience
keyword: comparative neurobiology
keyword: neurophysiology
keyword: computational neuroscience
keyword: cellular neuroscience
keyword: structure
0000005: 265
has provider formatter: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx
0000027: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx
0000029: neurondb

Dynamic Ecological Information Management System - Site and dataset registry
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
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.
is part of: bioregistry
has provider formatter: https://deims.org/$1
has local unique identifier pattern: ^[0-9a-f\-]+$
is deprecated: false
has responsible: Christoph Wohner
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: deims.id
has URI prefix: https://deims.org/
0000029: deims.site

GXA Gene
type: Resource
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.
is part of: bioregistry
0000005: AT4G01080
has provider formatter: https://www.ebi.ac.uk/gxa/genes/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/gxa/genes/
0000026: 02catss52
0000027: AT4G01080
0000029: gxa.gene

Patrice Buche

Prefix Commons
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A registry of life science prefxes
is part of: bioregistry
0000005: ChEBI
has provider formatter: https://bioregistry.io/metaregistry/prefixcommons/$1
is deprecated: false
has URI prefix: https://bioregistry.io/metaregistry/prefixcommons/
0000027: ChEBI
0000029: prefixcommons

Polygenic Score Catalog
type: Resource
description: The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation.
is part of: bioregistry
0000005: PGS000018
has provider formatter: https://www.pgscatalog.org/pgs/$1
has local unique identifier pattern: ^PGS[0-9]{6}$
is deprecated: false
has URI prefix: https://www.pgscatalog.org/pgs/
0000027: PGS000018
0000029: pgs

ProGlycProt
type: Resource
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.
is part of: bioregistry
0000005: AC119
has provider formatter: http://www.proglycprot.org/detail.aspx
has local unique identifier pattern: ^[A-Z]C\d{1,3}$
is deprecated: true
has URI prefix: http://www.proglycprot.org/detail.aspx
0000027: http://www.proglycprot.org/detail.aspx
0000029: proglyc

Dorothea Iglezakis

Mobility Theme
type: Resource
description: Controlled vocabulary for the classification of the theme for a mobility dataset.
is part of: bioregistry
keyword: traffic engineering
keyword: fid move
keyword: nfdi4ing
0000005: accesibility-information-for-vehicles
has provider formatter: https://w3id.org/mobilitydcat-ap/mobility-theme/$1
is deprecated: false
has URI prefix: https://w3id.org/mobilitydcat-ap/mobility-theme/
0000027: accesibility-information-for-vehicles
0000029: tib.mt

BacDive
type: Resource
description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.
is part of: bioregistry
keyword: microbiology
keyword: life science
keyword: biodiversity
0000005: 131392
has provider formatter: https://bacdive.dsmz.de/strain/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: Lorenz Reimer
has URI prefix: https://bacdive.dsmz.de/strain/
0000027: https://bacdive.dsmz.de/strain/131392
0000029: bacdive

Trushar Shah

SWEET Ontology Representation Mathematics
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation mathematics
0000005: Array
has provider formatter: http://sweetontology.net/reprMath/$1
is deprecated: false
has alternative prefix: sorepm
has URI prefix: http://sweetontology.net/reprMath/
0000027: Array
0000029: sweet.repm

Library of Congress Format Description Document
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
keyword: media type
keyword: file format
0000005: fdd000613
has provider formatter: https://www.loc.gov/preservation/digital/formats/fdd/$1
has local unique identifier pattern: ^fdd\d+$
is deprecated: false
has URI prefix: https://www.loc.gov/preservation/digital/formats/fdd/
0000027: https://www.loc.gov/preservation/digital/formats/fdd/fdd000613
0000029: loc.fdd

Degree of Establishment Controlled Vocabulary
type: Resource
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
is part of: bioregistry
keyword: fair data spaces
keyword: life sciences, biology
0000005: d001
has provider formatter: http://rs.tdwg.org/dwcdoe/$1
is deprecated: false
has responsible: Steve Baskauf
has URI prefix: http://rs.tdwg.org/dwcdoe/
0000027: d001
0000029: dwc.doe

NeuroLex Anatomy
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: NLXANAT covers anatomy terms. Almost all terms are also in Uberon.
is part of: bioregistry
keyword: anatomy
0000005: 090201
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Tom Gillespie
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_anat_
0000027: nlx anat 090201
0000029: nlx.anat

Thomas Keane

SWEET Ontology Property Dimensionless Ratio
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Dimensionless Ratio
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: dimensionless ratio
0000005: BowenRatio
has provider formatter: http://sweetontology.net/propDimensionlessRatio/$1
is deprecated: false
has alternative prefix: sopropdr
has URI prefix: http://sweetontology.net/propDimensionlessRatio/
0000027: BowenRatio
0000029: sweet.propdr

Adrien Rougny

SWEET Ontology State Physical
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Physical
is part of: bioregistry
is part of: sweet
git repository: sweet
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/
0000027: MoistureState
0000029: sweet.stp

Sigma Aldrich
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Sigma Aldrich is a life sciences supply vendor.
is part of: bioregistry
keyword: chemistry
keyword: vendor
keyword: life sciences
keyword: biology
0000005: HPA000698
has provider formatter: https://www.sigmaaldrich.com/US/en/product/sigma/$1
is deprecated: false
has URI prefix: https://www.sigmaaldrich.com/US/en/product/sigma/
0000027: HPA000698
0000029: sigmaaldrich

An ontology of core ecological entities
type: Resource
description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.
is part of: bioregistry
git repository: ecocore
keyword: obo
keyword: ontology
0000005: 00000001
has provider formatter: http://purl.obolibrary.org/obo/ECOCORE_$1
has local unique identifier pattern: ^\d+$
0000010: ecocore.owl
is deprecated: false
depends on: Environment Ontology
depends on: ro
depends on: Information Artifact Ontology
depends on: pato
depends on: Uber Anatomy Ontology
depends on: Chemical Entities of Biological Interest
depends on: go
depends on: Plant Ontology
depends on: pco
depends on: bfo
has responsible: Pier Luigi Buttigieg
has URI prefix: http://purl.obolibrary.org/obo/ECOCORE_
0000027: ECOCORE_00000001
0000029: ecocore

AOPWiki (Key Event)
type: Resource
description: International repository of Adverse Outcome Pathways.
is part of: bioregistry
0000005: 3
has provider formatter: https://aopwiki.org/events/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://aopwiki.org/events/
0000027: https://aopwiki.org/events/3
0000029: aop.events

Representing Content in RDF
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
keyword: rdf
0000005: Content
has provider formatter: http://www.w3.org/2011/content#$1
is deprecated: false
has URI prefix: http://www.w3.org/2011/content#
0000027: Content
0000029: cnt

Higher Education Resource Types
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A controlled vocbualry of higher education resource types
is part of: bioregistry
git repository: hcrt
keyword: educational resources
keyword: educational science
0000005: simulation
has provider formatter: https://w3id.org/kim/hcrt/$1
is deprecated: false
has URI prefix: https://w3id.org/kim/hcrt/
0000027: simulation
0000029: kim.hcrt

NFDI Core Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A mid-level ontology for representing metadata related to NFDI resources, including individuals, organizations, projects, data portals, and more
is part of: bioregistry
git repository: nfdicore
keyword: ontology
0000005: 0000106
has provider formatter: https://nfdi.fiz-karlsruhe.de/ontology/NFDI_$1
has local unique identifier pattern: ^\d+$
0000010: nfdicore.owl
is deprecated: false
has responsible: Jörg Waitelonis
has URI prefix: https://nfdi.fiz-karlsruhe.de/ontology/NFDI_
0000027: NFDI_0000106
0000029: nfdi.core

International Fungal Working Group Fungal Barcoding.
type: Resource
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.
is part of: bioregistry
0000005: 2224
has provider formatter: http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: https://bioregistry.io/fbol:
0000029: fbol

Vlado Dancik

Isabel Sá-Correia

Genome Aggregation Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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).
is part of: bioregistry
0000005: 1-55516888-G-GA
has provider formatter: https://gnomad.broadinstitute.org/variant/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-6025-0015
has URI prefix: https://gnomad.broadinstitute.org/variant/
0000027: 1-55516888-G-GA
0000029: gnomad

Semantic Sensor Network Ontology
type: Resource
contributor: https://orcid.org/0000-0002-1595-3213
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.
is part of: bioregistry
git repository: sdw-sosa-ssn
keyword: methods
keyword: ontology
keyword: imaging
keyword: resource metadata
keyword: engineering
keyword: w3c rec
keyword: nfdi4chem
keyword: monitoring
keyword: iot
keyword: remote sensing
keyword: nfdi4ing
keyword: sensor data
keyword: web of things
keyword: ess
0000005: hasProperty
has provider formatter: http://www.w3.org/ns/ssn/$1
0000010: ssn.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-3884-3420
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.w3.org/ns/ssn/
0000027: hasProperty
0000029: ssn

Leafsnap
type: Resource
description: identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide
is part of: bioregistry
0000005: Amelanchier laevis
has provider formatter: http://leafsnap.com/species/$1/
is deprecated: false
has URI prefix: https://bioregistry.io/leafsnap:
0000029: leafsnap

Gavin H. Thomas

Mid-level Energy Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: midlevel-energy-ontology
keyword: ontology
0000005: 01013
has local unique identifier pattern: ^\d+$
0000010: midlevel-energy.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-3722-5564
0000029: meno

CranioMaxilloFacial ontology
type: Resource
description: This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/CMF_$1
is deprecated: true
has responsible: https://orcid.org/0000-0001-5889-4463
has URI prefix: http://purl.obolibrary.org/obo/CMF_
0000029: cmf

NCBI Protein
type: Resource
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.
is part of: bioregistry
keyword: protein
0000005: CAA71118.1
has provider formatter: https://www.ncbi.nlm.nih.gov/protein/$1
has local unique identifier pattern: ^\w+_?\d+(.\d+)?$
is deprecated: false
has URI prefix: https://www.ncbi.nlm.nih.gov/protein/
0000026: 02meqm098
0000027: CAA71118.1
0000029: ncbiprotein

MatrixDB
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: Sucharitha Balu
description: MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides
is part of: bioregistry
keyword: interaction
keyword: biology
keyword: small molecule
keyword: protein
0000005: MULT_4_VAR1_bovine
has provider formatter: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort
is deprecated: false
0000018: complexportal
has responsible: https://orcid.org/0000-0001-9263-1851
has URI prefix: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort
0000027: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort
0000029: matrixdb

Generative Artificial Intelligence Delegation Taxonomy
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: gaidet-declaration
keyword: attribution
keyword: ontology
keyword: contributor roles
keyword: artificial intelligence
keyword: delegation
0000005: 0000001
has provider formatter: https://w3id.org/gaidet/$1
has local unique identifier pattern: ^\d{7}$
0000010: gaidet.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-5067-4498
has URI prefix: https://w3id.org/gaidet/
0000027: https://w3id.org/gaidet/0000001
0000029: gaidet

Biological Imaging Methods Ontology
type: Resource
description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
is part of: bioregistry
git repository: Biological Imaging Methods Ontology
keyword: life science
keyword: obo
keyword: ontology
keyword: imaging
keyword: experiment
keyword: assay
keyword: biomedical science
0000005: 00000268
has provider formatter: http://purl.obolibrary.org/obo/FBbi_$1
has local unique identifier pattern: ^\d+$
0000010: fbbi.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-8841-5870
has alternative prefix: FBbi
has URI prefix: http://purl.obolibrary.org/obo/FBbi_
0000027: FBbi_00000268
0000029: fbbi

NIH RePORTER
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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.
is part of: bioregistry
keyword: ontology
keyword: bibliometrics
keyword: project
0000005: 10343835
has provider formatter: https://reporter.nih.gov/project-details/$1
has local unique identifier pattern: ^\d+$
0000010: nihreporter.project.owl.gz
is deprecated: false
has responsible: NIH Reporter Helpdesk
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://reporter.nih.gov/project-details/
0000027: https://reporter.nih.gov/project-details/10343835
0000029: nihreporter.project

Richard Cyganiak

Thin-film Solar Cells Ontology
type: Resource
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.
is part of: bioregistry
git repository: autoperosol
keyword: physics
keyword: mechanical engineering, energy technology
keyword: fairmat
keyword: material science
0000005: 00000001
has provider formatter: https://purl.archive.org/tfsco/TFSCO_$1
is deprecated: false
has URI prefix: https://purl.archive.org/tfsco/TFSCO_
0000027: TFSCO_00000001
0000029: tfsco

Activity Streams
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: Sumir Pandit
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.
is part of: bioregistry
keyword: semantic web
keyword: social media
0000005: Add
has provider formatter: http://www.w3.org/ns/activitystreams#$1
is deprecated: false
has alternative prefix: as
has URI prefix: http://www.w3.org/ns/activitystreams#
0000027: Add
0000029: ac

BioLegend
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: BioLegend is a life sciences supply vendor.
is part of: bioregistry
keyword: life sciences
keyword: reagents
keyword: antibodies
keyword: vendor
keyword: assays
0000005: 3403
has provider formatter: https://www.biolegend.com/Default.aspx
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.biolegend.com/Default.aspx
0000027: https://www.biolegend.com/Default.aspx
0000029: biolegend

FAIRmat Resources
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes for ontologies relevant for [FAIRmat](https://www.nfdi.de/consortia-fairmat).
has part: nexus
has part: Thin-film Solar Cells Ontology
has part: A vocabulary for the catalysis disciplines
has part: bfo

Bibliographic Framework Initiative Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: bibframe-ontology
keyword: computer science
keyword: subject agnostic
keyword: miscellaneous
keyword: ontology
0000005: DescriptionLevel
has provider formatter: http://id.loc.gov/ontologies/bibframe/$1
0000010: bibframe.rdf
is deprecated: false
has responsible: Kirk Hess
has alternative prefix: bf
has URI prefix: http://id.loc.gov/ontologies/bibframe/
0000027: DescriptionLevel
0000029: bibframe

NIAID ChemDB ID
type: Resource
description: ID in NIAID ChemDB
is part of: bioregistry
0000005: 059486
has provider formatter: http://chemdb.niaid.nih.gov/CompoundDetails.aspx
is deprecated: false
has URI prefix: http://chemdb.niaid.nih.gov/CompoundDetails.aspx
0000027: http://chemdb.niaid.nih.gov/CompoundDetails.aspx
0000029: niaid.chemdb

Minimum Anformation About a Phylogenetic Analysis Ontology
type: Resource
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.
is part of: bioregistry
git repository: miapa
keyword: phylogeny
keyword: phylogenetics
keyword: life science
keyword: obo
keyword: ontology
0000005: 0000010
has provider formatter: http://purl.obolibrary.org/obo/MIAPA_$1
has local unique identifier pattern: ^\d{7}$
0000010: miapa.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9107-0714
has URI prefix: http://purl.obolibrary.org/obo/MIAPA_
0000027: MIAPA_0000010
0000029: miapa

Jade Hotchkiss

An SKOS extension for representing statistical classifications
type: Resource
description: An extension of SKOS for representaion of nomenclatures
is part of: bioregistry
keyword: vocabularies
0000005: belongsTo
is deprecated: false
0000029: xkos

Allergome
type: Resource
contributor: Sumir Pandit
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.
is part of: bioregistry
keyword: biomedical science
keyword: allergen
keyword: health science
keyword: medicine
keyword: life science
0000005: 1948
has provider formatter: http://www.allergome.org/script/dettaglio.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9137-1442
has URI prefix: http://www.allergome.org/script/dettaglio.php
0000027: http://www.allergome.org/script/dettaglio.php
0000029: allergome

Type of Address
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Identifies the type of address entered as contact information for an individual or an organization.
is part of: bioregistry
0000005: Mailing
has provider formatter: https://vocabularies.cessda.eu/vocabulary/TypeOfAddress#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/TypeOfAddress#code_
0000026: 015em2733
0000027: code Mailing
0000029: ddi.typeofaddress

Abdelmoneim Amer Desouki

NFDI4Ing Resources
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes for ontologies relevant for the NFDI4Ing
has part: tib.mat
has part: PROV Namespace
has part: Building Topology Ontology
has part: physh
has part: Ontology of units of Measure
has part: The Software Description Ontology
has part: Smart Applications Reference ontology
has part: tib.n0
has part: m4i
has part: Building Ontology
has part: modsci
has part: General Process Ontology
has part: tib.dr
has part: fiesta.iot
has part: System capabilities, operating ranges, and survival ranges ontology
has part: saref.auto
has part: cora
has part: IOC: Internet of Construction Ontology
has part: Vehicle Signal Specification Core Ontology
has part: saref.lift
has part: saref.building
has part: saref.environment
has part: tib.mdo
has part: bfo
has part: commoncoreontology
has part: bonsai
has part: pmdco
has part: MobiVoc Open Mobility Vocabulary 1.1.4
has part: tib.sto
has part: Basisklassifikation
has part: kit.mtxx
has part: dogont
has part: ListDB Ontology
has part: edam
has part: idsa
has part: tib.mdv
has part: MathModDB Ontology
has part: SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain
has part: fair
has part: The COnCEPT upper-level Design Ontology
has part: sio
has part: swo
has part: tib.hpont
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: tib.bo
has part: cc
has part: findex.bau
has part: saref.water
has part: Code Ontology
has part: sweet
has part: infosecsos
has part: Open Energy Ontology
has part: dcterms
has part: tib.lis
has part: Data Use Ontology
has part: wot.td
has part: afo
has part: SAREF4EE: the EEbus/Energy@home extension of SAREF
has part: FINDEX Raum
has part: tribain
has part: Unified Astronomy Thesaurus
has part: battinfo
has part: DFG Classification of Subject Areas Ontology - 2020-2024
has part: digitalconstruction.lifecycle
has part: sh
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: sepio
has part: rosetta
has part: Elementary Multiperspective Material Ontology

Madeline Iseminger

Minimum Information about a Biosynthetic Gene Cluster data repository
type: Resource
contributor: Mitja M. Zdouc
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.
is part of: bioregistry
git repository: mibig-json
0000005: BGC0000001
has provider formatter: https://mibig.secondarymetabolites.org/go/$1
has local unique identifier pattern: ^BGC\d{7}$
is deprecated: false
has responsible: Kai Blin
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://mibig.secondarymetabolites.org/go/
0000027: BGC0000001
0000029: mibig

SWEET Ontology Phenomena Planetary Climate
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Planetary Climate
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
keyword: planetary climate
0000005: Climate
has provider formatter: http://sweetontology.net/phenPlanetClimate/$1
is deprecated: false
has alternative prefix: sophpc
has URI prefix: http://sweetontology.net/phenPlanetClimate/
0000027: Climate
0000029: sweet.phpc

Oryzabase Mutant
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.
is part of: bioregistry
0000005: 21393
has provider formatter: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/
0000027: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/21393
0000029: oryzabase.mutant

MIRIAM Legacy Registry Identifier
type: Resource
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.
is part of: bioregistry
keyword: registry
0000005: 00100005
has provider formatter: https://resolver.api.identifiers.org/resolveMirId/$1
has local unique identifier pattern: ^001\d{5}$
is deprecated: true
has URI prefix: https://resolver.api.identifiers.org/resolveMirId/
0000027: https://resolver.api.identifiers.org/resolveMirId/00100005
0000029: miriam.resource

LNCipedia
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A comprehensive compendium of human long non-coding RNAs
is part of: bioregistry
keyword: life science
0000005: SNHG3
is deprecated: false
has responsible: Pieter Mestdagh
0000029: lncipedia

Data Catalog
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web
is part of: bioregistry
git repository: dxwg
keyword: computer science
keyword: subject agnostic
keyword: data management
keyword: ess
keyword: ontology
keyword: w3c rec
0000005: Dataset
has provider formatter: http://www.w3.org/ns/dcat#$1
0000010: dcat3
is deprecated: false
has responsible: Kim Durante
has URI prefix: http://www.w3.org/ns/dcat#
0000027: Dataset
0000029: dcat

ExAC Gene
type: Resource
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.
is part of: bioregistry
0000005: ENSG00000169174
has provider formatter: http://exac.broadinstitute.org/gene/$1
has local unique identifier pattern: ^ENSG\d{11}$
is deprecated: false
has URI prefix: http://exac.broadinstitute.org/gene/
0000027: ENSG00000169174
0000029: exac.gene

AntiFam
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: AntiFam is a database of spurious protein families that have been removed from Pfam due to incorrect hidden Markov model prediction.
is part of: bioregistry
0000005: ANF00001
has provider formatter: https://www.ebi.ac.uk/interpro/entry/antifam/$1
has local unique identifier pattern: ^ANF\d{5}$
is deprecated: false
has responsible: Alex Bateman
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.ebi.ac.uk/interpro/entry/antifam/
0000027: ANF00001
0000029: antifam

Publons publication
type: Resource
description: identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID)
is part of: bioregistry
0000005: 18466622
has provider formatter: https://publons.com/publon/$1
is deprecated: false
has URI prefix: https://publons.com/publon/
0000027: https://publons.com/publon/18466622
0000029: publons.publication

NCBI Probe database Public registry of nucleic acid reagents
type: Resource
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 part of: bioregistry
keyword: nucleotide
0000005: 1000000
has provider formatter: https://www.ncbi.nlm.nih.gov/probe/
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: https://www.ncbi.nlm.nih.gov/probe/
0000027: https://www.ncbi.nlm.nih.gov/probe/
0000029: dbprobe

Austrian Library Network
type: Resource
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.
is part of: bioregistry
0000005: AC00963334
has provider formatter: https://permalink.obvsg.at/$1
has local unique identifier pattern: ^AC[0-9]{8}$
is deprecated: false
has URI prefix: https://permalink.obvsg.at/
0000027: https://permalink.obvsg.at/AC00963334
0000029: obv

EcoliWiki from EcoliHub
type: Resource
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
keyword: ontology and terminology
keyword: genomics
keyword: bioinformatics
keyword: life science
0000005: aaeA
has provider formatter: http://ecoliwiki.net/colipedia/index.php/$1:Gene
has local unique identifier pattern: ^[A-Za-z0-9-]+$
is deprecated: false
has responsible: Peter D. Karp
has URI prefix: https://bioregistry.io/ecoliwiki:
0000027: aaeA:Gene
0000029: ecoliwiki

E-cyanobacterium entity
type: Resource
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.
is part of: bioregistry
0000005: 23
has provider formatter: https://www.e-cyanobacterium.org/bcs/entity/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.e-cyanobacterium.org/bcs/entity/
0000027: https://www.e-cyanobacterium.org/bcs/entity/23
0000029: ecyano.entity

Federica Quaglia

NIF Standard Ontology: Investigations
type: Resource
contributor: Tom Gillespie
description: NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis.
is part of: bioregistry
git repository: NIF-Ontology
keyword: data analysis
keyword: funding agencies
0000005: 90901
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Tom Gillespie
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXINV
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_inv_
0000027: nlx inv 90901
0000029: nlx.inv

Agronomy Ontology
type: Resource
contributor: Sumir Pandit
description: AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities
is part of: bioregistry
git repository: agro
keyword: farming systems research
keyword: agriculture
keyword: agronomy
keyword: plant breeding
keyword: cropping systems
keyword: obo
keyword: ontology
keyword: dataplant
0000005: 00020007
has provider formatter: http://purl.obolibrary.org/obo/AGRO_$1
has local unique identifier pattern: ^\d{8}$
0000010: agro.owl
is deprecated: false
depends on: pato
depends on: Ontology for Biomedical Investigations
depends on: go
depends on: xco
depends on: Plant Ontology
depends on: NCBI Taxonomy
depends on: bfo
depends on: to
depends on: foodon
depends on: peco
depends on: Environment Ontology
depends on: ro
depends on: Information Artifact Ontology
depends on: Units of measurement ontology
has responsible: https://orcid.org/0000-0002-8461-9745
has URI prefix: http://purl.obolibrary.org/obo/AGRO_
0000027: AGRO_00020007
0000029: agro

Morpheus model repository
type: Resource
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 part of: bioregistry
0000005: M0001
has provider formatter: https://morpheus.gitlab.io/models/$1
has local unique identifier pattern: ^M[0-9]{4,}$
is deprecated: false
has URI prefix: https://morpheus.gitlab.io/models/
0000027: M0001
0000029: morpheus

Information Artifact Ontology
type: Resource
description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.
is part of: bioregistry
git repository: IAO
keyword: nfdi4ing
keyword: reagent
keyword: biomedical science
keyword: experimental measurement
keyword: subject agnostic
keyword: data identity and mapping
keyword: data management
keyword: fair data spaces
keyword: study design
keyword: obo
keyword: ontology
keyword: assay
keyword: nfdi4chem
keyword: knowledge and information systems
keyword: drug report
0000005: 0000030
has provider formatter: http://purl.obolibrary.org/obo/IAO_$1
has local unique identifier pattern: ^\d{7}$
0000010: iao.owl
is deprecated: false
0000018: mcro
0000018: maxo
0000018: labo
0000018: An ontology of core ecological entities
0000018: Agronomy Ontology
0000018: pco
0000018: Performance Summary Display Ontology
0000018: fovt
0000018: Clytia hemisphaerica Development and Anatomy Ontology
0000018: xpo
0000018: Data Use Ontology
0000018: Environmental conditions, treatments and exposures ontology
has responsible: https://orcid.org/0000-0002-2999-0103
has URI prefix: http://purl.obolibrary.org/obo/IAO_
0000027: IAO_0000030
0000029: iao

SWEET Ontology Realm Astrophysical
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Astrophysical
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: astrophysical
keyword: realm
0000005: ActiveRegion
has provider formatter: http://sweetontology.net/realmAstroStar/$1
is deprecated: false
has alternative prefix: soreaas
has URI prefix: http://sweetontology.net/realmAstroStar/
0000027: ActiveRegion
0000029: sweet.reaas

ClinVar Record
type: Resource
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.
is part of: bioregistry
0000005: RCV000033555.3
has provider formatter: http://www.ncbi.nlm.nih.gov/clinvar/$1
has local unique identifier pattern: ^RCV\d+(\.\d+)?$
is deprecated: false
has URI prefix: http://www.ncbi.nlm.nih.gov/clinvar/
0000027: RCV000033555.3
0000029: clinvar.record

Database of homology-derived secondary structure of proteins
type: Resource
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.
is part of: bioregistry
keyword: sequence
keyword: protein
keyword: clustering
0000005: 102l
has provider formatter: ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2
has local unique identifier pattern: ^\w{4}$
is deprecated: false
has responsible: https://orcid.org/0000-0001-6059-6270
has URI prefix: https://bioregistry.io/hssp:
0000027: 102l.hssp.bz2
0000029: hssp

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

Chris Hunter

Mathematical modeling ontology
type: Resource
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.
is part of: bioregistry
git repository: mamo-ontology
keyword: systems biology
keyword: obo
keyword: ontology
keyword: computational biology
keyword: mathematics
0000005: 0000026
has provider formatter: http://bioportal.bioontology.org/ontologies/MAMO/
has local unique identifier pattern: ^\d{7}$
0000010: mamo.owl
is deprecated: true
has responsible: Nicolas Le Novere
has URI prefix: http://bioportal.bioontology.org/ontologies/MAMO/
0000027: http://bioportal.bioontology.org/ontologies/MAMO/
0000029: mamo

Meng LIU

EDAM Data
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: edamontology
keyword: ontology
0000005: 1664
has provider formatter: http://edamontology.org/data_$1
has local unique identifier pattern: ^\d+$
0000010: EDAM.obo
is deprecated: false
has responsible: Matúš Kalaš
has URI prefix: http://edamontology.org/data_
0000027: data 1664
0000029: edam.data

Library of Congress Subject Headings
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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: lcsh.genreforms
is part of: bioregistry
keyword: subject agnostic
0000005: nb2018006591
has provider formatter: https://id.loc.gov/authorities/$1
has local unique identifier pattern: ^\w{1,2}\d{8,10}$
is deprecated: false
has alternative prefix: lcnafid
has alternative prefix: lcnaf
has URI prefix: https://id.loc.gov/authorities/
0000027: nb2018006591
0000029: lcsh

SWEET Ontology Human Technology Readiness
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Technology Readiness
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: technology readiness
0000005: TRL
has provider formatter: http://sweetontology.net/humanTechReadiness/$1
is deprecated: false
has alternative prefix: sohutr
has URI prefix: http://sweetontology.net/humanTechReadiness/
0000027: TRL
0000029: sweet.hutr

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.
is part of: bioregistry
keyword: nfdi4ing
keyword: computer science
keyword: civil engineering
keyword: digital planning and construction
keyword: fid baudigital
0000005: Goal
has provider formatter: http://bimerr.iot.linkeddata.es/def/key-performance-indicator#$1
is deprecated: false
has URI prefix: http://bimerr.iot.linkeddata.es/def/key-performance-indicator#
0000027: Goal
0000029: kpio

MeSH 2013
type: Resource
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.
is part of: bioregistry
0000005: 17165
has provider formatter: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi
has local unique identifier pattern: ^[A-Za-z0-9]+$
0000011: mesh
is deprecated: false
has URI prefix: https://bioregistry.io/mesh.2013:
0000027: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi
0000029: mesh.2013

has local unique identifier pattern
type: Property
description: The pattern for identifiers in the given resource
domain: Resource
range: string
equivalent property: hasRegexPattern
equivalent property: P1793
equivalent property: identifierPattern

ClinGen Clinical Genome Expert Panel
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: 40135
has provider formatter: https://clinicalgenome.org/affiliation/$1/
is deprecated: false
has URI prefix: https://bioregistry.io/clingen.affiliation:
0000027: https://clinicalgenome.org/affiliation/40135/
0000029: clingen.affiliation

Provisional Cell Ontology
type: Resource
description: Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties.
is part of: bioregistry
git repository: provisional cell ontology
keyword: annotation
keyword: sequencing assay
keyword: cell
keyword: anatomy
keyword: life science
keyword: obo
keyword: cell biology
keyword: ontology
keyword: single-cell multimodal omics
keyword: omics
keyword: phenomics
keyword: transcriptomics
0000005: 0011124
has provider formatter: http://purl.obolibrary.org/obo/PCL_$1
has local unique identifier pattern: ^\d{7}$
0000010: pcl.owl
is deprecated: false
depends on: pato
depends on: Uber Anatomy Ontology
depends on: go
depends on: so
depends on: Chemical Entities of Biological Interest
depends on: pr
depends on: NCBI Taxonomy
depends on: bfo
depends on: cl
depends on: ro
depends on: OBO Metadata Ontology
depends on: nbo
has responsible: David Osumi-Sutherland
has URI prefix: http://purl.obolibrary.org/obo/PCL_
0000027: PCL_0011124
0000029: pcl

Code Ontology
type: Resource
description: An ontology that represents object-oriented programming languages
is part of: bioregistry
git repository: parser
keyword: engineering
keyword: nfdi4ing
0000005: AccessModifier
has provider formatter: http://rdf.webofcode.org/woc/$1
is deprecated: false
has URI prefix: http://rdf.webofcode.org/woc/
0000027: AccessModifier
0000029: woc.ontology

PSI Extended File Format
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
keyword: ontology
0000005: 0001011
has provider formatter: https://biopragmatics.github.io/providers/peff/$1
has local unique identifier pattern: ^\d{7}$
0000010: psi-peff-OBSOLETE-DO NOT USE.obo
is deprecated: true
has URI prefix: https://biopragmatics.github.io/providers/peff/
0000027: https://biopragmatics.github.io/providers/peff/0001011
0000029: peff

SWEET Ontology State Energy Flux
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Energy Flux
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state energy flux
0000005: AClass
has provider formatter: http://sweetontology.net/stateEnergyFlux/$1
is deprecated: false
has alternative prefix: sostef
has URI prefix: http://sweetontology.net/stateEnergyFlux/
0000027: AClass
0000029: sweet.stef

Frédéric Bastian
label: Frederic Bastian

MeSH 2012
type: Resource
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.
is part of: bioregistry
0000005: 17186
has provider formatter: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi
has local unique identifier pattern: ^[A-Za-z0-9]+$
0000011: mesh
is deprecated: false
has URI prefix: https://bioregistry.io/mesh.2012:
0000027: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi
0000029: mesh.2012

Assembling the Fungal Tree of Life - Category
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Categories in the AFTOL database
is part of: bioregistry
0000005: 229
has provider formatter: https://aftol.umn.edu/glossary
is deprecated: false
has responsible: David J. McLaughlin
has URI prefix: https://aftol.umn.edu/glossary
0000027: https://aftol.umn.edu/glossary
0000029: aftol.category

Interlinking Ontology for Biological Concepts
type: Resource
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".
is part of: bioregistry
git repository: IOBC
keyword: ontology
0000005: 200906038218908385
has provider formatter: http://purl.jp/bio/4/id/$1
0000010: iobc.owl
is deprecated: false
has responsible: Tatsuya Kushida
has URI prefix: http://purl.jp/bio/4/id/
0000027: http://purl.jp/bio/4/id/200906038218908385
0000029: iobc

MolBiC Compound
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
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.
is part of: bioregistry
0000005: CP0041613
has provider formatter: https://molbic.idrblab.net/data/compound/details/$1
has local unique identifier pattern: ^CP\d+$
is deprecated: false
has responsible: Feng Zhu
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://molbic.idrblab.net/data/compound/details/
0000027: CP0041613
0000029: molbic.compound

OrthoDB
type: Resource
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
is part of: bioregistry
keyword: dna
keyword: protein
keyword: life science
keyword: eukaryotic
0000005: Q9P0K8
has provider formatter: http://cegg.unige.ch/orthodb/results
has local unique identifier pattern: ^\w+$
0000011: uniprot
is deprecated: false
has responsible: Evgeny M Zdobnov
has URI prefix: http://cegg.unige.ch/orthodb/results
0000027: http://cegg.unige.ch/orthodb/results
0000029: orthodb

GESIS Knowledge Graph Schema
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Predicates that are used to construct the GESIS Knowledge Graph, a bibliometrics KG.
is part of: bioregistry
keyword: nfdi
keyword: data schema
0000005: linkContext
has provider formatter: https://data.gesis.org/gesiskg/schema/$1
is deprecated: false
has URI prefix: https://data.gesis.org/gesiskg/schema/
0000027: linkContext
0000029: gesiskg

Basisklassifikation
type: Resource
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).
is part of: bioregistry
keyword: fid move
keyword: earth sciences
keyword: nfdi4ing
keyword: ess
keyword: digital planning and construction
keyword: fid baudigital
0000005: 0
has provider formatter: http://uri.gbv.de/terminology/bk/$1
is deprecated: false
has URI prefix: http://uri.gbv.de/terminology/bk/
0000027: http://uri.gbv.de/terminology/bk/0
0000029: tib.bk

TOKU-E Cell-culture Database
type: Resource
description: Cell line databases/resources
is part of: bioregistry
has provider formatter: http://cell-lines.toku-e.com/Cell-Lines_$1.html
is deprecated: true
has URI prefix: https://bioregistry.io/tokue:
0000029: tokue

Mass spectrometry ontology
type: Resource
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.
is part of: bioregistry
git repository: psi-ms-CV
keyword: nfdi4chem
keyword: obo
keyword: ontology
keyword: dataplant
keyword: chemistry
keyword: nfdi4cat
0000005: 1000560
has provider formatter: http://purl.obolibrary.org/obo/MS_$1
has local unique identifier pattern: ^\d{7}$
0000010: ms.owl
is deprecated: false
depends on: pato
depends on: Units of measurement ontology
has responsible: Joshua Klein
has URI prefix: http://purl.obolibrary.org/obo/MS_
0000027: MS_1000560
0000029: ms

SNP to Transcription Factor Binding Sites
type: Resource
description: SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome.
is part of: bioregistry
0000005: rs11603840
has provider formatter: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi
has local unique identifier pattern: ^rs[0-9]+$
0000011: dbSNP Reference SNP number
is deprecated: false
has URI prefix: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi
0000027: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi
0000029: snp2tfbs

FAIRSharing
type: https://bioregistry.io/schema/#0000002
description: A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies.
has part: FAIRsharing.b084yh
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has part: FAIRsharing.IziuCK
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has part: FAIRsharing.1413b5
has part: FAIRsharing.ay74mj
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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
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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

NFDI Knowledge Graph Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Assigns identifiers to knowledge graphs (KGs) that are used and/or maintained within any NFDI consortium.
is part of: bioregistry
git repository: kgi4nfdi registry data
keyword: knowledge graph
0000005: KGR1
has provider formatter: http://kgi.services.base4nfdi.de/entity/$1
has local unique identifier pattern: ^KGR\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5190-1867
has URI prefix: http://kgi.services.base4nfdi.de/entity/
0000027: KGR1
0000029: nfdi.kgi

Catalytic Site Atlas
type: Resource
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
keyword: enzyme
keyword: structure
keyword: life science
0000005: 1a05
has provider formatter: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php
has local unique identifier pattern: ^[0-9][A-Za-z0-9]{3}$
is deprecated: true
has responsible: Nicholas Furnham
has URI prefix: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php
0000027: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php
0000029: csa

E-cyanobacterium Experimental Data
type: Resource
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 part of: bioregistry
0000005: 18
has provider formatter: https://www.e-cyanobacterium.org/experiments-repository/
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.e-cyanobacterium.org/experiments-repository/
0000027: https://www.e-cyanobacterium.org/experiments-repository/
0000029: ecyano.experiment

CAS Registry Number
type: Resource
description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.
is part of: bioregistry
keyword: chemical
keyword: chemical entity
keyword: structure
keyword: physical chemistry
0000005: 50-00-0
has provider formatter: https://commonchemistry.cas.org/detail
has local unique identifier pattern: ^\d{1,7}\-\d{2}\-\d$
is deprecated: false
has responsible: Andrea Jacobs
has alternative prefix: CAS_RN
has alternative prefix: CASID
has alternative prefix: cas_id
has alternative prefix: SECONDARY_CAS_RN
has URI prefix: https://commonchemistry.cas.org/detail
0000027: https://commonchemistry.cas.org/detail
0000029: cas

Toxin and Toxin Target Database
type: Resource
description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.
is part of: bioregistry
keyword: biomedical science
keyword: molecule
keyword: life science
keyword: protein
0000005: T3D0001
has provider formatter: http://www.t3db.org/toxins/$1
has local unique identifier pattern: ^T3D\d+$
is deprecated: false
has responsible: David Wishart
has URI prefix: http://www.t3db.org/toxins/
0000027: T3D0001
0000029: t3db

Selventa Chemicals
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Selventa legacy chemical namespace used with the Biological Expression Language
is part of: bioregistry
keyword: selventa
keyword: chemistry
keyword: bel
0000005: A0001
has provider formatter: https://biopragmatics.github.io/providers/schem/$1
has local unique identifier pattern: ^A\d{4}$
is deprecated: false
has responsible: Natalie L Catlett
has URI prefix: https://biopragmatics.github.io/providers/schem/
0000027: A0001
0000029: schem

OpenCitations Meta Identifier
type: Resource
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.
is part of: bioregistry
0000005: br/0601
has provider formatter: https://w3id.org/oc/meta/$1
has local unique identifier pattern: ^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$
is deprecated: false
has URI prefix: https://w3id.org/oc/meta/
0000027: https://w3id.org/oc/meta/br/0601
0000029: omid

Plant Ontology
type: Resource
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 part of: bioregistry
git repository: plant-ontology
keyword: life science
keyword: ess
keyword: classification
keyword: obo
keyword: ontology
keyword: expression data
keyword: dataplant
keyword: botany
keyword: earth sciences
keyword: life cycle
keyword: structure
keyword: whole plant development stage
keyword: plant anatomy
0000005: 0009089
has provider formatter: http://purl.obolibrary.org/obo/PO_$1
has local unique identifier pattern: ^\d+$
0000010: po.owl
is deprecated: false
0000018: Genomic Epidemiology Ontology
0000018: gallont
0000018: An ontology of core ecological entities
0000018: Agronomy Ontology
0000018: Environment Ontology
has responsible: https://orcid.org/0000-0002-1005-8383
has URI prefix: http://purl.obolibrary.org/obo/PO_
0000027: PO_0009089
0000029: po

Quantities, Units, Dimensions, and Types Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.
is part of: bioregistry
git repository: qudt-public-repo
keyword: ontology
keyword: quantification
keyword: unit
keyword: experimental measurement
keyword: measurement systems
keyword: methods
keyword: units
0000005: baseDimensionEnumeration
has provider formatter: http://qudt.org/schema/qudt#$1
0000010: qudt.owl
is deprecated: false
has responsible: Unknown
has URI prefix: http://qudt.org/schema/qudt#
0000027: baseDimensionEnumeration
0000029: qudt

Global Proteome Machine Database
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.
is part of: bioregistry
keyword: bioinformatics
keyword: proteomics
0000005: GPM32310002988
has provider formatter: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1
has local unique identifier pattern: ^GPM\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-5782-1000
has URI prefix: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=
0000027: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002988
0000029: gpmdb

PDB ligand
type: Resource
description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands.
is part of: bioregistry
keyword: structure
keyword: interaction
keyword: small molecule
keyword: protein
0000005: TRQ
has provider formatter: http://www.rcsb.org/ligand/$1
has local unique identifier pattern: ^[A-Za-z0-9]+$
is deprecated: false
has alternative prefix: PDB_CHEM_ID
has URI prefix: http://www.rcsb.org/ligand/
0000027: TRQ
0000029: pdb.ligand

depends on
type: Property
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

Common Science and Technology Resources
type: Resource
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 part of: bioregistry
keyword: centrally registered identifier
keyword: open science
keyword: subject agnostic
0000005: 31253.11.sciencedb.j00001.00123
has provider formatter: https://cstr.cn/$1
has local unique identifier pattern: ^\w{5}\.\d{2}\..*$
is deprecated: false
has URI prefix: https://cstr.cn/
0000027: 31253.11.sciencedb.j00001.00123
0000029: cstr

GeoNames Ontology
type: Resource
description: An ontology used to enable annotating geospatial semantic information to entities in GeoNames
is part of: bioregistry
0000005: parentFeature
is deprecated: false
0000029: geonames.ontology

DockerHub User
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A user in DockerHub
is part of: bioregistry
0000005: cthoyt
has provider formatter: https://hub.docker.com/u/$1
is deprecated: false
has URI prefix: https://hub.docker.com/u/
0000027: cthoyt
0000029: dockerhub.user

David Brodbelt

SWEET Ontology Realm Landform
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Landform
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: landform
keyword: realm
0000005: CentralCreekCrater
has provider formatter: http://sweetontology.net/realmLandform/$1
is deprecated: false
has alternative prefix: soreal
has URI prefix: http://sweetontology.net/realmLandform/
0000027: CentralCreekCrater
0000029: sweet.real

Harshvardhan J. Pandit

MGnify Project
type: Resource
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.
is part of: bioregistry
0000005: ERP004492
has provider formatter: https://www.ebi.ac.uk/metagenomics/projects/$1
has local unique identifier pattern: ^[A-Z]+[0-9]+$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/metagenomics/projects/
0000027: ERP004492
0000029: mgnify.proj

Fetal Calf Serum-Free Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Cell line databases/resources
is part of: bioregistry
0000005: 240-17-488-3-4-12
has provider formatter: https://fcs-free.org/fcs-database
is deprecated: false
has URI prefix: https://fcs-free.org/fcs-database
0000027: https://fcs-free.org/fcs-database
0000029: fcsfree

European Commission Participant Identification Code (PIC)
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An identifier for an organization
is part of: bioregistry
0000005: 881104060
has provider formatter: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/org-details/$1
has local unique identifier pattern: ^\d{9}$
is deprecated: false
has URI prefix: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/org-details/
0000027: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/org-details/881104060
0000029: europe.pic

MOSAiC Ontology
type: Resource
contributor: https://orcid.org/0000-0001-5705-7831
description: An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io).
is part of: bioregistry
git repository: sem-prov-ontologies
keyword: ontology
0000005: 00005643
has provider formatter: https://purl.dataone.org/odo/MOSAIC_$1
has local unique identifier pattern: ^\d{8}$
0000010: MOSAiC.owl
is deprecated: false
has responsible: Bryce Mecum
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://purl.dataone.org/odo/MOSAIC_
0000027: MOSAIC_00005643
0000029: mosaic

Molecular Modeling Database
type: Resource
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.
is part of: bioregistry
keyword: dna
keyword: small molecule
keyword: protein
keyword: structure
keyword: interaction
0000005: 50885
has provider formatter: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi
has local unique identifier pattern: ^\d{1,5}$
is deprecated: false
has responsible: Siqian He
has URI prefix: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi
0000027: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi
0000029: mmdb

Kidney and Urinary Pathway Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
0000005: 0001009
has local unique identifier pattern: ^\d{7}$
is deprecated: true
0000018: cl
0000029: kupo

CIViC Molecular Profile
type: Resource
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.
is part of: bioregistry
0000005: 559
has provider formatter: https://civicdb.org/links/molecular_profile/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: Malachi Griffith
has alternative prefix: civic.molecularprofile
has URI prefix: https://civicdb.org/links/molecular_profile/
0000027: https://civicdb.org/links/molecular_profile/559
0000029: civic.mpid

Human Intermediate Filament Database
type: Resource
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 part of: bioregistry
keyword: genome
0000005: NM_006262
has provider formatter: http://www.interfil.org/details.php
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.interfil.org/details.php
0000027: http://www.interfil.org/details.php
0000029: interfil

GenBank
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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).
is part of: bioregistry
keyword: genomics
keyword: dna
keyword: bioinformatics
keyword: virology
keyword: functional genomics
keyword: transcriptomics
keyword: epidemiology
keyword: metagenomics
keyword: data management
0000005: U49845
has provider formatter: https://www.ncbi.nlm.nih.gov/nucleotide/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-2497-3427
has URI prefix: https://www.ncbi.nlm.nih.gov/nucleotide/
0000027: U49845
0000029: genbank

David Gloriam

Ligand-Gated Ion Channel database
type: Resource
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.
is part of: bioregistry
keyword: gene
keyword: sequence
keyword: protein
0000005: 5HT3Arano
has provider formatter: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php
has local unique identifier pattern: ^\w+$
is deprecated: true
has URI prefix: https://bioregistry.io/lgic:
0000027: 5HT3Arano.php
0000029: lgic

Hazardous Substances Data Bank
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: 5621
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/
0000027: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/5621
0000029: hsdb

Systems Biology Ontology
type: Resource
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.
is part of: bioregistry
git repository: SBO
keyword: earth sciences
keyword: life sciences, biology
keyword: molecular interaction
keyword: systems biology
keyword: ess
keyword: obo
keyword: ontology
keyword: pathway
keyword: nfdi4cat
0000005: 0000485
has provider formatter: http://purl.obolibrary.org/obo/SBO_$1
has local unique identifier pattern: ^\d{7}$
0000010: sbo.owl
is deprecated: false
0000018: scdo
0000018: Process Chemistry Ontology
has responsible: Rahuman Sheriff
has URI prefix: http://purl.obolibrary.org/obo/SBO_
0000027: SBO_0000485
0000029: sbo

Units of measurement ontology
type: Resource
description: Ontology of standardized units
is part of: bioregistry
git repository: unit-ontology
keyword: nfdi4chem
keyword: earth sciences
keyword: life sciences, biology
keyword: unit
keyword: nfdi4ing
keyword: life science
keyword: ess
keyword: units
keyword: physics
keyword: obo
keyword: measurement
keyword: ontology
keyword: mathematics
keyword: dataplant
0000005: 0000080
has provider formatter: http://purl.obolibrary.org/obo/UO_$1
has local unique identifier pattern: ^\d{7}$
0000010: uo.owl
is deprecated: false
0000018: Mass spectrometry ontology
0000018: rbo
0000018: scdo
0000018: Agronomy Ontology
has responsible: George Gkoutos
has URI prefix: http://purl.obolibrary.org/obo/UO_
0000027: UO_0000080
0000029: uo

Basic Access Control ontology
type: Resource
description: The Basic Access Control ontology describes how access rights (access control) are defined on the web.
is part of: bioregistry
keyword: api
0000005: Access
has provider formatter: http://www.w3.org/ns/auth/acl#$1
is deprecated: false
has URI prefix: http://www.w3.org/ns/auth/acl#
0000027: Access
0000029: acl

Feature Type Thesaurus
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: 273
has provider formatter: https://apps.usgs.gov/thesaurus/term-simple.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://apps.usgs.gov/thesaurus/term-simple.php
0000027: https://apps.usgs.gov/thesaurus/term-simple.php
0000029: ftt

NONCODE v3
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.
is part of: bioregistry
keyword: expression
keyword: nucleotide
0000005: 377550
has provider formatter: http://www.noncode.org/NONCODERv3/ncrna.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: https://orcid.org/0000-0001-6049-8347
has URI prefix: http://www.noncode.org/NONCODERv3/ncrna.php
0000027: http://www.noncode.org/NONCODERv3/ncrna.php
0000029: noncodev3

Pfam protein clan
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Higher order grouping of Pfam families
is part of: bioregistry
keyword: ontology
keyword: protein family
0000005: CL0192
has provider formatter: https://www.ebi.ac.uk/interpro/set/pfam/$1
has local unique identifier pattern: ^CL\d+$
0000010: pfam.clan.owl
is deprecated: false
has responsible: Alex Bateman
has URI prefix: https://www.ebi.ac.uk/interpro/set/pfam/
0000027: CL0192
0000029: pfam.clan

International Nonproprietary Names
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.
is part of: bioregistry
0000005: fluticasone
has provider formatter: https://mednet-communities.net/inn/db/ViewINN.aspx
is deprecated: false
has alternative prefix: INN_ID
has URI prefix: https://mednet-communities.net/inn/db/ViewINN.aspx
0000027: https://mednet-communities.net/inn/db/ViewINN.aspx
0000029: inn

Chris Stoeckert

Planarian Phenotype Ontology
type: Resource
description: Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.
is part of: bioregistry
git repository: planarian-phenotype-ontology
keyword: obo
keyword: ontology
0000005: 0000001
has provider formatter: http://purl.obolibrary.org/obo/PLANP_$1
has local unique identifier pattern: ^\d+$
0000010: planp.owl
is deprecated: false
depends on: ro
depends on: pato
depends on: plana
depends on: go
has responsible: Sofia Robb
has URI prefix: http://purl.obolibrary.org/obo/PLANP_
0000027: PLANP_0000001
0000029: planp

DragonDB Allele
type: Resource
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information.
is part of: bioregistry
0000005: cho
has provider formatter: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
has local unique identifier pattern: ^\w+$
is deprecated: true
has URI prefix: https://bioregistry.io/dragondb.allele:
0000027: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
0000029: dragondb.allele

Unified Astronomy Thesaurus
type: Resource
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.
is part of: bioregistry
git repository: UAT
keyword: nfdi4ing
keyword: ess
keyword: astronomy and astrophysics
keyword: physics
0000005: 0
has provider formatter: http://astrothesaurus.org/uat/$1
is deprecated: false
has URI prefix: http://astrothesaurus.org/uat/
0000027: http://astrothesaurus.org/uat/0
0000029: uat

NFDI4Culture Metadata API
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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).
is part of: bioregistry
keyword: digital humanities
keyword: organization
keyword: generic
0000005: E4330
has provider formatter: https://nfdi4culture.de/id/$1
is deprecated: false
has URI prefix: https://nfdi4culture.de/id/
0000027: E4330
0000029: nfdi4culture.id

Ontology of Physics for Biology
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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.
is part of: bioregistry
keyword: ontology
keyword: concentration
keyword: structure
keyword: life science
keyword: physics
0000005: 00573
has provider formatter: https://bioportal.bioontology.org/ontologies/OPB/
has local unique identifier pattern: ^\d+$
0000010: opb.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-2390-6572
has URI prefix: https://bioportal.bioontology.org/ontologies/OPB/
0000027: https://bioportal.bioontology.org/ontologies/OPB/
0000029: opb

Protein covalent bond
type: Resource
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.
is part of: bioregistry
keyword: small molecule
keyword: protein
keyword: structure
keyword: obo
keyword: ontology
0000005: AA0001
has provider formatter: https://proteininformationresource.org/cgi-bin/resid
has local unique identifier pattern: ^AA\d{4}$
is deprecated: true
has responsible: 0000-0002-4131-735X
has URI prefix: https://proteininformationresource.org/cgi-bin/resid
0000027: https://proteininformationresource.org/cgi-bin/resid
0000029: resid

BioSystems
type: Resource
contributor: Tim Vandermeersch
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.
is part of: bioregistry
keyword: biology
keyword: pathways
keyword: systems biology
keyword: molecules
0000005: 001
has provider formatter: https://www.ncbi.nlm.nih.gov/biosystems/$1
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: https://orcid.org/0000-0003-1516-0712
has URI prefix: https://www.ncbi.nlm.nih.gov/biosystems/
0000027: https://www.ncbi.nlm.nih.gov/biosystems/001
0000029: biosystems

Justin Whorton

OMIM Phenotypic Series
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: https://orcid.org/0000-0002-8719-7760
description: A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.
is part of: bioregistry
keyword: phenotype
keyword: ontology
keyword: disease
0000005: 214100
has provider formatter: https://omim.org/MIM:PS$1
has local unique identifier pattern: ^\d+$
0000010: omim.ps.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1780-5230
has alternative prefix: mim.ps
has alternative prefix: MIMPS
has alternative prefix: PS
has alternative prefix: OMIMPS
has URI prefix: https://omim.org/MIM:PS
0000027: MIM:PS214100
0000029: omim.ps

Michal Linial

Bioregistry Metaregistry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Bioregistry's meta-registry
is part of: bioregistry
keyword: registry
keyword: metaregistry
keyword: data science
keyword: data integration
0000005: miriam
has provider formatter: https://bioregistry.io/metaregistry/$1
is deprecated: false
has responsible: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://bioregistry.io/metaregistry/
0000027: miriam
0000029: bioregistry.registry

Digical Object Container Identifier
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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: cultural heritage
keyword: publishing
keyword: bibliometrics
keyword: digital humanities
0000005: 20.500.14351/5a7cdd09d9b65bc39697
has provider formatter: https://docid.africapidalliance.org/docid/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-3910-2691
has alternative prefix: DOCiD
has URI prefix: https://docid.africapidalliance.org/docid/
0000026: 02y9nww90
0000027: https://docid.africapidalliance.org/docid/20.500.14351/5a7cdd09d9b65bc39697
0000029: docid

National Drug Data File
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: medicinal chemistry
keyword: chemical entity
keyword: biomedical science
keyword: drug
keyword: ontology
0000005: 002678
has provider formatter: http://purl.bioontology.org/ontology/NDDF/$1
has local unique identifier pattern: ^\d{6}$
is deprecated: false
has responsible: First DataBank Customer Support
has URI prefix: http://purl.bioontology.org/ontology/NDDF/
0000027: http://purl.bioontology.org/ontology/NDDF/002678
0000029: nddf

SWEET Ontology Phenomena Energy
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Energy
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
keyword: energy
0000005: ActiveSolarEnergy
has provider formatter: http://sweetontology.net/phenEnergy/$1
is deprecated: false
has alternative prefix: sophen
has URI prefix: http://sweetontology.net/phenEnergy/
0000027: ActiveSolarEnergy
0000029: sweet.phen

Potato Ontology
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 Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
is part of: bioregistry
git repository: Crop-Ontology
keyword: botany
keyword: agriculture
keyword: life science
keyword: ontology
keyword: plant phenotypes and traits
keyword: phenotype
0000005: 0000106
has provider formatter: https://cropontology.org/rdf/CO_330:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 330.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_330:
0000027: CO 330:0000106
0000029: co_330

Science Data Discovery Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
git repository: sddo
keyword: ontology
0000005: 3000001
has provider formatter: http://purl.obolibrary.org/obo/SDDO_$1
has local unique identifier pattern: ^\d{7}$
0000010: sddo.owl
is deprecated: false
has responsible: Daniel C. Berrios
has URI prefix: http://purl.obolibrary.org/obo/SDDO_
0000027: SDDO_3000001
0000029: sddo

Health Surveillance Ontology
type: Resource
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.
is part of: bioregistry
git repository: HSO
keyword: obo
keyword: ontology
0000005: 0000062
has provider formatter: http://purl.obolibrary.org/obo/HSO_$1
has local unique identifier pattern: ^\d{7}$
0000010: hso.owl
is deprecated: false
depends on: Ontology for Biomedical Investigations
depends on: Uber Anatomy Ontology
depends on: NCBI Taxonomy
depends on: bfo
depends on: ro
has responsible: Fernanda Dorea
has URI prefix: http://purl.obolibrary.org/obo/HSO_
0000027: HSO_0000062
0000029: hso

Célia Michotey

Protein Structural Change Database
type: Resource
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.
is part of: bioregistry
keyword: life science
0000005: 051
has provider formatter: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: 0000-0001-9090-668X
has URI prefix: https://bioregistry.io/pscdb:
0000027: 051.html
0000029: pscdb

Robert Court

BioTools
type: Resource
description: BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.
is part of: bioregistry
git repository: biotoolsregistry
keyword: biomedical science
keyword: biology
keyword: bioinformatics
0000005: bioregistry
has provider formatter: https://bio.tools/$1
has local unique identifier pattern: ^[-A-Za-z0-9\_]*$
is deprecated: false
has responsible: Hans Ienasescu
has URI prefix: https://bio.tools/
0000027: bioregistry
0000029: biotools

PyPI
type: Resource
description: The Python Package Index (PyPI) is a repository for Python packages.
is part of: bioregistry
0000005: numpy
has provider formatter: https://pypi.org/project/$1
has local unique identifier pattern: ^[a-zA-Z_][a-zA-Z0-9\-_]+$
is deprecated: false
has URI prefix: https://pypi.org/project/
0000027: numpy
0000029: pypi

Sensor, Observation, Sample, and Actuator Ontology
type: Resource
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.
is part of: bioregistry
git repository: sdw
keyword: engineering
keyword: environment
keyword: nfdi4chem
keyword: iot
keyword: nfdi4ing
keyword: ess
0000005: FeatureOfInterest
has provider formatter: http://www.w3.org/ns/sosa/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-3884-3420
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.w3.org/ns/sosa/
0000027: FeatureOfInterest
0000029: sosa

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.
is part of: bioregistry
keyword: genomics
0000005: CNBG_0001
has provider formatter: https://fungidb.org/fungidb/app/record/gene/$1
has local unique identifier pattern: ^[A-Za-z_0-9]+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7591-0020
has URI prefix: https://fungidb.org/fungidb/app/record/gene/
0000027: CNBG_0001
0000029: fungidb

BDGP insertion DB
type: Resource
description: BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.
is part of: bioregistry
keyword: sequence
keyword: gene
0000005: KG09531
has provider formatter: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5251-1801
has URI prefix: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php
0000027: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php
0000029: bdgp.insertion

Ontology of Biological Attributes
type: Resource
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.
is part of: bioregistry
git repository: bio-attribute-ontology
keyword: biology
keyword: obo
keyword: ontology
0000005: 0000001
has provider formatter: http://purl.obolibrary.org/obo/OBA_$1
has local unique identifier pattern: ^(VT)?\d{7}$
0000010: oba.owl
is deprecated: false
0000018: fovt
has responsible: https://orcid.org/0000-0002-6601-2165
has URI prefix: http://purl.obolibrary.org/obo/OBA_
0000027: OBA_0000001
0000029: oba

Unified Code for Units of Measure
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: ucum
keyword: subject agnostic
keyword: data identity and mapping
keyword: measurement
keyword: general & upper
keyword: unit
0000005: aBq
has provider formatter: https://units-of-measurement.org/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-3884-3420
has URI prefix: https://units-of-measurement.org/
0000027: aBq
0000029: ucum

Simplified molecular-input line-entry system
type: Resource
contributor: Nisha Sharma
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: opensmiles
keyword: chemistry
keyword: metabolomics
keyword: molecular entity
keyword: lipidomics
keyword: data analysis
keyword: structure
keyword: life science
keyword: bioinformatics
0000005: CC2(C)C\1CCC(C)/C=C/12
has provider formatter: https://www.simolecule.com/cdkdepict/depict/bow/svg
has local unique identifier pattern: ^[A-Za-z0-9+\-\*=#$:().>/\\\[\]%]+$
is deprecated: false
has responsible: Tim Vandermeersch
has URI prefix: https://bioregistry.io/smiles:
0000029: smiles

Open Tree of Life
type: Resource
contributor: https://orcid.org/0000-0003-2699-3066
description: Identifier for an entity in open tree of life
is part of: bioregistry
0000005: 3905431
has provider formatter: https://tree.opentreeoflife.org/taxonomy/browse
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://tree.opentreeoflife.org/taxonomy/browse
0000027: https://tree.opentreeoflife.org/taxonomy/browse
0000029: otol

LINCS Protein
type: Resource
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.
is part of: bioregistry
0000005: 200282
has provider formatter: https://lincs.hms.harvard.edu/db/proteins/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://lincs.hms.harvard.edu/db/proteins/
0000027: https://lincs.hms.harvard.edu/db/proteins/200282
0000029: lincs.protein

NASA Open Science Data Repository Hardware
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for hardware used in experiments that investigate biological and health responses of terrestrial life to spaceflight
is part of: bioregistry
0000005: 2011
has provider formatter: https://osdr.nasa.gov/bio/repo/data/hardware/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8542-2389
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://osdr.nasa.gov/bio/repo/data/hardware/
0000027: https://osdr.nasa.gov/bio/repo/data/hardware/2011
0000029: nasaosdr.hardware

GlycoMapsDB
type: Resource
description: A database of GlycoMaps containing 2585 conformational maps.
is part of: bioregistry
keyword: small molecule
0000005: 6819
has provider formatter: http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php
0000027: http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php
0000029: glycomapsdb

DBLP author ID
type: Resource
description: identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/)
is part of: bioregistry
0000005: 199/2168
has provider formatter: https://dblp.org/pid/$1
is deprecated: false
has URI prefix: https://dblp.org/pid/
0000027: https://dblp.org/pid/199/2168
0000029: dblp.author

Docker Hub repository
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Docker repository hosted on Docker Hub
is part of: bioregistry
0000005: gitea/gitea
has provider formatter: https://hub.docker.com/r/$1
is deprecated: false
has URI prefix: https://hub.docker.com/r/
0000027: gitea
0000029: dockerhub.repo

Vaccine Adjuvant Compendium
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: vaccines
keyword: immunology
keyword: biology
0000005: 15
has provider formatter: https://vac.niaid.nih.gov/view
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://vac.niaid.nih.gov/view
0000027: https://vac.niaid.nih.gov/view
0000029: vac

NameRXN
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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).
is part of: bioregistry
keyword: reactions
keyword: chemistry
keyword: text mining
0000005: 4.2.78
is deprecated: false
has responsible: https://orcid.org/0000-0001-6279-4481
0000029: namerxn

GND-Ontologie
type: Resource
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.
is part of: bioregistry
keyword: catalogs
keyword: computer science
keyword: ess
0000005: AdministrativeUnit
has provider formatter: https://d-nb.info/standards/elementset/gnd#$1
is deprecated: false
has URI prefix: https://d-nb.info/standards/elementset/gnd#
0000027: AdministrativeUnit
0000029: gndo

European Nucleotide Archive
type: Resource
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 part of: bioregistry
keyword: biodiversity
keyword: genomics
keyword: dna
keyword: bioinformatics
keyword: functional genomics
keyword: transcriptomics
keyword: metagenomics
keyword: data management
0000005: BN000065
has provider formatter: https://www.ebi.ac.uk/ena/browser/view/$1
has local unique identifier pattern: ^[A-Z]+[0-9]+(\.\d+)?$
is deprecated: false
has canonical: International Nucleotide Sequence Database Collaboration (INSDC) Run
has responsible: Guy Cochrane
has alternative prefix: ena
has URI prefix: https://www.ebi.ac.uk/ena/browser/view/
0000026: 02catss52
0000027: BN000065
0000029: ena.embl

EuroVoc
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
keyword: food
keyword: employment
keyword: international relations
keyword: political science
keyword: forest management
keyword: economics
keyword: social science
keyword: geography
keyword: business administration
keyword: social policy
keyword: transport
keyword: energy engineering
keyword: agriculture
keyword: linguistics
keyword: public finance
keyword: transportation planning
keyword: trade
keyword: environmental science
keyword: fisheries science
0000005: 1837
has provider formatter: http://eurovoc.europa.eu/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Publications Office of the European Union
has URI prefix: http://eurovoc.europa.eu/
0000027: http://eurovoc.europa.eu/1837
0000029: eurovoc

Orientation of Proteins in Realistic Lipid Membranes
type: Resource
contributor: 0009-0008-8406-631X
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.
is part of: bioregistry
0000005: 6782
has provider formatter: https://oprlm.org/proteins/$1
has local unique identifier pattern: ^\d*$
is deprecated: false
has responsible: https://orcid.org/0000-0001-5642-6041
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://oprlm.org/proteins/
0000027: https://oprlm.org/proteins/6782
0000029: oprlm

SWEET Ontology Representation Data Service Geospatial
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Service Geospatial
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation data service geospatial
0000005: Buffer
has provider formatter: http://sweetontology.net/reprDataServiceGeospatial/$1
is deprecated: false
has alternative prefix: sorepdsg
has URI prefix: http://sweetontology.net/reprDataServiceGeospatial/
0000027: Buffer
0000029: sweet.repdsg

TAIR Protein
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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
is part of: bioregistry
keyword: protein
0000005: 1009107926
has provider formatter: https://www.arabidopsis.org/protein
has local unique identifier pattern: ^\d{10}$
is deprecated: false
has responsible: 0000-0003-3871-858X
has URI prefix: https://www.arabidopsis.org/protein
0000027: https://www.arabidopsis.org/protein
0000029: tair.protein

Viral Bioinformatics Resource Center
type: Resource
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.
is part of: bioregistry
0000005: 35742
has provider formatter: http://vbrc.org/gene_detail.asp
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: http://vbrc.org/gene_detail.asp
0000027: http://vbrc.org/gene_detail.asp
0000029: vbrc

MetaboLights Compound
type: Resource
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.
is part of: bioregistry
0000005: MTBLS1
has provider formatter: https://www.ebi.ac.uk/metabolights/$1
has local unique identifier pattern: ^MTBL[CS]\d+$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/metabolights/
0000027: MTBLS1
0000029: metabolights

Protocol for Web Description Resources (POWDER) Schema
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Underlying schema for POWDER
is part of: bioregistry
0000005: tag
has provider formatter: http://www.w3.org/2007/05/powder#$1
is deprecated: false
has URI prefix: http://www.w3.org/2007/05/powder#
0000027: tag
0000029: wdr

LifeWatch Metadata Catalogue
type: Resource
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
has provider formatter: https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/$1
has local unique identifier pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$
is deprecated: false
has URI prefix: https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/
0000029: lw

RNACentral
type: Resource
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.
is part of: bioregistry
git repository: RNAcentral
keyword: bioinformatics
keyword: biology
0000005: URS0000759CF4
has provider formatter: https://rnacentral.org/rna/$1
has local unique identifier pattern: ^URS[0-9A-F]{10}(\_\d+)?$
is deprecated: false
has responsible: Blake A Sweeney
has alternative prefix: LNCRNADB
has URI prefix: https://rnacentral.org/rna/
0000027: URS0000759CF4
0000029: rnacentral

SWEET Ontology Phenomena Hydrosphere
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Hydrosphere
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: hydrosphere
keyword: phenomena
0000005: BaseFlow
has provider formatter: http://sweetontology.net/phenHydro/$1
is deprecated: false
has alternative prefix: sophhy
has URI prefix: http://sweetontology.net/phenHydro/
0000027: BaseFlow
0000029: sweet.phhy

Lyle Burgoon

PharmGKB Variant
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: SNPs and other variants that can be mapped to dbSNP.
is part of: bioregistry
keyword: snp
keyword: genetic variation
keyword: ontology
keyword: genetic variant
0000005: PA166156302
has provider formatter: https://www.pharmgkb.org/variant/$1
has local unique identifier pattern: ^PA\d+$
0000010: pharmgkb.variant.owl
is deprecated: false
has responsible: Teri E Klein
has URI prefix: https://www.pharmgkb.org/variant/
0000027: PA166156302
0000029: pharmgkb.variant

Sebastian Lobentanzer

Proteomics Identification Database Ontology
type: Resource
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.
is part of: bioregistry
git repository: pride-ontology
keyword: ontology
keyword: protein
keyword: proteomics
0000005: 0000006
has provider formatter: http://purl.obolibrary.org/obo/PRIDE_$1
has local unique identifier pattern: ^\d{7}$
0000010: pride.owl
is deprecated: true
has responsible: Yasset Perez-Riverol
has URI prefix: http://purl.obolibrary.org/obo/PRIDE_
0000027: PRIDE_0000006
0000029: pride

Fungal Nomenclature and Species Bank
type: Resource
contributor: https://orcid.org/0000-0003-0066-1717
description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.
is part of: bioregistry
keyword: classification
keyword: biology
keyword: taxonomy
0000005: 349124
has provider formatter: https://www.mycobank.org/page/Name%20details%20page/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9370-4677
has URI prefix: https://www.mycobank.org/page/Name%20details%20page/
0000027: https://www.mycobank.org/page/Name%20details%20page/349124
0000029: mycobank

NFDI4DS Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
0000005: City
has provider formatter: https://nfdi.fiz-karlsruhe.de/nfdi4dso/$1
is deprecated: false
has URI prefix: https://nfdi.fiz-karlsruhe.de/nfdi4dso/
0000027: City
0000029: nfdi4dso

DrugBank Salts
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.
is part of: bioregistry
keyword: chemical
keyword: salt
keyword: compound
keyword: small molecule
0000005: DBSALT001211
has provider formatter: https://go.drugbank.com/salts/$1
has local unique identifier pattern: ^DBSALT\d{6}$
is deprecated: false
has responsible: David Wishart
has URI prefix: https://go.drugbank.com/salts/
0000027: DBSALT001211
0000029: drugbank.salt

BiGG Metabolite
type: Resource
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.
is part of: bioregistry
keyword: small molecule
keyword: chemical
keyword: metabolite
keyword: compound
keyword: ontology
0000005: 12dgr161
has provider formatter: http://bigg.ucsd.edu/models/universal/metabolites/$1
has local unique identifier pattern: ^[a-z_A-Z0-9]+(\[[c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y]\])?$
0000010: bigg.metabolite.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-1238-1499
has URI prefix: http://bigg.ucsd.edu/models/universal/metabolites/
0000027: 12dgr161
0000029: bigg.metabolite

DFG Classification of Subject Areas Ontology - 2020-2024
type: Resource
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.
is part of: bioregistry
git repository: DFG-Fachsystematik-Ontology
keyword: digital planning and construction
keyword: fid baudigital
keyword: fid move
keyword: educational resources
keyword: open educational resources
keyword: open educational resource
keyword: nfdi4ing
keyword: educational science
keyword: ess
0000005: 101-01
has provider formatter: https://w3id.org/dfgfo/2020/$1
is deprecated: false
has URI prefix: https://w3id.org/dfgfo/2020/
0000027: https://w3id.org/dfgfo/2020/101-01
0000029: dfg.fo

Character Set
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Standard set of characters upon which many character encodings are based (Wikipedia).
is part of: bioregistry
0000005: ASCII
has provider formatter: https://vocabularies.cessda.eu/vocabulary/CharacterSet#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/CharacterSet#code_
0000026: 015em2733
0000027: code ASCII
0000029: ddi.characterset

UNESCO Thesaurus
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
keyword: political science
keyword: education science
keyword: culture
keyword: subject agnostic
keyword: communication science
0000005: 585
has provider formatter: http://vocabularies.unesco.org/thesaurus/concept$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://vocabularies.unesco.org/thesaurus/concept
0000027: concept585
0000029: unesco.thesaurus

PharmGKB Disease
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.
is part of: bioregistry
keyword: ontology
keyword: pharmacogenomics
0000005: PA447218
has provider formatter: http://www.pharmgkb.org/disease/$1
has local unique identifier pattern: ^PA\d+$
0000010: pharmgkb.disease.owl
is deprecated: false
has responsible: Teri E Klein
has URI prefix: http://www.pharmgkb.org/disease/
0000027: PA447218
0000029: pharmgkb.disease

Gramene protein
type: Resource
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.
is part of: bioregistry
0000005: 78073
has provider formatter: http://www.gramene.org/db/protein/protein_search
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: GR_PROTEIN
has URI prefix: http://www.gramene.org/db/protein/protein_search
0000027: http://www.gramene.org/db/protein/protein_search
0000029: gramene.protein

Joe Flack

LRMI Educational Audience Role Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A concept scheme that defines the primary or intended roles of the audience (beneficiary) of the resource being described.
is part of: bioregistry
git repository: lrmi
keyword: open educational resource
keyword: learning resource
0000005: mentor
has provider formatter: http://purl.org/dcx/lrmi-vocabs/educationalAudienceRole/$1
is deprecated: false
has URI prefix: http://purl.org/dcx/lrmi-vocabs/educationalAudienceRole/
0000027: mentor
0000029: lrmi.educationalaudiencerole

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.
is part of: bioregistry
0000005: 2555646
has provider formatter: http://www.ubio.org/browser/details.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: http://www.ubio.org/browser/details.php
0000027: http://www.ubio.org/browser/details.php
0000029: ubio.namebank

CiteXplore
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes.
is part of: bioregistry
0000005: C6155
has provider formatter: https://europepmc.org/article/CTX/$1
is deprecated: false
has alternative prefix: CTX
has URI prefix: https://europepmc.org/article/CTX/
0000027: C6155
0000029: citexplore

has reviewer
type: Property
description: The reviewer of a prefix
domain: Resource
range: Person

mirTarBase
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: life science
0000005: MIRT000002
has provider formatter: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php
has local unique identifier pattern: ^MIRT\d{6}$
is deprecated: true
has responsible: Sheng-Da Hsu
has URI prefix: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php
0000027: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php
0000029: mirtarbase

Biomarker Ontology
type: Resource
description: An application ontology that represents comprehensive knowledge involving a variety of fields of medical and biological aspects.
is part of: bioregistry
git repository: BiomarkerOntology
keyword: obo
keyword: ontology
0000005: 0000006
has provider formatter: http://purl.obolibrary.org/obo/BMONT_$1
0000010: bmont.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9896-3531
has URI prefix: http://purl.obolibrary.org/obo/BMONT_
0000029: bmont

Emotion Ontology
type: Resource
description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.
is part of: bioregistry
git repository: emotion-ontology
keyword: ontology
keyword: biomedical science
keyword: mental health
keyword: emotion process
keyword: obo
0000005: 000204
has provider formatter: http://purl.obolibrary.org/obo/MFOEM_$1
has local unique identifier pattern: ^\d{6}$
0000010: mfoem.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-3469-4923
has URI prefix: http://purl.obolibrary.org/obo/MFOEM_
0000027: MFOEM_000204
0000029: mfoem

Cell Cycle Ontology
type: Resource
description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.
is part of: bioregistry
keyword: obo
keyword: ontology
keyword: genomics
keyword: proteomics
keyword: molecular_function
keyword: functional genomics
keyword: cell cycle
keyword: cell
keyword: life science
0000005: 0000003
has provider formatter: https://www.ebi.ac.uk/ols4/ontologies/cco/terms
has local unique identifier pattern: ^\w+$
0000010: cco.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1171-9876
has URI prefix: https://www.ebi.ac.uk/ols4/ontologies/cco/terms
0000027: https://www.ebi.ac.uk/ols4/ontologies/cco/terms
0000029: cco

NCI Metathesaurus
type: Resource
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.
is part of: bioregistry
0000005: C0026339
has provider formatter: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp
has local unique identifier pattern: ^C\d+$
is deprecated: false
has URI prefix: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp
0000026: 040gcmg81
0000027: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp
0000029: ncim

Gene Normal Tissue Expression
type: Resource
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 part of: bioregistry
keyword: gene expression
0000005: GC06M052656
has provider formatter: http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl
is deprecated: false
has URI prefix: https://bioregistry.io/genecards.genenote:
0000027: http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl
0000029: genecards.genenote

Bioregistry Collections
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Manually curated collections of resources stored in the bioregistry
is part of: bioregistry
keyword: registry
0000005: 0000001
has provider formatter: https://bioregistry.io/collection/$1
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://bioregistry.io/collection/
0000027: Resources mentioned in "Sharing biological data: why, when, and how"
0000029: bioregistry.collection

Arabidopsis Information Portal
type: Resource
description: Website with general information about Arabidopsis and functionalities such as a genomic viewer
is part of: bioregistry
0000005: AT5G05330
has provider formatter: https://www.arabidopsis.org/servlets/TairObject
has local unique identifier pattern: ^AT.G[0-9]{5}$
is deprecated: false
has responsible: Vivek Krishnakuma
has URI prefix: https://www.arabidopsis.org/servlets/TairObject
0000027: https://www.arabidopsis.org/servlets/TairObject
0000029: araport

Kinetic Data of RNA-Protein Interactions Database
type: Resource
contributor: https://orcid.org/0009-0009-3402-8013
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.
is part of: bioregistry
keyword: kinetics
keyword: rna-protein interactions
keyword: binding affinity
0000005: 183
has provider formatter: http://www.kdbirp.aiddlab.com/detail/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: 0000-0002-1397-554X
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.kdbirp.aiddlab.com/detail/
0000027: http://www.kdbirp.aiddlab.com/detail/183
0000029: kdbirp

EST database maintained at the NCBI.
type: Resource
description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
is part of: bioregistry
keyword: life science
keyword: dna
keyword: bioinformatics
0000005: BP100000
has provider formatter: https://www.ncbi.nlm.nih.gov/nucest/$1
has local unique identifier pattern: ^([A-Z]+)?\d+(\.\d+)?$
is deprecated: false
has responsible: Todd M Lowe
has URI prefix: https://www.ncbi.nlm.nih.gov/nucest/
0000027: BP100000
0000029: dbest

Peruvian Clinical Trial Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
0000005: 046-19
has provider formatter: https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp
has local unique identifier pattern: ^\d+-\d+(-[A-Z])?$
is deprecated: false
has URI prefix: https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp
0000027: https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp
0000029: repec

SoyBase
type: Resource
description: SoyBase is a repository for curated genetics, genomics and related data resources for soybean.
is part of: bioregistry
keyword: development
keyword: plant breeding
keyword: comparative genomics
keyword: spider
keyword: life science
keyword: obo
keyword: phenotype
keyword: agriculture
0000005: BARC-013845-01256
has provider formatter: https://legacy.soybase.org/sbt/search/search_results.php
has local unique identifier pattern: ^\w+(\-)?\w+(\-)?\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-2787-3955
has URI prefix: https://legacy.soybase.org/sbt/search/search_results.php
0000027: https://legacy.soybase.org/sbt/search/search_results.php
0000029: soybase

SIDER Side Effect
type: Resource
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.
is part of: bioregistry
0000005: C0017565
has provider formatter: http://sideeffects.embl.de/se/$1
has local unique identifier pattern: ^C\d+$
0000011: umls
is deprecated: false
has URI prefix: http://sideeffects.embl.de/se/
0000027: http://sideeffects.embl.de/se/C0017565
0000029: sider.effect

Vehicle Signal Specification Core Ontology
type: Resource
description: This ontology describes the car's attributes, branches and signals defined in the Vehicle Signal Specification.
is part of: bioregistry
keyword: fid move
keyword: nfdi4ing
keyword: traffic engineering
0000005: VehicleProperty
has provider formatter: https://github.com/w3c/vsso-core#$1
is deprecated: false
has URI prefix: https://github.com/w3c/vsso-core#
0000027: VehicleProperty
0000029: vssocore

Category Scheme Election Studies
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Category Scheme Election Studies provides the ability to categorize election studies at the question and/or variable level.
is part of: bioregistry
0000005: 01
has provider formatter: https://vocabularies.cessda.eu/vocabulary/KategorienschemaWahlstudien#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/KategorienschemaWahlstudien#code_
0000026: 018afyw53
0000027: code_01
0000029: gesis.kategorienschemawahlstudien

FuncBase Human
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 human data.
is part of: bioregistry
0000005: 119514
has provider formatter: http://func.mshri.on.ca/human/genes/list_functional_scores/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://func.mshri.on.ca/human/genes/list_functional_scores/
0000027: http://func.mshri.on.ca/human/genes/list_functional_scores/119514
0000029: funcbase.human

Human Disease Ontology
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.
is part of: bioregistry
git repository: HumanDiseaseOntology
keyword: ontology
keyword: human
keyword: infection process
keyword: disease
keyword: disease course
keyword: genetic disorder
keyword: biomedical science
keyword: disease phenotype
keyword: mental health
keyword: life science
keyword: classification
keyword: obo
0000005: 0110974
has provider formatter: http://purl.obolibrary.org/obo/DOID_$1
has local unique identifier pattern: ^\d+$
0000010: doid.owl
is deprecated: false
0000018: scdo
0000018: Cell Line Ontology
has responsible: Lynn Schriml
has alternative prefix: do
has URI prefix: http://purl.obolibrary.org/obo/DOID_
0000027: DOID_0110974
0000029: doid

has provider formatter
type: Property
description: The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved.
domain: Resource
range: string
equivalent property: accessPattern
equivalent property: hasPrimaryUriPattern
equivalent property: P1630

NCBI Data Repository Service
type: Resource
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 part of: bioregistry
has provider formatter: https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/$1
has local unique identifier pattern: ^[0-9a-fA-F]{32}$
is deprecated: false
has URI prefix: https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/
0000029: ncbidrs

Melek Chaouch

Yam Ontology
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 Yam Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
is part of: bioregistry
git repository: Crop-Ontology
keyword: life science
keyword: food
keyword: ontology
keyword: plant phenotypes and traits
keyword: phenotype
keyword: botany
keyword: agriculture
0000005: 0100010
has provider formatter: https://cropontology.org/rdf/CO_343:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 343.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_343:
0000027: CO 343:0100010
0000029: co_343

KEGG Metagenome
type: Resource
description: The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.
is part of: bioregistry
is part of: kegg
keyword: genome
0000005: T30002
has provider formatter: http://www.kegg.jp/entry/$1
has local unique identifier pattern: ^T3\d+$
is deprecated: false
has responsible: 0000-0001-6123-540X
has URI prefix: http://www.kegg.jp/entry/
0000027: T30002
0000029: kegg.metagenome

James Alastair McLaughlin
label: James McLaughlin

Lehrplan Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: school-curriculum-pg
keyword: ontology
0000005: 0000141
has provider formatter: https://w3id.org/lehrplan/ontology/LP_$1
has local unique identifier pattern: ^\d{7}$
0000010: lp.owl
is deprecated: false
has URI prefix: https://w3id.org/lehrplan/ontology/LP_
0000027: LP_0000141
0000029: kim.lp

NFDI4Culture Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The NFDI4Culture Ontology (CTO) is a domain-specific ontology module developed within the Task Area 5 of the NFDI4Culture initiative. (from homepage)
is part of: bioregistry
git repository: nfdi4culture
keyword: other subjects
keyword: architecture
keyword: nfdi4culture
keyword: ontology
0000005: 0001003
has provider formatter: https://nfdi4culture.de/ontology/CTO_$1
has local unique identifier pattern: ^\d{7}$
0000010: cto.owl
is deprecated: false
has URI prefix: https://nfdi4culture.de/ontology/CTO_
0000027: CTO_0001003
0000029: nfdi4culture.cto

Swiss Personalized Health Network Schema
type: Resource
contributor: Deepak Unni
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/).
is part of: bioregistry
git repository: sphn-ontology
keyword: ontology
0000005: Allergy
has provider formatter: https://biomedit.ch/rdf/sphn-ontology/sphn#$1
has local unique identifier pattern: ^\S+$
0000010: sphn rdf schema.owl
is deprecated: false
has responsible: Sabine Oesterle
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://biomedit.ch/rdf/sphn-ontology/sphn#
0000027: Allergy
0000029: sphn

PREMIS 3 Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Ontology for PREMIS 3, the international standard for metadata to support the preservation of digital objects and ensure their long-term usability.
is part of: bioregistry
keyword: catalogs
keyword: nfdi4culture
0000005: Agent
has provider formatter: http://www.loc.gov/premis/rdf/v3/$1
is deprecated: false
has alternative prefix: premis3
has URI prefix: http://www.loc.gov/premis/rdf/v3/
0000027: Agent
0000029: premis

YRC PDR
type: Resource
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.
is part of: bioregistry
keyword: computational biology
keyword: protein
keyword: life science
0000005: 2673500
has provider formatter: http://yeastrc.org/pdr/viewProtein.do
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Michael Riffle
has URI prefix: http://yeastrc.org/pdr/viewProtein.do
0000027: http://yeastrc.org/pdr/viewProtein.do
0000029: yrcpdr

Resources for modeling Open Educational Resources
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
creator: Martin Voigt
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: kim.esv
has part: International Standard Classification of Education, 1997 Edition
has part: OER Schema
has part: vivo
has part: OpenEduHub Education Level
has part: isced2013
has part: kim.educationlevel
has part: kim.amb
has part: International Standard Classification of Education, 2011 Edition
has part: ans.educationlevel
has part: Higher Education Resource Types
has part: kim.conditionsofaccess
has part: lrmi.eduse
has part: KIM School Subjects
has part: ccso
has part: LRMI Interact Type Vocabulary
has part: LRMI Educational Audience Role Vocabulary
has part: t4fs
has part: German University Subject Classification System
has part: Lehrplan Ontology
has part: Library of Congress Format Description Document
has part: schema
has part: kim.schularten
has part: iana.mediatype
has part: UNESCO Thesaurus
has part: edam
has part: adcad
has part: lrmi.alignmenttype
has part: lrmi
has part: lrmi.resourcetype
has part: openeduhub.context
has part: modalia
has part: gsso
has part: CEDS Learning Resource Type

NCI Pathway Interaction Database: Pathway
type: Resource
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.
is part of: bioregistry
keyword: gene
keyword: life science
keyword: ontology
keyword: pathway
keyword: small molecule
keyword: protein
has provider formatter: http://pid.nci.nih.gov/search/pathway_landing.shtml
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$
0000010: pid.pathway.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-5941-3390
has alternative prefix: pid
has URI prefix: http://pid.nci.nih.gov/search/pathway_landing.shtml
0000027: http://pid.nci.nih.gov/search/pathway_landing.shtml
0000029: pid.pathway

SED-ML data format
type: Resource
description: Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).
is part of: bioregistry
0000005: csv
has provider formatter: https://sed-ml.org/urns.html#format:$1
has local unique identifier pattern: ^[a-z]+(\..*?)?$
is deprecated: false
has URI prefix: https://sed-ml.org/urns.html#format:
0000027: format:csv
0000029: sedml.format

PharmGKB Gene
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.
is part of: bioregistry
keyword: pharmacogenomics
keyword: gene
keyword: ontology
0000005: PA131
has provider formatter: http://www.pharmgkb.org/gene/$1
has local unique identifier pattern: ^PA\w+$
0000010: pharmgkb.gene.owl
is deprecated: false
has responsible: Teri E Klein
has URI prefix: http://www.pharmgkb.org/gene/
0000027: PA131
0000029: pharmgkb.gene

Person
type: Class
description: A person
equivalent class: Person

Jingshan Huang

Information Objects Ontology
type: Resource
description: An ontology for the description of information objects.
is part of: bioregistry
keyword: computer science
keyword: digital planning and construction
keyword: fid baudigital
keyword: nfdi4ing
0000005: InformationObject
has provider formatter: http://bimerr.iot.linkeddata.es/def/information-objects#$1
is deprecated: false
has URI prefix: http://bimerr.iot.linkeddata.es/def/information-objects#
0000027: InformationObject
0000029: tib.io

FID BAUdigital Subject Headings
type: Resource
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.
is part of: bioregistry
keyword: nfdi4ing
keyword: architecture
keyword: civil engineering
keyword: digital planning and construction
keyword: fid baudigital
has provider formatter: https://purl.org/fidbaudigital/subjects#$1
is deprecated: false
has URI prefix: https://purl.org/fidbaudigital/subjects#
0000029: fidbaudigital.subject

LiceBase
type: Resource
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
keyword: life science
0000005: EMLSAT00000003403
has provider formatter: https://licebase.org/
has local unique identifier pattern: ^[A-Za-z0-9\-\/]+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4110-0748
has URI prefix: https://licebase.org/
0000027: https://licebase.org/
0000029: licebase

OpenAlex
type: Resource
contributor: https://orcid.org/0000-0002-3012-7446
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 part of: bioregistry
keyword: wikidata
keyword: knowledge graph
0000005: W2741809807
has provider formatter: https://openalex.org/$1
has local unique identifier pattern: ^[WAICV]\d{2,}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-1613-5981
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://openalex.org/
0000027: W2741809807
0000029: openalex

Database of Spatially Interacting Motifs in Proteins
type: Resource
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 part of: bioregistry
keyword: protein
keyword: interaction
0000005: 53784
has provider formatter: http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi
0000027: http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi
0000029: imotdb

Gramene Reference
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Literature references in Gramene
is part of: bioregistry
0000005: 6200
has provider formatter: http://www.gramene.org/db/literature/pub_search
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: gramene.ref
has URI prefix: http://www.gramene.org/db/literature/pub_search
0000027: http://www.gramene.org/db/literature/pub_search
0000029: gramene.reference

UK Higher Education Statistics Agency
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An identifier for institutions in the United Kingdom, used in GRID and ROR.
is part of: bioregistry
keyword: bibliometrics
keyword: institution
0000005: 0154
has local unique identifier pattern: ^\d+$
is deprecated: false
0000029: hesa

ChEMBL Compound
type: Resource
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.
is part of: bioregistry
keyword: ontology
keyword: small molecule
keyword: chemical
keyword: compound
0000005: CHEMBL465070
has provider formatter: https://www.ebi.ac.uk/chembl/compound/inspect/$1
has local unique identifier pattern: ^CHEMBL\d+$
0000010: chembl.compound.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-0294-5484
has URI prefix: https://www.ebi.ac.uk/chembl/compound/inspect/
0000027: CHEMBL465070
0000029: chembl.compound

Cardiovascular Disease Ontology
type: Resource
description: An ontology to describe entities related to cardiovascular diseases
is part of: bioregistry
git repository: CVDO
keyword: cardiovascular disease
keyword: obo
keyword: ontology
keyword: cardiology
0000005: 0000546
has provider formatter: http://purl.obolibrary.org/obo/CVDO_$1
has local unique identifier pattern: ^\d{7}$
0000010: cvdo.owl
is deprecated: false
has responsible: Paul Fabry
has URI prefix: http://purl.obolibrary.org/obo/CVDO_
0000027: CVDO_0000546
0000029: cvdo

PharmGKB 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.
is part of: bioregistry
keyword: drug
keyword: ontology
keyword: pharmacogenomics
0000005: PA448710
has provider formatter: http://www.pharmgkb.org/drug/$1
has local unique identifier pattern: ^PA\d+$
0000010: pharmgkb.drug.owl
is deprecated: false
has responsible: Teri E Klein
has URI prefix: http://www.pharmgkb.org/drug/
0000027: PA448710
0000029: pharmgkb.drug

Animal Genome Size Database
type: Resource
contributor: Sumir Pandit
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.
is part of: bioregistry
keyword: life science
keyword: dna
keyword: genome
0000005: 4779
has provider formatter: http://www.genomesize.com/result_species.php
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.genomesize.com/result_species.php
0000027: http://www.genomesize.com/result_species.php
0000029: agsd

Descriptive Ontology for Linguistic and Cognitive Engineering
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: knowledge and information systems
keyword: linguistics
keyword: computer science
keyword: subject agnostic
keyword: classification
is deprecated: true
0000029: dolce

Supply Chain Operation Reference
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.
is part of: bioregistry
keyword: coypu
keyword: economics
0000005: ActiviateOrArchiveContract
has provider formatter: http://purl.org/eis/vocab/scor#$1
is deprecated: false
has URI prefix: http://purl.org/eis/vocab/scor#
0000027: ActiviateOrArchiveContract
0000029: scor

LigandBox
type: Resource
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.
is part of: bioregistry
0000005: D00001
has provider formatter: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi
has local unique identifier pattern: ^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$
is deprecated: false
has URI prefix: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi
0000027: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi
0000029: ligandbox

International Molecular Exchange
type: Resource
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
keyword: interaction
keyword: molecule
0000005: 19210-3
has provider formatter: https://www.ebi.ac.uk/intact/imex/main.xhtml
has local unique identifier pattern: ^\d+(-\d+)?$
is deprecated: false
has responsible: Sandra Orchard
has URI prefix: https://www.ebi.ac.uk/intact/imex/main.xhtml
0000026: 02catss52
0000027: https://www.ebi.ac.uk/intact/imex/main.xhtml
0000029: imex

NFDI4Health Collection
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Health
has part: bioregistry

AntiBodies Chemically Defined database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: Sumir Pandit
description: The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies
is part of: bioregistry
keyword: immunology
keyword: molecular biology
0000005: AD834
has provider formatter: https://web.expasy.org/abcd/ABCD_$1
is deprecated: false
has responsible: Pierre Cosson
has URI prefix: https://web.expasy.org/abcd/ABCD_
0000027: ABCD AD834
0000029: abcd

Drosophila RNAi Screening Center
type: Resource
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.
is part of: bioregistry
0000005: DRSC05221
has provider formatter: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl
has local unique identifier pattern: ^DRSC\d+$
is deprecated: false
has URI prefix: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl
0000027: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl
0000029: drsc

KEGG Compound
type: Resource
description: KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.
is part of: bioregistry
is part of: kegg
keyword: small molecule
0000005: C12345
has provider formatter: https://www.kegg.jp/entry/$1
has local unique identifier pattern: ^C\d+$
is deprecated: false
has responsible: 0000-0001-6123-540X
has alternative prefix: KEGG.COMPOUND
has alternative prefix: KEGG COMPOUND
has URI prefix: https://www.kegg.jp/entry/
0000027: C12345
0000029: kegg.compound

VEuPathDB ontology
type: Resource
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.
is part of: bioregistry
git repository: VEuPathDB-ontology
keyword: obo
keyword: ontology
keyword: population genetics
keyword: microbiome
keyword: functional genomics
keyword: epidemiology
keyword: biomedical science
0000005: 0010316
has provider formatter: http://purl.obolibrary.org/obo/EUPATH_$1
has local unique identifier pattern: ^\d{7}$
0000010: eupath.owl
is deprecated: true
0000018: scdo
has responsible: https://orcid.org/0000-0002-2999-0103
has URI prefix: http://purl.obolibrary.org/obo/EUPATH_
0000027: EUPATH_0010316
0000029: eupath

MetaCyc Reaction
type: Resource
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.
is part of: bioregistry
0000005: RXN-14904
has provider formatter: https://metacyc.org/META/NEW-IMAGE
has local unique identifier pattern: ^[A-Za-z0-9+_.%-:]+$
is deprecated: false
has responsible: Peter D. Karp
has URI prefix: https://metacyc.org/META/NEW-IMAGE
0000027: https://metacyc.org/META/NEW-IMAGE
0000029: metacyc.reaction

EAWAG Biocatalysis/Biodegradation Database pathway
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.
is part of: bioregistry
0000005: ala
has provider formatter: http://umbbd.ethz.ch/servlets/pageservlet
has local unique identifier pattern: ^\w+$
is deprecated: false
has alternative prefix: UM-BBD_pathwayID
has URI prefix: http://umbbd.ethz.ch/servlets/pageservlet
0000027: http://umbbd.ethz.ch/servlets/pageservlet
0000029: umbbd.pathway

CIÊNCIAVITAE ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier of scientific author in www.cienciavitae.pt
is part of: bioregistry
keyword: person
keyword: researcher
0000005: 0C1F-DA6C-4B02
has provider formatter: https://www.cienciavitae.pt/$1
has local unique identifier pattern: ^([0-9A-F]{4}-){2}[0-9A-F]{4}$
is deprecated: false
has URI prefix: https://www.cienciavitae.pt/
0000027: https://www.cienciavitae.pt/0C1F-DA6C-4B02
0000029: cienciavitae

Genomics of Drug Sensitivity in Cancer
type: Resource
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
0000005: 1242
has provider formatter: https://www.cancerrxgene.org/translation/Drug/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has URI prefix: https://www.cancerrxgene.org/translation/Drug/
0000027: https://www.cancerrxgene.org/translation/Drug/1242
0000029: gdsc

Chemical Entity Materials and Reactions Ontological Framework
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A data model for managing information about chemical entities, ranging from atoms through molecules to complex mixtures.
is part of: bioregistry
git repository: chemrof
keyword: ontology
keyword: chemistry
keyword: nfdi4chem
0000005: FullySpecifiedAtom
has provider formatter: https://chemkg.github.io/chemrof/$1
0000010: chemrof.owl.ttl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
has URI prefix: https://chemkg.github.io/chemrof/
0000027: FullySpecifiedAtom
0000029: chemrof

Multiplexed Assays of Variant Effect Database
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
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
is part of: bioregistry
git repository: mavedb-api
0000005: 00000011-a
has provider formatter: https://www.mavedb.org/#/experiments/urn:mavedb:$1
has local unique identifier pattern: ^\S+$
is deprecated: false
has responsible: 0000-0003-1474-605X
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.mavedb.org/#/experiments/urn:mavedb:
0000027: experiments/urn:mavedb:00000011-a
0000029: mavedb

CohesinDB - cohesin site
type: Resource
contributor: https://orcid.org/0009-0000-6974-6386
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.
is part of: bioregistry
keyword: binding site
keyword: protein
keyword: cohesin
0000005: CDBP00415501
has provider formatter: https://cohesindb.iqb.u-tokyo.ac.jp/browsepeak/eachpeak/$1
has local unique identifier pattern: ^CDBP00\d{6}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-3019-5817
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://cohesindb.iqb.u-tokyo.ac.jp/browsepeak/eachpeak/
0000027: CDBP00415501
0000029: cohesindb.binding

Steven G. E. Marsh

Stemcell Knowledge and Information Portal
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: SKIP001214
has provider formatter: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail
has local unique identifier pattern: ^SKIP\d+$
is deprecated: false
has URI prefix: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail
0000027: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail
0000029: skip

dictyBase
type: Resource
description: A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics
has part: dictybase.gene
is part of: bioregistry
keyword: comparative genomics
keyword: anatomy
keyword: life science
keyword: genome
0000005: DDB0191090
has provider formatter: http://dictybase.org/gene/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-4532-2703
has alternative prefix: dictyBase
has URI prefix: http://dictybase.org/gene/
0000027: http://dictybase.org/gene/DDB0191090
0000029: dictybase

Anatomical Therapeutic Chemical Classification System
type: Resource
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.
is part of: bioregistry
keyword: ontology
keyword: chemical biology
keyword: pharmacology
keyword: chemical
keyword: biomedical science
keyword: approved drug
keyword: drug
keyword: pharmacological family classification
keyword: atc code
0000005: A10BA02
has provider formatter: http://www.whocc.no/atc_ddd_index/
has local unique identifier pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$
is deprecated: false
has responsible: WHO Collaborating Centre for Drug Statistics Methodology
has alternative prefix: ATC_code
has alternative prefix: ATTC
has URI prefix: http://www.whocc.no/atc_ddd_index/
0000027: http://www.whocc.no/atc_ddd_index/
0000029: atc

AberOWL
type: https://bioregistry.io/schema/#0000002
description: AberOWL is a framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of webservices which provide access to OWL(-EL) reasoning over the ontologies, and several frontends which utilise the ontology repository and reasoning services to provide access to specific biological datasets.
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

Intelligence Task Ontology
type: Resource
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.
is part of: bioregistry
git repository: ITO
keyword: artificial intelligence
keyword: natural language processing
keyword: ontology
keyword: machine learning
0000005: 01625
has provider formatter: https://bioportal.bioontology.org/ontologies/ITO/
has local unique identifier pattern: ^\d+$
0000010: ito.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-4855-2571
has URI prefix: https://bioportal.bioontology.org/ontologies/ITO/
0000027: https://bioportal.bioontology.org/ontologies/ITO/
0000029: ito

Oliver Fiehn

SWEET Ontology Phenomena Atmosphere Cloud
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Cloud
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: atmosphere cloud
keyword: phenomena
0000005: Altostratus
has provider formatter: http://sweetontology.net/phenAtmoCloud/$1
is deprecated: false
has alternative prefix: sophatmoc
has URI prefix: http://sweetontology.net/phenAtmoCloud/
0000027: Altostratus
0000029: sweet.phatmoc

Development Data Object Service
type: Resource
description: Assists in resolving data across cloud resources.
is part of: bioregistry
has provider formatter: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1
has local unique identifier pattern: ^[a-zA-Z0-9\-:#\.]+$
is deprecated: false
has URI prefix: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/
0000027: 2017-03-24T18:43:16.886826-05:00
0000029: dev.ga4ghdos

Allen Institute Ontologies
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
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
has part: Primate Brain Atlas
has part: dhba

SUM Breast Cancer Cell Line Knowledge Base
type: Resource
description: Cell line databases/resources
is part of: bioregistry
0000005: 3618
has provider formatter: https://sumlineknowledgebase.com/
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://sumlineknowledgebase.com/
0000027: https://sumlineknowledgebase.com/
0000029: slkbase

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.
is part of: bioregistry
git repository: caro
keyword: annotation
keyword: anatomy
keyword: life science
keyword: obo
keyword: ontology
0000005: 0000000
has provider formatter: http://purl.obolibrary.org/obo/CARO_$1
has local unique identifier pattern: ^\d{7}$
0000010: caro.owl
is deprecated: true
0000018: lepao
0000018: gallont
0000018: pco
0000018: Coleoptera Anatomy Ontology
0000018: ehdaa2
0000018: aism
has responsible: https://orcid.org/0000-0001-9114-8737
has URI prefix: http://purl.obolibrary.org/obo/CARO_
0000027: CARO_0000000
0000029: caro

Nikolaus Schultz

NMR Restraints Grid
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: nmr
keyword: chemistry
keyword: spectrometry
0000005: 28789
has provider formatter: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
0000027: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
0000029: bmrb.restraint

Database of RNA Junctions and Kissing loop Structures
type: Resource
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.
is part of: bioregistry
keyword: structure
keyword: structural biology
keyword: rna
0000005: 8668
has provider formatter: https://rnajunction.ncifcrf.gov/JunctionPage.php
is deprecated: false
has responsible: Yaroslava G Yingling
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://rnajunction.ncifcrf.gov/JunctionPage.php
0000027: https://rnajunction.ncifcrf.gov/JunctionPage.php
0000029: rnajunction

MLCommons Association
type: Resource
description: MLCommons Association artifacts, including benchmark results, datasets, and saved models.
is part of: bioregistry
0000005: 0.7-123
has provider formatter: https://www.mlcommons.org/mlc-id/$1
has local unique identifier pattern: ^[0-9a-zA-Z\.\-\_]+$
is deprecated: false
has URI prefix: https://www.mlcommons.org/mlc-id/
0000027: https://www.mlcommons.org/mlc-id/0.7-123
0000029: mlc

Gwen Frishkoff

Food Classification and Description System (from FSA Food Type identifiers)
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.
is part of: bioregistry
0000005: A0TMC
has provider formatter: http://data.food.gov.uk/codes/foodtype/id/$1
is deprecated: false
has responsible: UK Food Standard Agency
has URI prefix: http://data.food.gov.uk/codes/foodtype/id/
0000027: A0TMC
0000029: foodex2

SWEET Ontology Phenomena Atmosphere Sky
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Sky
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: atmosphere sky
keyword: phenomena
0000005: AirPollution
has provider formatter: http://sweetontology.net/phenAtmoSky/$1
is deprecated: false
has alternative prefix: sophatmos
has URI prefix: http://sweetontology.net/phenAtmoSky/
0000027: AirPollution
0000029: sweet.phatmos

SAREF4INMA: an extension of SAREF for the industry and manufacturing domain
type: Resource
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.
is part of: bioregistry
keyword: industry
keyword: engineering
keyword: iot
keyword: nfdi4ing
0000005: Area
has provider formatter: https://saref.etsi.org/saref4inma/$1
is deprecated: false
has alternative prefix: s4inma
has URI prefix: https://saref.etsi.org/saref4inma/
0000027: Area
0000029: saref.industry

Experimental Factor Ontology
type: Resource
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.
is part of: bioregistry
git repository: efo
keyword: genome-wide association study
keyword: experimental measurement
keyword: ess
keyword: medicine
keyword: study design
keyword: study design independent variable
keyword: ontology
keyword: dataplant
keyword: experimental condition
keyword: genomics
keyword: assay
keyword: nfdi4chem
keyword: omics
keyword: proteomics
keyword: earth sciences
keyword: life sciences, biology
0000005: 0005147
has provider formatter: http://www.ebi.ac.uk/efo/EFO_$1
has local unique identifier pattern: ^\d{7}$
0000010: efo.owl
is deprecated: false
has responsible: Trish Whetzel
has URI prefix: http://www.ebi.ac.uk/efo/EFO_
0000026: 02catss52
0000027: EFO_0005147
0000029: efo

Probability Distribution Ontology
type: Resource
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.
is part of: bioregistry
git repository: ontology
keyword: systems biology
keyword: computational biology
keyword: mathematics
keyword: statistics
0000005: c0000005
has provider formatter: http://www.probonto.org/ontology#PROB_$1
has local unique identifier pattern: ^(c|k)\d{7}$
is deprecated: false
has responsible: Pierre Grenon
has URI prefix: http://www.probonto.org/ontology#PROB_
0000027: PROB c0000005
0000029: probonto

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 part of: bioregistry
0000005: 1
has provider formatter: http://pombe.oridb.org/details.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://pombe.oridb.org/details.php
0000027: http://pombe.oridb.org/details.php
0000029: oridb.schizo

Cryo Electron Microscopy
type: Resource
description: The CryoEM Ontology for describing objects and workflows in Single Particle Analysis by Cryo Electron Microscopy.
is part of: bioregistry
git repository: cryoem
keyword: electron microscopy
keyword: structural biology
keyword: bioimaging
keyword: ontology
0000005: 0000052
has provider formatter: http://scipion.i2pc.es/ontology/CRYOEM_$1
has local unique identifier pattern: ^\d{7}$
0000010: cryoem.owl
is deprecated: false
has responsible: 0000-0002-9473-283X
has URI prefix: http://scipion.i2pc.es/ontology/CRYOEM_
0000027: CRYOEM_0000052
0000029: cryoem

Data Repository of Antimicrobial Peptides
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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 part of: bioregistry
keyword: antimicrobial peptides
0000005: DRAMP00005
has provider formatter: http://dramp.cpu-bioinfor.org/browse/All_Information.php
has local unique identifier pattern: ^DRAMP\d{5}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-1810-5842
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://dramp.cpu-bioinfor.org/browse/All_Information.php
0000027: http://dramp.cpu-bioinfor.org/browse/All_Information.php
0000029: dramp

Bitbucket
type: Resource
description: Bitbucket is a Git-based source code repository hosting service owned by Atlassian.
is part of: bioregistry
keyword: knowledge and information systems
keyword: subject agnostic
keyword: software engineering
0000005: andreadega/systems-biology-compiler
has provider formatter: https://bitbucket.org/$1
has local unique identifier pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$
is deprecated: false
has URI prefix: https://bitbucket.org/
0000027: systems-biology-compiler
0000029: bitbucket

ChemPro Probe
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for chemoproteomic probes used to label human proteins in living cells.
is part of: bioregistry
0000005: LDPC0032
has provider formatter: https://chemprosquare.idrblab.net/data/probe/details/$1
has local unique identifier pattern: ^LDPC\d+$
is deprecated: false
has responsible: Feng Zhu
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://chemprosquare.idrblab.net/data/probe/details/
0000027: LDPC0032
0000029: chempro.probe

Pathogen Host Interaction Phenotype Ontology
type: Resource
description: Ontology of species-neutral phenotypes observed in pathogen-host interactions.
is part of: bioregistry
git repository: phipo
keyword: obo
keyword: ontology
0000005: 0000001
has provider formatter: http://purl.obolibrary.org/obo/PHIPO_$1
has local unique identifier pattern: ^\d{7}$
0000010: phipo.owl
is deprecated: false
depends on: pato
has responsible: https://orcid.org/0000-0001-8941-3984
has URI prefix: http://purl.obolibrary.org/obo/PHIPO_
0000027: PHIPO_0000001
0000029: phipo

Database of Interacting Proteins
type: Resource
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
is part of: bioregistry
keyword: interaction
keyword: biology
keyword: protein
0000005: DIP-743N
has provider formatter: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi
has local unique identifier pattern: ^DIP(\:)?\-\d{1,}[ENXS]$
is deprecated: false
has responsible: https://orcid.org/0000-0003-2432-5419
has URI prefix: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi
0000027: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi
0000029: dip

EAWAG Biocatalysis/Biodegradation Database enzyme
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 enzyme information.
is part of: bioregistry
0000005: e0333
has provider formatter: http://eawag-bbd.ethz.ch/servlets/pageservlet
has local unique identifier pattern: ^e\d+$
is deprecated: false
has alternative prefix: UM-BBD_enzymeID
has URI prefix: http://eawag-bbd.ethz.ch/servlets/pageservlet
0000027: http://eawag-bbd.ethz.ch/servlets/pageservlet
0000029: umbbd.enzyme

Human Metabolome Database
type: Resource
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.
is part of: bioregistry
keyword: biochemistry
keyword: life science
keyword: human
keyword: molecular biology
keyword: metabolomics
keyword: bioinformatics
keyword: omics
keyword: proteomics
keyword: chemical
keyword: phenomics
keyword: metabolite
0000005: HMDB00001
has provider formatter: http://www.hmdb.ca/metabolites/$1
has local unique identifier pattern: ^HMDB\d+$
is deprecated: false
has responsible: David Wishart
has alternative prefix: HMDB
has URI prefix: http://www.hmdb.ca/metabolites/
0000027: HMDB00001
0000029: hmdb

Cancer cell LInes GEne fusions portAl
type: Resource
description: Polymorphism and mutation databases
is part of: bioregistry
0000005: CCLE_867
has provider formatter: http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1
is deprecated: false
has URI prefix: http://hpc-bioinformatics.cineca.it/fusion/cell_line/
0000027: CCLE 867
0000029: ligea

Semantic Resource Types Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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'.
is part of: bioregistry
git repository: srt
keyword: semantic resource
0000005: 000001
has provider formatter: http://cor.esipfed.org/ont/earthcube/srt_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4808-4736
has URI prefix: http://cor.esipfed.org/ont/earthcube/srt_
0000027: srt_000001
0000029: earthcube.srt

InterLex
type: Resource
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.
is part of: bioregistry
keyword: anatomy
keyword: imaging
keyword: neurobiology
keyword: brain
keyword: biomedical science
0000005: 0101963
has provider formatter: https://scicrunch.org/scicrunch/interlex/view/ilx_$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: Maryann Elizabeth Martone
has alternative prefix: ILX
has URI prefix: https://scicrunch.org/scicrunch/interlex/view/ilx_
0000027: ilx_0101963
0000029: interlex

Network of Different Plant Genomic Research Projects
type: Resource
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'.
is part of: bioregistry
keyword: plant
keyword: gene
keyword: genome
0000005: 2679240
has provider formatter: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi
has local unique identifier pattern: ^\w+$
is deprecated: true
has responsible: https://orcid.org/0000-0001-9900-9133
has URI prefix: https://bioregistry.io/gabi:
0000027: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi
0000029: gabi

Robert Hoehndorf

Satya S. Sahoo

SciProfiles ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: numerical identifier for an author in SciProfiles by MDPI
is part of: bioregistry
keyword: person
keyword: researcher
0000005: 118021
has provider formatter: https://sciprofiles.com/profile/$1
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has URI prefix: https://sciprofiles.com/profile/
0000027: https://sciprofiles.com/profile/118021
0000029: sciprofiles

UniProt Isoform
type: Resource
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.
is part of: bioregistry
0000005: Q5BJF6-3
has provider formatter: http://purl.uniprot.org/isoforms/$1
has local unique identifier pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$
is deprecated: false
has responsible: Alex Bateman
has alternative prefix: UPISO
has URI prefix: http://purl.uniprot.org/isoforms/
0000027: Q5BJF6-3
0000029: uniprot.isoform

The Comprehensive R Archive Network
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Repository of packages for the R programming language
is part of: bioregistry
0000005: ggplot2
has provider formatter: https://cran.r-project.org/web/packages/$1
is deprecated: false
has URI prefix: https://cran.r-project.org/web/packages/
0000027: ggplot2
0000029: cran

Pathway ontology
type: Resource
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.
is part of: bioregistry
git repository: PW-Pathway-Ontology
keyword: molecular entity
keyword: enzymatic reaction
keyword: drug metabolism
keyword: life science
keyword: drug
keyword: obo
keyword: biological regulation
keyword: human
keyword: ontology
keyword: pathway
keyword: signaling
keyword: disease
0000005: 0000423
has provider formatter: http://purl.obolibrary.org/obo/PW_$1
has local unique identifier pattern: ^\d{7}$
0000010: pw.owl
is deprecated: false
has responsible: G. Thomas Hayman
has URI prefix: http://purl.obolibrary.org/obo/PW_
0000027: PW_0000423
0000029: pw

RiceNetDB Compound
type: Resource
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.
is part of: bioregistry
0000005: OSC1416
has provider formatter: http://bis.zju.edu.cn/ricenetdb/compounddetails.php
has local unique identifier pattern: ^OSC\d{4}$
is deprecated: false
has URI prefix: http://bis.zju.edu.cn/ricenetdb/compounddetails.php
0000027: http://bis.zju.edu.cn/ricenetdb/compounddetails.php
0000029: ricenetdb.compound

Jens Klump

Sweet Potato Ontology
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 Sweet Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
is part of: bioregistry
git repository: Crop-Ontology
keyword: life science
keyword: food
keyword: ontology
keyword: botany
keyword: agriculture
0000005: 0000088
has provider formatter: https://cropontology.org/rdf/CO_331:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 331.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-0595-5271
has URI prefix: https://cropontology.org/rdf/CO_331:
0000027: CO 331:0000088
0000029: co_331

SWEET Ontology Material Organic Compound
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Organic Compound
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: organic compound
keyword: materials
0000005: Alkane
has provider formatter: http://sweetontology.net/matrOrganicCompound/$1
is deprecated: false
has alternative prefix: somaoc
has URI prefix: http://sweetontology.net/matrOrganicCompound/
0000027: Alkane
0000029: sweet.maoc

Hymenoptera Anatomy Reference
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Literature references in the Hymenoptera Anatomy Ontology Portal
is part of: bioregistry
0000005: 98127
has provider formatter: http://api.hymao.org/api/ref/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5640-5491
has URI prefix: http://api.hymao.org/api/ref/
0000027: http://api.hymao.org/api/ref/98127
0000029: hao.ref

Rebecca Jackson

Cell Line Ontology
type: Resource
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.
is part of: bioregistry
git repository: CLO
keyword: cell line
keyword: obo
keyword: cell biology
keyword: ontology
keyword: cell
keyword: morphology
keyword: life science
0000005: 0000091
has provider formatter: http://purl.obolibrary.org/obo/CLO_$1
has local unique identifier pattern: ^\d{7}$
0000010: clo.owl
is deprecated: false
depends on: NCBI Taxonomy
depends on: Human Disease Ontology
depends on: cl
depends on: Uber Anatomy Ontology
0000018: Microbial Conditions Ontology
has responsible: https://orcid.org/0000-0002-2999-0103
has alternative prefix: CLO
has URI prefix: http://purl.obolibrary.org/obo/CLO_
0000027: CLO_0000091
0000029: clo

Tick Anatomy Ontology
type: Resource
description: The anatomy of the Tick, Families: Ixodidae, Argassidae
is part of: bioregistry
git repository: TADS
keyword: ontology
keyword: anatomy
keyword: life science
keyword: obo
0000005: 0000547
has provider formatter: http://purl.obolibrary.org/obo/TADS_$1
has local unique identifier pattern: ^\d{7}$
0000010: tads.owl
is deprecated: true
has responsible: Daniel Sonenshine
has URI prefix: http://purl.obolibrary.org/obo/TADS_
0000027: TADS_0000547
0000029: tads

Allotrope quality
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The quality component of the Allotrope ontology suite
is part of: bioregistry
is part of: afo
0000005: 0000236
has provider formatter: http://purl.allotrope.org/ontologies/quality#AFQ_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://purl.allotrope.org/ontologies/quality#AFQ_
0000027: AFQ_0000236
0000029: allotrope.quality

Clinical Trials Information System
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
0000005: 2023-503698-40-00
has provider formatter: https://euclinicaltrials.eu/app/#/view/$1
has local unique identifier pattern: ^\d{4}-\d+-\d+-\d+$
is deprecated: false
has URI prefix: https://euclinicaltrials.eu/app/#/view/
0000027: view/2023-503698-40-00
0000029: ctis

Ruili Huang

BiGG Model
type: Resource
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.
is part of: bioregistry
keyword: ontology
keyword: pathway
keyword: metabolic model
0000005: iECABU_c1320
has provider formatter: http://bigg.ucsd.edu/models/$1
has local unique identifier pattern: ^[a-z_A-Z0-9]+$
0000010: bigg.model.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-1238-1499
has URI prefix: http://bigg.ucsd.edu/models/
0000027: iECABU c1320
0000029: bigg.model

LINCS Small Molecule
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 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 part of: bioregistry
0000005: LSM-6306
has provider formatter: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1
has local unique identifier pattern: ^LSM-\d+$
is deprecated: false
has alternative prefix: lincs
has URI prefix: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/
0000027: view/LSM-6306
0000029: lincs.smallmolecule

Lentil Ontology
type: Resource
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.
is part of: bioregistry
git repository: Crop-Ontology
keyword: life science
keyword: food
keyword: ontology
keyword: plant phenotypes and traits
keyword: phenotype
keyword: botany
keyword: agriculture
0000005: 0000032
has provider formatter: https://cropontology.org/rdf/CO_339:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 339.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_339:
0000027: CO 339:0000032
0000029: co_339

PEPhub
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
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
0000005: geo
has provider formatter: https://pephub.databio.org/$1
has local unique identifier pattern: ^[A-Za-z0-9_\-]+(/[A-Za-z0-9_\-]+)?$
is deprecated: false
has responsible: https://orcid.org/0000-0001-5643-4068
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://pephub.databio.org/
0000027: geo
0000029: pephub

The International Harmonization of Nomenclature and Diagnostic criteria
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.
is part of: bioregistry
keyword: biomedical science
keyword: toxicity
keyword: disease
is deprecated: false
has responsible: https://orcid.org/0000-0003-4682-0824
0000029: inhand

SAREF4GRID: an extension of SAREF for the Smart Grid domain
type: Resource
description: This ontology extends the SAREF ontology for the smart grid domain.
is part of: bioregistry
keyword: engineering
keyword: nfdi4energy
0000005: ActionOperation
has provider formatter: https://saref.etsi.org/saref4grid/$1
is deprecated: false
has alternative prefix: s4grid
has URI prefix: https://saref.etsi.org/saref4grid/
0000027: ActionOperation
0000029: saref.grid

Environment Ontology
type: Resource
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.
is part of: bioregistry
git repository: envo
keyword: epidemiology
keyword: environmental science
keyword: life science
keyword: ess
keyword: nutritional science
keyword: fair data spaces
keyword: obo
keyword: ontology
keyword: marine metagenome
keyword: dataplant
keyword: ecology
keyword: nfdi4cat
keyword: microbiome
keyword: nfdi4chem
keyword: environmental material
keyword: earth sciences
keyword: life sciences, biology
0000005: 09200010
has provider formatter: http://purl.obolibrary.org/obo/ENVO_$1
has local unique identifier pattern: ^\d{7,8}$
0000010: envo.owl
is deprecated: false
depends on: NCBI Taxonomy
depends on: Plant Ontology
depends on: pco
depends on: foodon
depends on: ro
depends on: Uber Anatomy Ontology
depends on: Chemical Entities of Biological Interest
depends on: go
0000018: Ontology for Nutritional Studies
0000018: rbo
0000018: An ontology of core ecological entities
0000018: scdo
0000018: Agronomy Ontology
0000018: pco
0000018: cdno
0000018: foodon
0000018: Environmental conditions, treatments and exposures ontology
0000018: Uber Anatomy Ontology
has responsible: Pier Luigi Buttigieg
has URI prefix: http://purl.obolibrary.org/obo/ENVO_
0000027: ENVO_09200010
0000029: envo

NeuroVault Collection
type: Resource
description: Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images.
is part of: bioregistry
0000005: 3304
has provider formatter: https://neurovault.org/collections/$1
has local unique identifier pattern: ^[1-9][0-9]*$
is deprecated: false
has URI prefix: https://neurovault.org/collections/
0000027: https://neurovault.org/collections/3304
0000029: neurovault.collection

PANTHER Pathway Component
type: Resource
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.
is part of: bioregistry
0000005: P00266
has provider formatter: http://www.pantherdb.org/pathway/pathCatDetail.do
has local unique identifier pattern: ^(G|P|U|C|S)\d{5}$
is deprecated: false
has URI prefix: http://www.pantherdb.org/pathway/pathCatDetail.do
0000027: http://www.pantherdb.org/pathway/pathCatDetail.do
0000029: panther.pthcmp

MicroScope
type: Resource
description: MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.
is part of: bioregistry
keyword: comparative genomics
keyword: life science
0000005: 5601141
has provider formatter: http://www.genoscope.cns.fr/agc/microscope/mage/info.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: MEDIGUE Claudine
has URI prefix: http://www.genoscope.cns.fr/agc/microscope/mage/info.php
0000027: http://www.genoscope.cns.fr/agc/microscope/mage/info.php
0000029: microscope

Fission Yeast Experimental Conditions Ontology
type: Resource
contributor: Valerie Wood
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.
is part of: bioregistry
git repository: fypo
0000005: 0000003
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: Valerie Wood
has reviewer: https://orcid.org/0000-0003-4423-4370
0000029: fyeco

SWEET Ontology State Chemical
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Chemical
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state chemical
0000005: BiochemicalState
has provider formatter: http://sweetontology.net/stateChemical/$1
is deprecated: false
has alternative prefix: sostc
has URI prefix: http://sweetontology.net/stateChemical/
0000027: BiochemicalState
0000029: sweet.stc

BitterDB Receptor
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 receptors.
is part of: bioregistry
0000005: 1
has provider formatter: http://bitterdb.agri.huji.ac.il/Receptor.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://bitterdb.agri.huji.ac.il/Receptor.php
0000027: http://bitterdb.agri.huji.ac.il/Receptor.php
0000029: bitterdb.rec

UniProt Proteomes
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
contributor: JervenBolleman
contributor: https://orcid.org/0000-0003-4423-4370
description: UniProt provides proteome sets of proteins whose genomes have been completely sequenced.
is part of: bioregistry
0000005: UP000005640
has provider formatter: https://www.uniprot.org/proteomes/$1
has local unique identifier pattern: ^UP\d{9}$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.uniprot.org/proteomes/
0000027: UP000005640
0000029: uniprot.proteome

NCBI PubChem database of bioassay records
type: Resource
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.
is part of: bioregistry
keyword: small molecule
0000005: 1018
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/bioassay/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-7950-1374
has alternative prefix: pubchem.aid
has alternative prefix: pubchem.assay
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/bioassay/
0000027: https://pubchem.ncbi.nlm.nih.gov/bioassay/1018
0000029: pubchem.bioassay

Valerie Wood
label: Val Wood

Beta Cell Genomics Ontology
type: Resource
description: An application ontology built for beta cell genomics studies.
is part of: bioregistry
git repository: bcgo
keyword: obo
keyword: ontology
0000005: 0000015
has provider formatter: http://purl.obolibrary.org/obo/BCGO_$1
has local unique identifier pattern: ^\d{7}$
0000010: bcgo.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-2999-0103
has URI prefix: http://purl.obolibrary.org/obo/BCGO_
0000027: BCGO_0000015
0000029: bcgo

The Drug Ontology
type: Resource
description: An ontology to support comparative effectiveness researchers studying claims data.
is part of: bioregistry
git repository: dron
keyword: approved drug
keyword: drug
keyword: obo
keyword: ontology
keyword: small molecule
keyword: biomedical science
0000005: 00023232
has provider formatter: http://purl.obolibrary.org/obo/DRON_$1
has local unique identifier pattern: ^\d{8}$
0000010: dron.owl
is deprecated: false
0000018: scdo
has responsible: https://orcid.org/0000-0002-9881-1017
has URI prefix: http://purl.obolibrary.org/obo/DRON_
0000027: DRON_00023232
0000029: dron

Decentralized Identifier
type: Resource
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.
is part of: bioregistry
0000005: sov:WRfXPg8dantKVubE3HX8pw
has provider formatter: https://uniresolver.io/#did:$1
has local unique identifier pattern: ^[a-z0-9]+:[A-Za-z0-9.\-:]+$
is deprecated: false
has URI prefix: https://uniresolver.io/#did:
0000027: did:sov:WRfXPg8dantKVubE3HX8pw
0000029: did

eVOC (Expressed Sequence Annotation for Humans)
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.
is part of: bioregistry
keyword: anatomy
keyword: obo
keyword: experiment
keyword: ontology
keyword: development
keyword: cell
0000005: 0100011
has provider formatter: http://purl.obolibrary.org/obo/EV_$1
has local unique identifier pattern: ^\d{7}$
is deprecated: true
0000018: cl
has responsible: eVOC mailing list
has URI prefix: http://purl.obolibrary.org/obo/EV_
0000027: EV_0100011
0000029: ev

Nicole Vasilevsky

Canadian Drug Product Database
type: Resource
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).
is part of: bioregistry
0000005: 63250
has provider formatter: https://health-products.canada.ca/dpd-bdpp/info
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://health-products.canada.ca/dpd-bdpp/info
0000027: https://health-products.canada.ca/dpd-bdpp/info
0000029: cdpd

NFDI4Immuno Collection
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Immuno
has part: bioregistry

SWEET Ontology Phenomena Geologic Seismicity
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Seismicity
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
keyword: geologic seismicity
0000005: Aftershock
has provider formatter: http://sweetontology.net/phenGeolSeismicity/$1
is deprecated: false
has alternative prefix: sophgs
has URI prefix: http://sweetontology.net/phenGeolSeismicity/
0000027: Aftershock
0000029: sweet.phgs

Vocabulary of Interlinked Datasets
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: metadata
0000005: feature
has provider formatter: http://rdfs.org/ns/void#$1
is deprecated: false
has URI prefix: http://rdfs.org/ns/void#
0000027: feature
0000029: void

GeoSPARQL Function
type: Resource
description: Functions for GeoSPARQL
is part of: bioregistry
0000005: sfEquals
is deprecated: false
0000029: geosparql.function

HoloFood animal
type: Resource
contributor: 0009-0008-8406-631X
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.
is part of: bioregistry
0000005: SAMEA112904733
has provider formatter: https://www.holofooddata.org/animal/$1
has local unique identifier pattern: ^SAMEA\d{9}$
is deprecated: false
has responsible: Tom Gilbert
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.holofooddata.org/animal/
0000027: SAMEA112904733
0000029: holofood.animal

SWEET Ontology Representation Mathematics Graph
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Graph
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation mathematics graph
0000005: Arc
has provider formatter: http://sweetontology.net/reprMathGraph/$1
is deprecated: false
has alternative prefix: sorepmg
has URI prefix: http://sweetontology.net/reprMathGraph/
0000027: Arc
0000029: sweet.repmg

BioCatalogue Service
type: Resource
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 part of: bioregistry
keyword: registry
0000005: 614
has provider formatter: https://www.biocatalogue.org/services/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-1219-2137
has URI prefix: https://www.biocatalogue.org/services/
0000027: https://www.biocatalogue.org/services/614
0000029: biocatalogue.service

Susan J. Brown

GLIDA GPCR
type: Resource
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.
is part of: bioregistry
0000005: ACM1_HUMAN
has provider formatter: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php
has local unique identifier pattern: ^[A-Z-_0-9]+$
is deprecated: true
has URI prefix: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php
0000027: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php
0000029: glida.gpcr

SupraBank Additive
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Identifiers for chemicals used as additives
is part of: bioregistry
keyword: molecule
keyword: chemical
0000005: 10
has provider formatter: https://suprabank.org/additives/$1
is deprecated: false
has responsible: Stephan Sinn
has URI prefix: https://suprabank.org/additives/
0000027: https://suprabank.org/additives/10
0000029: suprabank.additive

PK-DB
type: Resource
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.
is part of: bioregistry
git repository: issues
keyword: pharmacogenomics
keyword: pharmacology
keyword: clinical veterinary medicine
keyword: preclinical studies
keyword: clinical studies
keyword: life science
keyword: personalized medicine
0000005: PKDB00198
has provider formatter: https://pk-db.com/data/$1
has local unique identifier pattern: ^PKDB[0-9]{5}$
is deprecated: false
has responsible: Matthias König
has URI prefix: https://pk-db.com/data/
0000027: PKDB00198
0000029: pkdb

Brian Aevermann

SWEET Ontology Phenomena Mixing
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Mixing
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: phenomena
keyword: mixing
0000005: Aeration
has provider formatter: http://sweetontology.net/phenMixing/$1
is deprecated: false
has alternative prefix: sophm
has URI prefix: http://sweetontology.net/phenMixing/
0000027: Aeration
0000029: sweet.phm

ArchDB
type: Resource
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.
is part of: bioregistry
keyword: life science
keyword: classification
keyword: protein
0000005: 39421
has provider formatter: http://sbi.imim.es/cgi-bin/archdb//loops.pl
is deprecated: false
has responsible: Narcis Fernandez-Fuentes
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://sbi.imim.es/cgi-bin/archdb//loops.pl
0000027: http://sbi.imim.es/cgi-bin/archdb//loops.pl
0000029: archdb

EM-DAT Disaster Classification Ontology
type: Resource
description: Crisis and hazard related taxonomy developed by CRED for disaster preparedness and humanitarian actions at national and international level.
is part of: bioregistry
keyword: life sciences, biology
keyword: coypu
keyword: earth sciences
0000005: Air
has provider formatter: https://schema.coypu.org/em-dat#$1
is deprecated: false
has URI prefix: https://schema.coypu.org/em-dat#
0000027: Air
0000029: coypu.emdat

SWEET Ontology Representation Data Format
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Format
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation data format
0000005: ByteOrder
has provider formatter: http://sweetontology.net/reprDataFormat/$1
is deprecated: false
has alternative prefix: sorepdf
has URI prefix: http://sweetontology.net/reprDataFormat/
0000027: ByteOrder
0000029: sweet.repdf

MolBiC Cell Line
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
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.
is part of: bioregistry
0000005: CL000025
has provider formatter: https://molbic.idrblab.net/data/cellline/details/$1
has local unique identifier pattern: ^CL\d+$
is deprecated: false
has responsible: Feng Zhu
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://molbic.idrblab.net/data/cellline/details/
0000027: CL000025
0000029: molbic.cellline

SEED Compound
type: Resource
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.
is part of: bioregistry
git repository: TheSEED
0000005: cpd15380
has provider formatter: http://modelseed.org/biochem/compounds/$1
has local unique identifier pattern: ^cpd\d+$
is deprecated: false
has URI prefix: http://modelseed.org/biochem/compounds/
0000027: cpd15380
0000029: seed.compound

SWEET Ontology State Space Scale
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Space Scale
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state space scale
0000005: Continental
has provider formatter: http://sweetontology.net/stateSpaceScale/$1
is deprecated: false
has alternative prefix: sostss
has URI prefix: http://sweetontology.net/stateSpaceScale/
0000027: Continental
0000029: sweet.stss

Web of Things Security Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: an RDF vocabulary for the security metadata definitions
is part of: bioregistry
0000005: APIKeySecurityScheme
has provider formatter: https://www.w3.org/2019/wot/security#$1
is deprecated: false
has URI prefix: https://www.w3.org/2019/wot/security#
0000027: APIKeySecurityScheme
0000029: wot.security

SWEET Ontology Phenomena Wave
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Wave
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: wave
keyword: phenomena
0000005: Acoustic
has provider formatter: http://sweetontology.net/phenWave/$1
is deprecated: false
has alternative prefix: sophw
has URI prefix: http://sweetontology.net/phenWave/
0000027: Acoustic
0000029: sweet.phw

Irina Medvedeva

MathModDB Ontology
type: Resource
description: This is the MathModDB Ontology for documenting mathematical models.
is part of: bioregistry
git repository: MathModDB
keyword: nfdi4ing
keyword: computer science
keyword: mathematics
keyword: engineering
0000005: ComputationalTask
has provider formatter: https://mardi4nfdi.de/mathmoddb#$1
is deprecated: false
has URI prefix: https://mardi4nfdi.de/mathmoddb#
0000027: ComputationalTask
0000029: mathmoddb

DiscoverX cell line products
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
0000005: 95-0166C6
has provider formatter: https://emea.discoverx.com/catalog/$1
is deprecated: false
has URI prefix: https://emea.discoverx.com/catalog/
0000027: https://emea.discoverx.com/catalog/95-0166C6
0000029: discoverx

Yeast Genome Order Browser
type: Resource
description: YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes.
is part of: bioregistry
keyword: gene
keyword: genome
0000005: ADH1
has provider formatter: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl
0000011: hgnc.symbol
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl
0000027: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl
0000029: ygob

SWEET Ontology Representation Time Season
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Time Season
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation time season
0000005: ColdestMonth
has provider formatter: http://sweetontology.net/reprTimeSeason/$1
is deprecated: false
has alternative prefix: sorepts
has URI prefix: http://sweetontology.net/reprTimeSeason/
0000027: ColdestMonth
0000029: sweet.repts

NCBI Gene Expression Omnibus
type: Resource
description: The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.
is part of: bioregistry
keyword: gene expression
keyword: phenomics
keyword: transcriptomics
keyword: comparative genomics
keyword: life science
keyword: epigenomics
keyword: genome
keyword: genomics
keyword: omics
0000005: GDS1234
has provider formatter: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
has local unique identifier pattern: ^G(PL|SM|SE|DS)\d+$
is deprecated: false
has responsible: Tanya Barrett
has URI prefix: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
0000027: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
0000029: geo

FAIRsharing Organization
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An organization in FAIRsharing, including universities, labs, etc.
is part of: bioregistry
0000005: 3851
has provider formatter: https://fairsharing.org/organisations/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7702-4495
has URI prefix: https://fairsharing.org/organisations/
0000027: https://fairsharing.org/organisations/3851
0000029: fairsharing.organization

Database of Genomic Structural Variation - Variant
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Variants in dbVar.
is part of: bioregistry
0000005: nsv3875336
has provider formatter: https://www.ncbi.nlm.nih.gov/dbvar/variants/$1
is deprecated: false
has alternative prefix: dbvar.variants
has URI prefix: https://www.ncbi.nlm.nih.gov/dbvar/variants/
0000027: nsv3875336
0000029: dbvar.variant

Urmas Kõljalg

Networked Knowledge Organization Systems/Services/Structures
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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).
is part of: bioregistry
0000005: alignedWith
has provider formatter: http://w3id.org/nkos/$1
is deprecated: false
has URI prefix: http://w3id.org/nkos/
0000027: alignedWith
0000029: nkos

Functional Requirements for Bibliographic Records
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: frbr
keyword: subject agnostic
keyword: frbr
0000005: Expression
has provider formatter: http://purl.org/vocab/frbr/core#$1
is deprecated: false
has responsible: Silvio Peroni
has URI prefix: http://purl.org/vocab/frbr/core#
0000027: Expression
0000029: frbr

Universal Spectrum Identifier
type: Resource
contributor: https://orcid.org/0000-0002-8741-7823
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.
is part of: bioregistry
git repository: usi
keyword: metabolomics
keyword: proteomics
keyword: lipidomics
keyword: data retrieval
keyword: data analysis
keyword: mass spectrum
keyword: data identity and mapping
0000005: PXD002255:ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2
has provider formatter: http://proteomecentral.proteomexchange.org/usi/
has local unique identifier pattern: ^.+$
is deprecated: false
has responsible: Gerhard Mayer
has URI prefix: http://proteomecentral.proteomexchange.org/usi/
0000027: http://proteomecentral.proteomexchange.org/usi/
0000029: mzspec

InChI
type: Resource
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.
is part of: bioregistry
git repository: InChI
keyword: centrally registered identifier
keyword: cheminformatics
keyword: chemical structure image
keyword: chemistry
keyword: molecular entity
keyword: chemical entity
keyword: structure
0000005: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3
has provider formatter: 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\-\+\(\)\,\/\?\;\.]+)*$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5538-8482
has URI prefix: https://www.ebi.ac.uk/chebi/advancedSearchFT.do
0000027: https://www.ebi.ac.uk/chebi/advancedSearchFT.do
0000029: inchi

COG Pathways
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: NAD%20biosynthesis
has provider formatter: https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-2265-5572
has URI prefix: https://www.ncbi.nlm.nih.gov/research/cog/pathway/
0000027: NAD biosynthesis
0000029: cog.pathway

Orthology Ontology
type: Resource
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.
is part of: bioregistry
git repository: OrthologyOntology
keyword: comparative genomics
keyword: orthologous
keyword: region
keyword: ontology
keyword: homologous
keyword: protein
keyword: paralogous
keyword: gene
0000005: HomologyRelation
has provider formatter: http://purl.org/net/orth#$1
0000010: orthOntology RC v2 A.owl
is deprecated: false
has responsible: Jesualdo Tomás Fernández-Breis
has URI prefix: http://purl.org/net/orth#
0000027: HomologyRelation
0000029: orth

NONCODE v4 Transcript
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 individual transcripts.
is part of: bioregistry
0000005: NONHSAT000001
has provider formatter: http://www.bioinfo.org/NONCODEv4/show_rna.php
has local unique identifier pattern: ^NONHSAT\d{6}$
is deprecated: true
has URI prefix: http://www.bioinfo.org/NONCODEv4/show_rna.php
0000027: http://www.bioinfo.org/NONCODEv4/show_rna.php
0000029: noncodev4.rna

Ontology of Microbial Phenotypes
type: Resource
description: An ontology of phenotypes covering microbes
is part of: bioregistry
git repository: OMP-ontology
keyword: microbial ecology
keyword: obo
keyword: ontology
keyword: dataplant
keyword: chemical biology
keyword: phenotype
keyword: omics
keyword: life sciences, biology
keyword: phenomics
keyword: microbiology
keyword: data analysis
keyword: microbe-host interaction phenotype
0000005: 0005067
has provider formatter: http://purl.obolibrary.org/obo/OMP_$1
has local unique identifier pattern: ^\d{7}$
0000010: omp.owl
is deprecated: false
0000018: Microbial Conditions Ontology
has responsible: James C. Hu
has URI prefix: http://purl.obolibrary.org/obo/OMP_
0000027: OMP_0005067
0000029: omp

SWEET Ontology Realm Astrophysical Heliosphere
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Astrophysical Heliosphere
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: astrophysical heliosphere
keyword: realm
0000005: DLayer
has provider formatter: http://sweetontology.net/realmAstroHelio/$1
is deprecated: false
has alternative prefix: soreaah
has URI prefix: http://sweetontology.net/realmAstroHelio/
0000027: DLayer
0000029: sweet.reaah

SWEET Ontology Representation Mathematics Operation
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Operation
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation mathematics operation
0000005: AreaIntegral
has provider formatter: http://sweetontology.net/reprMathOperation/$1
is deprecated: false
has alternative prefix: sorepmo
has URI prefix: http://sweetontology.net/reprMathOperation/
0000027: AreaIntegral
0000029: sweet.repmo

Suggested Ontology for Pharmacogenomics
type: Resource
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.
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/SOPHARM_$1
0000010: sopharm.owl
is deprecated: true
has responsible: Adrien Coulet
has URI prefix: http://purl.obolibrary.org/obo/SOPHARM_
0000029: sopharm

Health Procedure Ontology
type: Resource
contributor: Paul Fabry
description: HEPRO is an ontology of informational entities and processes related to health procedures and health activities.
is part of: bioregistry
git repository: HEPRO
keyword: ontology
0000005: 0000001
has provider formatter: http://purl.obolibrary.org/obo/HEPRO_$1
has local unique identifier pattern: ^\d{7}$
0000010: HEPRO.owl
is deprecated: false
has responsible: Paul Fabry
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://purl.obolibrary.org/obo/HEPRO_
0000026: 00kybxq39
0000027: HEPRO_0000001
0000029: hepro

EDAM Ontology
type: https://bioregistry.io/schema/#0000002
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 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
has part: data 2298
has part: data 2343
has part: data 2632
has part: data 1002
has part: data 2609
has part: data 2642
has part: data 1182
has part: data 2344
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
has part: data 1176
has part: data 2386

ChemPro Competitor
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for compounds that compete with probes for binding to target proteins.
is part of: bioregistry
0000005: LDCM0160
has provider formatter: https://chemprosquare.idrblab.net/data/competitor/details/$1
has local unique identifier pattern: ^LDCM\d+$
is deprecated: false
has responsible: Feng Zhu
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://chemprosquare.idrblab.net/data/competitor/details/
0000027: LDCM0160
0000029: chempro.competitor

Martin Ramirez

Uber Anatomy Ontology
type: Resource
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.
is part of: bioregistry
git repository: uberon
keyword: life sciences, biology
keyword: anatomy
keyword: taxonomy
keyword: life science
keyword: obo
keyword: ontology
keyword: developmental biology
keyword: dataplant
0000005: 2005080
has provider formatter: http://purl.obolibrary.org/obo/UBERON_$1
has local unique identifier pattern: ^\d+$
0000010: uberon.owl
is deprecated: false
depends on: pato
depends on: go
depends on: Chemical Entities of Biological Interest
depends on: pr
depends on: NCBI Taxonomy
depends on: bspo
depends on: bfo
depends on: Environment Ontology
depends on: cl
depends on: ro
depends on: OBO Metadata Ontology
depends on: nbo
0000018: The Echinoderm Anatomy and Development Ontology
0000018: Health Surveillance Ontology
0000018: Porifera Ontology
0000018: lepao
0000018: plana
0000018: Genomic Epidemiology Ontology
0000018: Provisional Cell Ontology
0000018: Ontology for Nutritional Studies
0000018: go
0000018: maxo
0000018: cteno
0000018: An ontology of core ecological entities
0000018: mfmo
0000018: Coleoptera Anatomy Ontology
0000018: Cell Line Ontology
0000018: fovt
0000018: foodon
0000018: Clytia hemisphaerica Development and Anatomy Ontology
0000018: chiro
0000018: zp
0000018: Environment Ontology
0000018: The Amphioxus Development and Anatomy Ontology
0000018: Environmental conditions, treatments and exposures ontology
0000018: cl
0000018: Microbial Conditions Ontology
0000018: aism
has responsible: https://orcid.org/0000-0002-6601-2165
has alternative prefix: Uberon
has alternative prefix: UBERON
has alternative prefix: Uber-anatomy ontology
has URI prefix: http://purl.obolibrary.org/obo/UBERON_
0000027: UBERON_2005080
0000029: uberon

C. Robin Buell

Dendritic cell
type: Resource
is part of: bioregistry
keyword: obo
keyword: ontology
0000005: 0000003
has provider formatter: http://purl.obolibrary.org/obo/DC_CL_$1
has local unique identifier pattern: ^\d{7}$
is deprecated: true
has responsible: https://orcid.org/0000-0003-1617-8244
has URI prefix: http://purl.obolibrary.org/obo/DC_CL_
0000027: DC CL 0000003
0000029: dc_cl

Carsten Linder

Genetics Home Reference
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
0000005: saddan
has provider formatter: https://medlineplus.gov/genetics/condition/$1
is deprecated: false
has URI prefix: https://medlineplus.gov/genetics/condition/
0000027: saddan
0000029: ghr

Plant Anatomy Ontology
type: Resource
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/PAO_$1
is deprecated: true
has responsible: https://orcid.org/0000-0002-1005-8383
has URI prefix: http://purl.obolibrary.org/obo/PAO_
0000029: pao

BRENDA Tissue Ontology
type: Resource
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.
is part of: bioregistry
git repository: BTO
keyword: life sciences, biology
keyword: enzymology
keyword: tissue
keyword: experimental measurement
keyword: cell
keyword: medicine
keyword: anatomy
keyword: life science
keyword: enzyme
keyword: obo
keyword: ontology
keyword: organ
keyword: cell biology
keyword: dataplant
keyword: genomics
keyword: sample annotation
keyword: nfdi4chem
keyword: omics
keyword: proteomics
0000005: 0000590
has provider formatter: http://purl.obolibrary.org/obo/BTO_$1
has local unique identifier pattern: ^\d{7}$
0000010: bto.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9117-7909
has alternative prefix: BTO
has URI prefix: http://purl.obolibrary.org/obo/BTO_
0000027: BTO_0000590
0000029: bto

ISO 3166-1 Country Code
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An identifier for a country in numeric format per ISO 3166-1
is part of: bioregistry
0000005: 554
has provider formatter: https://data.who.int/countries/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.who.int/countries/
0000027: https://data.who.int/countries/554
0000029: iso.3166

MarDB
type: Resource
description: MarDB includes all sequenced marine microbial genomes regardless of level of completeness.
is part of: bioregistry
0000005: MMP02954345.1
has provider formatter: https://mmp.sfb.uit.no/databases/mardb/#/records/$1
has local unique identifier pattern: ^MMP\d+.\d+$
is deprecated: false
has URI prefix: https://mmp.sfb.uit.no/databases/mardb/#/records/
0000027: records/MMP02954345.1
0000029: mmp.db

Andrew I Su

BacMap Map
type: Resource
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.
is part of: bioregistry
0000005: AP011135
has provider formatter: http://bacmap.wishartlab.com/maps/$1/index.html
has local unique identifier pattern: ^\w+(\_)?\d+(\.\d+)?$
is deprecated: false
has URI prefix: https://bioregistry.io/bacmap.map:
0000027: index.html
0000029: bacmap.map

PubMed Central
type: Resource
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 part of: bioregistry
keyword: biomedical science
keyword: bibliography
keyword: centrally registered identifier
0000005: PMC3084216
has provider formatter: http://europepmc.org/articles/$1
has local unique identifier pattern: ^PMC\d+(\.\d+)?$
is deprecated: false
has responsible: https://orcid.org/0000-0002-1798-9797
has alternative prefix: PMC
has alternative prefix: PMCID
has URI prefix: http://europepmc.org/articles/
0000027: PMC3084216
0000029: pmc

SWEET Ontology State
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state
0000005: BinaryState
has provider formatter: http://sweetontology.net/state/$1
is deprecated: false
has alternative prefix: sost
has URI prefix: http://sweetontology.net/state/
0000027: BinaryState
0000029: sweet.st

Fababean Ontology
type: Resource
description: to add
is part of: bioregistry
git repository: Crop-Ontology
keyword: ontology
0000005: 0000205
has provider formatter: https://cropontology.org/rdf/CO_365:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 365.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_365:
0000027: CO 365:0000205
0000029: co_365

The Cert Ontology
type: Resource
description: Ontology for Certificates and crypto stuff.
is part of: bioregistry
keyword: quality
0000005: Certificate
is deprecated: false
0000029: cert

Name Reaction Ontology
type: Resource
description: RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization.
is part of: bioregistry
git repository: rxno
keyword: obo
keyword: ontology
keyword: chemistry
keyword: nfdi4cat
keyword: nfdi4chem
keyword: molecular chemistry
keyword: reaction data
0000005: 0000253
has provider formatter: http://purl.obolibrary.org/obo/RXNO_$1
has local unique identifier pattern: ^\d{7}$
0000010: rxno.owl
is deprecated: false
has responsible: Colin Batchelor
has URI prefix: http://purl.obolibrary.org/obo/RXNO_
0000027: RXNO_0000253
0000029: rxno

FAIRsharing
type: Resource
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.
is part of: bioregistry
git repository: FAIRsharing
keyword: biomedical science
keyword: life science
keyword: environmental science
keyword: natural science
keyword: ontology and terminology
keyword: policy
keyword: agriculture
keyword: data governance
keyword: database management
keyword: humanities
keyword: earth science
0000005: bsg-000052
has provider formatter: https://fairsharing.org/$1
has local unique identifier pattern: ^(bsg-[dscp]?\d{6})|(FAIRsharing\.\w+)$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7702-4495
has URI prefix: https://fairsharing.org/
0000027: bsg-000052
0000029: fairsharing

GO Evidence Code
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported.
is part of: bioregistry
0000005: IPI
is deprecated: false
0000029: goeco

MediaDive Medium
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
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
0000005: 77
has provider formatter: https://mediadive.dsmz.de/medium/$1
has local unique identifier pattern: ^\d+\w?$
is deprecated: false
has responsible: https://orcid.org/0000-0003-3909-7201
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://mediadive.dsmz.de/medium/
0000027: https://mediadive.dsmz.de/medium/77
0000029: mediadive.medium

SWEET Ontology Material Biomass
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Biomass
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: materials
keyword: biomass
0000005: AnimalWaste
has provider formatter: http://sweetontology.net/matrBiomass/$1
is deprecated: false
has alternative prefix: somab
has URI prefix: http://sweetontology.net/matrBiomass/
0000027: AnimalWaste
0000029: sweet.mab

Bgee stage
type: Resource
contributor: Sébastien Moretti
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.
is part of: bioregistry
0000005: HsapDO:0000004
has provider formatter: http://bgee.unil.ch/bgee/bgee
has local unique identifier pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$
is deprecated: true
has URI prefix: http://bgee.unil.ch/bgee/bgee
0000027: http://bgee.unil.ch/bgee/bgee
0000029: bgee.stage

KEGG Drug
type: Resource
description: KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.
is part of: bioregistry
is part of: kegg
keyword: small molecule
0000005: D00123
has provider formatter: https://www.kegg.jp/entry/$1
has local unique identifier pattern: ^D\d+$
is deprecated: false
has responsible: 0000-0001-6123-540X
has alternative prefix: KEGG DRUG
has alternative prefix: KEGG.DRUG
has URI prefix: https://www.kegg.jp/entry/
0000027: D00123
0000029: kegg.drug

EDAM Topic
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: edamontology
keyword: ontology
0000005: 0003
has provider formatter: http://edamontology.org/topic_$1
has local unique identifier pattern: ^\d+$
0000010: EDAM.obo
is deprecated: false
has responsible: Matúš Kalaš
has URI prefix: http://edamontology.org/topic_
0000027: topic_0003
0000029: edam.topic

SAGE Social Science Thesaurus
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: -LHR8P7WS-K
has provider formatter: http://data.loterre.fr/ark:/67375/N9J$1
is deprecated: false
has URI prefix: http://data.loterre.fr/ark:/67375/N9J
0000027: N9J-LHR8P7WS-K
0000029: sage.socialsciencethesaurus

Ruben Abagyan

Gene Ontology Database references
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.
is part of: bioregistry
0000005: 0000041
has provider formatter: https://geneontology.org/GO_REF/$1
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has URI prefix: https://geneontology.org/GO_REF/
0000027: https://geneontology.org/GO_REF/0000041
0000029: go.ref

Integrated Microbial Genomes Gene
type: Resource
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.
is part of: bioregistry
keyword: gene
keyword: genome
0000005: 638309541
has provider formatter: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6131-0462
has URI prefix: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
0000027: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
0000029: img.gene

Homosaurus
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An international LGBTQ+ linked data vocabulary
is part of: bioregistry
git repository: homosaurus site
0000005: queerNewspapers
has provider formatter: http://homosaurus.org/terms/$1
is deprecated: false
0000018: gsso
has responsible: 0000-0003-1769-112X
has URI prefix: http://homosaurus.org/terms/
0000027: queerNewspapers
0000029: homosaurus

Metabolic Atlas
type: Resource
contributor: https://orcid.org/0000-0002-7753-9042
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 part: metatlas.metabolite
has part: metatlas.reaction
is part of: bioregistry
keyword: reactions
keyword: metabolites
keyword: chemistry
0000005: MAM01234c
has provider formatter: https://metabolicatlas.org/identifier/MetabolicAtlas/$1
has local unique identifier pattern: ^(MAM\d{5}\w)|(MAR\d{5})$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7753-9042
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://metabolicatlas.org/identifier/MetabolicAtlas/
0000027: MAM01234c
0000029: metatlas

Archival Resource Key
type: Resource
contributor: https://orcid.org/0000-0001-7604-8041
contributor: Sumir Pandit
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: arks-org
keyword: data retrieval
keyword: subject agnostic
0000005: /53355/cl010066723
has provider formatter: http://n2t.net/ark:$1
has local unique identifier pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$
is deprecated: false
has responsible: https://orcid.org/0000-0001-7604-8041
has URI prefix: http://n2t.net/ark:
0000027: cl010066723
0000029: ark

ISA Programme Location Core Vocabulary
type: Resource
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.
is part of: bioregistry
keyword: geography
keyword: geometry
0000005: Address
is deprecated: false
0000029: locn

FuncBase Yeast
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 yeast.
is part of: bioregistry
0000005: 2701
has provider formatter: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://func.mshri.on.ca/yeast/genes/list_functional_scores/
0000027: http://func.mshri.on.ca/yeast/genes/list_functional_scores/2701
0000029: funcbase.yeast

Datanator Gene
type: Resource
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 part of: bioregistry
0000005: K00973
has provider formatter: https://www.datanator.info/gene/$1
has local unique identifier pattern: ^K[0-9]+$
is deprecated: false
has URI prefix: https://www.datanator.info/gene/
0000027: K00973
0000029: datanator.gene

TAIR Gene
type: Resource
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.
is part of: bioregistry
keyword: gene
0000005: 2200934
has provider formatter: http://arabidopsis.org/servlets/TairObject
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: 0000-0003-3871-858X
has URI prefix: http://arabidopsis.org/servlets/TairObject
0000027: http://arabidopsis.org/servlets/TairObject
0000029: tair.gene

SCancerRNA
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
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.
is part of: bioregistry
0000005: 9530
has provider formatter: http://www.scancerrna.com/toDetail
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Tianyi Zhao
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: http://www.scancerrna.com/toDetail
0000027: http://www.scancerrna.com/toDetail
0000029: scancerrna

WiCell Research Institute Cell Collection
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
0000005: ai10e-kctd13b
has provider formatter: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx
is deprecated: false
has URI prefix: https://bioregistry.io/wicell:
0000027: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/ai10e-kctd13b.cmsx
0000029: wicell

International Traditional Medicine Clinical Trial Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
0000005: ITMCTR2023000002
has local unique identifier pattern: ^ITMCTR\d+$
is deprecated: false
0000029: itmctr

CATH superfamily
type: Resource
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.
is part of: bioregistry
is part of: cath
0000005: 1.10.10.200
has provider formatter: http://www.cathdb.info/cathnode/$1
has local unique identifier pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$
is deprecated: false
has URI prefix: http://www.cathdb.info/cathnode/
0000027: http://www.cathdb.info/cathnode/1.10.10.200
0000029: cath.superfamily

European Language Social Science Thesaurus
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
keyword: economics
keyword: social science
has provider formatter: https://elsst.cessda.eu/id/3/$1
is deprecated: false
has responsible: https://orcid.org/0000-0003-1003-0281
has URI prefix: https://elsst.cessda.eu/id/3/
0000029: elsst

C. elegans phenotype
type: Resource
description: Ontology about C. elegans and other nematode phenotypes
is part of: bioregistry
git repository: c-elegans-phenotype-ontology
keyword: phenomics
keyword: anatomy
keyword: life science
keyword: obo
keyword: ontology
keyword: worm
keyword: phenotype
keyword: omics
0000005: 0000983
has provider formatter: http://purl.obolibrary.org/obo/WBPhenotype_$1
has local unique identifier pattern: ^\d{7}$
0000010: wbphenotype.owl
is deprecated: false
has responsible: Chris Grove
has alternative prefix: WBPhenotype
has URI prefix: http://purl.obolibrary.org/obo/WBPhenotype_
0000027: WBPhenotype_0000983
0000029: wbphenotype

Document Components Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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).
is part of: bioregistry
git repository: doco
keyword: spar
keyword: subject agnostic
0000005: Paragraph
has provider formatter: http://purl.org/spar/doco/$1
is deprecated: false
has responsible: Silvio Peroni
has URI prefix: http://purl.org/spar/doco/
0000027: Paragraph
0000029: doco

GitHub account
type: Resource
description: GitHub is an online host of Git source code repositories.
is part of: bioregistry
git repository: services.github.com
keyword: knowledge and information systems
keyword: subject agnostic
keyword: software engineering
0000005: biopragmatics/bioregistry
has provider formatter: https://github.com/$1
has local unique identifier pattern: ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$
is deprecated: false
has URI prefix: https://github.com/
0000027: bioregistry
0000029: github

Glottolog
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Comprehensive reference information for the world's languages, especially the lesser known languages. [from homepage]
is part of: bioregistry
0000005: nort3314
has provider formatter: https://glottolog.org/resource/languoid/id/$1
is deprecated: false
0000018: gsso
has URI prefix: https://glottolog.org/resource/languoid/id/
0000027: nort3314
0000029: glottolog

Ensembl Plants
type: Resource
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
keyword: genome
0000005: AT1G73965
has provider formatter: https://plants.ensembl.org/id/$1
has local unique identifier pattern: ^\w+(\.\d+)?(\.\d+)?$
is deprecated: false
has URI prefix: https://plants.ensembl.org/id/
0000027: AT1G73965
0000029: ensembl.plant

CTD Chemical
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.
is part of: bioregistry
0000005: D001151
has provider formatter: http://ctdbase.org/detail.go
has local unique identifier pattern: ^[CD]\d+$
0000011: mesh
is deprecated: false
has URI prefix: http://ctdbase.org/detail.go
0000027: http://ctdbase.org/detail.go
0000029: ctd.chemical

StoreDB Dataset
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Datasets inside StoreDB at University of Cambridge
is part of: bioregistry
0000005: 1251
has provider formatter: https://www.storedb.org/
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: https://www.storedb.org/
0000027: https://www.storedb.org/
0000029: storedb.dataset

Minimum Information about a Tailoring Enzyme data repository
type: Resource
contributor: Mitja M. Zdouc
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.
is part of: bioregistry
git repository: mite data
0000005: MITE0000001
has provider formatter: https://mite.bioinformatics.nl/repository/$1
has local unique identifier pattern: ^MITE\d{7}$
is deprecated: false
has responsible: Mitja M. Zdouc
has reviewer: https://orcid.org/0000-0003-4423-4370
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://mite.bioinformatics.nl/repository/
0000027: MITE0000001
0000029: mite

Sorghum Ontology
type: Resource
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.
is part of: bioregistry
git repository: Crop-Ontology
keyword: food
keyword: ontology
keyword: phenotype
keyword: botany
keyword: agriculture
0000005: 0000111
has provider formatter: https://cropontology.org/rdf/CO_324:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 324.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_324:
0000027: CO 324:0000111
0000029: co_324

Genome Taxonomy Database
type: Resource
contributor: https://orcid.org/0000-0003-1982-9065
description: The Genome Taxonomy Database (GTDB) is an initiative to establish a standardized microbial taxonomy based on genome phylogeny.
is part of: bioregistry
keyword: taxonomy
keyword: ontology
0000005: g__Prochlorococcus_A
has provider formatter: https://gtdb.ecogenomic.org/tree
has local unique identifier pattern: ^[cdfgops]__\w+\S+$
0000010: gtdb.owl
is deprecated: false
has responsible: Donovan Parks
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://gtdb.ecogenomic.org/tree
0000027: https://gtdb.ecogenomic.org/tree
0000029: gtdb

Homologous Organ Groups
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc.
is part of: bioregistry
keyword: ontology
0000005: 0000255
has provider formatter: https://biopragmatics.github.io/providers/hog/$1
has local unique identifier pattern: ^\d{7}$
0000010: HOG.obo
is deprecated: false
has URI prefix: https://biopragmatics.github.io/providers/hog/
0000027: https://biopragmatics.github.io/providers/hog/0000255
0000029: hog

LigandBook
type: Resource
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.
is part of: bioregistry
0000005: 785
has provider formatter: https://ligandbook.org/package/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has URI prefix: https://ligandbook.org/package/
0000027: https://ligandbook.org/package/785
0000029: ligandbook

SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain
type: Resource
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…
is part of: bioregistry
keyword: ontology
keyword: engineering
keyword: iot
keyword: nfdi4ing
0000005: Activity
has provider formatter: https://saref.etsi.org/saref4ehaw/$1
0000010: s4ehaw.owl
is deprecated: false
has responsible: LOV Migration
has alternative prefix: s4ehaw
has URI prefix: https://saref.etsi.org/saref4ehaw/
0000027: Activity
0000029: saref.ehaw

Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse
type: Resource
description: The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.
is part of: bioregistry
keyword: gene
keyword: life science
0000005: humIGHV025
has provider formatter: http://www.vbase2.org/vgene.php
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-1297-9725
has URI prefix: http://www.vbase2.org/vgene.php
0000027: http://www.vbase2.org/vgene.php
0000029: vbase2

NASA Open Science Data Repository Experiment
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for space-related data from experiments that investigate biological and health responses of terrestrial life to spaceflight
is part of: bioregistry
0000005: OS-27
has provider formatter: https://osdr.nasa.gov/bio/repo/data/experiments/$1
has local unique identifier pattern: ^OS-\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8542-2389
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://osdr.nasa.gov/bio/repo/data/experiments/
0000027: OS-27
0000029: nasaosdr.experiment

Subcellular Anatomy Ontology
type: Resource
description: SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.
is part of: bioregistry
keyword: owl
keyword: biochemistry
keyword: obo
keyword: ontology
0000005: 5277619
has provider formatter: http://uri.neuinfo.org/nif/nifstd/sao$1
has local unique identifier pattern: ^\d+$
0000010: sao.owl
is deprecated: true
has responsible: Stephen Larson
has URI prefix: http://uri.neuinfo.org/nif/nifstd/sao
0000027: sao5277619
0000029: sao

Korean Clinical Research Information Service
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
0000005: KCT0008394
has local unique identifier pattern: ^KCT\d+$
is deprecated: false
0000029: kcris

NIF Dysfunction
type: Resource
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1
is deprecated: true
has responsible: 0000-0003-4752-543X
has URI prefix: http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_
0000029: nif.dysfunction

SWEET Ontology Property Ordinal
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Ordinal
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: ordinal
0000005: ActivityLevel
has provider formatter: http://sweetontology.net/propOrdinal/$1
is deprecated: false
has alternative prefix: sopropo
has URI prefix: http://sweetontology.net/propOrdinal/
0000027: ActivityLevel
0000029: sweet.propo

The COnCEPT upper-level Design Ontology
type: Resource
description: The COnCEPT upper-level Design Ontology (COnDO).
is part of: bioregistry
keyword: engineering
keyword: nfdi4ing
0000005: AestheticFunction
has provider formatter: http://www.w3id.org/Concept/Ontology/COnDO#$1
is deprecated: false
has URI prefix: http://www.w3id.org/Concept/Ontology/COnDO#
0000027: AestheticFunction
0000029: condo

Ontology for Nutritional Studies
type: Resource
description: An ontology for description of concepts in the nutritional studies domain.
is part of: bioregistry
git repository: Ontology-for-Nutritional-Studies
keyword: biomedical science
keyword: nutritional science
keyword: obo
keyword: ontology
0000005: 0000060
has provider formatter: http://purl.obolibrary.org/obo/ONS_$1
has local unique identifier pattern: ^\d{7}$
0000010: ons.owl
is deprecated: false
depends on: Chemical Entities of Biological Interest
depends on: NCBI Taxonomy
depends on: bfo
depends on: foodon
depends on: Environment Ontology
depends on: ro
depends on: Ontology for Biomedical Investigations
depends on: Uber Anatomy Ontology
0000018: one
has responsible: Francesco Vitali
has URI prefix: http://purl.obolibrary.org/obo/ONS_
0000027: ONS_0000060
0000029: ons

BacMap Biography
type: Resource
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 part of: bioregistry
0000005: 1050
has provider formatter: http://bacmap.wishartlab.com/organisms/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://bacmap.wishartlab.com/organisms/
0000027: http://bacmap.wishartlab.com/organisms/1050
0000029: bacmap.biog

OBO in OWL
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties
is part of: bioregistry
git repository: go-ontology
keyword: life science
keyword: ontology
0000005: hasDbXref
has provider formatter: http://www.geneontology.org/formats/oboInOwl#$1
has local unique identifier pattern: ^[\w-]+$
0000010: oboInOwl.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
has alternative prefix: oboformat
has alternative prefix: oio
has URI prefix: http://www.geneontology.org/formats/oboInOwl#
0000027: hasDbXref
0000029: oboinowl

Dutch Research Council File Number
type: Resource
contributor: Tim Vandermeersch
description: Dutch Research Council file numbers are used for approved grants.
is part of: bioregistry
0000005: osf232097
has provider formatter: https://www.nwo.nl/en/projects/$1
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.nwo.nl/en/projects/
0000027: osf232097
0000029: drc.filenumber

National Uniform Claim Committee Taxonomy
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: 207LH0002X
has local unique identifier pattern: ^\d{3}\w(\w|\d_)\d{4}X$
is deprecated: false
0000029: nucc.taxonomy

Novus Biologicals
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vendor of antibodies and other biologics
is part of: bioregistry
0000005: nb100-56351
has provider formatter: https://www.novusbio.com/products/$1
is deprecated: false
has URI prefix: https://www.novusbio.com/products/
0000027: nb100-56351
0000029: novus

COMBINE specifications
type: Resource
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 part of: bioregistry
0000005: sed-ml.level-1.version-1
has provider formatter: https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md
has local unique identifier pattern: ^\w+(\-|\.|\w)*$
is deprecated: false
has URI prefix: https://bioregistry.io/combine.specifications:
0000027: sed-ml.level-1.version-1.md
0000029: combine.specifications

Broad Fungal Genome Initiative
type: Resource
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.
is part of: bioregistry
0000005: S7000002168151102
has provider formatter: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html
has local unique identifier pattern: ^S\d+$
is deprecated: false
has URI prefix: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html
0000027: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html
0000029: broad

GoodRelations
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary for e-commerce
is part of: bioregistry
keyword: ebusiness
0000005: category
has provider formatter: http://purl.org/goodrelations/v1#$1
is deprecated: false
has URI prefix: http://purl.org/goodrelations/v1#
0000027: category
0000029: gr

Allotrope result
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The result component of the Allotrope ontology suite
is part of: bioregistry
is part of: afo
0000005: 0001055
has provider formatter: http://purl.allotrope.org/ontologies/result#AFR_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://purl.allotrope.org/ontologies/result#AFR_
0000027: AFR_0001055
0000029: allotrope.result

AspGD Protein
type: Resource
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.
is part of: bioregistry
0000005: ASPL0000349247
has provider formatter: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl
has local unique identifier pattern: ^[A-Za-z_0-9]+$
is deprecated: true
has URI prefix: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl
0000027: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl
0000029: aspgd.protein

Integrated Chemical Environment - Chemical data
type: Resource
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.
is part of: bioregistry
0000005: DTXSID7032004
has provider formatter: https://ice.ntp.niehs.nih.gov/api/v1/search
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]$
is deprecated: false
has URI prefix: https://ice.ntp.niehs.nih.gov/api/v1/search
0000027: https://ice.ntp.niehs.nih.gov/api/v1/search
0000029: icechem

Candida Genome Database
type: Resource
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.
is part of: bioregistry
keyword: nucleotide
keyword: life science
keyword: eukaryotic
keyword: genome
0000005: CAL0003079
has provider formatter: http://www.candidagenome.org/cgi-bin/locus.pl
has local unique identifier pattern: ^CAL\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-1692-4983
has URI prefix: http://www.candidagenome.org/cgi-bin/locus.pl
0000027: http://www.candidagenome.org/cgi-bin/locus.pl
0000029: cgd

Next Generation Biobanking Ontology
type: Resource
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
git repository: NGBO
keyword: obo
keyword: ontology
0000005: 6000122
has provider formatter: http://purl.obolibrary.org/obo/NGBO_$1
has local unique identifier pattern: ^\d{7}$
0000010: ngbo.owl
is deprecated: false
has responsible: Dalia Alghamdi
has URI prefix: http://purl.obolibrary.org/obo/NGBO_
0000027: NGBO_6000122
0000029: ngbo

Hathi Trust Digital Library
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world.
is part of: bioregistry
0000005: 008893080
has provider formatter: https://catalog.hathitrust.org/Record/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://catalog.hathitrust.org/Record/
0000027: https://catalog.hathitrust.org/Record/008893080
0000029: hathitrust

Clinical Trials Ontology
type: Resource
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.
is part of: bioregistry
git repository: CTO
keyword: neurobiology
keyword: disease
keyword: preclinical studies
keyword: biomedical science
keyword: obo
keyword: ontology
0000005: 0000022
has provider formatter: http://purl.obolibrary.org/obo/CTO_$1
has local unique identifier pattern: ^\d{7}$
0000010: cto.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9896-3531
has URI prefix: http://purl.obolibrary.org/obo/CTO_
0000027: CTO_0000022
0000029: cto

Metadata Management and distribution system for Multiple GNSS Networks
type: Resource
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 part of: bioregistry
0000005: station.6051b2f8b9142a5b8c676342
has provider formatter: https://gnss-metadata.eu/MOID/$1
has local unique identifier pattern: ^[a-zA-Z0-9]+\.[a-f0-9]{24}$
is deprecated: false
has URI prefix: https://gnss-metadata.eu/MOID/
0000027: station.6051b2f8b9142a5b8c676342
0000029: moid

NASA Open Science Data Repository Subject
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for subjects of experiments that investigate biological and health responses of terrestrial life to spaceflight
is part of: bioregistry
0000005: 58
has provider formatter: https://osdr.nasa.gov/bio/repo/data/subjects/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8542-2389
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://osdr.nasa.gov/bio/repo/data/subjects/
0000027: https://osdr.nasa.gov/bio/repo/data/subjects/58
0000029: nasaosdr.subject

Simple Modular Architecture Research Tool
type: Resource
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.
is part of: bioregistry
keyword: structure
keyword: life science
keyword: domain
keyword: protein
0000005: SM00015
has provider formatter: http://smart.embl-heidelberg.de/smart/do_annotation.pl
has local unique identifier pattern: ^SM\d{5}$
is deprecated: false
has responsible: Chris P. Ponting
has URI prefix: http://smart.embl-heidelberg.de/smart/do_annotation.pl
0000027: http://smart.embl-heidelberg.de/smart/do_annotation.pl
0000029: smart

JRC Data Catalogue
type: Resource
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.
is part of: bioregistry
0000005: jrc-eurl-ecvam-chemagora
has provider formatter: http://data.europa.eu/89h/$1
has local unique identifier pattern: ^[a-z0-9\-_]+$
is deprecated: false
has URI prefix: http://data.europa.eu/89h/
0000027: jrc-eurl-ecvam-chemagora
0000029: eu89h

Metabolomics Standards Initiative Ontology
type: Resource
description: an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.
is part of: bioregistry
git repository: MSIO
keyword: omics
keyword: life sciences, biology
keyword: data analysis
keyword: annotation
keyword: experimental measurement
keyword: mass spectrum
keyword: nmr
keyword: nuclear magnetic resonance spectroscopy
keyword: ontology
keyword: functional magnetic resonance imaging
keyword: dataplant
keyword: metabolomics
0000005: 0000111
has provider formatter: http://purl.obolibrary.org/obo/MSIO_$1
has local unique identifier pattern: ^\d{7}$
0000010: MSIO-merged-reasoned.owl
is deprecated: false
has responsible: Philippe Rocca-Serra
has URI prefix: http://purl.obolibrary.org/obo/MSIO_
0000027: MSIO_0000111
0000029: msio

Oryzabase Stage
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 development stage information.
is part of: bioregistry
0000005: 34
has provider formatter: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/
0000027: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/34
0000029: oryzabase.stage

Li-San Wang

Human developmental anatomy, abstract version
type: Resource
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 part of: bioregistry
keyword: development
keyword: anatomy
keyword: obo
keyword: human
keyword: ontology
0000005: 1
has provider formatter: http://purl.obolibrary.org/obo/EHDAA_$1
has local unique identifier pattern: ^\d+$
0000010: ehdaa.obo
is deprecated: true
has responsible: Jonathan Bard
has URI prefix: http://purl.obolibrary.org/obo/EHDAA_
0000027: EHDAA 1
0000029: ehdaa

Agilent Probe
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: transcriptomics
0000005: A_24_P98555
has local unique identifier pattern: ^A_\d+_.+$
is deprecated: false
0000029: agilent.probe

nmrXiv compound
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: compounds appearing in nmrXiv that have associated spectra.
is part of: bioregistry
keyword: chemical
keyword: compound
0000005: 188
has provider formatter: https://nmrxiv.org/spectra
is deprecated: false
has responsible: https://orcid.org/0000-0002-2564-3243
has URI prefix: https://nmrxiv.org/spectra
0000027: https://nmrxiv.org/spectra
0000029: nmrxiv.compound

SWEET Ontology Process Physical
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process Physical
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: physical
0000005: Abrasion
has provider formatter: http://sweetontology.net/procPhysical/$1
is deprecated: false
has alternative prefix: soprocp
has URI prefix: http://sweetontology.net/procPhysical/
0000027: Abrasion
0000029: sweet.procp

Lipid Ontology
type: Resource
description: An ontology representation of the LIPIDMAPS nomenclature classification.
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/LIPRO_$1
0000010: lipro.owl
is deprecated: true
has responsible: Christopher Baker
has URI prefix: http://purl.obolibrary.org/obo/LIPRO_
0000029: lipro

UM-BBD compound
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 compound information.
is part of: bioregistry
0000005: c0001
has provider formatter: http://eawag-bbd.ethz.ch/servlets/pageservlet
has local unique identifier pattern: ^c\d+$
is deprecated: false
has alternative prefix: UM-BBD_compID
has URI prefix: http://eawag-bbd.ethz.ch/servlets/pageservlet
0000027: http://eawag-bbd.ethz.ch/servlets/pageservlet
0000029: umbbd.compound

SEED Subsystem
type: Resource
contributor: Sam Seaver
contributor: https://orcid.org/0000-0003-1982-9065
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.
is part of: bioregistry
git repository: TheSEED
0000005: Biotin_biosynthesis
has provider formatter: https://pubseed.theseed.org/SubsysEditor.cgi
has local unique identifier pattern: ^\w+$
is deprecated: true
has alternative prefix: seed
has URI prefix: https://pubseed.theseed.org/SubsysEditor.cgi
0000027: https://pubseed.theseed.org/SubsysEditor.cgi
0000029: seed.subsystem

Crop Ontology Curation Tool
type: https://bioregistry.io/schema/#0000002
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 343
has part: CO 323
has part: CO 358
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
has part: CO 321
has part: CO 335
has part: CO 324
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
0000005: CO_325
has provider formatter: https://cropontology.org/ontology/$1
has resolver formatter: https://cropontology.org/term/$1:$2
has responsible: https://orcid.org/0000-0002-6020-5919

Lattes Platform number
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: number for the Lattes Platform entry on the person or group. Relationship between entry and subject must be supported by a source.
is part of: bioregistry
keyword: person
keyword: researcher
0000005: 0061106995455595
has provider formatter: https://lattes.cnpq.br/$1
has local unique identifier pattern: ^\d{16}$
is deprecated: false
has URI prefix: https://lattes.cnpq.br/
0000027: https://lattes.cnpq.br/0061106995455595
0000029: lattes

Henning Hermjakob

SWEET Ontology Property Difference
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Difference
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: difference
0000005: Amplitude
has provider formatter: http://sweetontology.net/propDifference/$1
is deprecated: false
has alternative prefix: sopropdife
has URI prefix: http://sweetontology.net/propDifference/
0000027: Amplitude
0000029: sweet.propdife

Current Procedural Terminology
type: Resource
contributor: 0000-0003-2975-882X
contributor: https://orcid.org/0000-0002-8719-7760
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
keyword: biomedical science
keyword: health science
keyword: medicine
keyword: ontology
0000005: 00103
has provider formatter: https://www.aapc.com/codes/cpt-codes/$1
has local unique identifier pattern: ^\d+$
0000010: cpt.owl
is deprecated: false
has responsible: American Medical Association
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: ama-cpt
has URI prefix: https://www.aapc.com/codes/cpt-codes/
0000027: https://www.aapc.com/codes/cpt-codes/00103
0000029: cpt

Mouse adult gross anatomy
type: Resource
description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus)
is part of: bioregistry
git repository: adult-mouse-anatomy-ontology
keyword: organ
keyword: ontology
keyword: mouse
keyword: tissue
keyword: anatomy
keyword: obo
0000005: 0002502
has provider formatter: http://purl.obolibrary.org/obo/MA_$1
has local unique identifier pattern: ^\d+$
0000010: ma.owl
is deprecated: false
has responsible: Terry Hayamizu
has URI prefix: http://purl.obolibrary.org/obo/MA_
0000027: MA_0002502
0000029: ma

FlyBrain Neuron Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A database of fly neurons and pathways with an associated 3D viewer.
is part of: bioregistry
0000005: 10531
has provider formatter: https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://bioregistry.io/flybrain.ndb:
0000027: https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=10531&-find=-find.html
0000029: flybrain.ndb

Provenance, Authoring, and Versioning Vocabulary
type: Resource
contributor: https://orcid.org/0000-0002-7356-1779
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: pav
keyword: subject agnostic
keyword: data management
keyword: ontology
keyword: resource metadata
keyword: quality
0000005: authoredBy
has provider formatter: http://purl.org/pav/$1
has local unique identifier pattern: ^[a-z][a-zA-Z]+$
0000010: pav.owl
is deprecated: false
has responsible: Stian Soiland-Reyes
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://purl.org/pav/
0000027: authoredBy
0000029: pav

EVORA Ontology
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]
is part of: bioregistry
git repository: evora-ontology
keyword: ontology
0000005: AlternateName
has provider formatter: https://w3id.org/evorao/$1
0000010: evorao.owl
is deprecated: false
has responsible: d3fk
has URI prefix: https://w3id.org/evorao/
0000027: AlternateName
0000029: evorao

The S/MAR transaction DataBase
type: Resource
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.
is part of: bioregistry
keyword: protein
0000005: SM0000020
has provider formatter: http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi
0000027: http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi
0000029: s_mart_db

Dublin Core Types
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
keyword: ontology
0000005: Collection
has provider formatter: http://purl.org/dc/dcmitype/$1
0000010: dcmitype.owl
is deprecated: false
has responsible: Kim Durante
has alternative prefix: dcmitype
has alternative prefix: dcmitypes
has URI prefix: http://purl.org/dc/dcmitype/
0000027: Collection
0000029: dctypes

Wikidata Property
type: https://bioregistry.io/schema/#0000002
description: An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries.
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 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

WikiData Support

The SEED
type: Resource
contributor: Sam Seaver
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.
is part of: bioregistry
git repository: TheSEED
0000005: Histidinol dehydrogenase (EC 1.1.1.23)
has provider formatter: https://pubseed.theseed.org/SubsysEditor.cgi
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://pubseed.theseed.org/SubsysEditor.cgi
0000029: seed.role

Mungbean Ontology
type: Resource
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.
is part of: bioregistry
git repository: Crop-Ontology
keyword: food
keyword: ontology
keyword: plant phenotypes and traits
keyword: phenotype
keyword: agriculture
keyword: life science
0000005: 0000199
has provider formatter: https://cropontology.org/rdf/CO_346:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 346.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_346:
0000027: CO 346:0000199
0000029: co_346

MIRIAM Registry collection
type: Resource
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.
is part of: bioregistry
0000005: 00000008
has provider formatter: https://www.ebi.ac.uk/miriam/main/$1
has local unique identifier pattern: ^000\d{5}$
is deprecated: true
has URI prefix: https://www.ebi.ac.uk/miriam/main/
0000027: https://www.ebi.ac.uk/miriam/main/00000008
0000029: miriam.collection

Erik van Nimwegen

Flybase Cell Line
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The cell line vocabulary inside FlyBase
is part of: bioregistry
0000005: 0000190
has provider formatter: https://flybase.org/reports/FBtc$1
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has alternative prefix: FlyBase_Cell_line
has URI prefix: https://flybase.org/reports/FBtc
0000027: FBtc0000190
0000029: fbtc

NeuroLex Dysfunction
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc.
is part of: bioregistry
keyword: disorders
keyword: disease
keyword: phenotypes
0000005: 20090602
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
0000018: Mondo Disease Ontology
has responsible: Tom Gillespie
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_dys_
0000027: nlx dys 20090602
0000029: nlx.dys

Regulation of Transcription Ontology
type: Resource
description: Regulation of Transcription
is part of: bioregistry
keyword: life science
keyword: ontology
keyword: regulation of gene expression
keyword: transcriptomics
keyword: transcript
0000010: reto.owl
is deprecated: false
has responsible: Vladimir Mironov
0000029: reto

ISO Object Identifier
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: https://orcid.org/0009-0001-5055-9262
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.
is part of: bioregistry
0000005: 2.16.840
has provider formatter: https://oid-base.com/get/$1
has local unique identifier pattern: ^[\d.]+$
is deprecated: false
has responsible: https://orcid.org/0009-0001-5055-9262
has URI prefix: https://oid-base.com/get/
0000027: https://oid-base.com/get/2.16.840
0000029: oid

HUGO Gene Nomenclature Committee
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. HGNC identifiers refer to records in the HGNC symbol database.
is part of: bioregistry
keyword: gene
keyword: life science
keyword: pseudogene
keyword: ncrna
keyword: classification
keyword: ontology
keyword: protein
keyword: gene name
0000005: 16793
has provider formatter: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1
has local unique identifier pattern: ^\d{1,5}$
0000010: hgnc.owl.gz
is deprecated: false
has responsible: Elspeth Bruford
has responsible: Susan Tweedie
has URI prefix: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/
0000027: !/hgnc id/16793
0000029: hgnc

Jose P. Faria

Human Pluripotent Stem Cell Registry
type: Resource
description: hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).
is part of: bioregistry
keyword: life science
keyword: biomedical science
0000005: BCRTi001-A
has provider formatter: https://hpscreg.eu/cell-line/$1
has local unique identifier pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8411-3226
has URI prefix: https://hpscreg.eu/cell-line/
0000027: BCRTi001-A
0000029: hpscreg

The Amphioxus Development and Anatomy Ontology
type: Resource
contributor: Sumir Pandit
description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).
is part of: bioregistry
git repository: amphx ontology
keyword: obo
keyword: ontology
0000005: 1000160
has provider formatter: http://purl.obolibrary.org/obo/AMPHX_$1
has local unique identifier pattern: ^\d+$
0000010: amphx.owl
is deprecated: false
depends on: Uber Anatomy Ontology
has responsible: Hector Escriva
has URI prefix: http://purl.obolibrary.org/obo/AMPHX_
0000027: AMPHX_1000160
0000029: amphx

SWEET Ontology State Role Chemical
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Chemical
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state role chemical
0000005: ChemicalRole
has provider formatter: http://sweetontology.net/stateRoleChemical/$1
is deprecated: false
has alternative prefix: sostrc
has URI prefix: http://sweetontology.net/stateRoleChemical/
0000027: ChemicalRole
0000029: sweet.strc

GeneAnnot: Microarray Gene Annotation
type: Resource
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.
is part of: bioregistry
keyword: gene expression
0000005: GSTA1
is deprecated: false
0000029: genecards.geneannot

CropMRepository
type: Resource
description: CropMRespository is a database of soil and crop biophysical process models.
is part of: bioregistry
0000005: 000000001
has provider formatter: http://www.crop2ml.org/cropmdb/$1
has local unique identifier pattern: ^[0-9]{9}$
is deprecated: false
has URI prefix: http://www.crop2ml.org/cropmdb/
0000027: http://www.crop2ml.org/cropmdb/000000001
0000029: crop2ml

Protein Interaction Network Analysis
type: Resource
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.
is part of: bioregistry
keyword: life science
keyword: data visualization
0000005: Q13485
has provider formatter: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do
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])$
0000011: uniprot
is deprecated: false
has responsible: 0000-0002-8876-128X
has URI prefix: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do
0000027: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do
0000029: pina

Conserved Domain Database at NCBI
type: Resource
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.
is part of: bioregistry
keyword: structure
keyword: protein
0000005: cd00400
has provider formatter: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi
has local unique identifier pattern: ^(cd)?\d{5}$
is deprecated: false
has URI prefix: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi
0000027: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi
0000029: cdd

Discourse Elements Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: deo
keyword: spar
keyword: subject agnostic
0000005: Reference
has provider formatter: http://purl.org/spar/deo/$1
is deprecated: false
has responsible: Silvio Peroni
has URI prefix: http://purl.org/spar/deo/
0000027: Reference
0000029: deo

Mauno Vihinen

has resolver formatter
type: Property
description: The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved.
domain: https://bioregistry.io/schema/#0000002
range: string

Genome Properties
type: Resource
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.
is part of: bioregistry
keyword: genome
keyword: classification
0000005: GenProp0699
has provider formatter: https://www.ebi.ac.uk/interpro/genomeproperties/#$1
has local unique identifier pattern: ^GenProp\d+$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/interpro/genomeproperties/#
0000026: 02catss52
0000027: GenProp0699
0000029: genprop

Rodent Unidentified Gene-Encoded Large Proteins
type: Resource
description: The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.
is part of: bioregistry
keyword: life science
keyword: dna
keyword: protein
0000005: mKIAA4200
has provider formatter: https://www.kazusa.or.jp/rouge/gfpage/$1
has local unique identifier pattern: ^m\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3328-9571
has URI prefix: https://www.kazusa.or.jp/rouge/gfpage/
0000027: mKIAA4200
0000029: rouge

Europe PMC Preprints
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: Javier Millán Acosta
contributor: Tim Vandermeersch
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.
is part of: bioregistry
keyword: bibliometrics
keyword: preprints
keyword: publishing
0000005: PPR103739
has provider formatter: https://europepmc.org/article/ppr/$1
has local unique identifier pattern: ^PPR\d+$
is deprecated: false
has URI prefix: https://europepmc.org/article/ppr/
0000027: PPR103739
0000029: ppr

SWEET Ontology Process
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: process
0000005: Force
has provider formatter: http://sweetontology.net/proc/$1
is deprecated: false
has alternative prefix: soproc
has URI prefix: http://sweetontology.net/proc/
0000027: Force
0000029: sweet.proc

Richard John Roberts

SAREF4EE: the EEbus/Energy@home extension of SAREF
type: Resource
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.
is part of: bioregistry
keyword: nfdi4ing
keyword: services
keyword: digital planning and construction
keyword: engineering
keyword: environment
keyword: fid baudigital
keyword: nfdi4energy
0000005: ActuatorLevel
has provider formatter: https://saref.etsi.org/saref4ener/$1
is deprecated: false
has alternative prefix: s4ener
has URI prefix: https://saref.etsi.org/saref4ener/
0000027: ActuatorLevel
0000029: saref.ener

Open Citation Identifier
type: Resource
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.
is part of: bioregistry
0000005: 01027931310-01022252312
has provider formatter: https://opencitations.net/index/ci/$1
has local unique identifier pattern: ^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$
is deprecated: false
has URI prefix: https://opencitations.net/index/ci/
0000027: https://opencitations.net/index/ci/01027931310-01022252312
0000029: oci

HomoloGene
type: Resource
description: HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.
is part of: bioregistry
keyword: genome
keyword: gene
keyword: life science
0000005: 1000
has provider formatter: https://www.ncbi.nlm.nih.gov/homologene/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Eric W. Sayers
has URI prefix: https://www.ncbi.nlm.nih.gov/homologene/
0000027: https://www.ncbi.nlm.nih.gov/homologene/1000
0000029: homologene

Microbial Protein Interaction Database
type: Resource
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
keyword: small molecule
keyword: protein
keyword: interaction
keyword: life science
0000005: 1776
has provider formatter: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9968-4080
has alternative prefix: mpidb
has URI prefix: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-
0000027: interaction id:MPIDB-INT-1776
0000029: mpid

BioDeep Database
type: Resource
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.
is part of: bioregistry
0000005: 00000000001
has provider formatter: https://query.biodeep.cn/metabolite/$1
has local unique identifier pattern: ^\d{11}$
is deprecated: false
has URI prefix: https://query.biodeep.cn/metabolite/
0000027: https://query.biodeep.cn/metabolite/00000000001
0000029: biodeep

Role Ontology
type: Resource
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.
is part of: bioregistry
keyword: obo
keyword: ontology
0000005: 0000002
has provider formatter: http://purl.obolibrary.org/obo/RoleO_$1
has local unique identifier pattern: ^\d{7}$
0000010: roleo.owl
is deprecated: true
has responsible: https://orcid.org/0000-0001-9189-9661
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://purl.obolibrary.org/obo/RoleO_
0000027: RoleO_0000002
0000029: roleo

Digital Object Identifier
type: Resource
contributor: https://orcid.org/0000-0002-3012-7446
contributor: https://orcid.org/0000-0002-6601-2165
description: The Digital Object Identifier System is for identifying content objects in the digital environment.
is part of: bioregistry
keyword: subject agnostic
keyword: bibliography
keyword: centrally registered identifier
0000005: 10.1038/s41597-022-01807-3
has provider formatter: https://doi.org/$1
has local unique identifier pattern: ^10.\d{2,9}/.*$
is deprecated: false
has responsible: https://orcid.org/0000-0001-9551-9662
has URI prefix: https://doi.org/
0000027: s41597-022-01807-3
0000029: doi

Ontology for Biomedical Investigations
type: Resource
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).
is part of: bioregistry
git repository: obi
keyword: life sciences, biology
keyword: reagent
keyword: biomedical science
keyword: life science
keyword: study design
keyword: obo
keyword: device
keyword: ontology
keyword: data transformation
keyword: dataplant
keyword: nfdi4cat
keyword: assay
keyword: nfdi4chem
keyword: functional genomics
0000005: 0400109
has provider formatter: http://purl.obolibrary.org/obo/OBI_$1
has local unique identifier pattern: ^\d{7}$
0000010: obi.owl
is deprecated: false
0000018: Microbial Conditions Ontology
0000018: Health Surveillance Ontology
0000018: one
0000018: rbo
0000018: Ontology for Nutritional Studies
0000018: maxo
0000018: gallont
0000018: labo
0000018: scdo
0000018: Agronomy Ontology
0000018: Process Chemistry Ontology
0000018: foodon
has responsible: https://orcid.org/0000-0002-8457-6693
has URI prefix: http://purl.obolibrary.org/obo/OBI_
0000027: OBI_0400109
0000029: obi

Competence Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A small ontology expressing skills and competencies.
is part of: bioregistry
git repository: competence-ontology
keyword: skills
keyword: competence
keyword: ontology
0000005: CognitiveCompetence
has provider formatter: http://purl.org/nemo/competence#$1
is deprecated: false
has responsible: João Paulo A. Almeida
has URI prefix: http://purl.org/nemo/competence#
0000027: CognitiveCompetence
0000029: nemo.competence

ValidatorDB
type: Resource
description: Database of validation results for ligands and non-standard residues in the Protein Data Bank.
is part of: bioregistry
keyword: life science
0000005: 2h6o
has provider formatter: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1
has local unique identifier pattern: ^[A-Za-z0-9\/]+$
0000011: pdb
is deprecated: false
has responsible: David Sehnal
has URI prefix: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/
0000027: 2h6o
0000029: validatordb

SWEET Ontology Property Space Location
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Location
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: space location
0000005: Center
has provider formatter: http://sweetontology.net/propSpaceLocation/$1
is deprecated: false
has alternative prefix: sopropsl
has URI prefix: http://sweetontology.net/propSpaceLocation/
0000027: Center
0000029: sweet.propsl

OBOE Standard
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Units in OBOE
is part of: bioregistry
keyword: units
keyword: ontology
keyword: unit
0000005: Acre
has provider formatter: http://ecoinformatics.org/oboe/oboe.1.2/oboe-standards.owl$1
is deprecated: false
has URI prefix: http://ecoinformatics.org/oboe/oboe.1.2/oboe-standards.owl
0000027: oboe-standards.owlAcre
0000029: oboe.standard

BioStudies database
type: Resource
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.
is part of: bioregistry
keyword: life science
keyword: biomedical science
0000005: S-EPMC6266652
has provider formatter: https://www.ebi.ac.uk/biostudies/studies/$1
has local unique identifier pattern: ^S-[A-Z]{4}[\-\_A-Z\d]+$
is deprecated: false
has responsible: Ugis Sarkans
has URI prefix: https://www.ebi.ac.uk/biostudies/studies/
0000027: S-EPMC6266652
0000029: biostudies

SWEET Ontology State Biological
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Biological
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state biological
0000005: BiologicalState
has provider formatter: http://sweetontology.net/stateBiological/$1
is deprecated: false
has alternative prefix: sostb
has URI prefix: http://sweetontology.net/stateBiological/
0000027: BiologicalState
0000029: sweet.stb

SWEET Ontology Representation Space Direction
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space Direction
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: representation space direction
0000005: Counterclockwise
has provider formatter: http://sweetontology.net/reprSpaceDirection/$1
is deprecated: false
has alternative prefix: sorepsd
has URI prefix: http://sweetontology.net/reprSpaceDirection/
0000027: Counterclockwise
0000029: sweet.repsd

SWEET Ontology Relationships Physical
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Physical
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: physical
0000005: colderThan
has provider formatter: http://sweetontology.net/relaPhysical/$1
is deprecated: false
has alternative prefix: sorelph
has URI prefix: http://sweetontology.net/relaPhysical/
0000027: colderThan
0000029: sweet.relph

NASA Open Science Data Repository Study
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for space-related data from studies that investigate biological and health responses of terrestrial life to spaceflight
is part of: bioregistry
0000005: OSD-678
has provider formatter: https://osdr.nasa.gov/bio/repo/data/studies/$1
has local unique identifier pattern: ^OSD-\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8542-2389
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://osdr.nasa.gov/bio/repo/data/studies/
0000027: OSD-678
0000029: nasaosdr.study

Salmon Ontology
type: Resource
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.
is part of: bioregistry
keyword: ontology
0000005: 00000674
has provider formatter: https://purl.dataone.org/odo/SALMON_$1
has local unique identifier pattern: ^\d+$
0000010: salmon.owl
is deprecated: false
has responsible: Bryce Mecum
has URI prefix: https://purl.dataone.org/odo/SALMON_
0000027: SALMON_00000674
0000029: salmon

ChemBioSys Institution
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An institution in the ChemBioSys data platform
is part of: bioregistry
0000005: 13
has provider formatter: https://data.chembiosys.de/institutions/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.chembiosys.de/institutions/
0000027: https://data.chembiosys.de/institutions/13
0000029: chembiosys.institution

Anita Caron

HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
type: Resource
description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.
is part of: bioregistry
git repository: xlmod-CV
keyword: reagent
keyword: experimental measurement
keyword: mass spectrum
keyword: mass spectrometry assay
keyword: obo
keyword: ontology
keyword: gas chromatography
keyword: chemical biology
keyword: metabolomics
keyword: omics
0000005: 00050
has provider formatter: http://purl.obolibrary.org/obo/XLMOD_$1
has local unique identifier pattern: ^\d{5}$
0000010: xlmod.owl
is deprecated: false
has responsible: Gerhard Mayer
has URI prefix: http://purl.obolibrary.org/obo/XLMOD_
0000027: XLMOD_00050
0000029: xlmod

SWAP Logic Ontology
type: Resource
description: Une ontologie "historique" utilisée par l'outil en ligne de commande cwm, au temps des balbutiements du web sémantique (~ 2000 - 2003 ?)
is part of: bioregistry
keyword: rdf
0000005: dtlit
is deprecated: false
0000029: log

Toni Gabaldón

Cell Biolabs cell line products
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
0000005: AKR-270
has provider formatter: https://www.cellbiolabs.com/search
is deprecated: false
has URI prefix: https://www.cellbiolabs.com/search
0000027: https://www.cellbiolabs.com/search
0000029: cell_biolabs

National Organization for Rare Disorders
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A website containing information about rare diseases, powered by Wordpress.
is part of: bioregistry
0000005: 1693
has provider formatter: https://rarediseases.org/
has local unique identifier pattern: ^\d+$
is deprecated: false
0000018: Mondo Disease Ontology
has responsible: Sean Roberts
has URI prefix: https://rarediseases.org/
0000027: https://rarediseases.org/
0000029: nord

BioProject
type: Resource
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.
is part of: bioregistry
keyword: life science
0000005: PRJDB3
has provider formatter: https://www.ncbi.nlm.nih.gov/bioproject/
has local unique identifier pattern: ^PRJ[DEN][A-Z]\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-0289-7101
has URI prefix: https://www.ncbi.nlm.nih.gov/bioproject/
0000027: https://www.ncbi.nlm.nih.gov/bioproject/
0000029: bioproject

Building Topology Ontology
type: Resource
description: The Building Topology Ontology (BOT) is a minimal ontology for describing the core topological concepts of a building.
is part of: bioregistry
git repository: bot
keyword: fid baudigital
keyword: architecture
keyword: nfdi4ing
keyword: nfdi4culture
keyword: civil engineering
keyword: digital planning and construction
0000005: Building
has provider formatter: https://w3id.org/bot#$1
is deprecated: false
has URI prefix: https://w3id.org/bot#
0000027: Building
0000029: bot

BioCarta Pathway
type: Resource
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.
is part of: bioregistry
0000005: h_aktPathway
has provider formatter: https://cgap.nci.nih.gov/Pathways/BioCarta/$1
has local unique identifier pattern: ^([hm]\_)?\w+Pathway$
is deprecated: false
has URI prefix: https://cgap.nci.nih.gov/Pathways/BioCarta/
0000027: h aktPathway
0000029: biocarta.pathway

E. coli Metabolite Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: ECMDB00005
has provider formatter: http://ecmdb.ca/compounds/$1
has local unique identifier pattern: ^ECMDB\d+$
is deprecated: false
has alternative prefix: ECMDB
has URI prefix: http://ecmdb.ca/compounds/
0000027: ECMDB00005
0000029: ecmdb

Merck Millipore (EMD Millipore)
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
0000005: SCC111
has provider formatter: https://www.merckmillipore.com/catalogue/item/$1
is deprecated: false
has URI prefix: https://www.merckmillipore.com/catalogue/item/
0000027: SCC111
0000029: millipore

EBI Ontology Lookup Service
type: https://bioregistry.io/schema/#0000002
description: The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions.
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

Mondo Disease Ontology
type: Resource
description: The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world.
is part of: bioregistry
git repository: mondo
keyword: medicine
keyword: infectious disease medicine
keyword: obo
keyword: ontology
keyword: biocuration
0000005: 0000001
has provider formatter: http://purl.obolibrary.org/obo/MONDO_$1
has local unique identifier pattern: ^\d{7}$
0000010: mondo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-4142-7153
has URI prefix: http://purl.obolibrary.org/obo/MONDO_
0000027: MONDO_0000001
0000029: mondo

Getty Iconography Authority
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
0000005: 901001034
has provider formatter: http://vocab.getty.edu/page/ia/$1
is deprecated: false
has URI prefix: http://vocab.getty.edu/page/ia/
0000027: http://vocab.getty.edu/page/ia/901001034
0000029: getty.ia

Saurav Kumar

ChemBioSys Publication
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A publication in the ChemBioSys data platform
is part of: bioregistry
0000005: 157
has provider formatter: https://data.chembiosys.de/publications/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.chembiosys.de/publications/
0000027: https://data.chembiosys.de/publications/157
0000029: chembiosys.publication

Dilfuza Djamalova

Retail Energy Market of Great Britain
type: Resource
description: An ontology of the Retail Energy Market of Great Britain created by Lidcast Data Limited.
is part of: bioregistry
git repository: GBEnergy
keyword: nfdi4energy
0000005: Advanced_Meter
has provider formatter: https://www.lidcast.co.uk/ontologies/RE#$1
is deprecated: false
has URI prefix: https://www.lidcast.co.uk/ontologies/RE#
0000027: Advanced Meter
0000029: tib.re

Soybean Ontology
type: Resource
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.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: life science
keyword: food
keyword: ontology
keyword: plant phenotypes and traits
keyword: phenotype
0000005: 0000339
has provider formatter: https://cropontology.org/rdf/CO_336:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 336.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_336:
0000027: CO 336:0000339
0000029: co_336

Semantically-Interlinked Online Communities Types Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining subclasses and subproperties of SIOC terms.
is part of: bioregistry
0000005: AddressBook
has provider formatter: http://rdfs.org/sioc/types#$1
is deprecated: false
has URI prefix: http://rdfs.org/sioc/types#
0000027: AddressBook
0000029: sioc.types

Porifera Ontology
type: Resource
description: An ontology describing the anatomical structures and characteristics of Porifera (sponges)
is part of: bioregistry
git repository: porifera-ontology
keyword: phylogeny
keyword: anatomy
keyword: taxonomy
keyword: obo
keyword: ontology
keyword: taxonomic classification
0000005: 0000550
has provider formatter: http://purl.obolibrary.org/obo/PORO_$1
has local unique identifier pattern: ^\d{7}$
0000010: poro.owl
is deprecated: false
depends on: Uber Anatomy Ontology
depends on: ro
0000018: gallont
has responsible: https://orcid.org/0000-0002-9654-0073
has URI prefix: http://purl.obolibrary.org/obo/PORO_
0000027: PORO_0000550
0000029: poro

CGH Data Base
type: Resource
description: Cell line databases/resources
is part of: bioregistry
0000005: 300165/p13898_2106T
is deprecated: false
0000029: cghdb

Getty Vocabulary Program ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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).
is part of: bioregistry
0000005: prefLabelGVP
has provider formatter: http://vocab.getty.edu/ontology#$1
is deprecated: false
has URI prefix: http://vocab.getty.edu/ontology#
0000027: prefLabelGVP
0000029: getty.gvp

Zebrafish anatomy and development ontology
type: Resource
description: ZFA description.
is part of: bioregistry
git repository: zebrafish-anatomical-ontology
keyword: structure
keyword: zebrafish
keyword: anatomy
keyword: morphology
keyword: life science
keyword: obo
keyword: ontology
keyword: life cycle stage
keyword: developmental biology
keyword: life cycle
0000005: 0005926
has provider formatter: http://purl.obolibrary.org/obo/ZFA_$1
has local unique identifier pattern: ^\d{7}$
0000010: zfa.owl
is deprecated: false
0000018: zp
has responsible: https://orcid.org/0000-0002-2244-7917
has alternative prefix: ZFA_RETIRED
has URI prefix: http://purl.obolibrary.org/obo/ZFA_
0000027: ZFA_0005926
0000029: zfa

Mammalia Polymorphism Database
type: Resource
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).
is part of: bioregistry
keyword: dna
0000005: MAMpol005339
has provider formatter: http://mampol.uab.es/cgi-bin/MamPol_s2.pl
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://mampol.uab.es/cgi-bin/MamPol_s2.pl
0000027: http://mampol.uab.es/cgi-bin/MamPol_s2.pl
0000029: mampol

dictyBase Expressed Sequence Tag
type: Resource
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 provider formatter: http://dictybase.org/db/cgi-bin/feature_page.pl
has local unique identifier pattern: ^DDB\d+$
is deprecated: false
has URI prefix: http://dictybase.org/db/cgi-bin/feature_page.pl
0000027: http://dictybase.org/db/cgi-bin/feature_page.pl
0000029: dictybase.est

MaizeGDB Locus
type: Resource
description: MaizeGDB is the maize research community's central repository for genetics and genomics information.
is part of: bioregistry
keyword: life science
keyword: genetics
keyword: genome
keyword: genomics
keyword: dna
0000005: 25011
has provider formatter: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-2164-8300
has alternative prefix: MaizeGDB
has URI prefix: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi
0000027: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi
0000029: maizegdb.locus

Identifiers.org Terms
type: Resource
description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.
is part of: bioregistry
0000005: Namespace
has provider formatter: https://biomodels.net/vocab/idot.rdf#$1
has local unique identifier pattern: ^[A-Za-z]+$
is deprecated: false
has URI prefix: https://biomodels.net/vocab/idot.rdf#
0000027: Namespace
0000029: idot

RNA Virus Database
type: Resource
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.
is part of: bioregistry
keyword: rna
keyword: genome
0000005: 164750
has provider formatter: http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php
is deprecated: false
has URI prefix: http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php
0000027: http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php
0000029: rnavdb

DragonDB Protein
type: Resource
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.
is part of: bioregistry
0000005: AMDEFA
has provider formatter: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
has local unique identifier pattern: ^\w+$
is deprecated: true
has URI prefix: https://bioregistry.io/dragondb.protein:
0000027: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
0000029: dragondb.protein

Daniel C. Berrios
label: Dan Berrios

Orientations of Proteins in Membranes Database
type: Resource
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.
is part of: bioregistry
0000005: 1h68
has provider formatter: http://opm.phar.umich.edu/protein.php
has local unique identifier pattern: ^[0-9][A-Za-z0-9]{3}$
is deprecated: false
has URI prefix: http://opm.phar.umich.edu/protein.php
0000027: http://opm.phar.umich.edu/protein.php
0000029: opm

Synthetic Binding Protein Protein Scaffold
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
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
0000005: ps048
has provider formatter: http://synbip.idrblab.net/data/scaffold/details/$1
has local unique identifier pattern: ^ps\d+$
is deprecated: false
has responsible: 0000-0002-1846-639X
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: http://synbip.idrblab.net/data/scaffold/details/
0000027: ps048
0000029: synbip.pss

Shur-Jen Wang

Christine Pourcel

SWEET Ontology Phenomena System Complexity
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena System Complexity
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: phenomena
keyword: system complexity
0000005: Cascade
has provider formatter: http://sweetontology.net/phenSystemComplexity/$1
is deprecated: false
has alternative prefix: sophsyc
has URI prefix: http://sweetontology.net/phenSystemComplexity/
0000027: Cascade
0000029: sweet.phsyc

Library of Congress Control Number
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
0000005: 2011488555
has provider formatter: https://lccn.loc.gov/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://lccn.loc.gov/
0000027: https://lccn.loc.gov/2011488555
0000029: lccn

SWEET Ontology Phenomena Geologic Volcano
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Volcano
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: geologic volcano
keyword: phenomena
0000005: EruptionCloud
has provider formatter: http://sweetontology.net/phenGeolVolcano/$1
is deprecated: false
has alternative prefix: sophgv
has URI prefix: http://sweetontology.net/phenGeolVolcano/
0000027: EruptionCloud
0000029: sweet.phgv

Human BioMolecular Atlas Program Collection
type: Resource
contributor: 0009-0008-8406-631X
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.
is part of: bioregistry
has provider formatter: https://portal.hubmapconsortium.org/browse/collection/$1
has local unique identifier pattern: ^[a-f0-9]{32}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3321-6137
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://portal.hubmapconsortium.org/browse/collection/
0000029: hubmap.collection

Lars Eisen

BRENDA Ligand Group
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Information for ligand groups (chemical classes).
is part of: bioregistry
keyword: chemistry
keyword: grouping
keyword: structrual bioinformatics
0000005: 18030
has provider formatter: https://www.brenda-enzymes.de/ligand.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.brenda-enzymes.de/ligand.php
0000027: https://www.brenda-enzymes.de/ligand.php
0000029: brenda.ligandgroup

Lebanon Clinical Trials Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
0000005: LBCTR2023015204
has local unique identifier pattern: ^LBCTR\d+$
is deprecated: false
0000029: lbctr

Pierre-Marie Allard

Plant Reactome
type: Resource
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 part of: bioregistry
0000005: R-ACH-1120024
has provider formatter: https://plantreactome.gramene.org/content/detail/$1
has local unique identifier pattern: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$
is deprecated: false
has URI prefix: https://plantreactome.gramene.org/content/detail/
0000027: R-ACH-1120024
0000029: plant_reactome

NIF Standard Ontology
type: Resource
contributor: Tom Gillespie
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.
is part of: bioregistry
git repository: NIF-Ontology
keyword: neuroscience
keyword: ontology
keyword: disease
keyword: brain
0000005: BAMSC981
has provider formatter: http://uri.neuinfo.org/nif/nifstd/$1
has local unique identifier pattern: ^BAMSC\d+$
0000010: nifstd.owl
is deprecated: false
has responsible: Tom Gillespie
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NIFSTD
has URI prefix: http://uri.neuinfo.org/nif/nifstd/
0000027: BAMSC981
0000029: nif.std

Machine-readable Cataloging (MARC) List for Languages
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: amh
has provider formatter: https://id.loc.gov/vocabulary/languages/$1
is deprecated: false
has URI prefix: https://id.loc.gov/vocabulary/languages/
0000027: amh
0000029: marc21

Todd W Harris

Tobias Hamann

PlastChem
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A database of chemicals relevant for plastics and polymer sciences.
is part of: bioregistry
0000005: 1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-4402-3234
0000029: plastchem

Cassava Ontology
type: Resource
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.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: nutritional science
keyword: food
keyword: ontology
keyword: plant phenotypes and traits
keyword: phenotype
keyword: botany
0000005: 0000070
has provider formatter: https://cropontology.org/rdf/CO_334:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 334.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_334:
0000027: CO 334:0000070
0000029: co_334

Banco de Celulas do Rio de Janeiro
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
0000005: 0278
has provider formatter: https://bcrj.org.br/pesquisa/
has local unique identifier pattern: ^\d{4}$
is deprecated: false
has URI prefix: https://bcrj.org.br/pesquisa/
0000027: https://bcrj.org.br/pesquisa/
0000029: bcrj

OER Schema
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A RDF vocabulary for OER content on the web.
is part of: bioregistry
git repository: oerschema
keyword: education
keyword: oer
keyword: curricula
keyword: oers
keyword: curriculum
keyword: open educational resources
0000005: InstructionalPattern
has provider formatter: https://oerschema.org/$1
is deprecated: false
has responsible: Michael Collins
has URI prefix: https://oerschema.org/
0000027: InstructionalPattern
0000029: oerschema

Distributed Archives for Neurophysiology Data Integration
type: Resource
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.
is part of: bioregistry
git repository: dandiarchive
keyword: neurophysiology
0000005: 000017
has provider formatter: https://dandiarchive.org/dandiset/$1
has local unique identifier pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$
is deprecated: false
has responsible: https://orcid.org/0000-0003-3456-2493
has URI prefix: https://dandiarchive.org/dandiset/
0000027: https://dandiarchive.org/dandiset/000017
0000029: dandi

Graphic Descriptor Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
git repository: GDO-GDOA
keyword: ontology
0000005: 0000016
has provider formatter: https://gdo.endlessforms.info/view/classes
0000010: gdoa.owl
is deprecated: false
has responsible: 0000-0001-9979-176X
has URI prefix: https://gdo.endlessforms.info/view/classes
0000027: https://gdo.endlessforms.info/view/classes
0000029: gdo

Ontology for manufacturing and logistics
type: Resource
description: Ontology for manufacturing and logistics
is part of: bioregistry
git repository: OFM
keyword: engineering
keyword: nfdi4ing
0000005: Anthropomorphic_Robot
has provider formatter: http://www.ontologies.com/Ontology3197.owl#$1
is deprecated: false
has URI prefix: http://www.ontologies.com/Ontology3197.owl#
0000027: Anthropomorphic Robot
0000029: tib.ofm

ShareLoc
type: Resource
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.
is part of: bioregistry
keyword: ontology
0000005: 000004
has provider formatter: https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1
has local unique identifier pattern: ^\d{6}$
0000010: shareloc.owl
is deprecated: false
has URI prefix: https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_
0000027: ontology/vocabulary/SHARELOC 000004
0000029: shareloc

Confidence Information Ontology
type: Resource
description: An ontology to capture confidence information about annotations.
is part of: bioregistry
git repository: confidence-information-ontology
keyword: ontology
keyword: annotation
keyword: biology
keyword: obo
0000005: 0000040
has provider formatter: http://purl.obolibrary.org/obo/CIO_$1
has local unique identifier pattern: ^\d{7}$
0000010: cio.owl
is deprecated: false
has responsible: Frédéric Bastian
has URI prefix: http://purl.obolibrary.org/obo/CIO_
0000027: CIO_0000040
0000029: cio

has responsible
type: Property
description: The responsible person for a resource
domain: Resource
range: Person

United States Patent and Trademark Office
type: Resource
contributor: https://orcid.org/0000-0002-3012-7446
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.
is part of: bioregistry
0000005: 4145692
has provider formatter: http://patft.uspto.gov/netacgi/nph-Parser
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
0000027: http://patft.uspto.gov/netacgi/nph-Parser
0000029: uspto

Maria Gould

ListDB Ontology
type: Resource
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.
is part of: bioregistry
git repository: listdb
keyword: traffic engineering
keyword: fid move
keyword: nfdi4ing
0000005: C0000000001
has provider formatter: https://w3id.org/listdb/onto#$1
is deprecated: false
has URI prefix: https://w3id.org/listdb/onto#
0000027: https://w3id.org/listdb/onto#C0000000001
0000029: listdb.onto

Abcam
type: Resource
contributor: Sumir Pandit
contributor: https://orcid.org/0000-0003-4423-4370
description: Vendor for assays, cells, and antibodies
is part of: bioregistry
0000005: ab275461
has provider formatter: https://www.abcam.com/$1.html
is deprecated: false
has URI prefix: https://bioregistry.io/abcam:
0000027: ab275461.html
0000029: abcam

Signaling Network Open Resource
type: Resource
description: SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature.
is part of: bioregistry
keyword: ontology
keyword: biology
0000005: SIGNOR-C41
has provider formatter: https://signor.uniroma2.it/relation_result.php
has local unique identifier pattern: ^SIGNOR\-[A-Z]+\d+$
0000010: signor.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-9528-6018
has alternative prefix: SIGNOR
has URI prefix: https://signor.uniroma2.it/relation_result.php
0000027: https://signor.uniroma2.it/relation_result.php
0000029: signor

FDA Submission Tracking Number
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The pre-IND tracking number for submissions to the FDA
is part of: bioregistry
0000005: 125768
is deprecated: false
0000029: stn

Performance Summary Display Ontology
type: Resource
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
git repository: psdo
keyword: obo
keyword: ontology
0000005: 0000055
has provider formatter: http://purl.obolibrary.org/obo/PSDO_$1
has local unique identifier pattern: ^\d{7}$
0000010: psdo.owl
is deprecated: false
depends on: bfo
depends on: The Statistical Methods Ontology
depends on: ro
depends on: Information Artifact Ontology
has responsible: https://orcid.org/0000-0002-9117-9338
has URI prefix: http://purl.obolibrary.org/obo/PSDO_
0000027: PSDO_0000055
0000029: psdo

SWEET Ontology Property Chemical
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Chemical
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: chemical
0000005: Abundance
has provider formatter: http://sweetontology.net/propChemical/$1
is deprecated: false
has alternative prefix: sopropche
has URI prefix: http://sweetontology.net/propChemical/
0000027: Abundance
0000029: sweet.propche

PhosphoSite Residue
type: Resource
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.
is part of: bioregistry
0000005: 2842
has provider formatter: http://www.phosphosite.org/siteAction.do
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://www.phosphosite.org/siteAction.do
0000027: http://www.phosphosite.org/siteAction.do
0000029: phosphosite.residue

SIGNOR Relation
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: Identifiers for relationships between proteins and complexes, along with their type and provenance
is part of: bioregistry
keyword: protein-protein interactions
0000005: SIGNOR-252737
has local unique identifier pattern: ^SIGNOR-\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
0000029: signor.relation

Lifecycle Event Type
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Specifies the event happening over the data life cycle that is considered significant enough to document.
is part of: bioregistry
0000005: StudyProposal
has provider formatter: https://vocabularies.cessda.eu/vocabulary/LifecycleEventType#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/LifecycleEventType#code_
0000026: 015em2733
0000027: code StudyProposal
0000029: ddi.lifecycleeventtype

SWEET Ontology Phenomena
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
0000005: AirSeaExchange
has provider formatter: http://sweetontology.net/phen/$1
is deprecated: false
has alternative prefix: soph
has URI prefix: http://sweetontology.net/phen/
0000027: AirSeaExchange
0000029: sweet.ph

MimoDB
type: Resource
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.
is part of: bioregistry
keyword: interaction
keyword: life science
keyword: protein
0000005: 1
has provider formatter: http://immunet.cn/bdb/index.php/mimoset/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-2314-7104
has URI prefix: http://immunet.cn/bdb/index.php/mimoset/
0000027: http://immunet.cn/bdb/index.php/mimoset/1
0000029: mimodb

Rebuilding a Kidney
type: Resource
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.
is part of: bioregistry
git repository: Create-citable-datasets
keyword: cell biology
keyword: developmental biology
keyword: genomics
keyword: molecular biology
0000005: Q-2958
has provider formatter: https://www.rebuildingakidney.org/id/$1
has local unique identifier pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
is deprecated: false
has responsible: https://orcid.org/0000-0002-2825-7663
has URI prefix: https://www.rebuildingakidney.org/id/
0000027: Q-2958
0000029: rbk

NASA Open Science Data Repository Payload
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for payloads associated with experiments that investigate biological and health responses of terrestrial life to spaceflight
is part of: bioregistry
0000005: VEG-03D
has provider formatter: https://osdr.nasa.gov/bio/repo/data/payloads/$1
has local unique identifier pattern: ^.+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8542-2389
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://osdr.nasa.gov/bio/repo/data/payloads/
0000027: VEG-03D
0000029: nasaosdr.payload

SWEET Ontology Property Temperature
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Temperature
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: temperature
0000005: AntennaTemperature
has provider formatter: http://sweetontology.net/propTemperature/$1
is deprecated: false
has alternative prefix: sopropt
has URI prefix: http://sweetontology.net/propTemperature/
0000027: AntennaTemperature
0000029: sweet.propt

Selventa Diseases
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Selventa legacy disease namespace used with the Biological Expression Language
is part of: bioregistry
keyword: bel
keyword: diseases
keyword: selventa
0000005: D0001
has provider formatter: https://biopragmatics.github.io/providers/sdis/$1
has local unique identifier pattern: ^D\d{4}$
is deprecated: false
has responsible: Natalie L Catlett
has URI prefix: https://biopragmatics.github.io/providers/sdis/
0000027: D0001
0000029: sdis

SWEET Ontology Realm Land Protected
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Protected
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: protectedland
0000005: CityPark
has provider formatter: http://sweetontology.net/realmLandProtected/$1
is deprecated: false
has alternative prefix: sorealp
has URI prefix: http://sweetontology.net/realmLandProtected/
0000027: CityPark
0000029: sweet.realp

Brain Architecture Knowledge Management System Neuroanatomical Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
is deprecated: true
0000029: bams

SWEET Ontology Relationships Time
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Time
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: time
0000005: dayOfYear
has provider formatter: http://sweetontology.net/relaTime/$1
is deprecated: false
has alternative prefix: sorelt
has URI prefix: http://sweetontology.net/relaTime/
0000027: dayOfYear
0000029: sweet.relt

UniProt Chain
type: Resource
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
0000005: PRO_0000016681
has provider formatter: http://purl.uniprot.org/annotation/$1
has local unique identifier pattern: ^PRO_[0-9]{10}$
is deprecated: false
has responsible: Alex Bateman
has alternative prefix: UPPRO
has URI prefix: http://purl.uniprot.org/annotation/
0000027: PRO_0000016681
0000029: uniprot.chain

Human developmental anatomy, timed version
type: Resource
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
keyword: development
keyword: anatomy
keyword: obo
keyword: ontology
keyword: human
0000005: 1
has provider formatter: http://purl.obolibrary.org/obo/EHDA_$1
has local unique identifier pattern: ^\d+$
0000010: ehda.obo
is deprecated: true
has responsible: Jonathan Bard
has URI prefix: http://purl.obolibrary.org/obo/EHDA_
0000027: EHDA 1
0000029: ehda

ChemIDplus
type: Resource
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 part of: bioregistry
keyword: structure
keyword: biomedical science
keyword: molecules
keyword: chemistry
0000005: 57-27-2
has provider formatter: https://chem.nlm.nih.gov/chemidplus/rn/$1
has local unique identifier pattern: ^\d+\-\d+\-\d+$
is deprecated: false
has alternative prefix: ChemIDplus
has URI prefix: https://chem.nlm.nih.gov/chemidplus/rn/
0000027: https://chem.nlm.nih.gov/chemidplus/rn/57-27-2
0000029: chemidplus

CORDIS Project
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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
0000005: 817732
has provider formatter: https://cordis.europa.eu/project/id/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://cordis.europa.eu/project/id/
0000027: https://cordis.europa.eu/project/id/817732
0000029: cordis.project

Beet Ontology
type: Resource
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.
is part of: bioregistry
git repository: Crop-Ontology
keyword: phenotype
keyword: botany
keyword: agriculture
keyword: plant breeding
keyword: life science
keyword: food
keyword: ontology
keyword: plant phenotypes and traits
0000005: 3000045
has provider formatter: https://cropontology.org/rdf/CO_333:$1
has local unique identifier pattern: ^\d+$
0000010: CO 333.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_333:
0000027: CO 333:3000045
0000029: co_333

Tim Vandermeersch
label: Egon Willighagen

SWEET Ontology Phenomena Ocean
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Ocean
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: ocean
keyword: phenomena
0000005: OceanPhenomena
has provider formatter: http://sweetontology.net/phenOcean/$1
is deprecated: false
has alternative prefix: sopho
has URI prefix: http://sweetontology.net/phenOcean/
0000027: OceanPhenomena
0000029: sweet.pho

Dublin Core Elements (1.1)
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)).
is part of: bioregistry
keyword: subject agnostic
keyword: metadata
keyword: metadata standardization
keyword: life science
keyword: ontology
keyword: resource metadata
keyword: annotation
keyword: biomedical science
0000005: contributor
has provider formatter: http://purl.org/dc/elements/1.1/$1
0000010: dcelements.owl
is deprecated: true
has responsible: Kim Durante
has alternative prefix: dcelem
has alternative prefix: dc.elements
has alternative prefix: elements
has alternative prefix: dc11
has alternative prefix: dce
has URI prefix: http://purl.org/dc/elements/1.1/
0000027: contributor
0000029: dc

Alzheimer Gene Database
type: Resource
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.
is part of: bioregistry
keyword: gene
0000005: 88
has provider formatter: http://www.alzgene.org/geneoverview.asp
is deprecated: false
has responsible: Lars Bertram
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.alzgene.org/geneoverview.asp
0000027: http://www.alzgene.org/geneoverview.asp
0000029: alzgene

SWEET Ontology Material Industrial
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Industrial
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: industrial
keyword: materials
0000005: Alloy
has provider formatter: http://sweetontology.net/matrIndustrial/$1
is deprecated: false
has alternative prefix: somaind
has URI prefix: http://sweetontology.net/matrIndustrial/
0000027: Alloy
0000029: sweet.maind

Mark Gerstein

Jennifer Smith
label: Jennifer R Smith

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.
is part of: bioregistry
0000005: D0N5OV
has provider formatter: https://db.idrblab.net/ttd/data/drug/details/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has URI prefix: https://db.idrblab.net/ttd/data/drug/details/
0000027: D0N5OV
0000029: ttd.drug

Integrated Genomic Resources of human Cell Lines for Identification
type: Resource
description: Cell line databases/resources
is part of: bioregistry
0000005: ACHN
has provider formatter: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi
is deprecated: false
has URI prefix: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi
0000027: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi
0000029: igrhcellid

Alan Wood's Pesticides
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients.
is part of: bioregistry
has provider formatter: http://www.alanwood.net/pesticides/$1.html
is deprecated: false
has URI prefix: https://bioregistry.io/pesticides:
0000027: derivatives/thiocyclam hydrochloride.html
0000029: pesticides

Eukaryotic Genes
type: Resource
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.
is part of: bioregistry
keyword: life science
keyword: ontology
keyword: genome
0000005: MGgn0008978
has provider formatter: http://eugenes.org:7072/.bin/fbidq.html
is deprecated: false
has responsible: https://orcid.org/0000-0002-6646-7274
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://eugenes.org:7072/.bin/fbidq.html
0000027: http://eugenes.org:7072/.bin/fbidq.html
0000029: eugenes

Radiomics Ontology
type: Resource
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 part of: bioregistry
keyword: ontology
0000005: LK99
has provider formatter: http://www.radiomics.org/RO/$1
is deprecated: false
has responsible: https://orcid.org/0000-0001-6183-4429
has URI prefix: http://www.radiomics.org/RO/
0000027: LK99
0000029: radiomics

MIMIC III Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
is part of: bioregistry
git repository: mimic-omop
keyword: health sciences
keyword: clinical data
keyword: health
keyword: clinical trials
is deprecated: false
0000029: cohd

Coli Genetic Stock Center
type: Resource
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.
is part of: bioregistry
keyword: gene
keyword: life science
0000005: 74
has provider formatter: http://cgsc.biology.yale.edu/Site.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: Kelly T. Hughes
has URI prefix: http://cgsc.biology.yale.edu/Site.php
0000027: http://cgsc.biology.yale.edu/Site.php
0000029: cgsc

International Medical Device Regulators Forum
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
is deprecated: false
0000029: imdrf

Antimicrobial Peptide Database
type: Resource
description: The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.
is part of: bioregistry
keyword: protein
keyword: biology
0000005: 01001
has provider formatter: http://aps.unmc.edu/AP/database/query_output.php
has local unique identifier pattern: ^\d{5}$
is deprecated: true
has responsible: https://orcid.org/0000-0002-4841-7927
has URI prefix: http://aps.unmc.edu/AP/database/query_output.php
0000027: http://aps.unmc.edu/AP/database/query_output.php
0000029: apd

Fly taxonomy
type: Resource
description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.
is part of: bioregistry
keyword: obo
keyword: ontology
0000005: 00000000
has provider formatter: http://purl.obolibrary.org/obo/FBSP_$1
has local unique identifier pattern: ^\d{8}$
0000010: fbsp.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-1373-1705
has URI prefix: http://purl.obolibrary.org/obo/FBSP_
0000027: FBSP_00000000
0000029: fbsp

SWEET Ontology State Time
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Time
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state time
0000005: Age
has provider formatter: http://sweetontology.net/stateTime/$1
is deprecated: false
has alternative prefix: sostti
has URI prefix: http://sweetontology.net/stateTime/
0000027: Age
0000029: sweet.stti

Store DB
type: Resource
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.
is part of: bioregistry
keyword: preclinical studies
keyword: epidemiology
keyword: biomedical science
keyword: life science
keyword: ecology
0000005: STUDY1040
has provider formatter: https://www.storedb.org/
has local unique identifier pattern: ^(STUDY|FILE|DATASET)\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5111-7263
has URI prefix: https://www.storedb.org/
0000027: https://www.storedb.org/
0000029: storedb

SWEET Ontology Human Environmental Conservation
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Environmental Conservation
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: environmental conservation
0000005: Conservation
has provider formatter: http://sweetontology.net/humanEnvirConservation/$1
is deprecated: false
has alternative prefix: sohuecons
has URI prefix: http://sweetontology.net/humanEnvirConservation/
0000027: Conservation
0000029: sweet.huecons

Brick Ontology
type: Resource
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.
is part of: bioregistry
git repository: Brick
keyword: architecture
keyword: building design
keyword: civil engineering
keyword: systems engineering
keyword: building informatics
keyword: power engineering
keyword: digital planning and construction
keyword: engineering
keyword: fid baudigital
keyword: building information modeling
keyword: energy engineering
keyword: industrial engineering
keyword: nfdi4energy
keyword: nfdi4ing
0000005: Ablutions_Room
has provider formatter: https://brickschema.org/schema/Brick#$1
is deprecated: false
has URI prefix: https://brickschema.org/schema/Brick#
0000027: Ablutions Room
0000029: brick

Structural Classification of Protein - Stable Domain Identifier
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: d4akea1
has provider formatter: http://scop.berkeley.edu/sid=$1
is deprecated: false
has responsible: John-Marc Chandonia
has URI prefix: http://scop.berkeley.edu/sid=
0000027: http://scop.berkeley.edu/sid=d4akea1
0000029: scop.sid

The COVID-19 epidemiology and monitoring ontology
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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.
is part of: bioregistry
git repository: covid19-epidemiology-ontology
keyword: ontology
0000005: secondary_attack_rate
has provider formatter: https://biopragmatics.github.io/providers/cemo/$1
has local unique identifier pattern: ^[0-9a-z_-]+$
0000010: cemo.owl
is deprecated: false
has responsible: Núria Queralt Rosinach
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://biopragmatics.github.io/providers/cemo/
0000027: secondary attack rate
0000029: cemo

PLOS Thesaurus
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: subject agnostic
keyword: ontology
0000005: 1443
has provider formatter: http://localhost/plosthes.2017-1#$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: PLOS Taxonomy Team
has alternative prefix: PLOSTHES
has URI prefix: http://localhost/plosthes.2017-1#
0000027: http://localhost/plosthes.2017-1#1443
0000029: plos

Mouse Developmental Stages
type: Resource
description: Life cycle stages for Mus Musculus
is part of: bioregistry
git repository: developmental-stage-ontologies
keyword: obo
keyword: ontology
keyword: life cycle stage
keyword: embryology
keyword: developmental biology
keyword: anatomy
0000005: 0000066
has provider formatter: http://purl.obolibrary.org/obo/MmusDv_$1
has local unique identifier pattern: ^\d{7}$
0000010: mmusdv.owl
is deprecated: false
has responsible: Frédéric Bastian
has alternative prefix: MmusDv
has URI prefix: http://purl.obolibrary.org/obo/MmusDv_
0000027: MmusDv_0000066
0000029: mmusdv

Web Ontology Language
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages.
is part of: bioregistry
keyword: informatics
keyword: computer science
keyword: subject agnostic
keyword: ontology
keyword: ontology and terminology
keyword: w3c rec
0000005: Ontology
has provider formatter: http://www.w3.org/2002/07/owl#$1
0000010: download.trig.gz
is deprecated: false
has responsible: https://orcid.org/0000-0001-5699-0515
has URI prefix: http://www.w3.org/2002/07/owl#
0000027: Ontology
0000029: owl

Extensible Markup Language
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: subject agnostic
0000005: lang
has provider formatter: http://www.w3.org/XML/1998/namespace#$1
is deprecated: false
has URI prefix: http://www.w3.org/XML/1998/namespace#
0000027: lang
0000029: xml

COSMIC Gene
type: Resource
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.
is part of: bioregistry
keyword: genetics
keyword: biomedical science
0000005: BRAF
has provider formatter: http://cancer.sanger.ac.uk/cosmic/gene/overview
has local unique identifier pattern: ^[A-Z0-9][A-Z0-9-]*$
0000011: hgnc.symbol
is deprecated: false
has responsible: https://orcid.org/0000-0002-8315-6574
has alternative prefix: cosmic
has URI prefix: http://cancer.sanger.ac.uk/cosmic/gene/overview
0000027: http://cancer.sanger.ac.uk/cosmic/gene/overview
0000029: cosmic.gene

DBPedia Resource
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A semi-automatically generated knowledgebase
is part of: bioregistry
0000005: Grenada
has provider formatter: http://dbpedia.org/resource/$1
is deprecated: false
has alternative prefix: dbr
has alternative prefix: dbpedia
has URI prefix: http://dbpedia.org/resource/
0000027: Grenada
0000029: dbpedia.resource

Croissant Format Specification
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A data model describing machine learning experiments
is part of: bioregistry
keyword: artificial intelligence
keyword: machine learning
0000005: FileObject
has provider formatter: http://mlcommons.org/croissant/$1
is deprecated: false
has URI prefix: http://mlcommons.org/croissant/
0000027: FileObject
0000029: croissant

Product Types Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Identifiers for product types (product, price, and company data) based on Wikipedia
is part of: bioregistry
0000005: Atlas
has provider formatter: http://www.productontology.org/id/$1
is deprecated: false
has URI prefix: http://www.productontology.org/id/
0000027: Atlas
0000029: pto

Hypertension Ontology
type: Resource
description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines
is part of: bioregistry
git repository: htn owl
keyword: obo
keyword: ontology
0000005: 00000014
has provider formatter: http://purl.obolibrary.org/obo/HTN_$1
has local unique identifier pattern: ^\d{8}$
0000010: htn.owl
is deprecated: false
has responsible: Amanda Hicks
has URI prefix: http://purl.obolibrary.org/obo/HTN_
0000027: HTN_00000014
0000029: htn

ICD 11 Codes
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: NA06.8D
has local unique identifier pattern: ^[0-9A-Z]+(\.[0-9A-Z]+)?$
is deprecated: false
0000029: icd11.code

Synapse.org external links
type: https://bioregistry.io/schema/#0000003
creator: Robert Allaway
description: A curated list by Sage Bionetworks of external resources that are automatically linked on Synapse.org and affiliated data portals
has part: loinc
has part: ensembl.metazoa
has part: drugbank
has part: edam
has part: clinicaltrials
has part: Gramene protein
has part: nextProt
has part: mgi
has part: CTD Chemical
has part: ClinVar Record
has part: National Organization for Rare Disorders
has part: ncit
has part: clinvar.variation
has part: kegg.reaction
has part: UniProt Archive
has part: omop
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: tao
has part: Alliance of Genome Resources Knowledge Base
has part: exac.variant
has part: ndfrt
has part: biosample
has part: metacyc.compound
has part: KEGG Drug
has part: civic.gid
has part: Internet Standard -- IETF Request for Comments
has part: icdc
has part: arXiv
has part: peco
has part: Zenodo
has part: Open Science Framework ID
has part: kegg
has part: European Nucleotide Archive
has part: International Classification of Functioning, Disability and Health
has part: decipher
has part: Electron Microscopy Data Bank
has part: arrayexpress
has part: dhba
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
has part: imgt.hla
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
has part: bioportal
has part: FAIRsharing
has part: Orphanet
has part: biorxiv
has part: Data Use Ontology
has part: ec
has part: stitch
has part: Bgee gene
has part: zinc
has part: rhea
has part: Brazilian Registry of Clinical Trials
has part: cbioportal
has part: cellxgene.collection
has part: PomBase
has part: Mouse Brain Atlas
has part: uniprot
has part: System Science of Biological Dynamics project
has part: InterPro
has part: Ensembl Gene
has part: civic.aid
has part: BRENDA Ligand Group

biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology
type: Resource
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.
is part of: bioregistry
keyword: gene
keyword: interaction
0000005: 12
has provider formatter: http://avis.princeton.edu/pixie/viewgraph.php
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://avis.princeton.edu/pixie/viewgraph.php
0000027: http://avis.princeton.edu/pixie/viewgraph.php
0000029: biopixie

Process Chemistry Ontology
type: Resource
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.
is part of: bioregistry
git repository: PROCO
keyword: obo
keyword: chemical and environmental engineering
keyword: ontology
keyword: chemistry
keyword: nfdi4chem
0000005: 0000001
has provider formatter: http://purl.obolibrary.org/obo/PROCO_$1
has local unique identifier pattern: ^\d{7}$
0000010: proco.owl
is deprecated: false
depends on: cheminf
depends on: ro
depends on: pato
depends on: Systems Biology Ontology
depends on: Ontology for Biomedical Investigations
depends on: Chemical Entities of Biological Interest
has responsible: https://orcid.org/0000-0002-8786-1756
has URI prefix: http://purl.obolibrary.org/obo/PROCO_
0000027: PROCO_0000001
0000029: proco

Thomas Lütteke

Paul David Neil Hebert

Probes and Drugs
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: PD000596
has provider formatter: https://www.probes-drugs.org/compound/$1
has local unique identifier pattern: ^PD\d{6}$
is deprecated: false
has responsible: Ctibor Škuta
has URI prefix: https://www.probes-drugs.org/compound/
0000027: PD000596
0000029: probesanddrugs

SWEET Ontology Phenomena Geologic
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
keyword: geologic
0000005: CompositeProcess
has provider formatter: http://sweetontology.net/phenGeol/$1
is deprecated: false
has alternative prefix: sophg
has URI prefix: http://sweetontology.net/phenGeol/
0000027: CompositeProcess
0000029: sweet.phg

Numeric Type
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Specifies the type of numeric data.
is part of: bioregistry
0000005: Integer
has provider formatter: https://vocabularies.cessda.eu/vocabulary/NumericType#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/NumericType#code_
0000026: 015em2733
0000027: code Integer
0000029: ddi.numerictype

WikiPathways GPML Vocabulary
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
contributor: 0000-0001-5608-781X
description: The WikiPatwhays Graphical Pathway Markup Language (GPML) vocabulary.
is part of: bioregistry
git repository: WpVocabularies
keyword: ontology
0000005: DataNode
has provider formatter: http://vocabularies.wikipathways.org/gpml#$1
has local unique identifier pattern: ^[A-Za-z]+$
0000010: gpml.owl
is deprecated: false
has responsible: Tim Vandermeersch
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: wikipathways.gpml
has URI prefix: http://vocabularies.wikipathways.org/gpml#
0000027: DataNode
0000029: gpml

Functional Mock-up Interface Ontology
type: Resource
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
is part of: bioregistry
git repository: fmi2rdf
keyword: mechanical engineering, energy technology
keyword: nfdi4energy
0000005: FMU
has provider formatter: https://purl.org/fmi-ontology#$1
is deprecated: false
has URI prefix: https://purl.org/fmi-ontology#
0000027: FMU
0000029: udsaes.fmi

Cooperative Patent Classification
type: Resource
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.
is part of: bioregistry
0000005: A01M1/026
has provider formatter: https://worldwide.espacenet.com/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,})$
is deprecated: false
has URI prefix: https://worldwide.espacenet.com/classification
0000027: https://worldwide.espacenet.com/classification
0000029: cpc

nmrXiv sample
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: spectra (samples) in the nmrXiv database
is part of: bioregistry
keyword: spectrum
keyword: nmr
keyword: spectra
keyword: sample
0000005: S1295
has provider formatter: https://nmrxiv.org/sample/$1
has local unique identifier pattern: ^S\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-2564-3243
has URI prefix: https://nmrxiv.org/sample/
0000027: S1295
0000029: nmrxiv.sample

Petra C. Steiner

BlastRule
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
0000005: NBR016799
has provider formatter: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/$1
has local unique identifier pattern: ^NBR\d+$
is deprecated: false
has URI prefix: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/
0000027: NBR016799
0000029: blastrule

International Standard Classification of Education, 1997 Edition
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: open educational resources
keyword: education level
0000005: 1
has provider formatter: https://w3id.org/kim/isced-1997/level$1
is deprecated: false
has URI prefix: https://w3id.org/kim/isced-1997/level
0000027: level1
0000029: isced1997

World Health Organization Verbal Autopsy Code
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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.
is part of: bioregistry
keyword: cause of death
keyword: verbal autopsy
0000005: VAs-09.01
has local unique identifier pattern: ^VAs-\d{2}(?:\.\d{2})?$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
0000029: who.va

Global Biodiversity Information Facility
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: gbif
keyword: metagenomics
keyword: taxonomy
keyword: natural science
keyword: natural history
keyword: marine biology
keyword: biodiversity
keyword: bioinformatics
0000005: 4238
has provider formatter: https://www.gbif.org/species/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-6215-3617
has URI prefix: https://www.gbif.org/species/
0000027: https://www.gbif.org/species/4238
0000029: gbif

RGD Disease Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms.
is part of: bioregistry
keyword: ontology
0000005: 9002859
has provider formatter: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1
has local unique identifier pattern: ^\d{7}$
0000010: RDO.owl
is deprecated: false
has URI prefix: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#
0000027: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#9002859
0000029: rdo

OBO Metadata Ontology
type: Resource
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).
is part of: bioregistry
git repository: ontology-metadata
keyword: obo
keyword: ontology
0000005: 0003003
has provider formatter: http://purl.obolibrary.org/obo/OMO_$1
has local unique identifier pattern: ^\d{7}$
0000010: omo.owl
is deprecated: false
0000018: cl
0000018: Uber Anatomy Ontology
0000018: Provisional Cell Ontology
has responsible: https://orcid.org/0000-0002-6601-2165
has URI prefix: http://purl.obolibrary.org/obo/OMO_
0000027: OMO_0003003
0000029: omo

Nucleotide Sequence Database
type: Resource
description: The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.
is part of: bioregistry
keyword: dna
0000005: X58356
has provider formatter: https://www.ebi.ac.uk/ena/data/view/$1
has local unique identifier pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4,6}\d{8,10}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/ena/data/view/
0000027: X58356
0000029: insdc

SWEET Ontology State Role Representative
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Representative
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state role representative
0000005: RepresentativeRole
has provider formatter: http://sweetontology.net/stateRoleRepresentative/$1
is deprecated: false
has alternative prefix: sostrr
has URI prefix: http://sweetontology.net/stateRoleRepresentative/
0000027: RepresentativeRole
0000029: sweet.strr

RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
keyword: rdf
0000005: PrefixOrTermMapping
has provider formatter: http://www.w3.org/ns/rdfa#$1
is deprecated: false
has responsible: Ivan Herman
has URI prefix: http://www.w3.org/ns/rdfa#
0000027: PrefixOrTermMapping
0000029: rdfa

FHIR United States Implementation Guides
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A set of guides on implementing various processes within hospitals or healthcare systems.
is part of: bioregistry
0000005: immds
has provider formatter: https://hl7.org/fhir/us/$1
is deprecated: false
has URI prefix: https://hl7.org/fhir/us/
0000027: immds
0000029: fhir.implementation

The COVID-19 Infectious Disease Ontology
type: Resource
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
git repository: ido-covid-19
keyword: ontology
0000005: 0001191
has provider formatter: http://purl.obolibrary.org/obo/COVIDO_$1
has local unique identifier pattern: ^\d{7}$
0000010: ido covid-19
is deprecated: false
has responsible: https://orcid.org/0000-0002-1118-1738
has URI prefix: http://purl.obolibrary.org/obo/COVIDO_
0000027: COVIDO_0001191
0000029: idocovid19

OpenEduHub Education Level
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A list of values for class levels. Created in the context of the OpenEduHub
is part of: bioregistry
git repository: oeh-metadata-vocabs
keyword: education level
keyword: open educational resources
0000005: 1
has provider formatter: http://w3id.org/openeduhub/vocabs/educationalLevel/$1
is deprecated: false
has URI prefix: http://w3id.org/openeduhub/vocabs/educationalLevel/
0000027: http://w3id.org/openeduhub/vocabs/educationalLevel/1
0000029: oeh.educationlevel

Ontology of Prokaryotic Phenotypic and Metabolic Characters
type: Resource
description: An ontology of prokaryotic phenotypic and metabolic characters
is part of: bioregistry
git repository: MicrO
keyword: obo
keyword: ontology
keyword: bioinformatics
keyword: assay
keyword: phenotype
keyword: cell culture
keyword: microbiology
0000005: 0002999
has provider formatter: http://purl.obolibrary.org/obo/MICRO_$1
has local unique identifier pattern: ^\d{7}$
0000010: micro.owl
is deprecated: true
0000018: Microbial Conditions Ontology
has responsible: https://orcid.org/0000-0002-2100-6351
has URI prefix: http://purl.obolibrary.org/obo/MICRO_
0000027: MICRO_0002999
0000029: micro

Jacobo Miranda

has canonical
type: Property
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).
domain: Resource
range: Resource

LRMI Interact Type Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A concept scheme that defines the predominate interact mode of the learning resource being described.
is part of: bioregistry
git repository: lrmi
keyword: learning resource
keyword: open educational resource
0000005: active
has provider formatter: http://purl.org/dcx/lrmi-vocabs/interactivityType/$1
is deprecated: false
has URI prefix: http://purl.org/dcx/lrmi-vocabs/interactivityType/
0000027: active
0000029: lrmi.interact

European Science Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
keyword: computer science
keyword: educational resources
has provider formatter: http://data.europa.eu/8mn/euroscivoc/$1
is deprecated: false
has responsible: Publications Office of the European Union
has URI prefix: http://data.europa.eu/8mn/euroscivoc/
0000029: euroscivoc

UK Universities and Colleges Admissions Service
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An identifier for institutions in the United Kingdom, used in GRID and ROR.
is part of: bioregistry
keyword: bibliometrics
keyword: institution
0000005: N21
has local unique identifier pattern: ^\w\d+$
is deprecated: false
0000029: ucas

Database of Sequence Tagged Sites
type: Resource
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 part of: bioregistry
keyword: protein
keyword: gene
0000005: 456789
has provider formatter: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi
0000027: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi
0000029: unists

SWEET Ontology Property Mass
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Mass
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: mass
0000005: BulkDensity
has provider formatter: http://sweetontology.net/propMass/$1
is deprecated: false
has alternative prefix: sopropm
has URI prefix: http://sweetontology.net/propMass/
0000027: BulkDensity
0000029: sweet.propm

FunderRegistry
type: Resource
description: The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.
is part of: bioregistry
0000005: 100000001
has provider formatter: http://data.crossref.org/fundingdata/funder/10.13039/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: crossref.funder
has alternative prefix: FundRef
has URI prefix: http://data.crossref.org/fundingdata/funder/10.13039/
0000027: http://data.crossref.org/fundingdata/funder/10.13039/100000001
0000029: funderregistry

Research Resource Identification
type: Resource
contributor: https://orcid.org/0000-0002-5497-0243
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.
is part of: bioregistry
keyword: life science
keyword: biochemistry
keyword: community resource
keyword: resource discovery
keyword: centrally registered identifier
keyword: resource metadata
keyword: chemistry
keyword: omics
keyword: data retrieval
keyword: annotation
keyword: fair
keyword: biology
0000005: AB_262044
has provider formatter: https://scicrunch.org/resolver/RRID:$1
has local unique identifier pattern: ^[a-zA-Z]+.+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5497-0243
has URI prefix: https://scicrunch.org/resolver/RRID:
0000027: RRID:AB 262044
0000029: rrid

H-InvDb Protein
type: Resource
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
0000005: HIP000030660
has provider formatter: http://h-invitational.jp/hinv/protein/protein_view.cgi
has local unique identifier pattern: ^HIP\d{9}(\.\d+)?$
is deprecated: true
has URI prefix: http://h-invitational.jp/hinv/protein/protein_view.cgi
0000027: http://h-invitational.jp/hinv/protein/protein_view.cgi
0000029: hinv.protein

COlleCtion of Open Natural ProdUcTs
type: Resource
contributor: https://orcid.org/0000-0003-0443-9902
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 part of: bioregistry
keyword: natural producs
keyword: chemistry
keyword: organic chemistry
0000005: CNP0171505
has provider formatter: https://coconut.naturalproducts.net/compound/coconut_id/$1
has local unique identifier pattern: ^CNP\d{7}(\.\d+)?$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://coconut.naturalproducts.net/compound/coconut_id/
0000027: CNP0171505
0000029: coconut

Sumir Pandit
label: Sumir H Pandit

Biomarker Knowledgebase - Canonical Biomarker
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: https://orcid.org/0000-0002-5317-1458
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 part of: bioregistry
keyword: biomarker
0000005: AN6278
has provider formatter: https://biomarkerkb.org/canonical/$1
has local unique identifier pattern: ^A(N|O)\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-8823-9945
has URI prefix: https://biomarkerkb.org/canonical/
0000027: AN6278
0000029: biomarkerkb.canonical

MultiCellDS Digital Cell Line
type: Resource
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.
is part of: multicellds
is part of: bioregistry
0000005: MCDS_L_0000000001
has provider formatter: http://multicellds.org/MultiCellDB/$1
has local unique identifier pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$
is deprecated: false
has URI prefix: http://multicellds.org/MultiCellDB/
0000027: MCDS L 0000000001
0000029: multicellds.cell_line

Ontology for simulation, modelling, and optimization
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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/)
is part of: bioregistry
keyword: nfdi4cat
keyword: material science
keyword: computer science
0000005: application_case
has provider formatter: https://purl.org/vimmp/osmo#$1
is deprecated: true
has URI prefix: https://purl.org/vimmp/osmo#
0000027: application case
0000029: nfdi4chem.osmo

SWEET Ontology Representation Space
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: representation space
0000005: Space
has provider formatter: http://sweetontology.net/reprSpace/$1
is deprecated: false
has alternative prefix: soreps
has URI prefix: http://sweetontology.net/reprSpace/
0000027: Space
0000029: sweet.reps

Rat Genome Database RatMap
type: Resource
description: The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters
is part of: bioregistry
keyword: gene
keyword: dna
keyword: genome
0000005: 5
has provider formatter: http://ratmap.org/Showgene.php
0000011: Ensembl Gene
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://ratmap.org/Showgene.php
0000027: http://ratmap.org/Showgene.php
0000029: ratmap

SWEET Ontology Realm Region
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Region
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: realm
keyword: region
0000005: Austral
has provider formatter: http://sweetontology.net/realmRegion/$1
is deprecated: false
has alternative prefix: sorear
has URI prefix: http://sweetontology.net/realmRegion/
0000027: Austral
0000029: sweet.rear

Zebrafish developmental stages ontology
type: Resource
description: Developmental stages of the Zebrafish
is part of: bioregistry
git repository: zebrafish-anatomical-ontology
keyword: life cycle
keyword: anatomy
keyword: obo
keyword: zoology
keyword: ontology
keyword: marine biology
keyword: developmental biology
keyword: aging
0000005: 0000050
has provider formatter: http://purl.obolibrary.org/obo/ZFS_$1
has local unique identifier pattern: ^\d{7}$
0000010: zfs.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-2244-7917
has URI prefix: http://purl.obolibrary.org/obo/ZFS_
0000027: ZFS_0000050
0000029: zfs

Feature Annotation Location Description Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
is part of: bioregistry
git repository: FALDO
keyword: binding site
keyword: nucleic acid sequence
keyword: sequence feature
keyword: ontology
keyword: gene feature
keyword: genetics
keyword: geography
keyword: sequence annotation
0000005: ForwardStrandPosition
has provider formatter: http://biohackathon.org/resource/faldo#$1
0000010: faldo.owl
is deprecated: false
has responsible: FALDO group
has URI prefix: http://biohackathon.org/resource/faldo#
0000027: ForwardStrandPosition
0000029: faldo

GeneTree
type: Resource
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 part of: bioregistry
keyword: gene
keyword: classification
keyword: protein
0000005: ENSGT00550000074763
has provider formatter: http://www.ensembl.org/Multi/GeneTree/Image
has local unique identifier pattern: ^ENSGT\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3897-7955
has URI prefix: http://www.ensembl.org/Multi/GeneTree/Image
0000027: http://www.ensembl.org/Multi/GeneTree/Image
0000029: genetree

UniPathway Compound
type: Resource
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.
is part of: bioregistry
0000005: UPC04349
has provider formatter: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc
has local unique identifier pattern: ^UPC\d{5}$
is deprecated: false
has URI prefix: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc
0000027: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc
0000029: unipathway.compound

Darwin Core pathway controlled vocabulary
type: Resource
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 part of: bioregistry
keyword: life sciences, biology
keyword: fair data spaces
0000005: p001
has provider formatter: http://rs.tdwg.org/dwcpw/$1
is deprecated: false
has responsible: John Wieczorek
has URI prefix: http://rs.tdwg.org/dwcpw/
0000027: p001
0000029: dwc.pw

SWEET Ontology Phenomena Geologic Tectonic
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Tectonic
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
keyword: geologic tectonic
0000005: AsymmetricHeatFlow
has provider formatter: http://sweetontology.net/phenGeolTectonic/$1
is deprecated: false
has alternative prefix: sophgt
has URI prefix: http://sweetontology.net/phenGeolTectonic/
0000027: AsymmetricHeatFlow
0000029: sweet.phgt

SustainGraph Ontology
type: Resource
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.
is part of: bioregistry
keyword: miscellaneous
0000005: 6T
has provider formatter: https://netmode.gitlab.io/sustaingraph/$1
is deprecated: false
has URI prefix: https://netmode.gitlab.io/sustaingraph/
0000027: 6T
0000029: sustaingraph

SWEET Ontology Realm Atmospheric Boundary Layer
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Atmospheric Boundary Layer
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: atmospheric boundary layer
keyword: realm
0000005: AtmosphericBoundaryLayer
has provider formatter: http://sweetontology.net/realmAtmoBoundaryLayer/$1
is deprecated: false
has alternative prefix: soreaabl
has URI prefix: http://sweetontology.net/realmAtmoBoundaryLayer/
0000027: AtmosphericBoundaryLayer
0000029: sweet.reaabl

CATH domain
type: Resource
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 part of: bioregistry
0000005: 1cukA01
has provider formatter: http://www.cathdb.info/domain/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has URI prefix: http://www.cathdb.info/domain/
0000027: 1cukA01
0000029: cath.domain

NCBI Bookshelf
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover.
is part of: bioregistry
0000005: NBK331
has provider formatter: https://www.ncbi.nlm.nih.gov/books/$1
has local unique identifier pattern: ^NBK\d+$
is deprecated: false
has URI prefix: https://www.ncbi.nlm.nih.gov/books/
0000027: NBK331
0000029: ncbibook

Terence D. Murphy

SWEET Ontology Human Jurisdiction
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Jurisdiction
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: jurisdiction
0000005: AdministrativeRegion
has provider formatter: http://sweetontology.net/humanJurisdiction/$1
is deprecated: false
has alternative prefix: sohuj
has URI prefix: http://sweetontology.net/humanJurisdiction/
0000027: AdministrativeRegion
0000029: sweet.huj

Regulatory Elements Database for Drosophila
type: Resource
description: REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).
is part of: bioregistry
keyword: regulation
0000005: 8
has provider formatter: http://redfly.ccr.buffalo.edu/
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://redfly.ccr.buffalo.edu/
0000027: http://redfly.ccr.buffalo.edu/
0000029: redfly

ChEBI Data Sources
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
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: drugbank
has part: UM-BBD compound
has part: Protein covalent bond
has part: The Bioinorganic Motif Database
has part: Web Elements
has part: metacyc.compound
has part: KEGG Drug
has part: Chemical Component Dictionary
has part: knapsack
has part: smid
has part: pdb
has part: Alan Wood's Pesticides
has part: eurofir
has part: KEGG Compound
has part: Human Metabolome Database
has part: ymdb
has part: lipidmaps
has part: E. coli Metabolite Database
has part: Chemical Entities of Biological Interest
has part: kegg.glycan
has part: molbase.sheffield
has part: ChemIDplus
has part: LINCS Small Molecule
has part: google.patent

National Microbiome Data Collaborative
type: Resource
contributor: https://orcid.org/0000-0002-8424-0604
contributor: https://orcid.org/0000-0003-4423-4370
description: An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.
is part of: bioregistry
keyword: microbiome
0000005: y3ax-8bq3-60
has provider formatter: https://w3id.org/nmdc/$1
has local unique identifier pattern: ^.{2,}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8424-0604
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://w3id.org/nmdc/
0000027: y3ax-8bq3-60
0000029: nmdc

Fungal Growth Database
type: Resource
contributor: https://orcid.org/0009-0009-3402-8013
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
keyword: growth profiles
keyword: plant biomass
keyword: monosaccharides
keyword: polysaccharides
keyword: fungi
0000005: 86
has provider formatter: https://www.fung-growth.org/page/Display%20page%20FG/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9370-4677
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.fung-growth.org/page/Display%20page%20FG/
0000027: https://www.fung-growth.org/page/Display%20page%20FG/86
0000029: funggrowth

Ontology for Avida digital evolution platform
type: Resource
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
is part of: bioregistry
git repository: ontoavida
keyword: obo
keyword: ontology
0000005: 00000001
has provider formatter: http://purl.obolibrary.org/obo/ONTOAVIDA_$1
has local unique identifier pattern: ^\d{8}$
0000010: ontoavida.owl
is deprecated: false
depends on: ncit
depends on: The Statistical Methods Ontology
depends on: ro
depends on: gsso
depends on: fbcv
has responsible: Miguel A. Fortuna
has URI prefix: http://purl.obolibrary.org/obo/ONTOAVIDA_
0000027: ONTOAVIDA_00000001
0000029: ontoavida

Cancer Cell Line Encyclopedia Cells
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Datasets around different cancer cell lines generated by the Broad Institute and Novartis
is part of: bioregistry
keyword: cancer cell line
keyword: cell
keyword: cell line
keyword: ontology
0000005: BT20_BREAST
has provider formatter: https://www.cbioportal.org/patient
0000010: ccle.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-3539-9803
has alternative prefix: ccle.cell
has URI prefix: https://www.cbioportal.org/patient
0000027: https://www.cbioportal.org/patient
0000029: ccle

SWEET Ontology Property
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: property
0000005: Accuracy
has provider formatter: http://sweetontology.net/prop/$1
is deprecated: false
has alternative prefix: soprop
has URI prefix: http://sweetontology.net/prop/
0000027: Accuracy
0000029: sweet.prop

NASA Open Science Data Repository Biospecimen
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for biospecimens used in experiments that investigate biological and health responses of terrestrial life to spaceflight
is part of: bioregistry
0000005: 7943
has provider formatter: https://osdr.nasa.gov/bio/repo/data/biospecimens/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8542-2389
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://osdr.nasa.gov/bio/repo/data/biospecimens/
0000027: https://osdr.nasa.gov/bio/repo/data/biospecimens/7943
0000029: nasaosdr.biospecimen

ELI Metadata Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology to describe legislation, based on the FRBR model, that encodes the ELI metadata fields.
is part of: bioregistry
keyword: frbr
keyword: contracts
0000005: InForce
has provider formatter: http://data.europa.eu/eli/ontology#$1
is deprecated: false
has URI prefix: http://data.europa.eu/eli/ontology#
0000027: InForce
0000029: eli

FishBase
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: 6472
has provider formatter: https://www.fishbase.ca/summary/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: fishbase
has URI prefix: https://www.fishbase.ca/summary/
0000027: https://www.fishbase.ca/summary/6472
0000029: fishbase.species

European Union Publications Office dataset
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Datasets published by the Publications Office of the European Union
is part of: bioregistry
0000005: euvoc
has provider formatter: http://publications.europa.eu/resource/dataset/$1
is deprecated: false
has URI prefix: http://publications.europa.eu/resource/dataset/
0000027: euvoc
0000029: eu.publication

OECD Harmonised Templates
type: Resource
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 part of: bioregistry
0000005: 74.186
has local unique identifier pattern: ^\d+\.\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
0000029: oecd.template

CLAVAS: ISO 639-3 Language Codes
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Representation of languages
is part of: bioregistry
keyword: language
0000005: CDB-00133756-001
has provider formatter: http://cdb.iso.org/lg/$1
is deprecated: false
has URI prefix: http://cdb.iso.org/lg/
0000027: http://cdb.iso.org/lg/CDB-00133756-001
0000029: clarin.clavas

The ALlele FREquency Database
type: Resource
contributor: Sumir Pandit
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.
is part of: bioregistry
keyword: genome
keyword: classification
0000005: LO362836C
has provider formatter: https://alfred.med.yale.edu/alfred/recordinfo.asp
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://alfred.med.yale.edu/alfred/recordinfo.asp
0000027: https://alfred.med.yale.edu/alfred/recordinfo.asp
0000029: alfred

Biological Collections Ontology
type: Resource
description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.
is part of: bioregistry
git repository: bco
keyword: metagenomics
keyword: ess
keyword: taxonomy
keyword: obo
keyword: ontology
keyword: biospecimen
keyword: biodiversity
keyword: dataplant
keyword: ecology
keyword: sample annotation
keyword: taxonomic classification
keyword: environmental material
keyword: earth sciences
0000005: 0000081
has provider formatter: http://purl.obolibrary.org/obo/BCO_$1
has local unique identifier pattern: ^\d{7}$
0000010: bco.owl
is deprecated: false
0000018: fovt
has responsible: https://orcid.org/0000-0001-8815-0078
has URI prefix: http://purl.obolibrary.org/obo/BCO_
0000027: BCO_0000081
0000029: bco

DiabetesOmic
type: Resource
contributor: https://orcid.org/0009-0000-6974-6386
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
keyword: omics
keyword: sample
keyword: diabetes
0000005: sample_002
has provider formatter: https://bio.liclab.net/diabetesOmicdb/RNA-seq
has local unique identifier pattern: ^sample_\d{3}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-0344-3168
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://bio.liclab.net/diabetesOmicdb/RNA-seq
0000027: https://bio.liclab.net/diabetesOmicdb/RNA-seq
0000029: diabetesomic

Terminology for Description of Dynamics
type: Resource
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.
is part of: bioregistry
git repository: teddy.md
keyword: neurophysiology
keyword: systems biology
keyword: ontology
keyword: synthetic biology
0000005: 0000066
has provider formatter: https://www.ebi.ac.uk/ols/ontologies/teddy/terms
has local unique identifier pattern: ^\d+$
0000010: teddy-inferred.owl
is deprecated: false
has responsible: Michael Hucka
has alternative prefix: teddy
has URI prefix: https://www.ebi.ac.uk/ols/ontologies/teddy/terms
0000027: https://www.ebi.ac.uk/ols/ontologies/teddy/terms
0000029: biomodels.teddy

Tim Beck

has alternative prefix
type: Property
description: An alternative or synonymous prefix
domain: Resource
range: string
sub property of: hasExactSynonym
equivalent property: alternatePrefix

PaxDb Organism
type: Resource
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.
is part of: bioregistry
0000005: 9606
has provider formatter: http://pax-db.org/#!species/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://pax-db.org/#!species/
0000027: !species/9606
0000029: paxdb.organism

UniProt
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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.
is part of: bioregistry
0000005: BRAF_HUMAN
has provider formatter: https://www.uniprot.org/uniprotkb/$1
has local unique identifier pattern: ^[A-Z0-9]{1,10}_[A-Z0-9]{1,5}$
is deprecated: false
has responsible: Alex Bateman
has reviewer: https://orcid.org/0000-0003-2473-2313
has URI prefix: https://www.uniprot.org/uniprotkb/
0000027: BRAF HUMAN
0000029: uniprot.mnemonic

Resource
type: Class
description: A type for entries in the Bioregistry's registry.

KIM License
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary describing licenses for data and code
is part of: bioregistry
git repository: license
keyword: license
0000005: nonCommercial
has provider formatter: https://w3id.org/kim/license/$1
is deprecated: false
has URI prefix: https://w3id.org/kim/license/
0000027: nonCommercial
0000029: kim.license

GlyTouCan
type: Resource
description: GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.
is part of: bioregistry
keyword: glycomics
keyword: structural biology
0000005: G00054MO
has provider formatter: https://glytoucan.org/Structures/Glycans/$1
has local unique identifier pattern: ^G[0-9]{5}[A-Z]{2}$
is deprecated: false
has responsible: 0000-0003-3147-448X
has alternative prefix: glygen
has URI prefix: https://glytoucan.org/Structures/Glycans/
0000027: G00054MO
0000029: glytoucan

Bibliographic Reference Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.
is part of: bioregistry
git repository: biro
keyword: subject agnostic
keyword: spar
0000005: BibliographicRecord
has provider formatter: http://purl.org/spar/biro/$1
is deprecated: false
has responsible: Silvio Peroni
has URI prefix: http://purl.org/spar/biro/
0000027: BibliographicRecord
0000029: biro

SUPERFAMILY
type: Resource
description: SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt.
is part of: bioregistry
keyword: classification
keyword: genome
keyword: protein
keyword: structure
0000005: SSF57615
has provider formatter: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-7168-7143
has URI prefix: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi
0000027: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi
0000029: supfam

LinkML
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: linkml
keyword: ontology and terminology
keyword: data integration
0000005: SchemaDefinition
has provider formatter: https://w3id.org/linkml/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
has URI prefix: https://w3id.org/linkml/
0000027: SchemaDefinition
0000029: linkml

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.
is part of: bioregistry
0000005: CAE46076
has provider formatter: http://ardb.cbcb.umd.edu/cgi/search.cgi
has local unique identifier pattern: ^[A-Z_]{3}[0-9]{4,}$
is deprecated: true
has URI prefix: http://ardb.cbcb.umd.edu/cgi/search.cgi
0000027: http://ardb.cbcb.umd.edu/cgi/search.cgi
0000029: ardb

CohesinDB gene
type: Resource
contributor: https://orcid.org/0009-0000-6974-6386
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 part of: bioregistry
keyword: gene
0000005: CDBG00009781
has provider formatter: https://cohesindb.iqb.u-tokyo.ac.jp/browsegene/eachgene/$1
has local unique identifier pattern: ^CDBG000\d{5}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-3019-5817
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://cohesindb.iqb.u-tokyo.ac.jp/browsegene/eachgene/
0000027: CDBG00009781
0000029: cohesindb.gene

Job Dekker

RSNA Informatics RadLex
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: ontology
keyword: medical informatics
keyword: medical imaging
keyword: diagnosis
keyword: radiology
keyword: clinical studies
keyword: biomedical science
keyword: anatomy
0000005: RID1
has provider formatter: https://radlex.org/RID/$1
has local unique identifier pattern: ^RID\d+$
0000010: radlex.owl
is deprecated: false
has responsible: Radiological Society of North America
has URI prefix: https://radlex.org/RID/
0000027: RID1
0000029: radlex

NIF Standard Ontology: Organisms
type: Resource
contributor: Tom Gillespie
description: NLXORG covers organisms.
is part of: bioregistry
git repository: NIF-Ontology
keyword: taxonomy
0000005: 090701
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Tom Gillespie
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXORG
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_organ_
0000027: nlx organ 090701
0000029: nlx.org

SWEET Ontology Relationships Space
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Space
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: space
0000005: adjacentTo
has provider formatter: http://sweetontology.net/relaSpace/$1
is deprecated: false
has alternative prefix: sorelsp
has URI prefix: http://sweetontology.net/relaSpace/
0000027: adjacentTo
0000029: sweet.relsp

ShiBASE
type: Resource
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.
is part of: bioregistry
keyword: genome
0000005: SDY2614
has provider formatter: http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi
0000027: http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi
0000029: shibase

Protocol for Web Description Resources (POWDER): POWDER-S Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
keyword: api
0000005: structure
has provider formatter: http://www.w3.org/2007/05/powder-s#$1
is deprecated: false
has URI prefix: http://www.w3.org/2007/05/powder-s#
0000027: structure
0000029: wdrs

UCSC Genome Browser
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: uc001rvw.5
has provider formatter: ftp://hgdownload.cse.ucsc.edu/goldenPath/$1
is deprecated: false
has responsible: Maximilian Haeussler
has URI prefix: ftp://hgdownload.cse.ucsc.edu/goldenPath/
0000027: uc001rvw.5
0000029: ucsc

Transporter Classification Database
type: Resource
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.
is part of: bioregistry
keyword: structure
keyword: phylogenetics
keyword: life science
keyword: cell biology
keyword: computational biology
keyword: protein
keyword: knowledge and information systems
0000005: 5.A.1.1.1
has provider formatter: http://www.tcdb.org/search/result.php
has local unique identifier pattern: ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$
is deprecated: false
has responsible: https://orcid.org/0000-0001-5530-0017
has alternative prefix: TC
has URI prefix: http://www.tcdb.org/search/result.php
0000027: http://www.tcdb.org/search/result.php
0000029: tcdb

Ontology of units of Measure
type: Resource
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.
is part of: bioregistry
git repository: OM
keyword: unit
keyword: nfdi4ing
keyword: ess
keyword: units
keyword: physics
keyword: ontology
keyword: nfdi4cat
keyword: nfdi4chem
keyword: earth sciences
keyword: life sciences, biology
0000005: Dimension
has provider formatter: http://www.ontology-of-units-of-measure.org/resource/om-2/$1
0000010: om.owl
is deprecated: false
has responsible: Hajo Rijgersberg
has URI prefix: http://www.ontology-of-units-of-measure.org/resource/om-2/
0000027: Dimension
0000029: om

System capabilities, operating ranges, and survival ranges ontology
type: Resource
contributor: https://orcid.org/0000-0002-1595-3213
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
is part of: bioregistry
keyword: nfdi4chem
keyword: nfdi4ing
keyword: engineering
0000005: qualityOfObservation
has provider formatter: http://www.w3.org/ns/ssn/systems/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-3884-3420
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.w3.org/ns/ssn/systems/
0000027: qualityOfObservation
0000029: ssn.system

DSSTox substance
type: Resource
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.
is part of: bioregistry
0000005: DTXSID2021028
has provider formatter: https://comptox.epa.gov/dashboard/$1
has local unique identifier pattern: ^DTXSID\d+$
is deprecated: false
has URI prefix: https://comptox.epa.gov/dashboard/
0000027: DTXSID2021028
0000029: comptox

GXA Expt
type: Resource
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
0000005: E-MTAB-2037
has provider formatter: https://www.ebi.ac.uk/gxa/experiments/$1
has local unique identifier pattern: ^[AEP]-\w{4}-\d+$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/gxa/experiments/
0000026: 02catss52
0000027: E-MTAB-2037
0000029: gxa.expt

SWEET Ontology State System
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State System
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state system
0000005: Coherent
has provider formatter: http://sweetontology.net/stateSystem/$1
is deprecated: false
has alternative prefix: sostsy
has URI prefix: http://sweetontology.net/stateSystem/
0000027: Coherent
0000029: sweet.stsy

Academic Event Ontology
type: Resource
contributor: https://orcid.org/0000-0002-1595-3213
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).
is part of: bioregistry
git repository: aeon
keyword: history
keyword: educational science
keyword: miscellaneous
keyword: ontology
keyword: social sciences
0000005: 0000001
has provider formatter: http://purl.obolibrary.org/obo/AEON_$1
has local unique identifier pattern: ^\d{7}$
0000010: aeon.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1595-3213
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://purl.obolibrary.org/obo/AEON_
0000027: AEON_0000001
0000029: aeon

Merriam Webster Dictionary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Online Dictionary
is part of: bioregistry
0000005: buccal_gland
has provider formatter: https://www.merriam-webster.com/dictionary/$1
is deprecated: false
has alternative prefix: merriam_webster
has URI prefix: https://www.merriam-webster.com/dictionary/
0000027: buccal gland
0000029: merriamwebster

Shuichi Onami

Small Angle Scattering Biological Data Bank
type: Resource
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.
is part of: bioregistry
keyword: molecular biology
keyword: life science
0000005: SASDAX8
has provider formatter: http://www.sasbdb.org/data/$1
has local unique identifier pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$
is deprecated: false
has responsible: https://orcid.org/0000-0003-1321-3956
has URI prefix: http://www.sasbdb.org/data/
0000027: SASDAX8
0000029: sasbdb

Protein Structure and Stability Knowledge Base
type: Resource
contributor: 0009-0008-8406-631X
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.
is part of: bioregistry
0000005: 2VM6_A55_A135
has provider formatter: https://psskb.org/motif/card/$1
has local unique identifier pattern: ^[A-Za-z0-9_]+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4472-2016
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://psskb.org/motif/card/
0000027: 2VM6 A55 A135
0000029: psskb

Minimal Viable Identifier
type: Resource
description: Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.
has part: minid.test
is part of: bioregistry
keyword: data retrieval
keyword: subject agnostic
0000005: b97957
has provider formatter: https://hdl.handle.net/hdl:20.500.12582/$1
has local unique identifier pattern: ^[A-Za-z0-9]+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-2129-5269
has URI prefix: https://hdl.handle.net/hdl:20.500.12582/
0000027: b97957
0000029: minid

WikiGenes
type: Resource
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.
is part of: bioregistry
0000005: 3771877
has provider formatter: http://www.wikigenes.org/e/gene/e/$1.html
has local unique identifier pattern: ^\d+$
0000011: ncbigene
is deprecated: false
has URI prefix: https://bioregistry.io/wikigenes:
0000027: 3771877.html
0000029: wikigenes

Commonality Type
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Describes the degree of similarity between two items or schemes (collections of items).
is part of: bioregistry
0000005: Identical
has provider formatter: https://vocabularies.cessda.eu/vocabulary/CommonalityType#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/CommonalityType#code_
0000026: 015em2733
0000027: code Identical
0000029: ddi.commonalitytype

SeaDataNet device categories
type: Resource
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).
is part of: bioregistry
keyword: earth sciences
keyword: ess
0000005: 101
has provider formatter: http://vocab.nerc.ac.uk/collection/L05/current/$1
is deprecated: false
has URI prefix: http://vocab.nerc.ac.uk/collection/L05/current/
0000027: http://vocab.nerc.ac.uk/collection/L05/current/101
0000029: bodc.sdn

Exercise Medicine Ontology
type: Resource
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.
is part of: bioregistry
git repository: EXMO
keyword: obo
keyword: ontology
0000005: 0000008
has provider formatter: http://purl.obolibrary.org/obo/EXMO_$1
0000010: exmo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-9295-2767
has URI prefix: http://purl.obolibrary.org/obo/EXMO_
0000029: exmo

Database of Quantitative Cellular Signaling: Model
type: Resource
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.
is part of: bioregistry
keyword: model
0000005: 57
has provider formatter: http://doqcs.ncbs.res.in/template.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Upinder S. Bhalla
has URI prefix: http://doqcs.ncbs.res.in/template.php
0000027: http://doqcs.ncbs.res.in/template.php
0000029: doqcs.model

BridgeDb Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc.
is part of: bioregistry
0000005: hasPrimaryUriPattern
has provider formatter: http://vocabularies.bridgedb.org/ops#$1
is deprecated: false
has URI prefix: http://vocabularies.bridgedb.org/ops#
0000027: hasPrimaryUriPattern
0000029: bridgedb

Theiler Stage
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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))
is part of: bioregistry
0000005: 23
has provider formatter: https://www.emouseatlas.org/emap/ema/DAOAnatomyJSP/anatomy.html
has local unique identifier pattern: ^\d+[a-d]?$
is deprecated: false
0000018: emaps
0000018: Mouse Developmental Stages
has responsible: Terry Hayamizu
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: thielerstage
has URI prefix: https://www.emouseatlas.org/emap/ema/DAOAnatomyJSP/anatomy.html
0000027: https://www.emouseatlas.org/emap/ema/DAOAnatomyJSP/anatomy.html
0000029: theiler

Mosquito insecticide resistance
type: Resource
description: Application ontology for entities related to insecticide resistance in mosquitos
is part of: bioregistry
git repository: MIRO
keyword: mutation
keyword: life science
keyword: obo
keyword: ontology
keyword: phenotype
0000005: 40000617
has provider formatter: http://purl.obolibrary.org/obo/MIRO_$1
has local unique identifier pattern: ^\d{8}$
0000010: miro.owl
is deprecated: true
has responsible: https://orcid.org/0000-0003-2497-2210
has URI prefix: http://purl.obolibrary.org/obo/MIRO_
0000027: MIRO_40000617
0000029: miro

Stuart Chalk

Raimond Winslow

SWEET Ontology Property Index
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Index
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: index
0000005: AdaptiveCapacity
has provider formatter: http://sweetontology.net/propIndex/$1
is deprecated: false
has alternative prefix: sopropi
has URI prefix: http://sweetontology.net/propIndex/
0000027: AdaptiveCapacity
0000029: sweet.propi

National Uniform Claim Committee Characteristic
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: 2A
has local unique identifier pattern: ^\d(\d|\w)$
is deprecated: false
0000029: nucc.characteristic

ChemBioSys Dataset
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A dataset in the ChemBioSys data platform
is part of: bioregistry
0000005: 103
has provider formatter: https://data.chembiosys.de/data_files/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.chembiosys.de/data_files/
0000027: https://data.chembiosys.de/data_files/103
0000029: chembiosys.data

BioNumbers
type: Resource
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 part of: bioregistry
0000005: 104674
has provider formatter: https://bionumbers.hms.harvard.edu/bionumber.aspx
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://bionumbers.hms.harvard.edu/bionumber.aspx
0000027: https://bionumbers.hms.harvard.edu/bionumber.aspx
0000029: bionumbers

Nicolas Le Novere
label: Nicolas Le Novère

MicrosporidiaDB
type: Resource
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 part of: bioregistry
keyword: eukaryotic
keyword: genome
0000005: ECU03_0820i
has provider formatter: http://microsporidiadb.org/micro/showRecord.do
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: Omar S. Harb
has URI prefix: http://microsporidiadb.org/micro/showRecord.do
0000027: http://microsporidiadb.org/micro/showRecord.do
0000029: microsporidia

RiceNetDB Protein
type: Resource
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.
is part of: bioregistry
0000005: LOC_Os01g49190
has provider formatter: http://bis.zju.edu.cn/ricenetdb/proteindetails.php
has local unique identifier pattern: ^LOC\_Os\d{1,2}g\d{5}$
is deprecated: false
has URI prefix: http://bis.zju.edu.cn/ricenetdb/proteindetails.php
0000027: http://bis.zju.edu.cn/ricenetdb/proteindetails.php
0000029: ricenetdb.protein

Dewey Decimal Classification
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: 325.4
has provider formatter: http://dewey.info/class/$1/e23/
has local unique identifier pattern: ^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\.[0-9]+(-[0-9]{3}\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$
is deprecated: false
has URI prefix: https://bioregistry.io/ddc:
0000027: e23
0000029: ddc

SED-ML model format
type: Resource
description: Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).
is part of: bioregistry
0000005: sbml.level-3.version-2
has provider formatter: https://sed-ml.org/urns.html#language:$1
has local unique identifier pattern: ^[a-z]+(\..*?)?$
is deprecated: false
has URI prefix: https://sed-ml.org/urns.html#language:
0000027: language:sbml.level-3.version-2
0000029: sedml.language

MycoBrowser smegmatis
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 smegmatis information.
is part of: bioregistry
is part of: myco
keyword: sequence
keyword: genome
0000005: MSMEG_3769
has provider formatter: https://mycobrowser.epfl.ch/genes/$1
has local unique identifier pattern: ^MSMEG\w+$
is deprecated: false
has URI prefix: https://mycobrowser.epfl.ch/genes/
0000027: MSMEG 3769
0000029: myco.smeg

Affymetrix Probeset
type: Resource
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.
is part of: bioregistry
0000005: 243002_at
has provider formatter: http://bio2rdf.org/affymetrix:$1
has local unique identifier pattern: ^\d{4,}((_[asx])?_at)?$
is deprecated: false
has URI prefix: http://bio2rdf.org/affymetrix:
0000027: affymetrix:243002 at
0000029: affy.probeset

Zhi Xie

Fischertechnik Ontology
type: Resource
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]
is part of: bioregistry
git repository: ftonto
keyword: engineering
keyword: nfdi4ing
keyword: coypu
0000005: ADXL345_Pi_1_AccSensor_1_Result_2019-02-26_14_53_54.97
has provider formatter: http://iot.uni-trier.de/FTOnto#$1
is deprecated: false
has URI prefix: http://iot.uni-trier.de/FTOnto#
0000027: ADXL345 Pi 1 AccSensor 1 Result 2019-02-26 14 53 54.97
0000029: ftonto

Genomic Data Commons Data Portal
type: Resource
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.
is part of: bioregistry
has provider formatter: https://portal.gdc.cancer.gov/cases/$1
has local unique identifier pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$
is deprecated: false
has URI prefix: https://portal.gdc.cancer.gov/cases/
0000029: gdc

SWEET Ontology State Spectral Line
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Spectral Line
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: state spectral line
0000005: CaK
has provider formatter: http://sweetontology.net/stateSpectralLine/$1
is deprecated: false
has alternative prefix: sostsl
has URI prefix: http://sweetontology.net/stateSpectralLine/
0000027: CaK
0000029: sweet.stsl

SWEET Ontology Property Charge
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Charge
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: charge
0000005: Capacitance
has provider formatter: http://sweetontology.net/propCharge/$1
is deprecated: false
has alternative prefix: sopropcha
has URI prefix: http://sweetontology.net/propCharge/
0000027: Capacitance
0000029: sweet.propcha

SWEET Ontology Realm Land Orographic
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Orographic
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: orographicland
0000005: Alpine
has provider formatter: http://sweetontology.net/realmLandOrographic/$1
is deprecated: false
has alternative prefix: sorealo
has URI prefix: http://sweetontology.net/realmLandOrographic/
0000027: Alpine
0000029: sweet.realo

KEGG Drug Group
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
is part of: kegg
0000005: DG00301
has local unique identifier pattern: ^DG\d+$
is deprecated: false
has alternative prefix: KEGG_DRUG_GROUP
has alternative prefix: KEGG_DGROUP
0000029: kegg.dgroup

PepBank Peptide Database
type: Resource
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.
is part of: bioregistry
keyword: protein
keyword: structure
0000005: 21877
has provider formatter: http://pepbank.mgh.harvard.edu/interactions/details/$1
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://pepbank.mgh.harvard.edu/interactions/details/
0000027: http://pepbank.mgh.harvard.edu/interactions/details/21877
0000029: pepbank

Gene Regulation Ontology
type: Resource
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.
is part of: bioregistry
keyword: obo
keyword: ontology
0000005: Lipid
has provider formatter: http://www.bootstrep.eu/ontology/GRO#$1
0000010: gro.owl
is deprecated: true
has responsible: Vivian Lee
has alternative prefix: bootstrep
has URI prefix: http://www.bootstrep.eu/ontology/GRO#
0000027: Lipid
0000029: gro

Golm Metabolome Database Analyte
type: Resource
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.
is part of: bioregistry
has provider formatter: http://gmd.mpimp-golm.mpg.de/Analytes/$1
has local unique identifier pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
is deprecated: false
has URI prefix: http://gmd.mpimp-golm.mpg.de/Analytes/
0000029: gmd.analyte

GeneCards Gene
type: Resource
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.
is part of: bioregistry
keyword: transcriptomics
keyword: life science
keyword: genetics
keyword: genome
0000005: ABL1
has provider formatter: https://www.genecards.org/cgi-bin/carddisp.pl
has local unique identifier pattern: ^[A-Za-z-0-9_]+(\@)?$
is deprecated: false
has responsible: https://orcid.org/0000-0001-5424-1393
has alternative prefix: genecards
has URI prefix: https://www.genecards.org/cgi-bin/carddisp.pl
0000027: https://www.genecards.org/cgi-bin/carddisp.pl
0000029: genecards.gene

DevTox
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
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.
is part of: bioregistry
0000005: 311935300
has provider formatter: https://www.devtox.org/nomenclature/ml_manus.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Rupert Kellner
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.devtox.org/nomenclature/ml_manus.php
0000027: https://www.devtox.org/nomenclature/ml_manus.php
0000029: devtox

Continuous Automated Model Evaluation
type: Resource
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.
is part of: bioregistry
keyword: life science
0000005: 2019-08-03_00000089_1
has provider formatter: https://www.cameo3d.org/sp/targets/target/$1
has local unique identifier pattern: ^[0-9\-_]+$
is deprecated: false
has responsible: Torsten Schwede
has URI prefix: https://www.cameo3d.org/sp/targets/target/
0000027: 2019-08-03 00000089 1
0000029: cameo

Evan E Bolton

Art and Architecture Thesaurus
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
0000005: 300011154
has provider formatter: http://vocab.getty.edu/aat/$1
is deprecated: false
has URI prefix: http://vocab.getty.edu/aat/
0000027: http://vocab.getty.edu/aat/300011154
0000029: getty.att

Matteo Guenci

Animal Genome Cattle 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 references cattle QTLs.
is part of: bioregistry
is part of: qtldb
keyword: genome
keyword: dna
0000005: 4685
has provider formatter: https://www.animalgenome.org/QTLdb/q
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.animalgenome.org/QTLdb/q
0000027: https://www.animalgenome.org/QTLdb/q
0000029: cattleqtldb

SWEET Ontology Phenomena Biology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Biology
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
keyword: biology
0000005: Assimilation
has provider formatter: http://sweetontology.net/phenBiol/$1
is deprecated: false
has alternative prefix: sophb
has URI prefix: http://sweetontology.net/phenBiol/
0000027: Assimilation
0000029: sweet.phb

Electron Microscopy Public Image Archive
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
is part of: bioregistry
keyword: bioinformatics
keyword: biology
0000005: 10595
has provider formatter: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-7663-9028
has URI prefix: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/
0000026: 02catss52
0000027: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10595
0000029: empiar

IUPAC Compendium of Analytical Nomenclature (Orange Book)
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The first number is the chapter then the remainder are subsections.
is part of: bioregistry
0000005: 10.2.1.1.3
is deprecated: false
0000029: orangebook

Software Package
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Indicates the statistical software package used in the production/processing/dissemination of the data. Data collection software is not covered in this list.
is part of: bioregistry
0000005: AcaStat
has provider formatter: https://vocabularies.cessda.eu/vocabulary/SoftwarePackage#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/SoftwarePackage#code_
0000026: 015em2733
0000027: code AcaStat
0000029: ddi.softwarepackage

SWEET Ontology Realm Land Aeolian
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Aeolian
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: aeolianland
0000005: Aeolian
has provider formatter: http://sweetontology.net/realmLandAeolian/$1
is deprecated: false
has alternative prefix: soreala
has URI prefix: http://sweetontology.net/realmLandAeolian/
0000027: Aeolian
0000029: sweet.reala

Environmental Molecular Sciences Laboratory Project
type: Resource
contributor: Cody O'Donnell
contributor: https://orcid.org/0000-0002-6601-2165
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
is part of: bioregistry
0000005: 60141
has provider formatter: https://sc-data.emsl.pnnl.gov/
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8683-0050
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://sc-data.emsl.pnnl.gov/
0000027: https://sc-data.emsl.pnnl.gov/
0000029: emsl.project

UniProt Post-Translational Modification
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
contributor: https://orcid.org/0000-0003-4423-4370
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
is part of: bioregistry
keyword: post-translational modification
keyword: structural biology
keyword: biochemistry
keyword: ontology
0000005: PTM-0450
has provider formatter: https://biopragmatics.github.io/providers/uniprot.ptm/$1
has local unique identifier pattern: ^PTM-\d{4}$
0000010: uniprot.ptm.owl
is deprecated: false
has responsible: Alex Bateman
has alternative prefix: PTM
has URI prefix: https://biopragmatics.github.io/providers/uniprot.ptm/
0000027: PTM-0450
0000029: uniprot.ptm

Allotrope role
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The role component of the Allotrope ontology suite
is part of: bioregistry
is part of: afo
0000005: 0000248
has provider formatter: http://purl.allotrope.org/ontologies/role#AFRL_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://purl.allotrope.org/ontologies/role#AFRL_
0000027: AFRL_0000248
0000029: allotrope.role

Mark Jensen

Dynamic Ecological Information Management System - Site and Dataset Registry - Locations
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Locations in DEIMS SDR
is part of: bioregistry
has provider formatter: https://deims.org/locations/$1
has local unique identifier pattern: ^[0-9a-f\-]+$
is deprecated: false
has responsible: Christoph Wohner
has URI prefix: https://deims.org/locations/
0000029: deims.location

Secondary Metabolism Collaboratory - biosynthetic gene cluster
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
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.
is part of: bioregistry
0000005: 12039302
has provider formatter: https://smc.jgi.doe.gov/bgc/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3491-0198
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://smc.jgi.doe.gov/bgc/
0000027: https://smc.jgi.doe.gov/bgc/12039302
0000029: smc.bgc

tsRNADisease
type: Resource
contributor: https://orcid.org/0009-0009-3402-8013
description: Identifiers correspond to curated associations between diseases and tRNA-derived small RNAs (tsRNAs) in the tsRNADisease database.
is part of: bioregistry
keyword: cancer
keyword: disease
keyword: tsrna
0000005: TRD00001
has provider formatter: http://118.178.132.53/tsRNADisease/detail.php
has local unique identifier pattern: ^TRD\d{5}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6782-0316
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: http://118.178.132.53/tsRNADisease/detail.php
0000027: http://118.178.132.53/tsRNADisease/detail.php
0000029: tsrnadisease

Mode Of Collection
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The procedure, technique, or mode of inquiry used to attain the data.
is part of: bioregistry
0000005: Interview
has provider formatter: https://vocabularies.cessda.eu/vocabulary/ModeOfCollection#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/ModeOfCollection#code_
0000026: 015em2733
0000027: code Interview
0000029: ddi.modeofcollection

TTD Target
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 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.
is part of: bioregistry
0000005: t59328
has provider formatter: https://db.idrblab.net/ttd/data/target/details/$1
has local unique identifier pattern: ^t\d+$
is deprecated: false
has URI prefix: https://db.idrblab.net/ttd/data/target/details/
0000027: t59328
0000029: ttd.target

Genetic Testing Registry Labs
type: Resource
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.
is part of: bioregistry
0000005: 000320401
has provider formatter: https://www.ncbi.nlm.nih.gov/gtr/labs/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.ncbi.nlm.nih.gov/gtr/labs/
0000027: https://www.ncbi.nlm.nih.gov/gtr/labs/000320401
0000029: gtr.lab

Odor Molecules DataBase
type: Resource
description: OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors
is part of: bioregistry
0000005: 74
has provider formatter: https://ordb.biotech.ttu.edu/OdorDB/Data/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://ordb.biotech.ttu.edu/OdorDB/Data/
0000027: https://ordb.biotech.ttu.edu/OdorDB/Data/74
0000029: odor

General Process Ontology
type: Resource
description: Ontology to model processes
is part of: bioregistry
git repository: ontology
keyword: engineering
keyword: nfdi4ing
has provider formatter: https://gpo.ontology.link/GPO_$1
is deprecated: false
has URI prefix: https://gpo.ontology.link/GPO_
0000029: tib.gpo

MHC Restriction Ontology
type: Resource
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.
is part of: bioregistry
git repository: MRO
keyword: obo
keyword: ontology
keyword: immunology
keyword: immune system
keyword: major histocompatibility complex
0000005: 0000634
has provider formatter: http://purl.obolibrary.org/obo/MRO_$1
has local unique identifier pattern: ^\d{7}$
0000010: mro.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-8457-6693
has URI prefix: http://purl.obolibrary.org/obo/MRO_
0000027: MRO_0000634
0000029: mro

Genomic Distribution of structural Superfamilies
type: Resource
description: Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases.
is part of: bioregistry
keyword: classification
keyword: genome
0000005: 46946
has provider formatter: http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi
0000027: http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi
0000029: gendis

FlowRepository
type: Resource
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.
is part of: bioregistry
keyword: biology
keyword: life science
keyword: cell biology
0000005: FR-FCM-ZYGW
has provider formatter: http://flowrepository.org/id/$1
has local unique identifier pattern: ^FR\-FCM\-\w{4}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9765-2990
has URI prefix: http://flowrepository.org/id/
0000027: FR-FCM-ZYGW
0000029: flowrepository

SWEET Ontology Representation Mathematics Statistics
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Statistics
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation mathematics statistics
0000005: ANOVA
has provider formatter: http://sweetontology.net/reprMathStatistics/$1
is deprecated: false
has alternative prefix: sorepmst
has URI prefix: http://sweetontology.net/reprMathStatistics/
0000027: ANOVA
0000029: sweet.repmst

International Standard Classification of Education, 2011 Edition
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: education level
keyword: open educational resources
0000005: 1
has provider formatter: https://w3id.org/kim/isced-2011/level$1
is deprecated: false
has URI prefix: https://w3id.org/kim/isced-2011/level
0000027: level1
0000029: isced2011

Sample processing and separation techniques
type: Resource
description: A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.
is part of: bioregistry
keyword: obo
keyword: ontology
keyword: protein
0000005: 00073
has provider formatter: http://purl.obolibrary.org/obo/SEP_$1
has local unique identifier pattern: ^\d{5,6}$
0000010: sep.owl
is deprecated: true
has responsible: SEP developers via the PSI and MSI mailing lists
has URI prefix: http://purl.obolibrary.org/obo/SEP_
0000027: SEP_00073
0000029: sep

GeoSPARQL
type: Resource
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.
is part of: bioregistry
keyword: nfdi4ing
keyword: ess
keyword: fair data spaces
keyword: ontology
keyword: earth sciences
0000005: hasDefaultGeometry
has provider formatter: http://www.opengis.net/ont/geosparql#$1
0000010: geosparql.owl
is deprecated: false
has responsible: Kim Durante
has URI prefix: http://www.opengis.net/ont/geosparql#
0000027: hasDefaultGeometry
0000029: geosparql

Oat Ontology
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/).
is part of: bioregistry
git repository: Crop-Ontology
keyword: botany
keyword: agriculture
keyword: life science
keyword: ontology
keyword: plant phenotypes and traits
keyword: phenotype
0000005: 0000215
has provider formatter: https://cropontology.org/rdf/CO_350:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 350.owl
is deprecated: false
has responsible: Jean-Luc Jannink
has URI prefix: https://cropontology.org/rdf/CO_350:
0000027: CO 350:0000215
0000029: co_350

iNaturalist Place
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Identifier for a place in iNaturalist
is part of: bioregistry
0000005: 7207
has provider formatter: https://www.inaturalist.org/places/$1
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has URI prefix: https://www.inaturalist.org/places/
0000027: https://www.inaturalist.org/places/7207
0000029: inaturalist.place

Jeremy D. Glasner

Primate Brain Atlas
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the primate brain
is part of: bioregistry
git repository: primate brain atlas ontology
keyword: ontology
0000005: 128011350
has provider formatter: https://biopragmatics.github.io/providers/pba/$1
has local unique identifier pattern: ^\d+$
0000010: allen-pba.obo
is deprecated: false
has URI prefix: https://biopragmatics.github.io/providers/pba/
0000027: https://biopragmatics.github.io/providers/pba/128011350
0000029: pba

Establishment Means Controlled Vocabulary
type: Resource
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.
is part of: bioregistry
keyword: fair data spaces
keyword: life sciences, biology
0000005: e001
has provider formatter: http://rs.tdwg.org/dwcem/$1
is deprecated: false
has responsible: John Wieczorek
has URI prefix: http://rs.tdwg.org/dwcem/
0000027: e001
0000029: dwc.em

IOC: Internet of Construction Ontology
type: Resource
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.
is part of: bioregistry
keyword: digital planning and construction
keyword: fid baudigital
keyword: nfdi4ing
keyword: civil engineering
0000005: Actor
has provider formatter: http://w3id.org/ioc#$1
is deprecated: false
has URI prefix: http://w3id.org/ioc#
0000027: Actor
0000029: tib.ioc

OpenCitations Corpus
type: Resource
description: The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law.
is part of: bioregistry
0000005: br/1
has provider formatter: https://w3id.org/oc/corpus/$1
has local unique identifier pattern: ^[a-z][a-z]/[0-9]+$
is deprecated: false
has URI prefix: https://w3id.org/oc/corpus/
0000027: https://w3id.org/oc/corpus/br/1
0000029: occ

NCI Drug Dictionary ID
type: Resource
description: identifier of an entry in the NCI Drug Dictionary
is part of: bioregistry
0000005: beta-carotene
has provider formatter: https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1
is deprecated: false
has URI prefix: https://www.cancer.gov/publications/dictionaries/cancer-drug/def/
0000027: beta-carotene
0000029: nci.drug

MEROPS Clan
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.
is part of: bioregistry
0000005: IA
has provider formatter: https://www.ebi.ac.uk/merops/cgi-bin/clansum
is deprecated: false
has responsible: Neil D Rawlings
has URI prefix: https://www.ebi.ac.uk/merops/cgi-bin/clansum
0000027: https://www.ebi.ac.uk/merops/cgi-bin/clansum
0000029: merops.clan

Adverse Event Reporting Ontology
type: Resource
contributor: Sumir Pandit
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
is part of: bioregistry
keyword: preclinical studies
keyword: biomedical science
keyword: health science
keyword: medicine
keyword: obo
keyword: ontology
keyword: adverse reaction
keyword: electronic health record
0000005: 0000125
has provider formatter: http://purl.obolibrary.org/obo/AERO_$1
has local unique identifier pattern: ^\d{7}$
0000010: aero.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-9551-6370
has URI prefix: http://purl.obolibrary.org/obo/AERO_
0000027: AERO_0000125
0000029: aero

Pathguide
type: https://bioregistry.io/schema/#0000002
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)
has part: http://www.pathguide.org/fullrecord.php
0000005: 235
has provider formatter: http://www.pathguide.org/fullrecord.php
has responsible: https://orcid.org/0000-0003-0185-8861

Protein Ensemble Database ensemble
type: Resource
description: The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins.
is part of: ped
is part of: bioregistry
0000005: PED00017e001
has provider formatter: https://proteinensemble.org/$1
has local unique identifier pattern: ^PED\d{5}e\d{3}$
is deprecated: false
has URI prefix: https://proteinensemble.org/
0000027: PED00017e001
0000029: ped.ensemble

Aclame
type: Resource
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.
is part of: bioregistry
keyword: gene
keyword: life science
keyword: genome
0000005: 2
has provider formatter: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi
has local unique identifier pattern: ^\d+$
is deprecated: true
has alternative prefix: aclame
has URI prefix: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi
0000027: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi
0000029: mge

Human BioMolecular Atlas Program Dataset
type: Resource
contributor: 0009-0008-8406-631X
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.
is part of: bioregistry
has provider formatter: https://portal.hubmapconsortium.org/browse/dataset/$1
has local unique identifier pattern: ^[a-f0-9]{32}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3321-6137
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://portal.hubmapconsortium.org/browse/dataset/
0000029: hubmap.dataset

Microbial Conditions Ontology
type: Resource
description: Microbial Conditions Ontology is an ontology...
is part of: bioregistry
git repository: microbial-conditions-ontology
keyword: obo
keyword: ontology
0000005: 0000858
has provider formatter: http://purl.obolibrary.org/obo/MCO_$1
has local unique identifier pattern: ^\d+$
0000010: mco.owl
is deprecated: false
depends on: peco
depends on: Ontology of Microbial Phenotypes
depends on: cl
depends on: omit
depends on: Uber Anatomy Ontology
depends on: pato
depends on: Ontology for Biomedical Investigations
depends on: Chemical Entities of Biological Interest
depends on: zeco
depends on: NCBI Taxonomy
depends on: Cell Line Ontology
depends on: bfo
depends on: Ontology of Prokaryotic Phenotypic and Metabolic Characters
depends on: ncit
has responsible: https://orcid.org/0000-0002-0142-5591
has URI prefix: http://purl.obolibrary.org/obo/MCO_
0000027: MCO_0000858
0000029: mco

ChemSpider
type: Resource
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.
is part of: bioregistry
keyword: life science
keyword: molecules
keyword: chemistry
keyword: structure
0000005: 56586
has provider formatter: http://www.chemspider.com/Chemical-Structure.$1.html
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-0412-9018
has alternative prefix: ChemSpiderID
has alternative prefix: Chemspider
has URI prefix: https://bioregistry.io/chemspider:
0000027: Chemical-Structure.56586.html
0000029: chemspider

Alvis Brazma

Variation Modelling Collaboration
type: Resource
is part of: bioregistry
is deprecated: true
0000029: vmc

Ontology of Host Pathogen Interactions
type: Resource
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).
is part of: bioregistry
git repository: ohpi
keyword: obo
keyword: ontology
keyword: infection process
keyword: bioinformatics
keyword: biomedical science
keyword: host
keyword: pathogen
0000005: 9001411
has provider formatter: http://purl.obolibrary.org/obo/OHPI_$1
has local unique identifier pattern: ^\d+$
0000010: ohpi.owl
is deprecated: false
has responsible: 0000-0002-5159-414X
has URI prefix: http://purl.obolibrary.org/obo/OHPI_
0000027: OHPI_9001411
0000029: ohpi

International Classification of Functioning, Disability and Health
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: primary health care
keyword: biomedical science
keyword: health science
keyword: medicine
keyword: ontology
keyword: electronic health record
0000005: 326705068
has provider formatter: https://icd.who.int/dev11/l-icf/en#/http://id.who.int/icd/entity/$1
has local unique identifier pattern: ^\d+$
0000010: icf.owl
is deprecated: false
has responsible: The World Health Organization
has URI prefix: https://icd.who.int/dev11/l-icf/en#/http://id.who.int/icd/entity/
0000027: http://id.who.int/icd/entity/326705068
0000029: icf

Pierre Baldi

Andrew G. McArthur

Nanbyo Disease Ontology
type: Resource
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.
is part of: bioregistry
keyword: ontology
0000005: 1200031
has provider formatter: https://nanbyodata.jp/disease/NANDO:$1
has local unique identifier pattern: ^\d+$
0000010: nando.owl
is deprecated: false
has responsible: Terue Takatsuki
has URI prefix: https://nanbyodata.jp/disease/NANDO:
0000027: NANDO:1200031
0000029: nando

IEEE Xplore document ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for a document in IEEE Xplore
is part of: bioregistry
0000005: 1580791
has provider formatter: https://ieeexplore.ieee.org/document/$1
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has URI prefix: https://ieeexplore.ieee.org/document/
0000027: https://ieeexplore.ieee.org/document/1580791
0000029: ieee.document

Homeostasis imbalance process ontology
type: Resource
contributor: https://orcid.org/0000-0001-5705-7831
description: An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes.
is part of: bioregistry
git repository: hoip
keyword: ontology
0000005: 0040379
has provider formatter: http://purl.bioontology.org/ontology/HOIP/HOIP_$1
has local unique identifier pattern: ^\d{7}$
0000010: hoip 0308.owl
is deprecated: false
has responsible: Yuki Yamagata
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://purl.bioontology.org/ontology/HOIP/HOIP_
0000027: HOIP_0040379
0000029: hoip

NanoParticle Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
git repository: npo
keyword: ontology
keyword: molecular entity
keyword: nanoparticle
keyword: structure
keyword: life science
0000005: 1731
has provider formatter: http://purl.bioontology.org/ontology/npo#NPO_$1
has local unique identifier pattern: ^\d+$
0000010: npo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-5892-6506
has URI prefix: http://purl.bioontology.org/ontology/npo#NPO_
0000027: NPO 1731
0000029: npo

Yvonne Bradford

Neurofibromatosis Data Portal Tools
type: Resource
contributor: https://orcid.org/0009-0009-3402-8013
description: Identifiers represent experimental tools and resources for neurofibromatosis (NF) research in the NF Data Portal Tools catalog.
is part of: bioregistry
keyword: research resources
keyword: neurofibromatosis
keyword: experimental tools
has provider formatter: https://nf.synapse.org/Explore/Tools/DetailsPage
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 deprecated: false
has responsible: Robert Allaway
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://nf.synapse.org/Explore/Tools/DetailsPage
0000027: https://nf.synapse.org/Explore/Tools/DetailsPage
0000029: nfportal.tool

Internet Standard -- IETF Request for Comments
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Legacy site for IETF RFC proposals
is part of: bioregistry
0000005: 5013
has provider formatter: https://tools.ietf.org/rfc/rfc$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://tools.ietf.org/rfc/rfc
0000027: rfc5013
0000029: rfc

Coleoptera Anatomy Ontology
type: Resource
description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.
is part of: bioregistry
git repository: colao
keyword: obo
keyword: ontology
0000005: 0000000
has provider formatter: http://purl.obolibrary.org/obo/COLAO_$1
has local unique identifier pattern: ^\d{7}$
0000010: colao.owl
is deprecated: false
depends on: bspo
depends on: bfo
depends on: Common Anatomy Reference Ontology
depends on: ro
depends on: aism
depends on: Uber Anatomy Ontology
depends on: pato
has responsible: https://orcid.org/0000-0002-0851-6883
has URI prefix: http://purl.obolibrary.org/obo/COLAO_
0000027: COLAO_0000000
0000029: colao

BiGG Reaction
type: Resource
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.
is part of: bioregistry
keyword: ontology
keyword: reaction
0000005: 13GS
has provider formatter: http://bigg.ucsd.edu/models/universal/reactions/$1
has local unique identifier pattern: ^[a-z_A-Z0-9]+$
0000010: bigg.reaction.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-1238-1499
has URI prefix: http://bigg.ucsd.edu/models/universal/reactions/
0000027: 13GS
0000029: bigg.reaction

Enabling and Unlocking Biology in the Open
type: Resource
contributor: 0009-0008-8406-631X
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 part of: bioregistry
0000005: EUB0000221
has provider formatter: https://gateway.eubopen.org/compound/$1
has local unique identifier pattern: ^EUB\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0001-6518-3344
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://gateway.eubopen.org/compound/
0000027: EUB0000221
0000029: eubopen

MassIVE
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.
is part of: bioregistry
git repository: MassIVEDocumentation
keyword: metaproteomics
keyword: metabolomics
keyword: omics
keyword: proteomics
keyword: functional genomics
keyword: phenomics
0000005: MSV000082131
has provider formatter: https://www.omicsdi.org/dataset/massive/$1
has local unique identifier pattern: ^MSV\d+$
is deprecated: false
has responsible: Mingxun Wang
has URI prefix: https://www.omicsdi.org/dataset/massive/
0000027: MSV000082131
0000029: massive

Pfam protein family
type: Resource
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.
is part of: bioregistry
keyword: biology
keyword: domain
keyword: ontology
keyword: protein
0000005: PF11779
has provider formatter: https://www.ebi.ac.uk/interpro/entry/pfam/$1
has local unique identifier pattern: ^PF\d{5}$
0000010: pfam.owl
is deprecated: false
has responsible: Alex Bateman
has alternative prefix: PF
has URI prefix: https://www.ebi.ac.uk/interpro/entry/pfam/
0000027: PF11779
0000029: pfam

Molecular Interaction Database
type: Resource
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.
is part of: bioregistry
keyword: proteomics
keyword: interaction
keyword: life science
keyword: protein
0000005: 6978836
has provider formatter: https://mint.bio.uniroma2.it/index.php/detailed-curation/
has local unique identifier pattern: ^\d{1,7}$
is deprecated: false
has responsible: Luana Licata
has URI prefix: https://mint.bio.uniroma2.it/index.php/detailed-curation/
0000027: https://mint.bio.uniroma2.it/index.php/detailed-curation/
0000029: mint

Fabrice Legeai

Catalogue of Life
type: Resource
description: Identifier of a taxon or synonym in the Catalogue of Life
is part of: bioregistry
0000005: 4QHKG
has provider formatter: https://www.checklistbank.org/dataset/3LR/taxon/$1
has local unique identifier pattern: ^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$
is deprecated: false
has URI prefix: https://www.checklistbank.org/dataset/3LR/taxon/
0000027: 4QHKG
0000029: col

Integrated Taxonomic Information System
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world.
is part of: bioregistry
keyword: biodiversity
keyword: taxonomy
keyword: life science
keyword: ontology
0000005: 589462
has provider formatter: https://www.itis.gov/servlet/SingleRpt/SingleRpt
has local unique identifier pattern: ^\d+$
0000010: itis.owl.gz
is deprecated: false
has responsible: Gerald Guala
has URI prefix: https://www.itis.gov/servlet/SingleRpt/SingleRpt
0000027: https://www.itis.gov/servlet/SingleRpt/SingleRpt
0000029: itis

Fyler
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A hierarchical classification of congenital heart disease
is part of: bioregistry
0000005: 4447
has local unique identifier pattern: ^\d+$
is deprecated: false
0000029: fyler

Ontology of Arthropod Circulatory Systems
type: Resource
description: OArCS is an ontology describing the Arthropod ciruclatory system.
is part of: bioregistry
git repository: oarcs
keyword: angiology
keyword: anatomy
keyword: obo
keyword: ontology
0000005: 0000029
has provider formatter: http://purl.obolibrary.org/obo/OARCS_$1
has local unique identifier pattern: ^\d{7}$
0000010: oarcs.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-5640-5491
has URI prefix: http://purl.obolibrary.org/obo/OARCS_
0000027: OARCS_0000029
0000029: oarcs

Yeast Deletion and the Mitochondrial Proteomics Project
type: Resource
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.
is part of: bioregistry
keyword: protein
0000005: YAL001C
has provider formatter: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi
has local unique identifier pattern: ^Y[A-Z]{2}\d+[CW]$
is deprecated: true
has URI prefix: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi
0000027: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi
0000029: ydpm

Ontology of Adverse Events
type: Resource
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
git repository: OAE
keyword: biomedical science
keyword: drug
keyword: obo
keyword: adverse reaction
keyword: ontology
keyword: vaccine
0000005: 0002959
has provider formatter: http://purl.obolibrary.org/obo/OAE_$1
has local unique identifier pattern: ^\d{7}$
0000010: oae.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9189-9661
has URI prefix: http://purl.obolibrary.org/obo/OAE_
0000027: OAE_0002959
0000029: oae

Fachsystematik LinSearch
type: Resource
description: Fächer für die LinSearch-Fachzuordnung
is part of: bioregistry
git repository: annif automated indexing at tib
keyword: computer science
keyword: miscellaneous
0000005: arc
has provider formatter: https://purl.org/linsearch/$1
is deprecated: false
has URI prefix: https://purl.org/linsearch/
0000027: arc
0000029: tib.linsearch

Human Dermatological Disease Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
git repository: dermatology
keyword: disease
keyword: dermatology
keyword: ontology
0000005: 0000000
has provider formatter: http://purl.obolibrary.org/obo/DERMO_$1
has local unique identifier pattern: ^\d{7}$
0000010: dermo.obo
is deprecated: false
has responsible: https://orcid.org/0000-0002-5111-7263
has URI prefix: http://purl.obolibrary.org/obo/DERMO_
0000027: DERMO_0000000
0000029: dermo

Niclas Karlsson

SWEET Ontology Realm Ocean
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Ocean
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: ocean
keyword: realm
0000005: Abyss
has provider formatter: http://sweetontology.net/realmOcean/$1
is deprecated: false
has alternative prefix: soreao
has URI prefix: http://sweetontology.net/realmOcean/
0000027: Abyss
0000029: sweet.reao

Event Venue Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: evr
0000005: 0000001
has provider formatter: https://cthoyt.com/evr/$1
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://cthoyt.com/evr/
0000027: https://cthoyt.com/evr/0000001
0000029: evr

SWEET Ontology Property Space
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: space
0000005: AngularDistribution
has provider formatter: http://sweetontology.net/propSpace/$1
is deprecated: false
has alternative prefix: soprops
has URI prefix: http://sweetontology.net/propSpace/
0000027: AngularDistribution
0000029: sweet.props

Common Access to Biological Resources and Information Project
type: Resource
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.
is part of: bioregistry
keyword: medical microbiology
keyword: applied microbiology
keyword: molecular biology
keyword: virology
keyword: microbiology
keyword: molecular microbiology
0000005: dsmz_mutz-id:ACC 291
has provider formatter: http://www.cabri.org/CABRI/srs-bin/wgetz
has local unique identifier pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4694-3883
has URI prefix: https://bioregistry.io/cabri:
0000029: cabri

SWEET Ontology Representation Scientific Component
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Component
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation scientific component
0000005: Component
has provider formatter: http://sweetontology.net/reprSciComponent/$1
is deprecated: false
has alternative prefix: sorepsc
has URI prefix: http://sweetontology.net/reprSciComponent/
0000027: Component
0000029: sweet.repsc

Ion Channel Electrophysiology Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
keyword: ontology
0000005: 0000002
has provider formatter: https://biopragmatics.github.io/providers/icepo/$1
has local unique identifier pattern: ^\d{7}$
0000010: icepo.obo
is deprecated: false
has responsible: https://orcid.org/0000-0003-1813-6857
has URI prefix: https://biopragmatics.github.io/providers/icepo/
0000027: https://biopragmatics.github.io/providers/icepo/0000002
0000029: icepo

Michael Witt

Ontology of Core Data Mining Entities
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
git repository: ontodm-core
keyword: ontology
0000005: 000072
has provider formatter: http://www.ontodm.com/OntoDM-core/OntoDM_$1
has local unique identifier pattern: ^\d+$
0000010: OntoDM.owl
is deprecated: false
0000018: Experimental Factor Ontology
has responsible: Pance Panov
has URI prefix: http://www.ontodm.com/OntoDM-core/OntoDM_
0000027: OntoDM_000072
0000029: ontodm

UR-DBMS Syndrome Finder
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
0000005: 3567
has provider formatter: http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php
has local unique identifier pattern: ^\d+$
is deprecated: true
0000018: Nanbyo Disease Ontology
has responsible: Kenji Naritomi
has URI prefix: http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php
0000027: http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php
0000029: urdbms.syndromefinder

Molecular Signatures Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can
is part of: bioregistry
keyword: reaction
keyword: gene group
keyword: ontology
keyword: pathway
keyword: gene family
keyword: gene set
0000005: M1
has provider formatter: https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/$1
has local unique identifier pattern: ^M\d+$
0000010: msigdb.owl.gz
is deprecated: false
has responsible: https://orcid.org/0000-0002-9755-2818
has alternative prefix: msig
has URI prefix: https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/
0000027: M1
0000029: msigdb

The Echinoderm Anatomy and Development Ontology
type: Resource
description: None
is part of: bioregistry
git repository: ecao ontology
keyword: obo
keyword: ontology
0000005: 0107180
has provider formatter: http://purl.obolibrary.org/obo/ECAO_$1
has local unique identifier pattern: ^\d{7}$
0000010: ecao.owl
is deprecated: false
depends on: cl
depends on: ro
depends on: Uber Anatomy Ontology
has responsible: Charles Ettensohn
has URI prefix: http://purl.obolibrary.org/obo/ECAO_
0000027: ECAO_0107180
0000029: ecao

DALIA Resources
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes relevant for the [Data Literacy Alliance (DALIA)](https://dalia.education/en) project
has part: dcterms
has part: modalia
has part: spdx.term
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: ceds.element
has part: ans.educationlevel
has part: datacite
has part: codata.rdmt
has part: Bibliographic Framework Initiative Vocabulary
has part: t4fs
has part: DBPedia Resource
has part: Library of Congress Format Description Document
has part: bibo
has part: PROV Namespace
has part: Machine-readable Cataloging (MARC) List for Languages
has part: m4i
has part: schema
has part: Wikidata
has part: dai.thesauri
has part: bmbf.glossary
has part: iana.mediatype
has part: NFDI4DS Ontology
has part: spdx
has part: FaBiO, the FRBR-aligned Bibliographic Ontology
has part: UNESCO Thesaurus
has part: citedcat
has part: SAGE Social Science Thesaurus
has part: Protocol for Web Description Resources (POWDER): POWDER-S Vocabulary
has part: sio
has part: Web Ontology Language

WormBase RNAi
type: Resource
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.
is part of: bioregistry
0000005: WBRNAi00086878
has provider formatter: https://www.wormbase.org/species/c_elegans/rnai/$1
has local unique identifier pattern: ^WBRNAi\d{8}$
is deprecated: false
has URI prefix: https://www.wormbase.org/species/c_elegans/rnai/
0000027: WBRNAi00086878
0000029: wb.rnai

Infectious Disease Ontology
type: Resource
contributor: Yohann Paris
description: Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.
is part of: bioregistry
git repository: infectious-disease-ontology
keyword: preclinical studies
keyword: biomedical science
keyword: molecular infection biology
keyword: classification
keyword: obo
keyword: ontology
keyword: disease
keyword: disease course
0000005: 0000504
has provider formatter: http://purl.obolibrary.org/obo/IDO_$1
has local unique identifier pattern: ^\d{7}$
0000010: ido.owl
is deprecated: false
0000018: scdo
has responsible: https://orcid.org/0000-0003-1617-8244
has URI prefix: http://purl.obolibrary.org/obo/IDO_
0000027: IDO_0000504
0000029: ido

SABIO-RK Reaction
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.
is part of: bioregistry
keyword: pathway
keyword: biochemistry
keyword: life science
keyword: reaction
keyword: kinetics
0000005: 75
has provider formatter: http://sabiork.h-its.org/reacdetails.jsp
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Ulrike Wittig
has alternative prefix: SABIO-RK
has URI prefix: http://sabiork.h-its.org/reacdetails.jsp
0000027: http://sabiork.h-its.org/reacdetails.jsp
0000029: sabiork.reaction

Ontology for Modeling and Representation of Social Entities
type: Resource
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.
is part of: bioregistry
git repository: OMRSE
keyword: health science
keyword: patient care
keyword: obo
keyword: ontology
keyword: social science
keyword: demographics
keyword: biomedical science
keyword: hospital
0000005: 00000022
has provider formatter: http://purl.obolibrary.org/obo/OMRSE_$1
has local unique identifier pattern: ^\d{8}$
0000010: omrse.owl
is deprecated: false
0000018: labo
has responsible: https://orcid.org/0000-0002-9881-1017
has URI prefix: http://purl.obolibrary.org/obo/OMRSE_
0000027: OMRSE_00000022
0000029: omrse

David Lynn

The Hydra Core Vocabulary
type: Resource
description: A lightweight vocabulary for hypermedia-driven Web APIs
is part of: bioregistry
keyword: rdf
0000005: TemplatedLink
is deprecated: false
0000029: hydra

Google Scholar Researcher
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
0000005: PjrpzUIAAAAJ
has provider formatter: https://scholar.google.com/citations
has local unique identifier pattern: ^[-_0-9A-Za-z]{12}$
is deprecated: false
has URI prefix: https://scholar.google.com/citations
0000027: https://scholar.google.com/citations
0000029: google.scholar

Wikidata
type: Resource
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 part: wikidata.property
has part: wikidata.entity
is part of: bioregistry
keyword: genomics
keyword: chemistry
keyword: metabolomics
keyword: proteomics
keyword: subject agnostic
0000005: Q47475003
has provider formatter: http://www.wikidata.org/entity/$1
has local unique identifier pattern: ^(Q|P|E|L)\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9593-2294
has alternative prefix: WD_Entity
has alternative prefix: wd
has alternative prefix: wdeschema
has URI prefix: http://www.wikidata.org/entity/
0000027: Q47475003
0000029: wikidata

Semantically-Interlinked Online Communities Core Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: society
0000005: Item
has provider formatter: http://rdfs.org/sioc/ns#$1
is deprecated: false
has alternative prefix: sioc
has URI prefix: http://rdfs.org/sioc/ns#
0000027: Item
0000029: sioc.core

SWEET Ontology Realm Hydrosphere
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Hydrosphere
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: hydrosphere
keyword: realm
0000005: Aquiclude
has provider formatter: http://sweetontology.net/realmHydro/$1
is deprecated: false
has alternative prefix: soreah
has URI prefix: http://sweetontology.net/realmHydro/
0000027: Aquiclude
0000029: sweet.reah

Protege Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology of metadata from protege
is part of: bioregistry
0000005: defaultLanguage
has provider formatter: http://protege.stanford.edu/plugins/owl/protege#$1
is deprecated: false
has URI prefix: http://protege.stanford.edu/plugins/owl/protege#
0000027: defaultLanguage
0000029: protege

ChEMBL database of bioactive drug-like small molecules - Cell lines section
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Chemistry resources
is part of: bioregistry
keyword: cell lines
keyword: bioactivities
0000005: CHEMBL3307800
has provider formatter: https://www.ebi.ac.uk/chembl/cell_line_report_card/$1
has local unique identifier pattern: ^CHEMBL\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-0294-5484
has alternative prefix: ChEMBL-Cells
has URI prefix: https://www.ebi.ac.uk/chembl/cell_line_report_card/
0000027: CHEMBL3307800
0000029: chembl.cell

AmoebaDB
type: Resource
contributor: Sumir Pandit
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
keyword: model organism
keyword: genomics
keyword: functional genomics
0000005: EDI_244000
has provider formatter: https://amoebadb.org/amoeba/app/record/gene/$1
has local unique identifier pattern: ^EDI_\d+$
is deprecated: false
has responsible: Omar S. Harb
has URI prefix: https://amoebadb.org/amoeba/app/record/gene/
0000027: EDI_244000
0000029: amoebadb

Medical Subject Headings Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump
is part of: bioregistry
git repository: meshrdf
0000005: term
has provider formatter: http://id.nlm.nih.gov/mesh/vocab#$1
is deprecated: false
has URI prefix: http://id.nlm.nih.gov/mesh/vocab#
0000027: term
0000029: mesh.vocab

Flavor and Extract Manufacturers Association
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
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).
is part of: bioregistry
0000005: 4667
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7806-4173
has reviewer: https://orcid.org/0000-0001-9439-5346
0000029: fema

NeuroMorpho
type: Resource
description: NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons.
is part of: bioregistry
keyword: structure
keyword: anatomy
0000005: Rosa2
has provider formatter: http://neuromorpho.org/neuron_info.jsp
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: 0000-0002-0964-676X
has URI prefix: http://neuromorpho.org/neuron_info.jsp
0000027: http://neuromorpho.org/neuron_info.jsp
0000029: neuromorpho

Elementary Multiperspective Material Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
git repository: EMMO
keyword: nfdi4ing
keyword: material science
keyword: communication science
keyword: physics
keyword: industry
keyword: philosophy
keyword: nfdi4cat
has provider formatter: http://emmo.info/emmo#EMMO_$1
is deprecated: false
has responsible: 0000-0002-1560-809X
has URI prefix: http://emmo.info/emmo#EMMO_
0000029: emmo

Crates.io
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A repository of software packages written in Rust.
is part of: bioregistry
0000005: curies
has provider formatter: https://crates.io/crates/$1
is deprecated: false
has URI prefix: https://crates.io/crates/
0000027: curies
0000029: crates

Melanoma Molecular Map Project Biomaps
type: Resource
description: A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.
is part of: bioregistry
keyword: interaction
keyword: molecule
keyword: pathway
0000005: 37
has provider formatter: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: mmmp:biomaps
has URI prefix: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp
0000027: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp
0000029: mmmp.biomaps

Zazuko Prefix Server
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
0000005: frbr
has provider formatter: https://prefix.zazuko.com/prefix/$1:
is deprecated: false
has responsible: Adrian Gschwend
has URI prefix: https://bioregistry.io/zazuko:
0000027: frbr:
0000029: zazuko

Oryzabase Gene
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 gene information.
is part of: bioregistry
0000005: 117
has provider formatter: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/
0000027: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/117
0000029: oryzabase.gene

Orphanet
type: Resource
contributor: https://orcid.org/0000-0002-7356-1779
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.
is part of: bioregistry
keyword: ontology and terminology
keyword: human
keyword: ontology
keyword: disease
keyword: life science
keyword: drug
0000005: 85163
has provider formatter: http://www.orpha.net/ORDO/Orphanet_$1
has local unique identifier pattern: ^C?\d+$
0000010: ordo orphanet.owl
is deprecated: false
has responsible: Marc Hanauer
has alternative prefix: Orphanet
has alternative prefix: orphanet
has URI prefix: http://www.orpha.net/ORDO/Orphanet_
0000027: Orphanet_85163
0000029: orpha

COI Catalogue
type: Resource
contributor: Tanay Shah
description: COI Catalogue is a herbarium with c. 800.000 specimens, organised in separate collections due to the research priorities over the years.
is part of: bioregistry
0000005: 63812
has provider formatter: https://coicatalogue.uc.pt/index.php
is deprecated: false
has responsible: COI Catalogue
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://coicatalogue.uc.pt/index.php
0000027: https://coicatalogue.uc.pt/index.php
0000029: coi

PIR Superfamily Classification System
type: Resource
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
keyword: proteomics
keyword: structure
keyword: life science
0000005: PIRSF000100
has provider formatter: https://pir.georgetown.edu/cgi-bin/ipcSF
has local unique identifier pattern: ^PIRSF\d{6}$
is deprecated: false
has responsible: https://orcid.org/0000-0001-6379-8601
has URI prefix: https://pir.georgetown.edu/cgi-bin/ipcSF
0000027: https://pir.georgetown.edu/cgi-bin/ipcSF
0000029: pirsf

Ensembl Gene
type: Resource
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.
is part of: bioregistry
keyword: biomedical science
keyword: comparative genomics
keyword: genome
keyword: genomics
0000005: ENSG00000139618
has provider formatter: https://www.ensembl.org/id/$1
has local unique identifier pattern: ^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3897-7955
has alternative prefix: Ensembl
has URI prefix: https://www.ensembl.org/id/
0000027: ENSG00000139618
0000029: ensembl

CDC Publisher Names
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Names of organisations providing metadata for CESSDA Data Catalogue.
is part of: bioregistry
0000005: AUSSDA
has provider formatter: https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames#code_
0000026: 02wg9xc72
0000027: code AUSSDA
0000029: cessda.cdcpublishernames

is deprecated
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.
domain: Resource
range: boolean

Node Package Manager
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A repository of software packages written in Javascript, TypeScript, and related.
is part of: bioregistry
0000005: @biopragmatics/curies
has provider formatter: https://www.npmjs.com/package/$1
is deprecated: false
has URI prefix: https://www.npmjs.com/package/
0000027: curies
0000029: npm

FAIRsharing User
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A user of FAIRsharing
is part of: bioregistry
0000005: 5112
has provider formatter: https://fairsharing.org/users/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7702-4495
has URI prefix: https://fairsharing.org/users/
0000027: https://fairsharing.org/users/5112
0000029: fairsharing.user

SWEET Ontology Relationships Mathematical
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Mathematical
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: mathematical
0000005: averageOver
has provider formatter: http://sweetontology.net/relaMath/$1
is deprecated: false
has alternative prefix: sorelm
has URI prefix: http://sweetontology.net/relaMath/
0000027: averageOver
0000029: sweet.relm

SWEET Ontology Material Particle
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Particle
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: particle
keyword: materials
0000005: AnomalousEnergeticParticle
has provider formatter: http://sweetontology.net/matrParticle/$1
is deprecated: false
has alternative prefix: somapa
has URI prefix: http://sweetontology.net/matrParticle/
0000027: AnomalousEnergeticParticle
0000029: sweet.mapa

KEGG LIGAND
type: Resource
is part of: bioregistry
is part of: kegg
has provider formatter: http://www.genome.jp/dbget-bin/www_bget
is deprecated: true
has URI prefix: http://www.genome.jp/dbget-bin/www_bget
0000029: kegg.ligand

Bernd Müller

Smart Applications Reference ontology
type: Resource
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.
is part of: bioregistry
keyword: iot
keyword: nfdi4ing
keyword: industry
keyword: services
keyword: engineering
keyword: digital planning and construction
keyword: fid baudigital
0000005: Actuation
has provider formatter: https://saref.etsi.org/core/$1
is deprecated: false
has responsible: Maxime Lefrançois
has URI prefix: https://saref.etsi.org/core/
0000027: Actuation
0000029: saref

YeTFasCo
type: Resource
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.
is part of: bioregistry
0000005: YOR172W_571.0
has provider formatter: http://yetfasco.ccbr.utoronto.ca/showPFM.php
has local unique identifier pattern: ^\w+\_\d+(\.\d+)?$
is deprecated: false
has URI prefix: http://yetfasco.ccbr.utoronto.ca/showPFM.php
0000027: http://yetfasco.ccbr.utoronto.ca/showPFM.php
0000029: yetfasco

Neuroscience Multi-Omic BRAIN Initiative Data
type: Resource
description: This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects.
is part of: bioregistry
0000005: smp-m3w9hbe
has provider formatter: https://assets.nemoarchive.org/$1
has local unique identifier pattern: ^[a-z]{3}-[a-km-z0-9]{7}$
is deprecated: false
has URI prefix: https://assets.nemoarchive.org/
0000027: smp-m3w9hbe
0000029: nemo

Animal natural history and life history
type: Resource
contributor: Sumir Pandit
description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.
is part of: bioregistry
keyword: ontology
keyword: taxonomic classification
keyword: anatomy
keyword: life science
keyword: obo
0000005: Lycalopex_vetulus
has provider formatter: https://animaldiversity.org/accounts/$1
has local unique identifier pattern: ^[A-Z_a-z]+$
0000010: adw.owl
is deprecated: true
has responsible: Animal Diversity Web technical staff
has URI prefix: https://animaldiversity.org/accounts/
0000027: Lycalopex vetulus
0000029: adw

Curated Drug-Drug Interactions Database - Interaction
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
keyword: chemistry
keyword: drugs
keyword: drug-drug interactions
keyword: relationships
0000005: 1122888
has provider formatter: http://ddinter.scbdd.com/ddinter/interact/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Dongsheng Cao
has URI prefix: http://ddinter.scbdd.com/ddinter/interact/
0000027: http://ddinter.scbdd.com/ddinter/interact/1122888
0000029: ddinter.interaction

Transport Systems Tracker
type: Resource
description: The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes.
is part of: bioregistry
0000005: TR0000001
has provider formatter: https://transyt.bio.di.uminho.pt/reactions/$1
has local unique identifier pattern: ^T[A-Z]\d{7}$
is deprecated: false
has URI prefix: https://transyt.bio.di.uminho.pt/reactions/
0000027: TR0000001
0000029: transyt

Database of Genomic Structural Variation - Study
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Studies in dbVar.
is part of: bioregistry
0000005: nstd102
has provider formatter: https://www.ncbi.nlm.nih.gov/dbvar/studies/$1
is deprecated: false
has alternative prefix: dbvar.studies
has URI prefix: https://www.ncbi.nlm.nih.gov/dbvar/studies/
0000027: nstd102
0000029: dbvar.study

SWEET Ontology Phenomena Wave Noise
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Wave Noise
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
keyword: wave noise
0000005: AmbientNoise
has provider formatter: http://sweetontology.net/phenWaveNoise/$1
is deprecated: false
has alternative prefix: sophwn
has URI prefix: http://sweetontology.net/phenWaveNoise/
0000027: AmbientNoise
0000029: sweet.phwn

Psychology Ontology
type: Resource
contributor: Sumir Pandit
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: ontology
keyword: behavior
keyword: psychology
0000005: Abdomen
has provider formatter: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1
0000010: apaonto.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-1082-8760
has URI prefix: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#
0000027: Abdomen
0000029: apaonto

NIF Cell
type: Resource
description: Neuronal cell types
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/NIF_CELL_$1
0000010: nifcell.owl
is deprecated: true
has responsible: 0000-0003-4752-543X
has URI prefix: http://purl.obolibrary.org/obo/NIF_CELL_
0000029: nif.cell

Physico-chemical methods and properties
type: Resource
description: An ontology of physico-chemical methods and properties.
is part of: bioregistry
keyword: experimental measurement
keyword: property
keyword: obo
keyword: experiment
keyword: ontology
keyword: chemistry
0000005: 0000390
has provider formatter: http://purl.obolibrary.org/obo/FIX_$1
has local unique identifier pattern: ^\d{7}$
0000010: fix.owl
is deprecated: true
has responsible: https://orcid.org/0000-0001-8123-5351
has URI prefix: http://purl.obolibrary.org/obo/FIX_
0000026: 02catss52
0000027: FIX_0000390
0000029: fix

Information Artifact Ontology Issue Tracker
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An issue on the Information Artifact Ontology GitHub issue tracker
is part of: bioregistry
0000005: 206
has provider formatter: https://github.com/information-artifact-ontology/IAO/issues/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://github.com/information-artifact-ontology/IAO/issues/
0000027: https://github.com/information-artifact-ontology/IAO/issues/206
0000029: iao.issue

Zhang Zhang

ArrayMap
type: Resource
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.
is part of: bioregistry
keyword: genomics
keyword: bioinformatics
keyword: biomedical science
keyword: life science
0000005: icdom:8500_3
has provider formatter: https://www.arraymap.org/pgx:$1
has local unique identifier pattern: ^[\w\-:,]{3,64}$
is deprecated: false
has responsible: Michael Baudis
has URI prefix: https://www.arraymap.org/pgx:
0000027: pgx:icdom:8500 3
0000029: arraymap

Liz Allen

Southwestern Environmental Information Network
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary about species to support the environmental research community in Arizona and New Mexico
is part of: bioregistry
0000005: 762
has provider formatter: https://swbiodiversity.org/seinet/taxa/index.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has reviewer: Tiffany J. Callahan
has URI prefix: https://swbiodiversity.org/seinet/taxa/index.php
0000027: https://swbiodiversity.org/seinet/taxa/index.php
0000029: seinet

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).
is part of: bioregistry
keyword: genome
0000005: EY223054.1
has provider formatter: https://www.ncbi.nlm.nih.gov/nucest/$1
has local unique identifier pattern: ^\w+(\.)?(\d+)?$
is deprecated: false
has canonical: EST database maintained at the NCBI.
has URI prefix: https://www.ncbi.nlm.nih.gov/nucest/
0000027: EY223054.1
0000029: bdgp.est

CCDC Number
type: Resource
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.
is part of: bioregistry
0000005: 1829126
has provider formatter: https://www.ccdc.cam.ac.uk/services/structures
has local unique identifier pattern: ^\d{6,7}$
is deprecated: false
has URI prefix: https://bioregistry.io/ccdc:
0000027: https://www.ccdc.cam.ac.uk/services/structures
0000029: ccdc

BioModels Database
type: Resource
description: BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.
is part of: bioregistry
keyword: model
0000005: BIOMD0000000048
has provider formatter: https://biomodels.org/$1
has local unique identifier pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$
is deprecated: false
has responsible: Michael Hucka
has alternative prefix: BIOMD
has URI prefix: https://biomodels.org/
0000027: BIOMD0000000048
0000029: biomodels.db

Synthetic Binding Protein Epitope
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for synthetic binding protein-target complexes, detailing their components, 3D structures and docking statistics
is part of: bioregistry
0000005: mt002305
has provider formatter: http://synbip.idrblab.net/data/sbp-target-complex/details/$1
has local unique identifier pattern: ^mt\d+$
is deprecated: false
has responsible: 0000-0002-1846-639X
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: http://synbip.idrblab.net/data/sbp-target-complex/details/
0000027: mt002305
0000029: synbip.epitope

TreeFam
type: Resource
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
keyword: classification
keyword: gene
0000005: TF101014
has provider formatter: http://www.treefam.org/family/$1
has local unique identifier pattern: ^\w{1,2}\d+$
is deprecated: false
has responsible: Fabian Schreiber
has URI prefix: http://www.treefam.org/family/
0000027: TF101014
0000029: treefam

SWEET Ontology Realm Geologic Orogen
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Orogen
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: geologic orogen
keyword: realm
0000005: Arc
has provider formatter: http://sweetontology.net/realmGeolOrogen/$1
is deprecated: false
has alternative prefix: soreagor
has URI prefix: http://sweetontology.net/realmGeolOrogen/
0000027: Arc
0000029: sweet.reagor

Nicolas Terrapon

Xuetong Zhao

CIDOC Conceptual Reference Model
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
keyword: coypu
keyword: nfdi4culture
keyword: history
keyword: culture
keyword: ontology
keyword: anthropology
keyword: digital planning and construction
keyword: humanities and social science
keyword: fid baudigital
keyword: cultural studies
0000005: E1
has provider formatter: http://www.cidoc-crm.org/cidoc-crm/$1
0000010: cidoc-crm.owl
is deprecated: false
has responsible: Patrick Le Bœuf
has URI prefix: http://www.cidoc-crm.org/cidoc-crm/
0000027: E1
0000029: cidoc.crm

Eric Sid

European Commission Library Thesaurus
type: Resource
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.
is part of: bioregistry
keyword: literature
keyword: educational resources
0000005: 004.11.00.0100
has provider formatter: http://data.europa.eu/bkc/notation_$1
is deprecated: false
has URI prefix: http://data.europa.eu/bkc/notation_
0000027: notation 004.11.00.0100
0000029: eclas

ESCO - International Standard Classification of Occupations
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The European Skills, Competences, Qualifications and Occupations (ESCO) International Standard Classification of Occupations (ISCO).
is part of: bioregistry
0000005: C4
has provider formatter: http://data.europa.eu/esco/isco/$1
is deprecated: false
has URI prefix: http://data.europa.eu/esco/isco/
0000027: C4
0000029: esco.isco

Rfam database of RNA families
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.
is part of: bioregistry
keyword: genetics
0000005: RF00230
has provider formatter: https://rfam.org/family/$1
has local unique identifier pattern: ^RF\d{5}$
is deprecated: false
has responsible: https://orcid.org/0000-0001-7279-2682
has URI prefix: https://rfam.org/family/
0000027: RF00230
0000029: rfam

SWEET Ontology Realm Cryosphere
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Cryosphere
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: realm
keyword: cryosphere
0000005: AblationZone
has provider formatter: http://sweetontology.net/realmCryo/$1
is deprecated: false
has alternative prefix: soreac
has URI prefix: http://sweetontology.net/realmCryo/
0000027: AblationZone
0000029: sweet.reac

Open Researcher and Contributor
type: Resource
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.
is part of: bioregistry
git repository: ORCID
keyword: subject agnostic
keyword: person
0000005: 0000-0003-4423-4370
has provider formatter: https://orcid.org/$1
has local unique identifier pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4654-1403
has alternative prefix: ORCID
has alternative prefix: ORCiD
has URI prefix: https://orcid.org/
0000027: https://orcid.org/0000-0003-4423-4370
0000029: orcid

Library of Congress Relator
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Relator terms and their associated codes designate the relationship between an agent and a bibliographic resource.
is part of: bioregistry
0000005: arc
has provider formatter: https://id.loc.gov/vocabulary/relators/$1
is deprecated: false
has URI prefix: https://id.loc.gov/vocabulary/relators/
0000027: arc
0000029: loc.relator

Aquatic Sciences and Fisheries Information System
type: Resource
contributor: https://orcid.org/0000-0002-8844-9165
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)
is part of: bioregistry
0000005: 20560
has provider formatter: https://www.fao.org/fishery/en/species/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: asfis
has URI prefix: https://www.fao.org/fishery/en/species/
0000027: https://www.fao.org/fishery/en/species/20560
0000029: fao.asfis

Reece Hart

COG Categories
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Higher-level classifications of COG Pathways
is part of: bioregistry
keyword: pathways
0000005: K
has provider formatter: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-2265-5572
has URI prefix: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/
0000027: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/K
0000029: cog.category

IntAct protein interaction
type: Resource
contributor: Sucharitha Balu
description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data.
is part of: bioregistry
keyword: protein
keyword: interaction
keyword: biology
0000005: EBI-2307691
has provider formatter: https://www.ebi.ac.uk/intact/interaction/$1
has local unique identifier pattern: ^EBI\-[0-9]+$
is deprecated: false
has responsible: Juan Jose Medina Reyes
has responsible: Kalpana Panneerselvam
has URI prefix: https://www.ebi.ac.uk/intact/interaction/
0000026: 02catss52
0000027: EBI-2307691
0000029: intact

dbSNP Reference SNP number
type: Resource
description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.
is part of: bioregistry
git repository: tutorials
keyword: life science
keyword: genome
0000005: rs121909098
has provider formatter: https://www.ncbi.nlm.nih.gov/snp/$1
has local unique identifier pattern: ^rs\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-7950-1374
has URI prefix: https://www.ncbi.nlm.nih.gov/snp/
0000027: rs121909098
0000029: dbsnp

Loggerhead nesting
type: Resource
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/LOGGERHEAD_$1
is deprecated: true
has responsible: https://orcid.org/0000-0001-6512-3296
has URI prefix: http://purl.obolibrary.org/obo/LOGGERHEAD_
0000029: loggerhead

A vocabulary for the catalysis disciplines
type: Resource
contributor: David Linke
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.
is part of: bioregistry
git repository: voc4cat
keyword: chemistry
keyword: nfdi4cat
keyword: nfdi4chem
keyword: fairmat
0000005: 0000123
has provider formatter: https://w3id.org/nfdi4cat/voc4cat_$1
has local unique identifier pattern: ^\d{7,}$
is deprecated: false
has responsible: Nikolaos Moustakas
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://w3id.org/nfdi4cat/voc4cat_
0000027: voc4cat_0000123
0000029: voc4cat

SWEET Ontology Material Mineral
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Mineral
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: mineral
keyword: materials
0000005: Calcite
has provider formatter: http://sweetontology.net/matrMineral/$1
is deprecated: false
has alternative prefix: somamin
has URI prefix: http://sweetontology.net/matrMineral/
0000027: Calcite
0000029: sweet.mamin

Kyoto Stock Center
type: Resource
description: Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. [from RRID]
is part of: bioregistry
keyword: genetic resource
keyword: genomics
keyword: drosophila
keyword: organism supplier
0000005: 918902
has provider formatter: https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi
0000027: https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi
0000029: dggr

David Wishart
label: David S. Wishart

SWEET Ontology Representation
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: representation
0000005: CardinalScale
has provider formatter: http://sweetontology.net/repr/$1
is deprecated: false
has alternative prefix: sorep
has URI prefix: http://sweetontology.net/repr/
0000027: CardinalScale
0000029: sweet.rep

ASTD
type: Resource
description: Identifier of an object from the ASTD database.
is part of: bioregistry
keyword: alternative splicing
keyword: transcript
keyword: gene
0000005: ENSG00000136147
has provider formatter: http://www.ebi.ac.uk/astd/geneview.html
0000011: Ensembl Gene
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.ebi.ac.uk/astd/geneview.html
0000027: http://www.ebi.ac.uk/astd/geneview.html
0000029: astd

Pseudomonas Genome Database
type: Resource
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
0000005: PSEEN0001
has provider formatter: http://www.pseudomonas.com/feature/show/
has local unique identifier pattern: ^P\w+$
is deprecated: false
has URI prefix: http://www.pseudomonas.com/feature/show/
0000027: http://www.pseudomonas.com/feature/show/
0000029: pseudomonas

Organization
type: Class
description: An organization

Gene Expression Ontology
type: Resource
description: Gene Expression Ontology
is part of: bioregistry
keyword: life science
keyword: ontology
keyword: expression data
keyword: gene expression
0000010: gexo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1171-9876
0000029: gexo

SBML RDF Vocabulary
type: Resource
description: Vocabulary used in the RDF representation of SBML models.
is part of: bioregistry
0000005: rateRule
has provider formatter: http://biomodels.net/rdf/vocabulary.rdf#$1
has local unique identifier pattern: ^[A-Za-z]+$
is deprecated: false
has URI prefix: http://biomodels.net/rdf/vocabulary.rdf#
0000027: rateRule
0000029: biomodels.vocabulary

DBPedia Property
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Properties in DBPedia.
is part of: bioregistry
0000005: insertion
has provider formatter: http://dbpedia.org/property/$1
is deprecated: false
0000018: fovt
has URI prefix: http://dbpedia.org/property/
0000027: insertion
0000029: dbpedia.property

Semantically-Interlinked Online Communities Argumentation Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary of argumentation predicates for SIOC
is part of: bioregistry
0000005: decides
has provider formatter: http://rdfs.org/sioc/argument#$1
is deprecated: false
has URI prefix: http://rdfs.org/sioc/argument#
0000027: decides
0000029: sioc.argument

PerkinElmer
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A product catalog for PerkinElmer, a laboratory supplies vendor
is part of: bioregistry
0000005: SCC111
has provider formatter: https://www.perkinelmer.com/searchresult
is deprecated: false
has URI prefix: https://www.perkinelmer.com/searchresult
0000027: https://www.perkinelmer.com/searchresult
0000029: perkinelmer

Dynamic Ecological Information Management System - Site and Dataset Registry - Taxonomy
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Taxonomy in DEIMS SDR
is part of: bioregistry
0000005: 21157
has provider formatter: https://deims.org/taxonomy/term/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Christoph Wohner
has URI prefix: https://deims.org/taxonomy/term/
0000027: https://deims.org/taxonomy/term/21157
0000029: deims.taxonomy

Plant Phenotype Experiment Ontology
type: Resource
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
keyword: life sciences, biology
0000005: GPS_location
has provider formatter: http://purl.org/ppeo/PPEO.owl#$1
is deprecated: false
has responsible: Cyril Pommier
has URI prefix: http://purl.org/ppeo/PPEO.owl#
0000027: GPS location
0000029: ppeo

Bgee gene
type: Resource
contributor: Sébastien Moretti
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
keyword: gene expression
0000005: FBgn0000015
has provider formatter: https://www.bgee.org/gene/$1
has local unique identifier pattern: ^[A-Za-z0-9]+$
is deprecated: false
has responsible: Sébastien Moretti
has URI prefix: https://www.bgee.org/gene/
0000027: FBgn0000015
0000029: bgee.gene

Cell Version Control Repository
type: Resource
description: The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines
is part of: bioregistry
0000005: 82
has provider formatter: https://www.cellrepo.com/repositories/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has URI prefix: https://www.cellrepo.com/repositories/
0000027: https://www.cellrepo.com/repositories/82
0000029: cellrepo

Sri Lanka Clinical Trials Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
0000005: SLCTR/2023/010
has local unique identifier pattern: ^SLCTR/\d{4}/\d+$
is deprecated: false
0000029: slctr

Michael Feolo

nextProt
type: Resource
description: neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases.
is part of: bioregistry
keyword: life science
keyword: proteomics
0000005: NX_O00165
has provider formatter: https://www.nextprot.org/db/entry/$1
has local unique identifier pattern: ^NX_\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-7961-6091
has alternative prefix: NXP
has URI prefix: https://www.nextprot.org/db/entry/
0000027: NX O00165
0000029: nextprot

NITE Biological Resource Center
type: Resource
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.
is part of: bioregistry
keyword: microbiology
keyword: microbial
keyword: taxonomy
0000005: 00001234
has provider formatter: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet
0000027: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet
0000029: nbrc

John Cottrell

Sequence-Structural Templates of Single-member Superfamilies
type: Resource
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.
is part of: bioregistry
keyword: protein
keyword: structure
0000005: 01.01.005
has provider formatter: http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi
0000027: http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi
0000029: sstoss

Biolink Model
type: Resource
description: A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations.
is part of: bioregistry
git repository: biolink-model
keyword: ontology
keyword: medical informatics
keyword: translational medicine
keyword: functional genomics
keyword: medical biotechnology
keyword: biomedical science
0000005: Gene
has provider formatter: https://biolink.github.io/biolink-model/$1
has local unique identifier pattern: ^\S+$
0000010: biolink.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
has URI prefix: https://biolink.github.io/biolink-model/
0000027: Gene
0000029: biolink

MarkerDB
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
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.
is part of: bioregistry
0000005: MDB00000001
has local unique identifier pattern: ^MDB\d{8}$
is deprecated: false
has responsible: David Wishart
has reviewer: https://orcid.org/0000-0001-9439-5346
0000029: markerdb

Alexey M. Eroshkin

Mouse Tumor Biology Database
type: Resource
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.
is part of: bioregistry
keyword: dna
keyword: gene expression
0000005: 1374
has provider formatter: http://tumor.informatics.jax.org/mtbwi/strainDetails.do
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://tumor.informatics.jax.org/mtbwi/strainDetails.do
0000027: http://tumor.informatics.jax.org/mtbwi/strainDetails.do
0000029: mtbd

sébastien Aubourg

SPARQL 1.1 Service Description
type: Resource
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.
is part of: bioregistry
keyword: w3c rec
0000005: endpoint
is deprecated: false
0000029: sd

Josh Moore

InterPro
type: Resource
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.
is part of: bioregistry
git repository: interpro-blog
keyword: protein
keyword: bioinformatics
keyword: biology
keyword: domain
keyword: obo
keyword: ontology
0000005: IPR016380
has provider formatter: https://www.ebi.ac.uk/interpro/entry/InterPro/$1
has local unique identifier pattern: ^IPR\d{6}$
0000010: interpro.owl
is deprecated: false
has responsible: Alex Bateman
has alternative prefix: IP
has alternative prefix: IPR
has alternative prefix: InterPro
has URI prefix: https://www.ebi.ac.uk/interpro/entry/InterPro/
0000027: IPR016380
0000029: interpro

ICEberg cis-integrative and mobilizable element
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: genomics
keyword: biology
0000005: 6
has provider formatter: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-9439-1660
has URI prefix: https://bioregistry.io/iceberg.cime:
0000027: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php
0000029: iceberg.cime

Core Ontology for Biology and Biomedicine
type: Resource
description: COB brings together key terms from a wide range of OBO projects to improve interoperability.
is part of: bioregistry
git repository: COB
keyword: obo
keyword: ontology
keyword: dataplant
keyword: life sciences, biology
0000005: 0000080
has provider formatter: http://purl.obolibrary.org/obo/COB_$1
has local unique identifier pattern: ^\d{7}$
0000010: cob.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-8457-6693
has URI prefix: http://purl.obolibrary.org/obo/COB_
0000027: COB_0000080
0000029: cob

SWEET Ontology Material Animal
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Animal
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: materials
keyword: animal
0000005: AcornWorm
has provider formatter: http://sweetontology.net/matrAnimal/$1
is deprecated: false
has alternative prefix: soman
has URI prefix: http://sweetontology.net/matrAnimal/
0000027: AcornWorm
0000029: sweet.man

Yu Zong Chen

Vertebrate Gene Nomenclature Committee
type: Resource
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.
is part of: bioregistry
keyword: life science
0000005: 3792
has provider formatter: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1
has local unique identifier pattern: ^\d{1,9}$
is deprecated: false
has responsible: Susan Tweedie
has URI prefix: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/
0000027: !/vgnc id/3792
0000029: vgnc

SWEET Ontology Property Quantity
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Quantity
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: quantity
0000005: BalanceEquation
has provider formatter: http://sweetontology.net/propQuantity/$1
is deprecated: false
has alternative prefix: sopropq
has URI prefix: http://sweetontology.net/propQuantity/
0000027: BalanceEquation
0000029: sweet.propq

OntoSpecies - Chemical Species Ontology for Data Integration and Knowledge Discovery
type: Resource
description: OntoSpecies is an ontology developed for representing chemical species.
is part of: bioregistry
keyword: chemistry
keyword: nfdi4chem
0000005: Charge
has provider formatter: http://www.theworldavatar.com/ontology/ontospecies/OntoSpecies.owl#$1
is deprecated: false
has URI prefix: http://www.theworldavatar.com/ontology/ontospecies/OntoSpecies.owl#
0000027: Charge
0000029: worldavatar.os

Clytia hemisphaerica Development and Anatomy Ontology
type: Resource
description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.
is part of: bioregistry
git repository: clyh ontology
keyword: obo
keyword: ontology
0000005: 1000100
has provider formatter: http://purl.obolibrary.org/obo/CLYH_$1
has local unique identifier pattern: ^\d+$
0000010: clyh.owl
is deprecated: false
depends on: Uber Anatomy Ontology
depends on: ro
depends on: Information Artifact Ontology
has responsible: Lucas Leclere
has URI prefix: http://purl.obolibrary.org/obo/CLYH_
0000027: CLYH_1000100
0000029: clyh

Amphibian gross anatomy
type: Resource
description: A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon.
is part of: bioregistry
keyword: anatomy
keyword: obo
keyword: ontology
0000005: 0000138
has provider formatter: http://purl.obolibrary.org/obo/AAO_$1
has local unique identifier pattern: ^\d{7}$
is deprecated: true
has responsible: https://orcid.org/0000-0002-1810-9886
has URI prefix: http://purl.obolibrary.org/obo/AAO_
0000027: AAO_0000138
0000029: aao

Common Bean Ontology
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 Common Bean Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
is part of: bioregistry
git repository: Crop-Ontology
keyword: food
keyword: ontology
keyword: botany
keyword: agriculture
0000005: 0000189
has provider formatter: https://cropontology.org/rdf/CO_335:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 335.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_335:
0000027: CO 335:0000189
0000029: co_335

American Type Culture Collection
type: Resource
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.
is part of: bioregistry
keyword: virology
keyword: epidemiology
keyword: life science
0000005: 11303
has provider formatter: https://www.atcc.org/products/$1
has local unique identifier pattern: ^([a-zA-Z]+-)?\d+(\.\d)?$
is deprecated: false
has alternative prefix: ATCC(dna)
has alternative prefix: ATCC(in host)
has alternative prefix: ATCC number
has alternative prefix: ATCC
has URI prefix: https://www.atcc.org/products/
0000027: https://www.atcc.org/products/11303
0000029: atcc

COVID-19 Surveillance Ontology
type: Resource
description: Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease.
is part of: bioregistry
keyword: ontology
0000005: SFB_COVID19_MW286762
has provider formatter: https://covid19.sfb.uit.no/api/records/$1
has local unique identifier pattern: ^\w+_COVID19_[-\w]+$
0000010: covid19.owl
is deprecated: false
has responsible: Dylan McGagh
has URI prefix: https://covid19.sfb.uit.no/api/records/
0000027: SFB COVID19 MW286762
0000029: covid19

Human BioMolecular Atlas Program Sample
type: Resource
contributor: 0009-0008-8406-631X
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.
is part of: bioregistry
has provider formatter: https://portal.hubmapconsortium.org/browse/sample/$1
has local unique identifier pattern: ^[a-f0-9]{32}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3321-6137
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://portal.hubmapconsortium.org/browse/sample/
0000029: hubmap.sample

GiardiaDB
type: Resource
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.
is part of: bioregistry
keyword: eukaryotic
keyword: genome
keyword: genomics
0000005: GL50803_102438
has provider formatter: https://giardiadb.org/giardiadb/app/record/gene/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: Omar S. Harb
has URI prefix: https://giardiadb.org/giardiadb/app/record/gene/
0000027: GL50803_102438
0000029: giardiadb

GO Relations
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: Arslaan Zahid
description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.
is part of: bioregistry
keyword: ontology
0000005: 0002005
has provider formatter: http://purl.obolibrary.org/obo/GOREL_$1
has local unique identifier pattern: ^\d{7}$
0000010: gorel.owl
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/GOREL_
0000027: GOREL_0002005
0000029: gorel

CIViC Source
type: Resource
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.
is part of: bioregistry
0000005: 62
has provider formatter: https://civicdb.org/links/sources/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: Malachi Griffith
has alternative prefix: civic.source
has URI prefix: https://civicdb.org/links/sources/
0000027: https://civicdb.org/links/sources/62
0000029: civic.sid

mirEX
type: Resource
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.
is part of: bioregistry
keyword: life science
0000005: 165a
has provider formatter: http://comgen.pl/mirex1/
has local unique identifier pattern: ^\d+(\w+)?$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8086-5404
has URI prefix: https://bioregistry.io/mirex:
0000027: http://comgen.pl/mirex1/
0000029: mirex

Medical Dictionary for Regulatory Activities Terminology
type: Resource
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 part of: bioregistry
keyword: preclinical studies
keyword: biomedical science
keyword: medicine
keyword: ontology
keyword: disease
0000005: 10015919
has provider formatter: https://bioportal.bioontology.org/ontologies/MEDDRA
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: MedDRA MSSO
has alternative prefix: Medical Dictionary for Regulatory Activities
has alternative prefix: MEDRA
has alternative prefix: MedDRA
has alternative prefix: MeDRA
has URI prefix: https://bioportal.bioontology.org/ontologies/MEDDRA
0000027: https://bioportal.bioontology.org/ontologies/MEDDRA
0000029: meddra

OBO Foundry
type: https://bioregistry.io/schema/#0000002
description: The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate.
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 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

An Educational and Career-Oriented Recommendation Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: educor
0000005: stri
has provider formatter: https://github.com/tibonto/educor#$1
is deprecated: false
has responsible: Eleni Ilkou
has URI prefix: https://github.com/tibonto/educor#
0000027: stri
0000029: educor

Indian Crop Phenome Database Study
type: Resource
contributor: Sonia Balyan
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]
is part of: bioregistry
0000005: PST_100013
has provider formatter: https://ibdc.dbtindia.gov.in/icpd/study-view-home/$1
has local unique identifier pattern: ^PST_\d+$
is deprecated: false
has responsible: Sonia Balyan
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://ibdc.dbtindia.gov.in/icpd/study-view-home/
0000027: PST_100013
0000029: icpd.study

SWEET Ontology Realm Geologic Constituent
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Constituent
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: geologic constituent
keyword: realm
0000005: ArmoredRelictInclusion
has provider formatter: http://sweetontology.net/realmGeolConstituent/$1
is deprecated: false
has alternative prefix: soreagcons
has URI prefix: http://sweetontology.net/realmGeolConstituent/
0000027: ArmoredRelictInclusion
0000029: sweet.reagcons

Carnegie Stage
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: One of the 23 stages of embryo development
is part of: bioregistry
0000005: 20
has provider formatter: https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages#Stage_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages#Stage_
0000027: Stage 20
0000029: carnegie.stage

GlycoPOST
type: Resource
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.
is part of: bioregistry
keyword: life science
keyword: glycomics
0000005: GPST000024
has provider formatter: https://glycopost.glycosmos.org/entry/$1
has local unique identifier pattern: ^GPST[0-9]{6}$
is deprecated: false
has URI prefix: https://glycopost.glycosmos.org/entry/
0000027: GPST000024
0000029: glycopost

Open Graph protocol
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary for embedding provenance metadata into webpages via RDFa
is part of: bioregistry
keyword: data schema
keyword: linked open data
keyword: semantic web
keyword: api
0000005: title
has provider formatter: https://ogp.me/ns#$1
is deprecated: false
has URI prefix: https://ogp.me/ns#
0000027: title
0000029: og

Transcription Factor Database
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.
is part of: bioregistry
keyword: genome
keyword: regulation
0000005: 0045310
has provider formatter: http://www.transcriptionfactor.org/index.cgi
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://bioregistry.io/dbd:
0000027: http://www.transcriptionfactor.org/index.cgi
0000029: dbd

International Genome Sample Resource
type: 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.
is part of: bioregistry
keyword: genomics
keyword: comparative genomics
0000005: NA06985
has provider formatter: https://www.internationalgenome.org/data-portal/sample/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-3897-7955
has URI prefix: https://www.internationalgenome.org/data-portal/sample/
0000027: NA06985
0000029: igsr

Applied Biological Materials cell line products
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: Cell line collections (Providers)
is part of: bioregistry
0000005: T0599
has provider formatter: https://www.abmgood.com/search
is deprecated: false
has URI prefix: https://www.abmgood.com/search
0000027: https://www.abmgood.com/search
0000029: abm

HoloFood sample
type: Resource
contributor: 0009-0008-8406-631X
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.
is part of: bioregistry
0000005: SAMEA10104908
has provider formatter: https://www.holofooddata.org/sample/$1
has local unique identifier pattern: ^SAMEA\d{8}$
is deprecated: false
has responsible: Tom Gilbert
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.holofooddata.org/sample/
0000027: SAMEA10104908
0000029: holofood.sample

Curated Drug-Drug Interactions Database - Drug
type: Resource
contributor: https://orcid.org/0000-0002-8719-7760
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
keyword: relationships
keyword: chemistry
keyword: drugs
0000005: DDInter20
has provider formatter: http://ddinter.scbdd.com/ddinter/drug-detail/$1
has local unique identifier pattern: ^DDInter\d+$
is deprecated: false
has responsible: Dongsheng Cao
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://ddinter.scbdd.com/ddinter/drug-detail/
0000027: DDInter20
0000029: ddinter.drug

Japan Registry of Clinical Trials
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
0000005: jRCTs041220087
has provider formatter: https://jrct.niph.go.jp/en-latest-detail/$1
has local unique identifier pattern: ^jRCT\w?\d+$
is deprecated: false
has URI prefix: https://jrct.niph.go.jp/en-latest-detail/
0000027: jRCTs041220087
0000029: jrct

Henriette Harmse

GLIDA Ligand
type: Resource
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
0000005: L000001
has provider formatter: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php
has local unique identifier pattern: ^L\d+$
is deprecated: true
has URI prefix: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php
0000027: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php
0000029: glida.ligand

Evaluation and Report Language
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: EARL is a vocabulary, the terms of which are defined across a set of specifications and technical notes, and that is used to describe test results. The primary motivation for developing this vocabulary is to facilitate the exchange of test results between Web accessibility evaluation tools in a vendor-neutral and platform-independent format. It also provides reusable terms for generic quality assurance and validation purposes. [from homepage]
is part of: bioregistry
keyword: quality
0000005: Assertion
has provider formatter: http://www.w3.org/ns/earl#$1
is deprecated: false
has URI prefix: http://www.w3.org/ns/earl#
0000027: Assertion
0000029: earl

Transcriptional Regulatory Element Database
type: Resource
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.
is part of: bioregistry
keyword: dna
keyword: regulation
0000005: 21552
has provider formatter: http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi
0000027: http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi
0000029: tred

AOPWiki
type: Resource
contributor: Sumir Pandit
description: International repository of Adverse Outcome Pathways.
is part of: bioregistry
0000005: 98
has provider formatter: https://aopwiki.org/aops/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://aopwiki.org/aops/
0000027: https://aopwiki.org/aops/98
0000029: aop

Karen R. Christie

Frederique Lisacek

Web Elements
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Browser for the periodic table of the elements
is part of: bioregistry
keyword: chemistry
0000005: chromium
has provider formatter: https://www.webelements.com/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has URI prefix: https://www.webelements.com/
0000027: chromium
0000029: webelements

International Classifications of Diseases
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
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, 9th Revision
has part: icd9cm
has part: icd10pcs
has part: icd10cm
has part: International Classification of Diseases, 11th Revision (Foundation Component)
has part: icd10
has part: icdo
has part: ICD 11 Codes

Healthcare Organizations and Services Ontology
type: Resource
contributor: Paul Fabry
description: HOSO is an ontology of informational entities and processes related to healthcare organizations and services.
is part of: bioregistry
git repository: HOSO
0000005: 0000001
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: Paul Fabry
has reviewer: https://orcid.org/0000-0003-4423-4370
0000029: hoso

Immune Epitope Database Assays
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for specific experimental assays that serve as evidence for immune-related studies.
is part of: bioregistry
keyword: life science
keyword: immunology
keyword: bioinformatics
0000005: 1691753
has provider formatter: https://www.iedb.org/assay/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-8957-7612
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.iedb.org/assay/
0000027: https://www.iedb.org/assay/1691753
0000029: iedb.assay

Open Digital Rights Language Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
keyword: metadata
0000005: assetConcepts
has provider formatter: http://www.w3.org/ns/odrl/2/$1
is deprecated: false
has URI prefix: http://www.w3.org/ns/odrl/2/
0000027: assetConcepts
0000029: odrl

Gert Vriend

Wiktionary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A free dictionary
is part of: bioregistry
0000005: pharmacist
has provider formatter: https://en.wiktionary.org/wiki/$1
is deprecated: false
has URI prefix: https://en.wiktionary.org/wiki/
0000027: pharmacist
0000029: wiktionary

International Standard for Intelligent Information Request and Delivery Machinery Ontology
type: Resource
description: An ontology encoding machinery based on the Intelligent Information Request and Delivery (iiRDS) standard
is part of: bioregistry
git repository: models
keyword: nfdi4ing
keyword: computer science
0000005: ConsumableSupply
has provider formatter: http://iirds.tekom.de/iirds/domain/machinery#$1
is deprecated: false
has URI prefix: http://iirds.tekom.de/iirds/domain/machinery#
0000027: ConsumableSupply
0000029: iirds.mch

Tobias Schulze

Simple Standard for Sharing Ontological Mappings
type: Resource
contributor: https://orcid.org/0000-0002-7356-1779
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.
is part of: bioregistry
git repository: sssom
0000005: mapping_justification
has provider formatter: https://w3id.org/sssom/$1
has local unique identifier pattern: ^[A-Za-z_]+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7356-1779
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://w3id.org/sssom/
0000027: mapping justification
0000029: sssom

General Data Format
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Describes the physical format(s) of the data documented in the logical product(s) of a study unit.
is part of: bioregistry
0000005: Numeric
has provider formatter: https://vocabularies.cessda.eu/vocabulary/GeneralDataFormat#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/GeneralDataFormat#code_
0000026: 015em2733
0000027: code Numeric
0000029: ddi.generaldataformat

AGROVOC
type: Resource
contributor: https://orcid.org/0000-0002-2404-1582
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: food
keyword: forest management
keyword: knowledge and information systems
keyword: botany
keyword: agriculture
keyword: climate
keyword: agronomy
keyword: food security
keyword: aquaculture
keyword: water management
keyword: agricultural products
keyword: nutritional science
keyword: environmental science
keyword: fisheries science
keyword: data management
0000005: 2842
has provider formatter: http://aims.fao.org/aos/agrovoc/c_$1
has local unique identifier pattern: ^[a-z0-9]+$
is deprecated: false
has responsible: Alex Skrenchuk
has URI prefix: http://aims.fao.org/aos/agrovoc/c_
0000027: c 2842
0000029: agrovoc

MobiDB
type: Resource
description: MobiDB is a database of protein disorder and mobility annotations.
is part of: bioregistry
keyword: biomedical science
keyword: biology
0000005: P10636
has provider formatter: https://mobidb.org/$1
has local unique identifier pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$
0000011: uniprot
is deprecated: false
has responsible: https://orcid.org/0000-0003-4525-7793
has URI prefix: https://mobidb.org/
0000027: P10636
0000029: mobidb

Darwin-SW
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.
is part of: bioregistry
git repository: dsw
keyword: ess
keyword: fair data spaces
keyword: earth sciences
keyword: life sciences, biology
0000005: DriedSpecimen
has provider formatter: http://purl.org/dsw/$1
is deprecated: false
has responsible: Steve Baskauf
has URI prefix: http://purl.org/dsw/
0000027: DriedSpecimen
0000029: dsw

Glycan Naming and Subsumption Ontology
type: Resource
description: An ontology for glycans based on GlyTouCan, but organized by subsumption.
is part of: bioregistry
git repository: GNOme
keyword: obo
keyword: ontology
0000005: 10004892
has provider formatter: http://purl.obolibrary.org/obo/GNO_$1
has local unique identifier pattern: ^(\d{8}|(\w+\d+\w+))$
0000010: gno.owl
is deprecated: false
has responsible: Nathan Edwards
has alternative prefix: gnome
has URI prefix: http://purl.obolibrary.org/obo/GNO_
0000027: GNO_10004892
0000029: gno

NIF Standard Ontology: Qualities
type: Resource
contributor: Tom Gillespie
description: NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO).
is part of: bioregistry
git repository: NIF-Ontology
keyword: dispositions
keyword: qualities
0000005: 100810
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Tom Gillespie
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXQUAL
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_qual_
0000027: nlx qual 100810
0000029: nlx.qual

4D Nucleome Data Portal Experiment Replicate
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: https://orcid.org/0000-0001-5130-7705
contributor: https://orcid.org/0000-0002-6240-9325
contributor: Layla Michán Aguirre
description: Database portal containing replicate experiments of different assays and samples
is part of: bioregistry
0000005: 4DNESWX1J3QU
has provider formatter: https://data.4dnucleome.org/experiment-set-replicates/$1
is deprecated: false
has alternative prefix: 4dn.replicate
has URI prefix: https://data.4dnucleome.org/experiment-set-replicates/
0000027: 4DNESWX1J3QU
0000029: _4dn.replicate

Social Insect Behavior Ontology
type: Resource
description: Social Behavior in insects
is part of: bioregistry
git repository: sibo
keyword: biology
keyword: obo
keyword: ontology
0000005: 0000509
has provider formatter: http://purl.obolibrary.org/obo/SIBO_$1
has local unique identifier pattern: ^\d{7}$
0000010: sibo.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-6601-2165
has URI prefix: http://purl.obolibrary.org/obo/SIBO_
0000027: SIBO_0000509
0000029: sibo

SWEET Ontology Property Time Frequency
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Time Frequency
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: time frequency
0000005: Bandwidth
has provider formatter: http://sweetontology.net/propTimeFrequency/$1
is deprecated: false
has alternative prefix: soproptf
has URI prefix: http://sweetontology.net/propTimeFrequency/
0000027: Bandwidth
0000029: sweet.proptf

SWEET Ontology Phenomena Reaction
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Reaction
is part of: sweet
is part of: bioregistry
git repository: sweet
keyword: phenomena
keyword: reaction
0000005: Activation
has provider formatter: http://sweetontology.net/phenReaction/$1
is deprecated: false
has alternative prefix: sophr
has URI prefix: http://sweetontology.net/phenReaction/
0000027: Activation
0000029: sweet.phr

SWEET Ontology Realm Geologic Oceanic
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Oceanic
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: geologic oceanic
keyword: realm
0000005: AccretionaryPrism
has provider formatter: http://sweetontology.net/realmGeolOceanic/$1
is deprecated: false
has alternative prefix: soreagoc
has URI prefix: http://sweetontology.net/realmGeolOceanic/
0000027: AccretionaryPrism
0000029: sweet.reagoc

KEGG Disease
type: Resource
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.
is part of: bioregistry
is part of: kegg
keyword: classification
0000005: H00076
has provider formatter: http://www.kegg.jp/entry/$1
has local unique identifier pattern: ^H\d+$
is deprecated: false
has URI prefix: http://www.kegg.jp/entry/
0000027: H00076
0000029: kegg.disease

Unique Ingredient Identifier
type: Resource
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.
is part of: bioregistry
0000005: 3G6A5W338E
has provider formatter: https://precision.fda.gov/uniisearch/srs/unii/$1
has local unique identifier pattern: ^[A-Z0-9]+$
is deprecated: false
has URI prefix: https://precision.fda.gov/uniisearch/srs/unii/
0000027: 3G6A5W338E
0000029: unii

BioKC
type: Resource
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 part of: bioregistry
0000005: bkc640
has provider formatter: https://biokb.lcsb.uni.lu/fact/$1
has local unique identifier pattern: ^bkc[0-9]*$
is deprecated: false
has URI prefix: https://biokb.lcsb.uni.lu/fact/
0000027: bkc640
0000029: biokc

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.
is part of: bioregistry
0000005: 19333
has provider formatter: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail
0000027: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail
0000029: grin.taxonomy

Alliance of Genome Resources Knowledge Base
type: Resource
contributor: https://orcid.org/0000-0002-8719-7760
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)
is part of: bioregistry
keyword: model organism database
0000005: 100000000000001
has provider formatter: https://www.alliancegenome.org/accession/$1
has local unique identifier pattern: ^[1-9][0-9]{14}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.alliancegenome.org/accession/
0000027: https://www.alliancegenome.org/accession/100000000000001
0000029: agrkb

AOPWiki (Stressor)
type: Resource
description: International repository of Adverse Outcome Pathways.
is part of: bioregistry
0000005: 9
has provider formatter: https://aopwiki.org/stressors/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://aopwiki.org/stressors/
0000027: https://aopwiki.org/stressors/9
0000029: aop.stressor

Homology Ontology
type: Resource
description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.
is part of: bioregistry
git repository: homology-ontology
keyword: homologous
keyword: life cycle stage
keyword: molecular entity
keyword: anatomy
keyword: life science
keyword: obo
keyword: ontology
0000005: 0000049
has provider formatter: http://purl.obolibrary.org/obo/HOM_$1
has local unique identifier pattern: ^\d{7}$
0000010: hom.owl
is deprecated: false
has responsible: Frédéric Bastian
has URI prefix: http://purl.obolibrary.org/obo/HOM_
0000027: HOM_0000049
0000029: hom

arXiv
type: Resource
contributor: Sumir Pandit
description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.
is part of: bioregistry
keyword: preprints
keyword: publishing
keyword: bibliography
0000005: 0807.4956v1
has provider formatter: https://arxiv.org/abs/$1
has local unique identifier pattern: ^(\w+(\-\w+)?(\.\w+)?\/?)?\d{4,7}(\.\d+(v\d+)?)?$
is deprecated: false
has URI prefix: https://arxiv.org/abs/
0000027: 0807.4956v1
0000029: arxiv

Data Source Type
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Includes a typology of data sources.
is part of: bioregistry
0000005: RegistersRecordsAccounts
has provider formatter: https://vocabularies.cessda.eu/vocabulary/DataSourceType#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/DataSourceType#code_
0000026: 015em2733
0000027: code RegistersRecordsAccounts
0000029: ddi.datasourcetype

NIA Mouse cDNA Project
type: Resource
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.
is part of: bioregistry
keyword: life science
keyword: dna
0000005: J0705A10
has provider formatter: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3
has local unique identifier pattern: ^\w\d{4}\w\d{2}(\-[35])?$
is deprecated: true
has responsible: Dawood B. Dudekula
has URI prefix: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3
0000027: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3
0000029: niaest

Microbial Ecophysiological Trait and Phenotype Ontology
type: Resource
contributor: 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".
is part of: bioregistry
git repository: metpo
keyword: ontology
keyword: phenotypes
keyword: microbes
0000005: 1004005
has provider formatter: https://w3id.org/metpo/$1
has local unique identifier pattern: ^\d+$
0000010: metpo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9076-6066
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://w3id.org/metpo/
0000026: 02jbv0t02
0000027: https://w3id.org/metpo/1004005
0000029: metpo

Barry Smith

TIGR protein families
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
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.
is part of: bioregistry
keyword: protein
0000005: TIGR00010
has provider formatter: https://www.ncbi.nlm.nih.gov/cdd
has local unique identifier pattern: ^TIGR\d+$
is deprecated: false
has URI prefix: https://www.ncbi.nlm.nih.gov/cdd
0000027: https://www.ncbi.nlm.nih.gov/cdd
0000029: tigrfam

Joint FAO/WHO Expert Committee on Food Additives
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
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.
is part of: bioregistry
0000005: 2116
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Kim Petersen
has reviewer: https://orcid.org/0000-0001-9439-5346
0000029: jecfa

Virus Pathogen Resource
type: Resource
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.
is part of: bioregistry
git repository: VirusBRC
keyword: proteomics
keyword: epidemiology
keyword: biomedical science
keyword: life science
keyword: immunology
keyword: genomics
keyword: virology
0000005: BeAn 70563
has provider formatter: http://www.viprbrc.org/brc/viprStrainDetails.do
has local unique identifier pattern: ^[A-Za-z 0-9]+$
is deprecated: false
has responsible: 0000-0003-1355-892X
has URI prefix: https://bioregistry.io/vipr:
0000029: vipr

David Craik

eNanoMapper ontology
type: Resource
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 part of: bioregistry
keyword: health science
keyword: ontology
keyword: chemistry
keyword: nfdi4chem
keyword: nanosafety
keyword: nanoparticle
keyword: chemical entity
0000005: 8000221
has provider formatter: http://purl.enanomapper.org/onto/ENM_$1
has local unique identifier pattern: ^\d+$
0000010: enanomapper.owl
is deprecated: false
has responsible: Tim Vandermeersch
has URI prefix: http://purl.enanomapper.org/onto/ENM_
0000027: ENM_8000221
0000029: enm

Toxic Process Ontology
type: Resource
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
is part of: bioregistry
git repository: TXPO
keyword: ontology
keyword: obo
0000005: 0002066
has provider formatter: http://purl.obolibrary.org/obo/TXPO_$1
has local unique identifier pattern: ^\d{7}$
0000010: txpo.owl
is deprecated: false
has responsible: Yuki Yamagata
has URI prefix: http://purl.obolibrary.org/obo/TXPO_
0000027: TXPO_0002066
0000029: txpo

CIViC Therapy
type: Resource
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.
is part of: bioregistry
0000005: 14
has provider formatter: https://civicdb.org/links/drugs/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: Malachi Griffith
has alternative prefix: civic.therapy
has URI prefix: https://civicdb.org/links/drugs/
0000027: https://civicdb.org/links/drugs/14
0000029: civic.tid

Resources mentioned in "Sharing biological data: why, when, and how"
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
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: ega.dataset
has part: BioStudies database
has part: ssbd.dataset
has part: Electron Microscopy Public Image Archive
has part: peptideatlas.dataset
has part: Panorama Public
has part: Proteomics Identification Database Ontology
has part: ega.study
has part: bmrb.entry
has part: Electron Microscopy Data Bank
has part: GenBank
has part: pdb
has part: System Science of Biological Dynamics project
has part: insdc.sra
has part: NCBI Gene Expression Omnibus
has part: cellimage
has part: MassIVE
has part: idr

CharProt
type: Resource
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 part of: bioregistry
0000005: CH_001923
has provider formatter: http://www.jcvi.org/charprotdb/index.cgi/view/$1
has local unique identifier pattern: ^CH_\d+$
is deprecated: true
has URI prefix: http://www.jcvi.org/charprotdb/index.cgi/view/
0000027: CH_001923
0000029: charprot

Creative Commons Schema
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A precursor that was later replaced with the Creative Commons Rights Expression Language (ccREL)
is part of: bioregistry
keyword: license
keyword: schema
0000005: License
has provider formatter: http://web.resource.org/cc/$1
is deprecated: true
has URI prefix: http://web.resource.org/cc/
0000027: License
0000029: cc.legacy

Pathogen Transmission Ontology
type: Resource
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.
is part of: bioregistry
git repository: PathogenTransmissionOntology
keyword: biomedical science
keyword: host
keyword: pathogen
keyword: obo
keyword: ontology
keyword: infection process
0000005: 0000024
has provider formatter: http://purl.obolibrary.org/obo/TRANS_$1
has local unique identifier pattern: ^\d{7}$
0000010: trans.owl
is deprecated: false
has responsible: Lynn Schriml
has URI prefix: http://purl.obolibrary.org/obo/TRANS_
0000027: TRANS_0000024
0000029: trans

SWEET Ontology Human Decision
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Decision
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: decision
0000005: Allocation
has provider formatter: http://sweetontology.net/humanDecision/$1
is deprecated: false
has alternative prefix: sohud
has URI prefix: http://sweetontology.net/humanDecision/
0000027: Allocation
0000029: sweet.hud

Common Greenhouse Ontology
type: Resource
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.
is part of: bioregistry
keyword: horticulture
keyword: earth sciences
keyword: ess
keyword: chemical and environmental engineering
0000005: AbioticStressTrait
has provider formatter: https://www.tno.nl/agrifood/ontology/common-greenhouse-ontology#$1
is deprecated: false
has URI prefix: https://www.tno.nl/agrifood/ontology/common-greenhouse-ontology#
0000027: AbioticStressTrait
0000029: tib.cgo

Molbase
type: Resource
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.
is part of: bioregistry
0000005: 128796-39-4
has provider formatter: http://www.molbase.com/en/index.php
has local unique identifier pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$
is deprecated: false
has URI prefix: http://www.molbase.com/en/index.php
0000027: http://www.molbase.com/en/index.php
0000029: molbase

OMA Protein
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 individual protein records.
is part of: bioregistry
0000005: HUMAN16963
has provider formatter: https://omabrowser.org/oma/vps/$1
has local unique identifier pattern: ^[A-Z0-9]{5}\d+$
is deprecated: false
has URI prefix: https://omabrowser.org/oma/vps/
0000027: HUMAN16963
0000029: oma.protein

Corpus Vitrearum
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A digital photo archive
is part of: bioregistry
0000005: F3436
has provider formatter: https://corpusvitrearum.de/id/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-5101-5275
has URI prefix: https://corpusvitrearum.de/id/
0000027: F3436
0000029: corpusvitrearum

Assembling the Fungal Tree of Life - Taxonomy
type: Resource
contributor: Layla Michán Aguirre
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 part of: bioregistry
0000005: 959
has provider formatter: http://wasabi.lutzonilab.net/pub/displayTaxonInfo
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: David J. McLaughlin
has URI prefix: http://wasabi.lutzonilab.net/pub/displayTaxonInfo
0000027: http://wasabi.lutzonilab.net/pub/displayTaxonInfo
0000029: aftol.taxonomy

Comparative Data Analysis Ontology
type: Resource
description: a formalization of concepts and relations relevant to evolutionary comparative analysis
is part of: bioregistry
git repository: cdao
keyword: evolutionary biology
keyword: biomedical science
keyword: phylogenetics
keyword: taxonomy
keyword: life science
keyword: obo
keyword: ontology
keyword: molecular biology
keyword: bioinformatics
keyword: evolution
0000005: 0000072
has provider formatter: http://purl.obolibrary.org/obo/CDAO_$1
has local unique identifier pattern: ^\d{7}$
0000010: cdao.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-8688-6599
has URI prefix: http://purl.obolibrary.org/obo/CDAO_
0000027: CDAO_0000072
0000029: cdao

Semantically-Interlinked Online Communities Services Ontology - SWAN Mapping
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Mappings from SIOC to SWAN, with a small number of aux terms
is part of: bioregistry
0000005: OnlineJournal
has provider formatter: http://rdfs.org/sioc/swan#$1
is deprecated: false
has URI prefix: http://rdfs.org/sioc/swan#
0000027: OnlineJournal
0000029: sioc.swan

Biocuration Conference 2025 Collection
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of resources added during Biocuration 2025 in Kansas City, MO, USA.
has part: endlessforms.unit
has part: endlessforms.element
has part: AntiFam
has part: Biomarker Knowledgebase - Canonical Biomarker
has part: Graphic Descriptor Ontology
has part: BlastRule
has part: endlessforms.image
has part: endlessforms.graphic
has part: emi
has part: EndlessForms Studio Image Collections
has part: endlessforms.library
has part: biomarkerkb.biomarker

Database of Macromolecular Interactions
type: Resource
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.
is part of: bioregistry
0000005: 2GC4
has provider formatter: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1
has local unique identifier pattern: ^[0-9][A-Za-z0-9]{3}$
is deprecated: true
has URI prefix: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/
0000027: 2GC4
0000029: dommino

Structural Classification of Proteins - Unique Identifier
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.).
is part of: bioregistry
keyword: structure
keyword: protein
0000005: 47419
has provider formatter: http://scop.berkeley.edu/sunid=$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: John-Marc Chandonia
has alternative prefix: scop.sunid
has alternative prefix: scop.sun
has URI prefix: http://scop.berkeley.edu/sunid=
0000027: http://scop.berkeley.edu/sunid=47419
0000029: scop

Sunflower Ontology
type: Resource
description: To add
is part of: bioregistry
git repository: Crop-Ontology
keyword: ontology
0000005: 0000947
has provider formatter: https://cropontology.org/rdf/CO_359:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 359.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_359:
0000027: CO 359:0000947
0000029: co_359

OntoRXN
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: OntoRXN is an ontology for the description of reaction networks as undirected graphs characterized by energies.
is part of: bioregistry
keyword: ontology
keyword: chemistry
keyword: nfdi4chem
0000005: hasCalculation
0000010: OntoRXN.owl
is deprecated: false
0000029: ontorxn

eagle-i resource ontology
type: Resource
description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.
is part of: bioregistry
keyword: life science
keyword: study design
keyword: obo
keyword: ontology
keyword: biospecimen
keyword: reagent
keyword: biomedical science
0000005: 0001655
has provider formatter: http://purl.obolibrary.org/obo/ERO_$1
has local unique identifier pattern: ^\d{7}$
0000010: ero.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-3734-1859
has URI prefix: http://purl.obolibrary.org/obo/ERO_
0000027: ERO_0001655
0000029: ero

FaBiO, the FRBR-aligned Bibliographic Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: fabio
keyword: miscellaneous
keyword: ontology
keyword: literature
keyword: spar
keyword: subject agnostic
0000005: d4e2515
has provider formatter: https://sparontologies.github.io/fabio/current/fabio.html#$1
0000010: fabio.owl
is deprecated: false
has responsible: Silvio Peroni
has URI prefix: https://sparontologies.github.io/fabio/current/fabio.html#
0000027: d4e2515
0000029: fabio

Diagnostic and Statistical Manual of Mental Disorders (5th Edition)
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
0000005: 312.33
has local unique identifier pattern: ^\d{3}\.\d{2}$
is deprecated: false
has alternative prefix: dsm-v
0000029: dsm5

EcoPortal
type: https://bioregistry.io/schema/#0000002
description: The LifeWatch ERIC repository of semantic resources for the ecological domain.
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
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
has part: AGROVOC
has part: FABIO
has part: CMECS
has part: ENVTHES
has part: STY
0000005: AGROVOC
has provider formatter: http://ecoportal.lifewatch.eu/ontologies/$1
has responsible: 0000-0003-4494-839X

GeoNames Feature Code
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: ontology
keyword: geography
0000005: ADM1
has provider formatter: https://www.geonames.org/recent-changes/featurecode/$1/
0000010: geonames.feature.owl
is deprecated: false
has responsible: Marc Wick
has URI prefix: https://bioregistry.io/geonames.feature:
0000027: ADM1
0000029: geonames.feature

Interlab Cell Line Collection
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
0000005: ATL98012
has provider formatter: http://www.iclc.it/details/det_list.php
has local unique identifier pattern: ^\w{3}\d+$
is deprecated: false
has URI prefix: http://www.iclc.it/details/det_list.php
0000027: http://www.iclc.it/details/det_list.php
0000029: iclc

Panorama Public
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
keyword: metabolomics
keyword: proteomics
keyword: life science
0000005: FxnI151FMs
has provider formatter: https://panoramaweb.org/$1.url
is deprecated: false
has responsible: https://orcid.org/0000-0002-9575-0255
has URI prefix: https://bioregistry.io/panorama:
0000027: FxnI151FMs.url
0000029: panorama

ESCO Occupation
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
has provider formatter: http://data.europa.eu/esco/occupation/$1
is deprecated: false
has URI prefix: http://data.europa.eu/esco/occupation/
0000029: esco.occupation

SWEET Ontology Property Space Distance
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Distance
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: space distance
0000005: AttenuationCoefficient
has provider formatter: http://sweetontology.net/propSpaceDistance/$1
is deprecated: false
has alternative prefix: sopropsdis
has URI prefix: http://sweetontology.net/propSpaceDistance/
0000027: AttenuationCoefficient
0000029: sweet.propsdis

Wheat Ontology
type: Resource
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.
is part of: bioregistry
git repository: Crop-Ontology
keyword: phenotype
keyword: agriculture
keyword: life science
keyword: food
keyword: ontology
0000005: 0000449
has provider formatter: https://cropontology.org/rdf/CO_321:$1
has local unique identifier pattern: ^\d{7}$
0000010: CO 321.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-9399-8003
has URI prefix: https://cropontology.org/rdf/CO_321:
0000027: CO 321:0000449
0000029: co_321

NLFFF Database
type: Resource
description: Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database
is part of: bioregistry
0000005: 345201101230312003
has provider formatter: http://database.deepsolar.space:18080/dbs/nlfff/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has URI prefix: http://database.deepsolar.space:18080/dbs/nlfff/
0000027: http://database.deepsolar.space:18080/dbs/nlfff/345201101230312003
0000029: nlfff

ScerTF
type: Resource
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.
is part of: bioregistry
0000005: RSC3
has provider formatter: http://stormo.wustl.edu/ScerTF/details/$1
has local unique identifier pattern: ^\w+$
is deprecated: true
has URI prefix: http://stormo.wustl.edu/ScerTF/details/
0000027: RSC3
0000029: scretf

Bacillus subtilis genome sequencing project
type: Resource
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.
is part of: bioregistry
keyword: genome
keyword: dna
keyword: protein
0000005: BG11523
has provider formatter: http://genolist.pasteur.fr/SubtiList/genome.cgi
has local unique identifier pattern: ^BG\d+$
is deprecated: true
has responsible: Antoine Danchin
has URI prefix: http://genolist.pasteur.fr/SubtiList/genome.cgi
0000027: http://genolist.pasteur.fr/SubtiList/genome.cgi
0000029: subtilist

Echinobase
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species.
is part of: bioregistry
0000005: 23159291
has provider formatter: https://www.echinobase.org/entry/gene/showgene.do
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.echinobase.org/entry/gene/showgene.do
0000027: https://www.echinobase.org/entry/gene/showgene.do
0000029: echinobase

Brazilian Registry of Clinical Trials
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
0000005: RBR-6qvdftm
has provider formatter: https://ensaiosclinicos.gov.br/rg/$1
has local unique identifier pattern: ^RBR-\w+$
is deprecated: false
has URI prefix: https://ensaiosclinicos.gov.br/rg/
0000027: RBR-6qvdftm
0000029: rebec

Kinetic Simulation Algorithm Ontology
type: Resource
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.
is part of: bioregistry
git repository: KiSAO
keyword: bioinformatics
keyword: algorithm
keyword: computer science
keyword: obo
keyword: ontology
0000005: 0000057
has provider formatter: http://purl.obolibrary.org/obo/KISAO_$1
has local unique identifier pattern: ^\d+$
0000010: kisao.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-2605-5080
has alternative prefix: biomodels.kisao
has alternative prefix: kisao
has URI prefix: http://purl.obolibrary.org/obo/KISAO_
0000027: KISAO_0000057
0000029: biomodels.kisao

Epilepsy Ontology
type: Resource
description: A application driven Epilepsy Ontology with official terms from the ILAE.
is part of: bioregistry
git repository: EpilepsyOntology
keyword: ontology
keyword: obo
0000005: 0000011
has provider formatter: http://purl.obolibrary.org/obo/EPIO_$1
has local unique identifier pattern: ^\d{7}$
0000010: epio.owl
is deprecated: false
depends on: bfo
has responsible: https://orcid.org/0000-0001-9896-3531
has URI prefix: http://purl.obolibrary.org/obo/EPIO_
0000027: EPIO_0000011
0000029: epio

Protein Alignment organised as Structural Superfamily
type: Resource
description: The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.
is part of: bioregistry
keyword: classification
keyword: genome
keyword: dna
keyword: structure
0000005: 46977
has provider formatter: https://caps.ncbs.res.in/pass2.8/
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: https://caps.ncbs.res.in/pass2.8/
0000027: https://caps.ncbs.res.in/pass2.8/
0000029: pass2

SWEET Ontology Phenomena Atmosphere Fog
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Fog
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
keyword: atmosphere fog
0000005: AdvectionFog
has provider formatter: http://sweetontology.net/phenAtmoFog/$1
is deprecated: false
has alternative prefix: sophatmofo
has URI prefix: http://sweetontology.net/phenAtmoFog/
0000027: AdvectionFog
0000029: sweet.phatmofo

SWEET Ontology Phenomena Atmosphere
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
keyword: atmosphere
0000005: AirMass
has provider formatter: http://sweetontology.net/phenAtmo/$1
is deprecated: false
has alternative prefix: sophatmo
has URI prefix: http://sweetontology.net/phenAtmo/
0000027: AirMass
0000029: sweet.phatmo

ModelDB concept
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models.
is part of: bioregistry
0000005: 3639
has provider formatter: https://modeldb.science/modellist/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://modeldb.science/modellist/
0000027: https://modeldb.science/modellist/3639
0000029: modeldb.concept

Golm Metabolome Database
type: Resource
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.
is part of: bioregistry
keyword: metabolomics
keyword: life science
has provider formatter: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx
has local unique identifier pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
is deprecated: false
has responsible: Joachim Kopka
has URI prefix: https://bioregistry.io/gmd:
0000029: gmd

Jackson Laboratories Mouse Strain
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A catalogue of mouse strains supplied by The Jackson Laboratory. Each identifier corresponds to a mouse strain.
is part of: bioregistry
keyword: repository
keyword: genetic engineering
keyword: gene
keyword: subject
keyword: research
keyword: knockout
keyword: life science
keyword: supply
keyword: model
keyword: strain
keyword: mouse
keyword: mice
0000005: 004435
has provider formatter: https://www.jax.org/strain/$1
has local unique identifier pattern: ^\d{6}$
is deprecated: false
has alternative prefix: jaxMiceUID
has alternative prefix: jax
has URI prefix: https://www.jax.org/strain/
0000027: https://www.jax.org/strain/004435
0000029: jaxmice

SWEET Ontology Property Fraction
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Fraction
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: fraction
0000005: Absorptance
has provider formatter: http://sweetontology.net/propFraction/$1
is deprecated: false
has alternative prefix: sopropfr
has URI prefix: http://sweetontology.net/propFraction/
0000027: Absorptance
0000029: sweet.propfr

NMRShiftDB structure
type: Resource
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.
is part of: bioregistry
keyword: analytical chemistry
0000005: 234
has provider formatter: https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5990-4157
has alternative prefix: NMRShiftDB
has URI prefix: https://nmrshiftdb.nmr.uni-koeln.de/molecule/
0000027: https://nmrshiftdb.nmr.uni-koeln.de/molecule/234
0000029: nmrshiftdb2

Energy Market Roles ontology
type: Resource
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 part of: bioregistry
keyword: nfdi4energy
has provider formatter: http://www.purl.org/dabgeo/conceptual/energymarketroles#$1
is deprecated: false
has URI prefix: http://www.purl.org/dabgeo/conceptual/energymarketroles#
0000029: energymarketroles

Mouse pathology ontology
type: Resource
description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes
is part of: bioregistry
git repository: mpath
keyword: biomedical science
keyword: anatomy
keyword: mutation
keyword: histological assay
keyword: obo
keyword: ontology
keyword: strain
keyword: mouse
keyword: disease
keyword: phenotype
0000005: 728
has provider formatter: http://purl.obolibrary.org/obo/MPATH_$1
has local unique identifier pattern: ^\d+$
0000010: mpath.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-5111-7263
has alternative prefix: MPATH
has URI prefix: http://purl.obolibrary.org/obo/MPATH_
0000027: MPATH 728
0000029: mpath

SpBase
type: Resource
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.
is part of: bioregistry
keyword: rna
keyword: genome
keyword: dna
0000005: SPU_000001
has provider formatter: http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php
0000027: http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php
0000029: spbase

Snapshot
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
0000005: Quality
has provider formatter: http://www.ifomis.org/bfo/1.1/snap#$1
is deprecated: false
has alternative prefix: bfo11snap
has URI prefix: http://www.ifomis.org/bfo/1.1/snap#
0000027: Quality
0000029: snap

Japan Consortium for Glycobiology and Glycotechnology Database
type: Resource
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.
is part of: bioregistry
0000005: JCGG-STR008690
has provider formatter: http://jcggdb.jp/idb/jcggdb/$1
has local unique identifier pattern: ^JCGG-STR\d{6}$
is deprecated: true
has URI prefix: http://jcggdb.jp/idb/jcggdb/
0000027: JCGG-STR008690
0000029: jcggdb

Chromosome Ontology
type: Resource
contributor: https://orcid.org/0000-0001-5705-7831
description: The Chromosome Ontology is an automatically derived ontology of chromosomes and chromosome parts.
is part of: bioregistry
git repository: monochrom
keyword: ontology
0000005: 10090-chr10qC
has provider formatter: http://purl.obolibrary.org/obo/CHR_$1
0000010: chr.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://purl.obolibrary.org/obo/CHR_
0000027: CHR 10090-chr10qC
0000029: chr

Human Protein Complex Map
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The hu.MAP integrates several large scale protein interaction datasets to obtain a comprehensive view of protein complexes.
is part of: bioregistry
0000005: huMAP3_04143.1
has provider formatter: https://humap3.proteincomplexes.org/displayComplexes
is deprecated: false
has responsible: Kevin Drew
has alternative prefix: humap3
has URI prefix: https://humap3.proteincomplexes.org/displayComplexes
0000027: https://humap3.proteincomplexes.org/displayComplexes
0000029: humap

Insect Cell Line Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
0000005: 64ba
has provider formatter: https://entomology.ca.uky.edu/content/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-2212-4771
has URI prefix: https://entomology.ca.uky.edu/content/
0000027: 64ba
0000029: icldb

Roger Hyam

Human Dephosphorylation Database
type: Resource
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.
is part of: bioregistry
keyword: life science
0000005: PTPN1
has provider formatter: http://www.depod.bioss.uni-freiburg.de/showp.php
has local unique identifier pattern: ^[A-Z0-9]+$
0000011: hgnc.symbol
is deprecated: false
has responsible: https://orcid.org/0000-0003-3562-7869
has URI prefix: http://www.depod.bioss.uni-freiburg.de/showp.php
0000027: http://www.depod.bioss.uni-freiburg.de/showp.php
0000029: depod

Reaxys
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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 part of: bioregistry
0000005: 1257009
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: Beilstein
has alternative prefix: Reaxys
0000029: reaxys

Oryzabase Strain
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 wild strain information.
is part of: bioregistry
0000005: 1
has provider formatter: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/
0000027: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/1
0000029: oryzabase.strain

SWEET Ontology Relationships Human
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Human
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: human
0000005: hasAttribute
has provider formatter: http://sweetontology.net/relaHuman/$1
is deprecated: false
has alternative prefix: sorelh
has URI prefix: http://sweetontology.net/relaHuman/
0000027: hasAttribute
0000029: sweet.relh

Online Mendelian Inheritance in Animals
type: Resource
contributor: https://orcid.org/0000-0002-5520-6597
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)
is part of: bioregistry
keyword: traits
keyword: gene
keyword: model organism database
keyword: classification
keyword: disorders
0000005: 001000
has provider formatter: https://omia.org/phene/omia:$1
has local unique identifier pattern: ^\d{6}(-\d+)?$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5520-6597
has alternative prefix: OMIA
has URI prefix: https://omia.org/phene/omia:
0000027: omia:001000
0000029: omia

SWEET Ontology Phenomena Atmosphere Precipitation
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Precipitation
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: atmosphere precipitation
keyword: phenomena
0000005: AtmosphericPrecipitation
has provider formatter: http://sweetontology.net/phenAtmoPrecipitation/$1
is deprecated: false
has alternative prefix: sophatmopc
has URI prefix: http://sweetontology.net/phenAtmoPrecipitation/
0000027: AtmosphericPrecipitation
0000029: sweet.phatmopc

Vital Sign Ontology
type: Resource
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.
is part of: bioregistry
keyword: ontology
keyword: blood
keyword: owl
keyword: biomedical science
keyword: experimental measurement
keyword: health science
keyword: health
0000005: 0000041
has provider formatter: https://bioportal.bioontology.org/ontologies/VSO/
has local unique identifier pattern: ^\d{7}$
0000010: vso.owl
is deprecated: false
has responsible: Albert Goldfain
has URI prefix: https://bioportal.bioontology.org/ontologies/VSO/
0000027: https://bioportal.bioontology.org/ontologies/VSO/
0000029: vso

United States Department of Agriculture Veterinary Biological Product Code Number
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
keyword: vaccine
keyword: diagnostic product
keyword: bacterin
keyword: toxoid
keyword: bacterin-toxoid
keyword: antitoxin
0000005: 1011.00
has local unique identifier pattern: ^[A-Z0-9]{4}\.[A-Z0-9]{2}$
is deprecated: false
0000018: Vaccine Ontology
0000026: 0599wfz09
0000029: usda.cvb.pcn

Disease Drivers Ontology
type: Resource
description: Drivers of human diseases including environmental, maternal and social exposures.
is part of: bioregistry
git repository: DiseaseDriversOntology
keyword: obo
keyword: ontology
0000005: 0000000
has provider formatter: http://purl.obolibrary.org/obo/DISDRIV_$1
has local unique identifier pattern: ^\d+$
0000010: disdriv.owl
is deprecated: false
has responsible: Lynn Schriml
has URI prefix: http://purl.obolibrary.org/obo/DISDRIV_
0000027: DISDRIV_0000000
0000029: disdriv

International Standard Serial Number
type: Resource
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.
is part of: bioregistry
0000005: 0745-4570
has provider formatter: https://portal.issn.org/resource/ISSN/$1
has local unique identifier pattern: ^\d{4}-\d{3}[\dX]$
is deprecated: false
has URI prefix: https://portal.issn.org/resource/ISSN/
0000027: https://portal.issn.org/resource/ISSN/0745-4570
0000029: issn

MedlinePlus Health Topics
type: Resource
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.
is part of: bioregistry
keyword: biomedical science
keyword: health science
keyword: medicine
keyword: ontology
keyword: disease
0000005: 002804
has provider formatter: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: NLM Customer Service
has URI prefix: https://bioregistry.io/medlineplus:
0000027: 002804.htm
0000029: medlineplus

Idan Gabdank

International Classification of Diseases, 9th Revision
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics.
is part of: bioregistry
0000005: 277.9
has provider formatter: http://www.icd9data.com/getICD9Code.ashx
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})$
is deprecated: false
has alternative prefix: ICD9_2005
has alternative prefix: ICD9
has alternative prefix: MTHICD9_2006
has URI prefix: http://www.icd9data.com/getICD9Code.ashx
0000027: http://www.icd9data.com/getICD9Code.ashx
0000029: icd9

Metabolic Encyclopedia for Pathway/Genome Databases
type: Resource
contributor: Harshad Hegde
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
is part of: bioregistry
0000005: 12DICHLORETHDEG-PWY
has provider formatter: https://metacyc.org/META/NEW-IMAGE
is deprecated: false
has responsible: Peter D. Karp
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://metacyc.org/META/NEW-IMAGE
0000027: https://metacyc.org/META/NEW-IMAGE
0000029: metacyc.pathway

Plant Genome Network
type: Resource
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.
is part of: bioregistry
0000005: Glyma0021s00410
has provider formatter: http://www.phytozome.net/genePage.php
has local unique identifier pattern: ^[A-Za-z0-9]+$
is deprecated: false
has alternative prefix: JGI Phytozome
has URI prefix: http://www.phytozome.net/genePage.php
0000027: http://www.phytozome.net/genePage.php
0000029: phytozome.locus

UniChem compound
type: Resource
description: identifier of a compound in the UniChem database
is part of: bioregistry
0000005: 161671
has provider formatter: https://www.ebi.ac.uk/unichem/compoundsources
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/unichem/compoundsources
0000027: https://www.ebi.ac.uk/unichem/compoundsources
0000029: unichem

Encyclopedia of Life
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A collaborative project intended to create an encyclopedia documenting all living species known to science
is part of: bioregistry
keyword: biology
keyword: taxonomy
keyword: biodiversity
keyword: ecology
0000005: 1044544
has provider formatter: https://eol.org/pages/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: EOL Secretariat
has URI prefix: https://eol.org/pages/
0000027: https://eol.org/pages/1044544
0000029: eolife

RiceNetDB Gene
type: Resource
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.
is part of: bioregistry
0000005: LOC_Os01g49190.1
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
has URI prefix: http://bis.zju.edu.cn/ricenetdb/genedetails.php
0000027: http://bis.zju.edu.cn/ricenetdb/genedetails.php
0000029: ricenetdb.gene

Intrinsically Disordered proteins with Extensive Annotations and Literature
type: Resource
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.
is part of: bioregistry
keyword: biology
0000005: IID00001
has provider formatter: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php
has local unique identifier pattern: ^IID\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5705-3061
has URI prefix: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php
0000027: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php
0000029: ideal

APID Interactomes
type: Resource
contributor: Sumir Pandit
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
0000005: P01116
has provider formatter: http://cicblade.dep.usal.es:8080/APID/Interactions.action
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+)?$
0000011: uniprot
is deprecated: false
has URI prefix: http://cicblade.dep.usal.es:8080/APID/Interactions.action
0000027: http://cicblade.dep.usal.es:8080/APID/Interactions.action
0000029: apid.interactions

Data Object Service
type: Resource
description: Assists in resolving data across cloud resources.
is part of: bioregistry
has provider formatter: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1
has local unique identifier pattern: ^[a-zA-Z0-9\-:#/\.]+$
is deprecated: false
has URI prefix: https://dataguids.org/ga4gh/dos/v1/dataobjects/
0000029: ga4ghdos

Taconic Biosciences
type: Resource
description: Supplier of mice for research purposes. [from RRID]
is part of: bioregistry
keyword: supply
keyword: model
keyword: mouse
keyword: strain
keyword: mice
keyword: transgenic
keyword: repository
keyword: genetic engineering
keyword: gene
keyword: subject
keyword: research
keyword: knockout
0000005: 1178
has provider formatter: https://scicrunch.org/resolver/RRID:IMSR_TAC_$1
is deprecated: false
has URI prefix: https://scicrunch.org/resolver/RRID:IMSR_TAC_
0000027: RRID:IMSR TAC 1178
0000029: imsr_tac

NIF Standard Ontology: Digital Resources
type: Resource
contributor: Tom Gillespie
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
is part of: bioregistry
git repository: NIF-Ontology
keyword: software and information systems
0000005: 090924
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_res_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Tom Gillespie
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXRES
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_res_
0000027: nlx res 090924
0000029: nlx.res

Livestock Breed Ontology
type: Resource
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.
is part of: bioregistry
git repository: livestock-breed-ontology
keyword: animal breeding
keyword: animal husbandry
keyword: ontology
keyword: genetics
keyword: genomics
0000005: 0000487
has provider formatter: https://bioportal.bioontology.org/ontologies/LBO/
has local unique identifier pattern: ^\d{7}$
0000010: lbo.owl
is deprecated: false
has responsible: Carissa Park
has URI prefix: https://bioportal.bioontology.org/ontologies/LBO/
0000027: https://bioportal.bioontology.org/ontologies/LBO/
0000029: lbo

Progenetix
type: Resource
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
keyword: genomics
keyword: biomedical science
0000005: pgxbs-kftva5zv
has provider formatter: https://progenetix.org/services/ids/$1
has local unique identifier pattern: ^\w{3,15}[-_]\w[\w.-]{3,128}$
is deprecated: false
has responsible: Michael Baudis
has alternative prefix: Progenetix
has URI prefix: https://progenetix.org/services/ids/
0000027: pgxbs-kftva5zv
0000029: pgx

Biolink Model Registry
type: https://bioregistry.io/schema/#0000002
description: A modeling paradigm-specific registry of prefixes and their URL expansions
has part: XPO
has part: EDAM-FORMAT
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 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
has part: CPT

Molecule role (INOH Protein name/family name ontology)
type: Resource
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.
is part of: bioregistry
keyword: obo
keyword: ontology
keyword: small molecule
keyword: protein
0000005: 0000001
has provider formatter: http://purl.obolibrary.org/obo/IMR_$1
has local unique identifier pattern: ^\d{7}$
is deprecated: true
has responsible: INOH curators
has URI prefix: http://purl.obolibrary.org/obo/IMR_
0000027: IMR_0000001
0000029: imr

Hui Wu

Data Use Ontology
type: Resource
description: DUO is an ontology which represent data use conditions.
is part of: bioregistry
git repository: DUO
keyword: nfdi4ing
keyword: biomedical science
keyword: computer science
keyword: subject agnostic
keyword: metadata standardization
keyword: ess
keyword: obo
keyword: ontology
keyword: nfdi4chem
0000005: 0000046
has provider formatter: http://purl.obolibrary.org/obo/DUO_$1
has local unique identifier pattern: ^\d{7}$
0000010: duo.owl
is deprecated: false
depends on: bfo
depends on: Information Artifact Ontology
0000018: scdo
has responsible: https://orcid.org/0000-0002-9551-6370
has URI prefix: http://purl.obolibrary.org/obo/DUO_
0000027: DUO_0000046
0000029: duo

PathoPlant®
type: Resource
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.
is part of: bioregistry
keyword: pathway
keyword: small molecule
keyword: protein
keyword: gene expression
keyword: interaction
0000005: MO000027
has provider formatter: http://www.pathoplant.de/detail.php
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.pathoplant.de/detail.php
0000027: http://www.pathoplant.de/detail.php
0000029: pathoplant

Digital Competence Framework
type: Resource
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.
is part of: bioregistry
keyword: social sciences
keyword: educational resources
keyword: literature
0000005: 00b51s9rc5
has provider formatter: http://data.europa.eu/snb/dcf/$1
is deprecated: false
has URI prefix: http://data.europa.eu/snb/dcf/
0000027: 00b51s9rc5
0000029: europa.dcf

German University Subject Classification System
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A classification of subjects in Hochschule (universities of applied sciences)
is part of: bioregistry
git repository: hochschulfaechersystematik
keyword: educational science
keyword: educational resources
0000005: n2
has provider formatter: https://w3id.org/kim/hochschulfaechersystematik/$1
is deprecated: false
has URI prefix: https://w3id.org/kim/hochschulfaechersystematik/
0000027: n2
0000029: kim.hochschulfaechersystematik

ASKEM Epidemiology Prefixes
type: https://bioregistry.io/schema/#0000003
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project.
has part: hp
has part: RDF Schema
has part: symp
has part: Data Science Ontology
has part: Digital Object Identifier
has part: Ontology of Adverse Events
has part: ovae
has part: bfo
has part: Human Disease Ontology
has part: OBO in OWL
has part: pubmed
has part: Vaccine Ontology
has part: Common Anatomy Reference Ontology
has part: PubMed Central
has part: Infectious Disease Ontology
has part: Web Ontology Language
has part: ro
has part: Pathogen Transmission Ontology

Data Science Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: datascienceontology
keyword: data science
keyword: ontology
0000005: classification-model
has provider formatter: https://www.datascienceontology.org/concept/$1
is deprecated: false
has responsible: Evan Patterson
has URI prefix: https://www.datascienceontology.org/concept/
0000027: classification-model
0000029: dso

FooDB Food
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Foods in FooDB
is part of: bioregistry
0000005: FOOD00020
has provider formatter: https://foodb.ca/foods/$1
has local unique identifier pattern: ^FOOD\d+$
is deprecated: false
has URI prefix: https://foodb.ca/foods/
0000027: FOOD00020
0000029: foodb.food

GitHub Issue
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An issue in any public repository on GitHub.
is part of: bioregistry
keyword: software engineering
keyword: version control
keyword: knowledge and information systems
keyword: project management
0000005: biopragmatics/bioregistry/424
has provider formatter: https://bioregistry.io/resolve/github/issue/$1
is deprecated: false
has URI prefix: https://bioregistry.io/resolve/github/issue/
0000027: https://bioregistry.io/resolve/github/issue/biopragmatics/bioregistry/424
0000029: github.issue

Vertebrate Skeletal Anatomy Ontology
type: Resource
description: Vertebrate skeletal anatomy ontology.
is part of: bioregistry
keyword: obo
keyword: ontology
keyword: vertebrate
keyword: anatomy
0000005: 0000183
has provider formatter: http://purl.obolibrary.org/obo/VSAO_$1
has local unique identifier pattern: ^\d{7}$
0000010: vsao.owl
is deprecated: true
has responsible: https://orcid.org/0000-0003-3162-7490
has alternative prefix: VSAO_RETIRED
has URI prefix: http://purl.obolibrary.org/obo/VSAO_
0000027: VSAO_0000183
0000029: vsao

Jennifer L Harrow

SWEET Ontology Material Facility
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Facility
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: materials
keyword: facility
0000005: AgriculturalProductionFacility
has provider formatter: http://sweetontology.net/matrFacility/$1
is deprecated: false
has alternative prefix: somaf
has URI prefix: http://sweetontology.net/matrFacility/
0000027: AgriculturalProductionFacility
0000029: sweet.maf

Ribocentre
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: Ribocentre is designed to contain comprehensive information of all natural ribozymes.
is part of: bioregistry
git repository: ribocentre.github.io
0000005: hammer
has provider formatter: https://www.ribocentre.org/docs/$1
has local unique identifier pattern: ^[a-zA-Z0-9-]+$
is deprecated: false
has responsible: 0000-0002-2121-365X
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: ribocenter
has URI prefix: https://www.ribocentre.org/docs/
0000027: hammer
0000029: ribocentre

Cellular Microscopy Phenotype Ontology
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.
is part of: bioregistry
git repository: CMPO
keyword: cellular_component
keyword: microscopy
keyword: phenotype
keyword: phenomics
keyword: cell
keyword: bioimaging
keyword: imaging
keyword: cell biology
keyword: ontology
0000005: 0000435
has provider formatter: http://www.ebi.ac.uk/cmpo/CMPO_$1
has local unique identifier pattern: ^\d{7}$
0000010: cmpo.owl
is deprecated: false
has responsible: Simon Jupp
has URI prefix: http://www.ebi.ac.uk/cmpo/CMPO_
0000027: CMPO_0000435
0000029: cmpo

Audience Types Controlled Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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.
is part of: bioregistry
git repository: AUT
keyword: audience type
keyword: person
keyword: role
0000005: 0000001
has provider formatter: http://cor.esipfed.org/ont/earthcube/AUT_$1
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4808-4736
has URI prefix: http://cor.esipfed.org/ont/earthcube/AUT_
0000027: AUT_0000001
0000029: earthcube.aut

USA National Service Center Number
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Identifier used by the Cancer Chemotherapy National Service Center.
is part of: bioregistry
0000005: 27223
has provider formatter: https://dtp.cancer.gov/dtpstandard/servlet/ChemData
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://dtp.cancer.gov/dtpstandard/servlet/ChemData
0000027: https://dtp.cancer.gov/dtpstandard/servlet/ChemData
0000029: nsc

Babelon
type: Resource
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.
is part of: bioregistry
git repository: babelon
0000005: translation_language
has provider formatter: https://w3id.org/babelon/$1
has local unique identifier pattern: ^[a-z][a-z0-9_]+[a-z0-9]$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7356-1779
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://w3id.org/babelon/
0000027: translation language
0000029: babelon

Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
type: Resource
description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology
is part of: bioregistry
git repository: DIDEO
keyword: evidence
keyword: drug interaction
keyword: biochemistry
keyword: obo
keyword: natural product
keyword: ontology
0000005: 00000180
has provider formatter: http://purl.obolibrary.org/obo/DIDEO_$1
has local unique identifier pattern: ^\d{8}$
0000010: dideo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-1834-3856
has URI prefix: http://purl.obolibrary.org/obo/DIDEO_
0000027: DIDEO_00000180
0000029: dideo

Response Unit
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Indicates the entity that provided the information carried by the variable.
is part of: bioregistry
0000005: Self
has provider formatter: https://vocabularies.cessda.eu/vocabulary/ResponseUnit#code_$1
is deprecated: false
has URI prefix: https://vocabularies.cessda.eu/vocabulary/ResponseUnit#code_
0000026: 015em2733
0000027: code Self
0000029: ddi.responseunit

ArachnoServer
type: Resource
contributor: Sumir Pandit
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.
is part of: bioregistry
keyword: life science
keyword: drug
keyword: protein
0000005: AS000060
has provider formatter: http://www.arachnoserver.org/toxincard.html
has local unique identifier pattern: ^AS\d{6}$
is deprecated: false
has responsible: Glenn King
has URI prefix: http://www.arachnoserver.org/toxincard.html
0000027: http://www.arachnoserver.org/toxincard.html
0000029: arachnoserver

Electron Microscopy Glossary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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]
is part of: bioregistry
git repository: em glossary
keyword: ontology
0000005: 00000005
has provider formatter: https://purls.helmholtz-metadaten.de/emg/EMG_$1
has local unique identifier pattern: ^\d{8}$
0000010: ontology.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-0575-2853
has URI prefix: https://purls.helmholtz-metadaten.de/emg/EMG_
0000027: EMG_00000005
0000029: emg

SWEET Ontology Phenomena Star
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Star
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: phenomena
keyword: star
0000005: Asteroseismology
has provider formatter: http://sweetontology.net/phenStar/$1
is deprecated: false
has alternative prefix: sophst
has URI prefix: http://sweetontology.net/phenStar/
0000027: Asteroseismology
0000029: sweet.phst

Data Commons
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces.
is part of: bioregistry
git repository: website
0000005: Gene
has provider formatter: https://datacommons.org/browser/$1
is deprecated: false
has alternative prefix: dcid
has URI prefix: https://datacommons.org/browser/
0000027: Gene
0000029: datacommons

INSPIRE theme register
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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)
is part of: bioregistry
0000005: mr
has provider formatter: https://inspire.ec.europa.eu/theme/$1
is deprecated: false
has URI prefix: https://inspire.ec.europa.eu/theme/
0000027: mr
0000029: inspire.theme

CEDS Learning Resource Type
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary for learning resource types
is part of: bioregistry
keyword: educational resources
keyword: open educational resources
keyword: learning materials
0000005: AlternateAssessment
has provider formatter: https://ceds.ed.gov/element/000928#$1
is deprecated: false
has URI prefix: https://ceds.ed.gov/element/000928#
0000027: AlternateAssessment
0000029: ceds.learning_resource_type

Semantic Web Applications in Neuromedicine
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: SWAN ontology consists in a collection of ontologies used to create, manage and share scientific knowledge bases.
is part of: bioregistry
git repository: swan-ontology
keyword: ontology
0000010: swan.owl
is deprecated: true
0000029: swan

Maya Schuldiner

RNA SSTRAND
type: Resource
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.
is part of: bioregistry
keyword: rna
keyword: structure
0000005: CRW_00469
has provider formatter: http://www.rnasoft.ca/sstrand/show_results.php
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.rnasoft.ca/sstrand/show_results.php
0000027: http://www.rnasoft.ca/sstrand/show_results.php
0000029: rna_sstrand

SWEET Ontology Realm Climate Zone
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Climate Zone
is part of: bioregistry
is part of: sweet
git repository: sweet
keyword: realm
keyword: climate zone
0000005: A
has provider formatter: http://sweetontology.net/realmClimateZone/$1
is deprecated: false
has alternative prefix: soreacz
has URI prefix: http://sweetontology.net/realmClimateZone/
0000027: http://sweetontology.net/realmClimateZone/A
0000029: sweet.reacz

PomBase
type: Resource
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.
is part of: bioregistry
keyword: ontology
keyword: life science
0000005: SPCC13B11.01
has provider formatter: https://www.pombase.org/gene/$1
has local unique identifier pattern: ^S\w+(\.)?\w+(\.)?$
0000010: pombase.owl
is deprecated: false
has responsible: Valerie Wood
has alternative prefix: PomBase
has URI prefix: https://www.pombase.org/gene/
0000027: SPCC13B11.01
0000029: pombase

Vernon Putz-Anderson

FINDEX Raum
type: Resource
description: SKOS-Modellierung des Thesaurus FINDEX Raum des Fraunhofer-Informationszentrums Raum und Bau IRB
is part of: bioregistry
keyword: civil engineering
keyword: digital planning and construction
keyword: fid baudigital
keyword: earth sciences
keyword: nfdi4ing
0000005: R00000000000_3
has provider formatter: https://terminology.fraunhofer.de/voc/raum#$1
is deprecated: false
has URI prefix: https://terminology.fraunhofer.de/voc/raum#
0000027: R00000000000 3
0000029: findex.raum