Resource
type: Class
description: A type for entries in the Bioregistry's registry.

Registry
type: Class
description: A type for entries in the Bioregistry's metaregistry.

Collection
type: Class
description: A type for entries in the Bioregistry's collections

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

Organization
type: Class
description: An organization

Semantic Web Context
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: Resources used in the semantic web, drawing from lists in [BioContext](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) and [LinkML](https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/data/linked_data.curated.yaml) as well as W3C recommendations.
has part: ac
has part: bibo
has part: dc
has part: dcat
has part: dcterms
has part: dctypes
has part: doap
has part: faldo
has part: foaf
has part: idot
has part: oa
has part: oboinowl
has part: oslc
has part: owl
has part: pav
has part: prov
has part: qb
has part: qudt
has part: https://bioregistry.io/registry/rdf
has part: rdfs
has part: schema
has part: sh
has part: shex
has part: skos
has part: skosxl
has part: swrl
has part: vann
has part: void
has part: xsd

ChEBI Data Sources
type: Collection
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: chebi
has part: chemidplus
has part: come
has part: drugbank
has part: ecmdb
has part: eurofir
has part: google.patent
has part: hmdb
has part: kegg.compound
has part: kegg.drug
has part: kegg.glycan
has part: knapsack
has part: lincs.smallmolecule
has part: lipidmaps
has part: metacyc.compound
has part: molbase.sheffield
has part: pdb
has part: pdb-ccd
has part: pesticides
has part: resid
has part: smid
has part: umbbd.compound
has part: webelements
has part: ymdb

International Classifications of Diseases
type: Collection
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: icd10
has part: icd10cm
has part: icd10pcs
has part: icd11
has part: icd11.code
has part: icd9
has part: icd9cm
has part: icdo

Allen Institute Ontologies
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: This collection contains various brain atlases from the Allen Institute.
has part: dhba
has part: dmba
has part: hba
has part: mba
has part: pba

SPAR Ontologies
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF.
has part: bido
has part: biro
has part: c4o
has part: cito
has part: datacite
has part: deo
has part: doco
has part: fabio
has part: frapo
has part: mito
has part: pso
has part: puro
has part: pwo
has part: scoro

Publication Provenance Prefixes
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes useful in annotating documentation provenance.
has part: arxiv
has part: doi
has part: pmc
has part: pubmed

ASKEM Epidemiology Prefixes
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project.
has part: bfo
has part: caro
has part: doi
has part: doid
has part: dso
has part: hp
has part: ido
has part: oae
has part: oboinowl
has part: ovae
has part: owl
has part: pmc
has part: pubmed
has part: rdfs
has part: ro
has part: symp
has part: trans
has part: vo

FHIR External Terminologies
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes mentioned on the _external_ list on the FHIR [Code Systems](https://hl7.org/fhir/terminologies-systems.html) page. This list is mostly complete. Notably, some entries that have not been curated: - HGVS (see discussion at [#460](https://github.com/biopragmatics/bioregistry/issues/460)) - [NUBC](http://www.nubc.org) (National Uniform Billing Committee) - could not find information about the terminology or its entries - [ICPC](http://www.ph3c.org/) (International Classification of Primary Care) _same_ - [GTIN](https://www.gs1.org/standards/id-keys/gtin) (Global Trade Item Number) _same_ - [MDC](https://www.iso.org/standard/37890.html) (Medical Device Codes) since that appears to be part of a larger ISO standard vocabulary that needs further investigation
has part: atcc
has part: clinicaltrials
has part: clinvar.variation
has part: cosmic.gene
has part: cpt
has part: cvx
has part: dbsnp
has part: dicom
has part: dsm5
has part: ensembl
has part: hc.din
has part: hc.npn
has part: hgnc
has part: hl7.v2codesystem
has part: hl7.v3codesystem
has part: icd10
has part: icd9
has part: icf
has part: ietf.language
has part: imgt.hla
has part: iso.3166
has part: loinc
has part: lrg
has part: ncit
has part: ndc
has part: ndfrt
has part: nucc.taxonomy
has part: omim
has part: pharmgkb.gene
has part: pubmed
has part: radlex
has part: refseq
has part: rxnorm
has part: snomedct
has part: so
has part: ucum
has part: unii

Global Biodata Coalition - Global Core Biodata Resources
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: The [Global Biodata Coalition](https://globalbiodata.org) released a [curated list](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/) of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria [here](https://doi.org/10.5281/zenodo.5845116)). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). Among the databases that don't induce semantic spaces or have simple relationships to prefixes are: - [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.) - [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC) - [GENCODE](https://www.gencodegenes.org/) (uses GenBank) - [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc) - [STRING](https://string-db.org/) (uses UniProt)
has part: agrkb
has part: bacdive
has part: brenda
has part: brenda.ligand
has part: brenda.ligandgroup
has part: bto
has part: chebi
has part: chembl
has part: civic.aid
has part: civic.did
has part: civic.eid
has part: civic.gid
has part: civic.sid
has part: civic.tid
has part: civic.vid
has part: ecocyc
has part: ena.embl
has part: ensembl
has part: eupath
has part: flybase
has part: gbif
has part: gnomad
has part: go
has part: hgnc
has part: interpro
has part: mgi
has part: orpha
has part: orphanet.ordo
has part: panther.family
has part: panther.node
has part: panther.pathway
has part: panther.pthcmp
has part: pdb
has part: pharmgkb.disease
has part: pharmgkb.drug
has part: pharmgkb.gene
has part: pharmgkb.pathways
has part: pmc
has part: pombase
has part: px
has part: reactome
has part: rgd
has part: rhea
has part: sgd
has part: ucsc
has part: uniprot
has part: wormbase
has part: zfin

NDFI4Cat Collection
type: Collection
creator: Hendrik Borgelt
creator: https://orcid.org/0000-0003-4423-4370
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: afo
has part: bao
has part: bfo
has part: cao
has part: chebi
has part: cheminf
has part: chmo
has part: dolce
has part: edam
has part: emmo
has part: emmo.cif
has part: envo
has part: iso15926
has part: m4i
has part: mop
has part: ms
has part: nfdi4chem.ontocape
has part: nfdi4chem.osmo
has part: obi
has part: om
has part: rex
has part: rxno
has part: sbo
has part: voc4cat
has part: worldavatar.compchem
has part: worldavatar.kin

Clinical Trial Registries
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of clinical trial registries appearing in the World Health Organization's [International Clinical Trials Registry Platform (ICTRP)](https://trialsearch.who.int/)
has part: anzctr
has part: chictr
has part: clinicaltrials
has part: ctis
has part: ctri
has part: drks
has part: euclinicaltrials
has part: hc.trial
has part: irct
has part: isrctn
has part: itmctr
has part: jrct
has part: kcris
has part: lbctr
has part: pactr
has part: phrr
has part: rebec
has part: repec
has part: rpcec
has part: slctr
has part: snctp
has part: tctr
has part: uminctr

Software Package Repositories
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: These resources represent software repositories
has part: cran
has part: crates
has part: npm
has part: packagist
has part: pypi
has part: rubygems

NFDI4Chem Collection
type: Collection
creator: https://orcid.org/0000-0002-1595-3213
description: A collection of ontologies relevant within the [NFDI4Chem project](https://www.nfdi4chem.de/) that is mostly based on the overview paper [Ontologies4Chem: the landscape of ontologies in chemistry](https://doi.org/10.1515/pac-2021-2007). NFDI4Chem deploys a [custom instance](https://terminology.nfdi4chem.de/ts/) of the Ontology Lookup Service (OLS), called NFDI4Chem Terminology Services (TS), that provides the ontologies in this list. This list contains ontologies that cover various domains of chemistry (e.g. ChEBI, CHMO, and RXNO), those that are dependencies of these chemistry specific ontologies (e.g. BFO, RO, IAO, and OBI) as well as those ontologies, which where indexed in the NFDI4Chem TS for interoperability research purposes (e.g. PROV-O, SOSA, and OBOE).
has part: afo
has part: bfo
has part: bto
has part: chebi
has part: cheminf
has part: chemrof
has part: chiro
has part: chmo
has part: duo
has part: edam
has part: efo
has part: enm
has part: envo
has part: fair
has part: fix
has part: gainesville.core
has part: iao
has part: mod
has part: mop
has part: ms
has part: ncit
has part: nmr
has part: obi
has part: oboe
has part: om
has part: ontorxn
has part: pato
has part: proco
has part: prov
has part: reproduceme
has part: rex
has part: ro
has part: rxno
has part: sepio
has part: sio
has part: sosa
has part: ssn
has part: ssn.system
has part: suprabank.additive
has part: suprabank.buffer
has part: suprabank.interaction
has part: suprabank.molecule
has part: suprabank.solvent
has part: swo
has part: time
has part: uo
has part: vibso
has part: voc4cat
has part: worldavatar.compchem
has part: worldavatar.kin
has part: worldavatar.os

Biocuration Conference 2025 Collection
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of resources added during Biocuration 2025 in Kansas City, MO, USA.
has part: antifam
has part: biomarkerkb.biomarker
has part: biomarkerkb.canonical
has part: blastrule
has part: emi
has part: endlessforms.collection
has part: endlessforms.element
has part: endlessforms.graphic
has part: endlessforms.image
has part: endlessforms.library
has part: endlessforms.unit
has part: gdo

Synapse.org external links
type: Collection
creator: https://orcid.org/0000-0003-3573-3565
description: A curated list by Sage Bionetworks of external resources that are automatically linked on Synapse.org and affiliated data portals
has part: ado
has part: agrkb
has part: anzctr
has part: arrayexpress
has part: arxiv
has part: atc
has part: atcc
has part: bacdive
has part: bfo
has part: bgee.gene
has part: biocyc
has part: biogrid
has part: bioportal
has part: bioproject
has part: biorxiv
has part: biosample
has part: biostudies
has part: bmrb.entry
has part: brenda
has part: brenda.ligand
has part: brenda.ligandgroup
has part: bto
has part: cath
has part: cbioportal
has part: cdd
has part: cellimage
has part: cellxgene.collection
has part: chebi
has part: chembl
has part: chembl.compound
has part: chemspider
has part: civic.aid
has part: civic.did
has part: civic.eid
has part: civic.gid
has part: civic.sid
has part: civic.tid
has part: civic.vid
has part: clinicaltrials
has part: clinvar.record
has part: clinvar.variation
has part: complexportal
has part: cosmic.cell
has part: cosmic.gene
has part: cpt
has part: ctd.chemical
has part: ctri
has part: cvx
has part: dbgap
has part: dbsnp
has part: decipher
has part: depmap
has part: dhba
has part: disprot
has part: dmba
has part: doi
has part: doid
has part: drks
has part: drugbank
has part: drugcentral
has part: duo
has part: ec
has part: ecacc
has part: edam
has part: ega.dataset
has part: ega.study
has part: emdb
has part: empiar
has part: ena.embl
has part: ensembl
has part: ensembl.metazoa
has part: ensembl.plant
has part: euclinicaltrials
has part: eupath
has part: exac.variant
has part: fairsharing

DALIA Resources
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes relevant for the [Data Literacy Alliance (DALIA)](https://dalia.education/en) project
has part: ans.educationlevel
has part: bibframe
has part: bibo
has part: bmbf.glossary
has part: ceds.element
has part: citedcat
has part: codata.rdmt
has part: dai.thesauri
has part: datacite
has part: dbpedia.resource
has part: dcterms
has part: emmo
has part: fabio
has part: iana.mediatype
has part: isced1997
has part: isced2011
has part: loc.fdd
has part: m4i
has part: marc21
has part: modalia
has part: nfdi4dso
has part: owl
has part: prov
has part: sage.socialsciencethesaurus
has part: schema
has part: sio
has part: spdx
has part: spdx.term
has part: t4fs
has part: unesco.thesaurus
has part: wdrs
has part: wikidata

Resources for modeling Open Educational Resources
type: Collection
creator: 0000-0001-5556-838X
creator: https://orcid.org/0000-0003-4423-4370
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: adcad
has part: ans.educationlevel
has part: ccso
has part: ceds.learning resource type
has part: edam
has part: gsso
has part: iana.mediatype
has part: isced1997
has part: isced2011
has part: isced2013
has part: kim.amb
has part: kim.conditionsofaccess
has part: kim.educationlevel
has part: kim.esv
has part: kim.hcrt
has part: kim.hochschulfaechersystematik
has part: kim.lp
has part: kim.schularten
has part: kim.schulfaecher
has part: loc.fdd
has part: lrmi
has part: lrmi.alignmenttype
has part: lrmi.educationalaudiencerole
has part: lrmi.eduse
has part: lrmi.interact
has part: lrmi.resourcetype
has part: modalia
has part: oeh.educationlevel
has part: oerschema
has part: openeduhub.context
has part: schema
has part: t4fs
has part: unesco.thesaurus
has part: vivo

Digital Humanities
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes relevant for the digital humanities
has part: cidoc.crm
has part: edm
has part: getty.att
has part: getty.cona
has part: getty.gvp
has part: getty.ia
has part: getty.tgn
has part: getty.ulan
has part: iconclass

KonsortSWD
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: [KonsortSWD (Strengthen, Widen, Deepen)](https://www.nfdi.de/consortia-konsortswd) is the German National Data Infrastructure (NFDI) consortium for social, educational, behavioral, and economic sciences. This collection reflects the prefixes collected by NFDI Section Metadata for ontologies and controlled vocabularies used by members of the consortium.
has part: cessda
has part: cessda.cdcpublishernames
has part: cessda.cessdadatacataloguecollections
has part: cessda.cessdapersistentidentifiertypes
has part: cessda.countrynamesandcodes
has part: cessda.topicclassification
has part: ddi.aggregationmethod
has part: ddi.analysisunit
has part: ddi.characterset
has part: ddi.commonalitytype
has part: ddi.contributorrole
has part: ddi.datasourcetype
has part: ddi.datatype
has part: ddi.datetype
has part: ddi.generaldataformat
has part: ddi.languageproficiency
has part: ddi.lifecycleeventtype
has part: ddi.modeofcollection
has part: ddi.numerictype
has part: ddi.responseunit
has part: ddi.samplingprocedure
has part: ddi.softwarepackage
has part: ddi.summarystatistictype
has part: ddi.timemethod
has part: ddi.timezone
has part: ddi.typeofaddress
has part: ddi.typeofconceptgroup
has part: ddi.typeoffrequency
has part: ddi.typeofinstrument
has part: ddi.typeofnote
has part: ddi.typeoftelephone
has part: ddi.typeoftranslationmethod
has part: gesis.kategorienschemawahlstudien
has part: gesis.rexconcepts
has part: gesis.rexdatatype
has part: gesis.rexgroups
has part: gesis.variables-relations

NFDI4Energy Resources
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes for ontologies relevant for the NFDI4Energy
has part: bonsai
has part: brick
has part: digitalconstruction.energy
has part: dogont
has part: energymarketroles
has part: meno
has part: oeo
has part: openadr
has part: saref.ener
has part: saref.grid
has part: sargon
has part: tib.re
has part: udsaes.fmi
has part: udsaes.sms
has part: zbw.stw

NFDI4Ing Resources
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes for ontologies relevant for the NFDI4Ing
has part: afo
has part: atomistic
has part: battinfo
has part: bfo
has part: bonsai
has part: bot
has part: brick
has part: building
has part: cc
has part: commoncoreontology
has part: condo
has part: cora
has part: credit
has part: dcterms
has part: dfg.fo
has part: digitalconstruction.energy
has part: digitalconstruction.lifecycle
has part: digitalconstruction.occupancy
has part: dogont
has part: dpvocab
has part: duo
has part: edam
has part: emmo
has part: fair
has part: fidbaudigital.subject
has part: fiesta.iot
has part: findex.bau
has part: findex.raum
has part: ftonto
has part: geosparql
has part: gist
has part: iao
has part: idsa
has part: iirds.core
has part: iirds.mch
has part: iirds.sft
has part: infosecsos
has part: iofcore
has part: kdsf.ffk
has part: kit.mtxx
has part: kpio
has part: listdb.onto
has part: m4i
has part: mathmoddb
has part: mobivoc
has part: modsci
has part: oeo
has part: okn.sd
has part: om
has part: panet
has part: physh
has part: pmdco
has part: polymat
has part: prov
has part: rosetta
has part: saref
has part: saref.auto
has part: saref.building
has part: saref.ehaw
has part: saref.ener
has part: saref.environment
has part: saref.industry
has part: saref.lift
has part: saref.system
has part: saref.water
has part: saref.wearable
has part: sepio
has part: sh
has part: sio
has part: sosa
has part: ssn
has part: ssn.system
has part: sweet
has part: swo
has part: t4fs
has part: tib.bk

DataPLANT Resources
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes for ontologies relevant for the DataPLANT (i.e. the NFDI consortium for plants)
has part: agro
has part: bao
has part: bco
has part: bfo
has part: bto
has part: chebi
has part: chmo
has part: cob
has part: dpbo
has part: edam
has part: efo
has part: envo
has part: flopo
has part: go
has part: mmo
has part: mod
has part: ms
has part: msio
has part: ncit
has part: obi
has part: omp
has part: pato
has part: pco
has part: peco
has part: po
has part: ppeo
has part: ppo
has part: pso
has part: ro
has part: stato
has part: swo
has part: to
has part: uberon
has part: uo

FAIRmat Resources
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes for ontologies relevant for [FAIRmat](https://www.nfdi.de/consortia-fairmat).
has part: bfo
has part: nexus
has part: tfsco
has part: voc4cat

NFDI4Culture Resources
type: Collection
creator: https://orcid.org/0000-0002-0006-7542
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes for ontologies relevant for NFDI4Culture.
has part: bot
has part: cidoc.crm
has part: gesah
has part: iconclass
has part: nfdi4culture.cto
has part: premis

DAPHNE4NFDI Resources
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: Prefixes for ontologies relevant for DAPHNE4NFDI.
has part: emg

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

BERD@NFDI Collection
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for BERD@NFDI
has part: bioregistry

NFDI4DataScience Collection
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4DataScience
has part: bioregistry

NFDI4Earth Collection
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Earth
has part: bioregistry

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

PUNCH4NFDI Collection
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for PUNCH4NFDI
has part: bioregistry

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

NFDI4BIOIMAGE Collection
type: Collection
creator: Damien Goutte-Gattat
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4BIOIMAGE
has part: bioregistry
has part: chebi
has part: cl
has part: clo
has part: cmpo
has part: dicom
has part: doid
has part: edam
has part: efo
has part: fbbi
has part: go
has part: mesh
has part: mondo
has part: mp
has part: mpath
has part: ncbitaxon
has part: obi
has part: radlex
has part: snomedct
has part: swo
has part: uberon
has part: uo

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

NFDI4Objects Collection
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Objects
has part: bioregistry

NFDI4Memory Collection
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Memory
has part: bioregistry

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

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

NFDI4Biodiversity Collection
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Biodiversity
has part: bioregistry

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

NFDI4Microbiota Collection
type: Collection
creator: https://orcid.org/0000-0003-4423-4370
description: A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Microbiota
has part: bioregistry

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

Prefix.cc
type: Registry
description: A web-developer centric archive of prefixes and URI prefixes
has local unique identifier example: foaf
has provider formatter: https://prefix.cc/$1
has responsible: https://orcid.org/0000-0001-9950-5209

has local unique identifier example
type: Property
description: An identifier for a resource or metaresource.
domain: Resource
range: string
equivalent property: exampleIdentifier
equivalent property: example
equivalent property: idExample

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

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: Registry
range: string

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

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

provides for
type: Property
description: For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource.
domain: Resource
range: Resource

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

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

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

appears in
type: Property
description: Terms from the source appear in the target resource
domain: Resource
range: Resource

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

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

has responsible
type: Property
description: The main contact person for a registry
domain: Registry
range: Person

has alternative prefix
type: Property
description: An alternative or synonymous prefix
domain: Resource
range: string
sub property of: hasExactSynonym
equivalent property: alternatePrefix

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: preferredNamespaceUri
equivalent property: uriSpace
equivalent property: namespace

has identifier space owner
type: Property
description: An organization
domain: Resource
range: Organization

has resource example
type: Property
description: An expanded example URL for a resource or metaresource.
domain: Resource
range: string
equivalent property: exampleResource

has URI pattern
type: Property
description: The pattern for expanded URIs in the given resource
domain: Resource
range: string
equivalent property: accessIdentifierPattern
equivalent property: uriRegexPattern
equivalent property: P8966

has prefix
type: Property
description: has canonical prefix
domain: Resource
range: string
equivalent property: preferredPrefix
equivalent property: preferredNamespacePrefix
equivalent property: systemCode
equivalent property: prefix

Resources mentioned in "Sharing biological data: why, when, and how"
type: Collection
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: biostudies
has part: bmrb.entry
has part: cellimage
has part: ega.dataset
has part: ega.study
has part: emdb
has part: empiar
has part: genbank
has part: geo
has part: idr
has part: insdc.sra
has part: massive
has part: panorama
has part: pdb
has part: peptideatlas.dataset
has part: pride
has part: ssbd.dataset
has part: ssbd.project

3D Metabolites
type: Resource
description: 3DMET is a database collecting three-dimensional structures of natural metabolites.
is part of: bioregistry
keyword: chemical
keyword: life science
keyword: metabolite
keyword: metabolomics
keyword: structure
has local unique identifier example: B00162
has provider formatter: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php
has local unique identifier pattern: ^B\d{5}$
is deprecated: true
has alternative prefix: 3dmet
has URI prefix: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php
has resource example: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php
has prefix: _3dmet

4D Nucleome Data Portal Biosource
type: Resource
description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases.
is part of: bioregistry
keyword: dna
keyword: life science
keyword: protein
has local unique identifier example: 4DNSR73BT2A2
has provider formatter: https://data.4dnucleome.org/biosources/$1
has local unique identifier pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$
is deprecated: false
has responsible: Job Dekker
has alternative prefix: 4DN
has alternative prefix: 4dn.biosource
has URI prefix: https://data.4dnucleome.org/biosources/
has resource example: 4DNSR73BT2A2
has prefix: _4dn.biosource

4D Nucleome Data Portal Experiment Replicate
type: Resource
contributor: José Victorino Ruiz Lavida
contributor: 0000-0002-5798-662X
contributor: Minerva María Romero Pérez
contributor: https://orcid.org/0000-0003-4423-4370
description: Database portal containing replicate experiments of different assays and samples
is part of: bioregistry
has local unique identifier example: 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/
has resource example: 4DNESWX1J3QU
has prefix: _4dn.replicate

Antibody-Antigen Complex Database
type: Resource
contributor: https://orcid.org/0009-0009-3402-8013
description: Identifiers represent antibody-antigen complexes in the Antigen-Antibody Complex Database (AACDB), which provides comprehensive structural and functional annotations including paratope and epitope information, antibody developability data, and antigen-drug target relationships to support immunoinformatics research and therapeutic antibody development.
is part of: bioregistry
keyword: antibody
keyword: antigen
keyword: molecular biophysics
keyword: structural biology
has local unique identifier example: 61
has provider formatter: https://i.uestc.edu.cn/AACDB/details.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Jian Huang
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://i.uestc.edu.cn/AACDB/details.php
has resource example: https://i.uestc.edu.cn/AACDB/details.php
has prefix: aacdb

AAindex
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
description: Identifier of an entry from the AAindex database.
is part of: bioregistry
keyword: protein
has local unique identifier example: BUNA790102
has provider formatter: http://www.genome.jp/dbget-bin/www_bget
is deprecated: false
has responsible: https://orcid.org/0000-0001-7883-3756
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.genome.jp/dbget-bin/www_bget
has resource example: http://www.genome.jp/dbget-bin/www_bget
has prefix: aaindex

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
has local unique identifier example: 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_
has resource example: AAO_0000138
has prefix: aao

Abcam
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
contributor: https://orcid.org/0000-0003-4423-4370
description: Vendor for assays, cells, and antibodies
is part of: bioregistry
has local unique identifier example: ab275461
has provider formatter: https://www.abcam.com/$1.html
is deprecated: false
has URI prefix: https://bioregistry.io/abcam:
has resource example: ab275461.html
has prefix: abcam

AntiBodies Chemically Defined database
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
contributor: https://orcid.org/0000-0003-4423-4370
description: The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies
is part of: bioregistry
keyword: immunology
keyword: molecular biology
has local unique identifier example: 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_
has resource example: ABCD AD834
has prefix: abcd

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
has local unique identifier example: T0599
has provider formatter: https://www.abmgood.com/search
is deprecated: false
has URI prefix: https://www.abmgood.com/search
has resource example: https://www.abmgood.com/search
has prefix: abm

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

AntiBody Sequence Database
type: Resource
contributor: 0009-0008-8406-631X
description: The AntiBody Sequence Database is a public dataset for antibody sequence data. It provides unique identifiers for antibody sequences, including both immunoglobulin and single-chain variable fragment sequences. These are are critical for immunological studies, and allows users to search and retrieve antibody sequences based on sequence similarity and specificity, and other biological properties.
is part of: bioregistry
has provider formatter: https://absd.pasteur.cloud/antibody/$1
has local unique identifier pattern: ^[a-f0-9]{64}$
is deprecated: false
has responsible: Nicolas Maillet
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://absd.pasteur.cloud/antibody/
has prefix: absd

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
has local unique identifier example: 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/
has resource example: Animation
has prefix: ac.subtype

Audubon Core Variant Controlled Vocabulary
type: Resource
description: Audubon Core uses the terms ac:variant and ac:variantLiteral to provide information about the size, extent, and availability of the Service Access Point of a media item. This controlled vocabulary provides values for those terms.
is part of: bioregistry
keyword: fair data spaces
keyword: life sciences, biology
has local unique identifier example: v001
is deprecated: false
has responsible: Steve Baskauf
has prefix: ac.variant

Aceview Worm
type: Resource
description: AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression.
is part of: bioregistry
keyword: dna
keyword: gene
keyword: rna
has local unique identifier example: aap-1
has provider formatter: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi
has local unique identifier pattern: ^[a-z0-9-]+$
is deprecated: false
has responsible: Danielle Thierry-Mieg
has URI prefix: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi
has resource example: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi
has prefix: aceview.worm

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
has local unique identifier example: 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#
has resource example: Access
has prefix: acl

AddexBio cell line products
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: C0020004/4992
has provider formatter: https://www.addexbio.com/productdetail
is deprecated: false
has URI prefix: https://www.addexbio.com/productdetail
has resource example: https://www.addexbio.com/productdetail
has prefix: addexbio

Addgene Plasmid Repository
type: Resource
description: Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world.
is part of: bioregistry
keyword: bio.tools
keyword: faseb list
keyword: life science
keyword: molecular biology
keyword: plasmid
keyword: repository
keyword: sequence alignment
has local unique identifier example: 50943
has provider formatter: http://addgene.org/$1
has local unique identifier pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$
is deprecated: false
has responsible: Joanne Kamens
has URI prefix: http://addgene.org/
has resource example: http://addgene.org/50943
has prefix: addgene

Addiction Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Addiction Ontology (AddictO) is an ontology being developed all aspects of addiction research.
is part of: bioregistry
git repository: addiction-ontology
keyword: ontology
has local unique identifier example: 0000447
has provider formatter: http://addictovocab.org/ADDICTO_$1
has download URL: addicto.owl
is deprecated: false
has responsible: Robert J. West
has URI prefix: http://addictovocab.org/ADDICTO_
has resource example: ADDICTO_0000447
has prefix: addicto

Asset Description Metadata Schema Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies).
is part of: bioregistry
git repository: ADMS
keyword: metadata
has local unique identifier example: Asset
has provider formatter: http://www.w3.org/ns/adms#$1
is deprecated: false
has responsible: Bert Van Nuffelen
has URI prefix: http://www.w3.org/ns/adms#
has resource example: Asset
has prefix: adms

Animal natural history and life history
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.
is part of: bioregistry
keyword: anatomy
keyword: life science
keyword: obo
keyword: ontology
keyword: taxonomic classification
has local unique identifier example: Lycalopex_vetulus
has provider formatter: https://animaldiversity.org/accounts/$1
has local unique identifier pattern: ^[A-Z_a-z]+$
has download URL: adw.owl
is deprecated: true
has responsible: Animal Diversity Web technical staff
has URI prefix: https://animaldiversity.org/accounts/
has resource example: Lycalopex vetulus
has prefix: adw

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: educational science
keyword: history
keyword: miscellaneous
keyword: ontology
keyword: social sciences
has local unique identifier example: 0000001
has provider formatter: http://purl.obolibrary.org/obo/AEON_$1
has local unique identifier pattern: ^\d{7}$
has download URL: 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_
has resource example: AEON_0000001
has prefix: aeon

Adverse Event Reporting Ontology
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
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: adverse reaction
keyword: biomedical science
keyword: electronic health record
keyword: health science
keyword: medicine
keyword: obo
keyword: ontology
keyword: preclinical studies
has local unique identifier example: 0000125
has provider formatter: http://purl.obolibrary.org/obo/AERO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: aero.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-9551-6370
has URI prefix: http://purl.obolibrary.org/obo/AERO_
has resource example: AERO_0000125
has prefix: aero

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
has local unique identifier example: 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:
has resource example: affymetrix:243002 at
has prefix: affy.probeset

African Population Ontology
type: Resource
description: AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms.
is part of: bioregistry
git repository: afpo
keyword: obo
keyword: ontology
has local unique identifier example: 0000440
has provider formatter: http://purl.obolibrary.org/obo/AfPO_$1
has download URL: afpo.owl
is deprecated: false
has responsible: Melek Chaouch
has URI prefix: http://purl.obolibrary.org/obo/AfPO_
has prefix: afpo

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
has local unique identifier example: 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
has resource example: https://aftol.umn.edu/glossary
has prefix: aftol.category

Assembling the Fungal Tree of Life - Taxonomy
type: Resource
contributor: 0000-0002-5798-662X
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
has local unique identifier example: 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
has resource example: http://wasabi.lutzonilab.net/pub/displayTaxonInfo
has prefix: aftol.taxonomy

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
has local unique identifier example: A_24_P98555
has local unique identifier pattern: ^A_\d+_.+$
is deprecated: false
has prefix: agilent.probe

Agricultural Online Access
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0003-4423-4370
description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.
is part of: bioregistry
has local unique identifier example: IND608186955
has provider formatter: https://europepmc.org/article/AGR/$1
has local unique identifier pattern: ^(IND|GUA)\d+$
is deprecated: false
appears in: chebi
appears in: pmc
has responsible: Judith A Blake
has alternative prefix: AGR
has alternative prefix: AGRICOLA_ID
has URI prefix: https://europepmc.org/article/AGR/
has resource example: IND608186955
has prefix: agricola

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: agricultural products
keyword: agriculture
keyword: agronomy
keyword: aquaculture
keyword: botany
keyword: climate
keyword: data management
keyword: environmental science
keyword: fisheries science
keyword: food
keyword: food security
keyword: forest management
keyword: knowledge and information systems
keyword: nutritional science
keyword: water management
has local unique identifier example: 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_
has resource example: c 2842
has prefix: agrovoc

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

Animal Genome Size Database
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
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: dna
keyword: genome
keyword: life science
has local unique identifier example: 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
has resource example: http://www.genomesize.com/result_species.php
has prefix: agsd

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

The ALlele FREquency Database
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
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: classification
keyword: genome
has local unique identifier example: 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
has resource example: https://alfred.med.yale.edu/alfred/recordinfo.asp
has prefix: alfred

Allergome
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
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: allergen
keyword: biomedical science
keyword: health science
keyword: life science
keyword: medicine
has local unique identifier example: 1948
has provider formatter: http://www.allergome.org/script/dettaglio.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Adriano Mari
has URI prefix: http://www.allergome.org/script/dettaglio.php
has resource example: http://www.allergome.org/script/dettaglio.php
has prefix: allergome

Alzforum Mutations
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
contributor: https://orcid.org/0000-0003-4423-4370
description: Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease.
is part of: bioregistry
keyword: alzheimer's disease
keyword: genes
keyword: variants
has local unique identifier example: app-d678n-tottori
has provider formatter: https://www.alzforum.org/mutations/$1
is deprecated: false
has alternative prefix: Alzforum_mut
has URI prefix: https://www.alzforum.org/mutations/
has resource example: app-d678n-tottori
has prefix: alzforum.mutation

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
has local unique identifier example: 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
has resource example: http://www.alzgene.org/geneoverview.asp
has prefix: alzgene

AmoebaDB
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
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: functional genomics
keyword: genomics
keyword: model organism
has local unique identifier example: 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: https://orcid.org/0000-0003-4446-6200
has URI prefix: https://amoebadb.org/amoeba/app/record/gene/
has resource example: EDI_244000
has prefix: amoebadb

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
has local unique identifier example: 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/
has resource example: https://amphibiaweb.org/species/149
has prefix: amphibiaweb.species

Antibody Registry
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
description: The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.
is part of: bioregistry
keyword: antibody
keyword: reagent
keyword: unique identifiers
has local unique identifier example: 493771
has provider formatter: http://antibodyregistry.org/AB_$1
has local unique identifier pattern: ^\d{6}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5497-0243
has URI prefix: http://antibodyregistry.org/AB_
has resource example: AB_493771
has prefix: antibodyregistry

AntWeb
type: Resource
description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.
is part of: bioregistry
keyword: anatomy
keyword: classification
keyword: life science
has local unique identifier example: casent0106247
has provider formatter: http://www.antweb.org/specimen.do
has local unique identifier pattern: ^casent\d+(\-D\d+)?$
is deprecated: false
has URI prefix: http://www.antweb.org/specimen.do
has resource example: http://www.antweb.org/specimen.do
has prefix: antweb

AOPWiki
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
description: International repository of Adverse Outcome Pathways.
is part of: bioregistry
has local unique identifier example: 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/
has resource example: https://aopwiki.org/aops/98
has prefix: aop

AOPWiki (Key Event)
type: Resource
description: International repository of Adverse Outcome Pathways.
is part of: bioregistry
has local unique identifier example: 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/
has resource example: https://aopwiki.org/events/3
has prefix: aop.events

AOPWiki (Key Event Relationship)
type: Resource
description: International repository of Adverse Outcome Pathways.
is part of: bioregistry
has local unique identifier example: 5
has provider formatter: https://aopwiki.org/relationships/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://aopwiki.org/relationships/
has resource example: https://aopwiki.org/relationships/5
has prefix: aop.relationships

AOPWiki (Stressor)
type: Resource
description: International repository of Adverse Outcome Pathways.
is part of: bioregistry
has local unique identifier example: 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/
has resource example: https://aopwiki.org/stressors/9
has prefix: aop.stressor

Adverse Outcome Pathway Ontology
type: Resource
contributor: 0000-0001-5608-781X
description: The AOPO provides classes and relationships for the semantic representation of the Adverse Outcome Pathway framework.
is part of: bioregistry
git repository: aop-ontology
keyword: adverse outcome pathway
keyword: ontology
has local unique identifier example: AdverseOutcomePathway
has provider formatter: http://aopkb.org/aop_ontology#$1
has local unique identifier pattern: ^[A-Za-z_]+$
has download URL: aopo.owl
is deprecated: false
has responsible: Lyle Burgoon
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://aopkb.org/aop_ontology#
has resource example: AdverseOutcomePathway
has prefix: aopo

Psychology Ontology
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
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: behavior
keyword: ontology
keyword: psychology
has local unique identifier example: Abdomen
has provider formatter: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1
has download URL: apaonto.owl
is deprecated: false
has responsible: Alvin Walker
has URI prefix: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#
has resource example: Abdomen
has prefix: apaonto

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: biology
keyword: protein
has local unique identifier example: 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: Guangshun Wang
has URI prefix: http://aps.unmc.edu/AP/database/query_output.php
has resource example: http://aps.unmc.edu/AP/database/query_output.php
has prefix: apd

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

APID Interactomes
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
description: APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.
is part of: bioregistry
has local unique identifier example: 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+)?$
provides for: uniprot
is deprecated: false
has URI prefix: http://cicblade.dep.usal.es:8080/APID/Interactions.action
has resource example: http://cicblade.dep.usal.es:8080/APID/Interactions.action
has prefix: apid.interactions

Ascomycete phenotype ontology
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi.
is part of: bioregistry
git repository: ascomycete-phenotype-ontology
keyword: cell biology
keyword: genomics
keyword: life cycle stage
keyword: life science
keyword: morphology
keyword: mutation
keyword: obo
keyword: ontology
keyword: phenomics
keyword: phenotype
keyword: study design
has local unique identifier example: 0000184
has provider formatter: http://purl.obolibrary.org/obo/APO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: apo.owl
is deprecated: false
has responsible: Stacia R Engel
has URI prefix: http://purl.obolibrary.org/obo/APO_
has resource example: APO_0000184
has prefix: apo

ArachnoServer
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
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: drug
keyword: life science
keyword: protein
has local unique identifier example: 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
has resource example: http://www.arachnoserver.org/toxincard.html
has prefix: arachnoserver

Arabidopsis Information Portal
type: Resource
description: Website with general information about Arabidopsis and functionalities such as a genomic viewer
is part of: bioregistry
has local unique identifier example: 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
has resource example: https://www.arabidopsis.org/servlets/TairObject
has prefix: araport

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: classification
keyword: life science
keyword: protein
has local unique identifier example: 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
has resource example: http://sbi.imim.es/cgi-bin/archdb//loops.pl
has prefix: archdb

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
has local unique identifier example: 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
has resource example: http://ardb.cbcb.umd.edu/cgi/search.cgi
has prefix: ardb

Archival Resource Key
type: Resource
contributor: https://orcid.org/0000-0001-7604-8041
contributor: https://orcid.org/0000-0002-1216-4761
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
has local unique identifier example: /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:
has resource example: cl010066723
has prefix: ark

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
has local unique identifier example: 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/
has resource example: A-GEOD-50
has prefix: arrayexpress.platform

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: bioinformatics
keyword: biomedical science
keyword: genomics
keyword: life science
has local unique identifier example: 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: https://orcid.org/0000-0002-9903-4248
has URI prefix: https://www.arraymap.org/pgx:
has resource example: pgx:icdom:8500 3
has prefix: arraymap

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

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

Amazon Standard Identification Number
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
description: Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue.
is part of: bioregistry
has local unique identifier example: 0471491039
has provider formatter: https://amzn.com/$1
has local unique identifier pattern: ^[0-9]{10}$
is deprecated: false
has URI prefix: https://amzn.com/
has resource example: https://amzn.com/0471491039
has prefix: asin

Aspergillus Genome Database
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 gene information.
is part of: bioregistry
has local unique identifier example: ASPL0000349247
has provider formatter: http://www.aspergillusgenome.org/cgi-bin/locus.pl
has local unique identifier pattern: ^[A-Za-z_0-9]+$
is deprecated: true
has URI prefix: http://www.aspergillusgenome.org/cgi-bin/locus.pl
has resource example: http://www.aspergillusgenome.org/cgi-bin/locus.pl
has prefix: aspgd.locus

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
has local unique identifier example: 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
has resource example: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl
has prefix: aspgd.protein

Arabidopsis Small RNA Project
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes.
is part of: bioregistry
keyword: genome
keyword: regulation
keyword: rna
has local unique identifier example: ASRP1423
has provider formatter: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html
is deprecated: false
has responsible: Kristin D. Kasschau
has URI prefix: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html
has resource example: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html
has prefix: asrp

ASTD
type: Resource
description: Identifier of an object from the ASTD database.
is part of: bioregistry
keyword: alternative splicing
keyword: gene
keyword: transcript
has local unique identifier example: ENSG00000136147
has provider formatter: http://www.ebi.ac.uk/astd/geneview.html
provides for: ensembl
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.ebi.ac.uk/astd/geneview.html
has resource example: http://www.ebi.ac.uk/astd/geneview.html
has prefix: astd

Asteraceae Genome Database - Genome
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collection refers to the genomic data of Asteraceae species.
is part of: bioregistry
has local unique identifier example: 0002
has provider formatter: https://cbcb.cdutcm.edu.cn/AGD/genome/details/
has local unique identifier pattern: ^\d{4}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6857-7696
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://cbcb.cdutcm.edu.cn/AGD/genome/details/
has resource example: https://cbcb.cdutcm.edu.cn/AGD/genome/details/
has prefix: asteraceaegd.genome

Asteraceae Genome Database - Plant
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collections refers to the broader phenotypic and genetic resources of Asteraceae plants.
is part of: bioregistry
has local unique identifier example: 0016
has provider formatter: https://cbcb.cdutcm.edu.cn/AGD/plant/details/
has local unique identifier pattern: ^\d{4}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6857-7696
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://cbcb.cdutcm.edu.cn/AGD/plant/details/
has resource example: https://cbcb.cdutcm.edu.cn/AGD/plant/details/
has prefix: asteraceaegd.plant

Anatomical Therapeutic Chemical Vetinary
type: Resource
description: The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.
is part of: bioregistry
has local unique identifier example: QJ51RV02
has provider formatter: http://www.whocc.no/atcvet/atcvet_index/
has local unique identifier pattern: ^Q[A-Z0-9]+$
is deprecated: false
has URI prefix: http://www.whocc.no/atcvet/atcvet_index/
has resource example: http://www.whocc.no/atcvet/atcvet_index/
has prefix: atcvet

Animal TFDB Family
type: Resource
description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.
is part of: bioregistry
has local unique identifier example: CUT
has provider formatter: https://guolab.wchscu.cn/AnimalTFDB4//#/family_summary/TF/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has URI prefix: https://guolab.wchscu.cn/AnimalTFDB4//#/family_summary/TF/
has resource example: family summary/TF/CUT
has prefix: atfdb.family

Amphibian taxonomy
type: Resource
description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource
is part of: bioregistry
keyword: obo
keyword: ontology
keyword: taxonomic classification
keyword: taxonomy
has local unique identifier example: 0000000
has provider formatter: http://purl.obolibrary.org/obo/ATO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: ato.obo
is deprecated: true
has responsible: https://orcid.org/0000-0002-1810-9886
has URI prefix: http://purl.obolibrary.org/obo/ATO_
has resource example: ATO_0000000
has prefix: ato

Animal Trait Ontology for Livestock
type: Resource
description: ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment. ATOL aims to: provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; represent traits as generic as possible for livestock vertebrates; make the ATOL ontology as operational as possible and closely related to measurement techniques; and structure the ontology in relation to animal production.
is part of: bioregistry
keyword: agriculture
keyword: animal husbandry
keyword: life science
keyword: livestock
keyword: ontology
keyword: phenotype
has local unique identifier example: 0002233
has provider formatter: http://opendata.inra.fr/ATOL/ATOL_$1
has local unique identifier pattern: ^\d{7}$
has download URL: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php
is deprecated: false
has responsible: https://orcid.org/0000-0002-8310-5195
has URI prefix: http://opendata.inra.fr/ATOL/ATOL_
has resource example: ATOL_0002233
has prefix: atol

AutDB
type: Resource
description: AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.
is part of: bioregistry
has local unique identifier example: ADA
has provider formatter: http://autism.mindspec.org/GeneDetail/$1
has local unique identifier pattern: ^[A-Z]+[A-Z-0-9]{2,}$
is deprecated: true
has URI prefix: http://autism.mindspec.org/GeneDetail/
has resource example: ADA
has prefix: autdb

Authenticus ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: ID of a researcher in Authenticus website
is part of: bioregistry
keyword: person
keyword: researcher
has local unique identifier example: P-008-GD6
has provider formatter: https://www.authenticus.pt/$1
has local unique identifier pattern: ^[A-Z]-[0-9A-Z]{3}-[0-9A-Z]{3}$
is deprecated: false
has URI prefix: https://www.authenticus.pt/
has resource example: P-008-GD6
has prefix: authenticus

Authorea author ID
type: Resource
description: identifier for an author on the Authorea writing service
is part of: bioregistry
has local unique identifier example: 229233
has provider formatter: https://www.authorea.com/users/$1
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has URI prefix: https://www.authorea.com/users/
has resource example: https://www.authorea.com/users/229233
has prefix: authorea.author

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
has local unique identifier example: 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/
has resource example: translation language
has prefix: babelon

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
has local unique identifier example: 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/
has resource example: http://bacmap.wishartlab.com/organisms/1050
has prefix: bacmap.biog

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
has local unique identifier example: 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:
has resource example: index.html
has prefix: bacmap.map

Bactibase
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria.
is part of: bioregistry
keyword: life science
keyword: protein
has local unique identifier example: BAC045
has provider formatter: http://bactibase.hammamilab.org/$1
is deprecated: false
has responsible: Ismail Fliss
has URI prefix: http://bactibase.hammamilab.org/
has resource example: BAC045
has prefix: bactibase

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
has prefix: bams

Basic Register of Thesauri, Ontologies & Classifications
type: Resource
contributor: https://orcid.org/0000-0002-7613-4123
contributor: https://orcid.org/0000-0003-4423-4370
description: The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries. The main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).
is part of: bioregistry
git repository: bartoc.org
keyword: knowledge and information systems
keyword: ontology and terminology
has local unique identifier example: 241
has provider formatter: https://bartoc.org/en/node/$1
has local unique identifier pattern: ^[1-9][0-9]*$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7613-4123
has URI prefix: https://bartoc.org/en/node/
has identifier space owner: 048vdhs48
has resource example: https://bartoc.org/en/node/241
has prefix: bartoc

Blue Brain Project Knowledge Graph
type: Resource
description: Blue Brain Project's published data as knowledge graphs and Web Studios.
is part of: bioregistry
has provider formatter: https://bbp.epfl.ch/nexus/web/studios/public/$1
has local unique identifier pattern: ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$
is deprecated: true
has URI prefix: https://bbp.epfl.ch/nexus/web/studios/public/
has prefix: bbkg

Blue Brain Project Topological sampling Knowledge Graph
type: Resource
description: Input data and analysis results for the paper "Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ).
is part of: bioregistry
has provider formatter: https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1
has local unique identifier pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$
is deprecated: true
has URI prefix: https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:
has prefix: bbtp

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: adenovirus
keyword: antibody
keyword: basic research
keyword: basic science
keyword: beta cell
keyword: cell line
keyword: cell regeneration
keyword: cell replacement
keyword: cell reprogramming
keyword: data set
keyword: data sharing
keyword: embryonic stem cell
keyword: embryonic stem cell line
keyword: functional genomics
keyword: gene
keyword: gene expression
keyword: genomics
keyword: mouse
keyword: mouse embryonic stem cell line
keyword: mouse strain
keyword: pancreas
keyword: pancreatic development
keyword: pancreatic islet
keyword: pancreatic islet development
keyword: pancreatic islet function
keyword: protocol
has local unique identifier example: 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_
has resource example: RRID:BCBC 4623
has prefix: bcbc

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
has local unique identifier example: 0000015
has provider formatter: http://purl.obolibrary.org/obo/BCGO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: bcgo.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-2999-0103
has URI prefix: http://purl.obolibrary.org/obo/BCGO_
has resource example: BCGO_0000015
has prefix: bcgo

The Behaviour Change Intervention Ontology
type: Resource
description: The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.
is part of: bioregistry
keyword: ontology
has local unique identifier example: 040000
has provider formatter: https://w3id.org/BCI-ontology#$1
has local unique identifier pattern: ^\d{6}$
has download URL: bcio.owl
is deprecated: false
has responsible: Sergio José Rodríguez Méndez
has URI prefix: https://w3id.org/BCI-ontology#
has resource example: https://w3id.org/BCI-ontology#040000
has prefix: bcio

BCRC Strain Collection Catalog
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Cell line collections (Providers)
is part of: bioregistry
keyword: cell lines
has local unique identifier example: 60316
has provider formatter: https://catalog.bcrc.firdi.org.tw/BcrcContent
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://catalog.bcrc.firdi.org.tw/BcrcContent
has resource example: https://catalog.bcrc.firdi.org.tw/BcrcContent
has prefix: bcrc

Banco de Celulas do Rio de Janeiro
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: 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/
has resource example: https://bcrj.org.br/pesquisa/
has prefix: bcrj

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
has local unique identifier example: 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: dbest
has URI prefix: https://www.ncbi.nlm.nih.gov/nucest/
has resource example: EY223054.1
has prefix: bdgp.est

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: gene
keyword: sequence
has local unique identifier example: KG09531
has provider formatter: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: Allan Spradling
has URI prefix: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php
has resource example: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php
has prefix: bdgp.insertion

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

Tribolium Genome Database -- Insertion
type: Resource
description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.
is part of: bioregistry
keyword: computational biology
keyword: genome
keyword: life science
has local unique identifier example: TC010103
has provider formatter: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/
has local unique identifier pattern: ^TC\d+$
is deprecated: true
has responsible: Susan J. Brown
has URI prefix: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/
has resource example: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/
has prefix: beetlebase

Benchmark Energy & Geometry Database
type: Resource
description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.
is part of: bioregistry
keyword: life science
has local unique identifier example: 4214
has provider formatter: http://www.begdb.com/index.php
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: Pavel Hobza
has URI prefix: http://www.begdb.com/index.php
has resource example: http://www.begdb.com/index.php
has prefix: begdb

BEI Resources
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Cell line collections (Providers)
is part of: bioregistry
keyword: cell lines
has local unique identifier example: MRA-253
has provider formatter: https://www.beiresources.org/Catalog/cellBanks/$1.aspx
is deprecated: false
has alternative prefix: BEI_Resources
has URI prefix: https://bioregistry.io/beiresources:
has resource example: MRA-253.aspx
has prefix: beiresources

Biological Expression Language
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents.
is part of: bioregistry
keyword: biology
has local unique identifier example: 9-1-1 Complex
is deprecated: false
has responsible: https://orcid.org/0000-0003-4423-4370
has prefix: bel

Biological and Environmental Research Variable Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A representation of variables appearing in models in the environmental research space.
is part of: bioregistry
git repository: bervo
keyword: ontology
has local unique identifier example: 0000001
has provider formatter: https://w3id.org/bervo/BERVO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: bervo.owl
is deprecated: false
has responsible: Harry Caufield
has URI prefix: https://w3id.org/bervo/BERVO_
has resource example: BERVO_0000001
has prefix: bervo

Bgee family
type: Resource
contributor: 0000-0003-3947-488X
description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species.
is part of: bioregistry
has local unique identifier example: ENSFM00500000270089
has provider formatter: http://bgee.unil.ch/bgee/bgee
has local unique identifier pattern: ^(ENSFM|ENSGTV:)\d+$
is deprecated: true
has URI prefix: http://bgee.unil.ch/bgee/bgee
has resource example: http://bgee.unil.ch/bgee/bgee
has prefix: bgee.family

Bgee organ
type: Resource
contributor: 0000-0003-3947-488X
description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures.
is part of: bioregistry
has local unique identifier example: EHDAA:2185
has provider formatter: http://bgee.unil.ch/bgee/bgee
has local unique identifier pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$
is deprecated: true
has URI prefix: http://bgee.unil.ch/bgee/bgee
has resource example: http://bgee.unil.ch/bgee/bgee
has prefix: bgee.organ

Bgee stage
type: Resource
contributor: 0000-0003-3947-488X
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
has local unique identifier example: 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
has resource example: http://bgee.unil.ch/bgee/bgee
has prefix: bgee.stage

BiGG Compartment
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 model compartments.
is part of: bioregistry
keyword: cellular component
keyword: compartment
keyword: ontology
keyword: subcellular compartment
has local unique identifier example: c
has provider formatter: http://bigg.ucsd.edu/compartments/$1
has local unique identifier pattern: ^c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y$
has download URL: bigg.compartment.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-1238-1499
has URI prefix: http://bigg.ucsd.edu/compartments/
has resource example: http://bigg.ucsd.edu/compartments/c
has prefix: bigg.compartment

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: chemical
keyword: compound
keyword: metabolite
keyword: ontology
keyword: small molecule
has local unique identifier example: 12dgr161
has provider formatter: http://bigg.ucsd.edu/models/universal/metabolites/$1
has local unique identifier pattern: ^[a-z_A-Z0-9]+(\[[c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y]\])?$
has download URL: 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/
has resource example: 12dgr161
has prefix: bigg.metabolite

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: metabolic model
keyword: ontology
keyword: pathway
has local unique identifier example: iECABU_c1320
has provider formatter: http://bigg.ucsd.edu/models/$1
has local unique identifier pattern: ^[a-z_A-Z0-9]+$
has download URL: bigg.model.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-1238-1499
has URI prefix: http://bigg.ucsd.edu/models/
has resource example: iECABU c1320
has prefix: bigg.model

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
has local unique identifier example: 13GS
has provider formatter: http://bigg.ucsd.edu/models/universal/reactions/$1
has local unique identifier pattern: ^[a-z_A-Z0-9]+$
has download URL: 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/
has resource example: 13GS
has prefix: bigg.reaction

Bilateria anatomy
type: Resource
description: This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource.
is part of: bioregistry
keyword: anatomy
keyword: gene expression
keyword: obo
keyword: ontology
has local unique identifier example: 0000000
has provider formatter: http://purl.obolibrary.org/obo/BILA_$1
has local unique identifier pattern: ^\d{7}$
has download URL: bila.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-1548-3290
has URI prefix: http://purl.obolibrary.org/obo/BILA_
has resource example: BILA_0000000
has prefix: bila

BIND accession number
type: Resource
description: Accession number of an entry from the BIND database.
is part of: bioregistry
keyword: interaction
keyword: pathway
keyword: small molecule
has local unique identifier example: 98346
has provider formatter: http://www.bind.ca/Action
is deprecated: true
has URI prefix: http://www.bind.ca/Action
has resource example: http://www.bind.ca/Action
has prefix: bind

BindingDB
type: Resource
description: BindingDB is the first public database of protein-small molecule affinity data.
is part of: bioregistry
keyword: chemistry
keyword: computational chemistry
keyword: drug discovery
keyword: interaction
keyword: life science
keyword: medicinal chemistry
keyword: protein
has local unique identifier example: 999
has provider formatter: http://www.bindingdb.org/rwd/entry/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Michael K. Gilson
has URI prefix: http://www.bindingdb.org/rwd/entry/
has resource example: http://www.bindingdb.org/rwd/entry/999
has prefix: bindingdb

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
has local unique identifier example: 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/
has resource example: h aktPathway
has prefix: biocarta.pathway

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
has local unique identifier example: 614
has provider formatter: https://www.biocatalogue.org/services/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Carole Goble
has URI prefix: https://www.biocatalogue.org/services/
has resource example: https://www.biocatalogue.org/services/614
has prefix: biocatalogue.service

Biocompute Object
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication. This pipeline documentation approach has been adopted by a few FDA centers. The goal is to ease the communication burdens between research centers, organizations, and industries. This web portal allows users to build a BioCompute Objects through the interface in a human and machine readable format.
is part of: bioregistry
git repository: BCO Specification
has local unique identifier example: 000001
has provider formatter: https://biocomputeobject.org/BCO_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-8823-9945
has URI prefix: https://biocomputeobject.org/BCO_
has resource example: BCO_000001
has prefix: biocompute

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
has local unique identifier example: 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/
has resource example: https://query.biodeep.cn/metabolite/00000000001
has prefix: biodeep

BioDolphin
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for lipid-protein interactions, including details about protein functions, protein families, lipid classifications, lipid-protein binding affinities, membrane association type, and atomic structures.
is part of: bioregistry
has local unique identifier example: BD1a05-A-A-IPM1
has provider formatter: https://biodolphin.chemistry.gatech.edu/detail/$1
has local unique identifier pattern: ^BD\d[a-zA-Z0-9]+-[A-Za-z]-[A-Za-z]-[A-Za-z0-9]+$
is deprecated: false
has responsible: Andrew C. McShan
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://biodolphin.chemistry.gatech.edu/detail/
has resource example: BD1a05-A-A-IPM1
has prefix: biodolphin

Biofactoid
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications.
is part of: bioregistry
git repository: factoid
keyword: biocuration
keyword: database
keyword: relationships
has provider formatter: https://biofactoid.org/document/$1
has local unique identifier pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
is deprecated: false
has responsible: Jeffrey Wong
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://biofactoid.org/document/
has prefix: biofactoid

BioGRID Interactions
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.
is part of: bioregistry
has local unique identifier example: 2649230
has provider formatter: https://thebiogrid.org/interaction/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9713-9994
has URI prefix: https://thebiogrid.org/interaction/
has resource example: https://thebiogrid.org/interaction/2649230
has prefix: biogrid.interaction

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
has local unique identifier example: 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/
has resource example: bkc640
has prefix: biokc

BioLegend
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: BioLegend is a life sciences supply vendor.
is part of: bioregistry
keyword: antibodies
keyword: assays
keyword: life sciences
keyword: reagents
keyword: vendor
has local unique identifier example: 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
has resource example: https://www.biolegend.com/Default.aspx
has prefix: biolegend

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: biomedical science
keyword: functional genomics
keyword: medical biotechnology
keyword: medical informatics
keyword: ontology
keyword: translational medicine
has local unique identifier example: Gene
has provider formatter: https://biolink.github.io/biolink-model/$1
has local unique identifier pattern: ^\S+$
has download URL: biolink.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
has URI prefix: https://biolink.github.io/biolink-model/
has resource example: Gene
has prefix: biolink

BioMagResBank
type: Resource
description: A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids.
is part of: bioregistry
keyword: protein
has local unique identifier example: 10046
has provider formatter: http://www.bmrb.wisc.edu/data_library/generate_summary.php
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.bmrb.wisc.edu/data_library/generate_summary.php
has resource example: http://www.bmrb.wisc.edu/data_library/generate_summary.php
has prefix: biomagresbank

Bio-MINDER Tissue Database
type: Resource
description: Database of the dielectric properties of biological tissues.
is part of: bioregistry
has provider formatter: https://datalab.rwth-aachen.de/MINDER/resource/$1
has local unique identifier pattern: ^[a-z0-9\-]+$
is deprecated: false
has URI prefix: https://datalab.rwth-aachen.de/MINDER/resource/
has prefix: biominder

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
has local unique identifier example: 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: https://orcid.org/0000-0001-9105-5960
has alternative prefix: BIOMD
has URI prefix: https://biomodels.org/
has resource example: BIOMD0000000048
has prefix: biomodels.db

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: algorithm
keyword: bioinformatics
keyword: computer science
keyword: obo
keyword: ontology
has local unique identifier example: 0000057
has provider formatter: http://purl.obolibrary.org/obo/KISAO_$1
has local unique identifier pattern: ^\d+$
has download URL: 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_
has resource example: KISAO_0000057
has prefix: biomodels.kisao

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: ontology
keyword: synthetic biology
keyword: systems biology
has local unique identifier example: 0000066
has provider formatter: https://www.ebi.ac.uk/ols/ontologies/teddy/terms
has local unique identifier pattern: ^\d+$
has download URL: teddy-inferred.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9105-5960
has alternative prefix: teddy
has URI prefix: https://www.ebi.ac.uk/ols/ontologies/teddy/terms
has resource example: https://www.ebi.ac.uk/ols/ontologies/teddy/terms
has prefix: biomodels.teddy

SBML RDF Vocabulary
type: Resource
description: Vocabulary used in the RDF representation of SBML models.
is part of: bioregistry
has local unique identifier example: 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#
has resource example: rateRule
has prefix: biomodels.vocabulary

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
has local unique identifier example: 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
has resource example: https://bionumbers.hms.harvard.edu/bionumber.aspx
has prefix: bionumbers

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
has local unique identifier example: 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
has resource example: http://avis.princeton.edu/pixie/viewgraph.php
has prefix: biopixie

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
has local unique identifier example: 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/
has resource example: Resources mentioned in "Sharing biological data: why, when, and how"
has prefix: bioregistry.collection

Bioregistry Metaregistry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Bioregistry's meta-registry
is part of: bioregistry
keyword: data integration
keyword: data science
keyword: metaregistry
keyword: registry
has local unique identifier example: 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/
has resource example: miriam
has prefix: bioregistry.registry

Bioregistry Schema
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Schema for the export of the Bioregistry as RDF
is part of: bioregistry
keyword: registry
has local unique identifier example: 0000001
has provider formatter: https://bioregistry.io/schema/#$1
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://bioregistry.io/schema/#
has resource example: Resource
has prefix: bioregistry.schema

BioSchemas
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]
is part of: bioregistry
git repository: specifications
has local unique identifier example: Dataset
has provider formatter: https://bioschemas.org/profiles/$1
is deprecated: false
has alternative prefix: bioschema
has alternative prefix: bioschemas_draft
has URI prefix: https://bioschemas.org/profiles/
has resource example: Dataset
has prefix: bioschemas

biosimulations
type: Resource
description: BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools.
is part of: bioregistry
has local unique identifier example: Yeast-cell-cycle-Irons-J-Theor-Biol-2009
has provider formatter: https://biosimulations.org/projects/$1
has local unique identifier pattern: ^[a-zA-Z0-9_-]{3,}$
is deprecated: false
has URI prefix: https://biosimulations.org/projects/
has resource example: Yeast-cell-cycle-Irons-J-Theor-Biol-2009
has prefix: biosimulations

BioSimulators
type: Resource
description: BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML).
is part of: bioregistry
git repository: choose
keyword: computational biology
keyword: systems biology
has local unique identifier example: vcell
has provider formatter: https://biosimulators.org/simulators/$1
has local unique identifier pattern: ^[a-zA-Z0-9-_]+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-2605-5080
has URI prefix: https://biosimulators.org/simulators/
has resource example: vcell
has prefix: biosimulators

BioSystems
type: Resource
contributor: https://orcid.org/0000-0001-7542-0286
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: molecules
keyword: pathways
keyword: systems biology
has local unique identifier example: 001
has provider formatter: https://www.ncbi.nlm.nih.gov/biosystems/$1
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: Aron Marchler-Bauer
has URI prefix: https://www.ncbi.nlm.nih.gov/biosystems/
has resource example: https://www.ncbi.nlm.nih.gov/biosystems/001
has prefix: biosystems

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: bioinformatics
keyword: biology
keyword: biomedical science
has local unique identifier example: 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/
has resource example: bioregistry
has prefix: biotools

BioTop
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network
is part of: bioregistry
git repository: biotop
keyword: biology
keyword: ontology
has local unique identifier example: attachedTo
has provider formatter: http://purl.org/biotop/biotop.owl#$1
has download URL: biotop.owl
is deprecated: false
has responsible: Stefan Schulz
has URI prefix: http://purl.org/biotop/biotop.owl#
has resource example: attachedTo
has prefix: biotop

BIOZIL
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Redistributor of bilogics and biomedical supplies
is part of: bioregistry
keyword: biologics
keyword: life sciences
keyword: vendor
has local unique identifier example: ls-c35719-120
has provider formatter: https://www.biozol.de/en/product/$1
is deprecated: false
has URI prefix: https://www.biozol.de/en/product/
has resource example: ls-c35719-120
has prefix: biozil

Biomedical Informatics Research Network Lexicon
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.
is part of: bioregistry
keyword: anatomy
keyword: biomedical science
keyword: disease
keyword: ontology
keyword: study design
has local unique identifier example: 2023
has provider formatter: http://uri.neuinfo.org/nif/nifstd/birnlex_$1
has local unique identifier pattern: ^\d+$
has download URL: birnlex.owl
is deprecated: false
has responsible: William Bug
has URI prefix: http://uri.neuinfo.org/nif/nifstd/birnlex_
has resource example: birnlex 2023
has prefix: birnlex

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: software engineering
keyword: subject agnostic
has local unique identifier example: 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/
has resource example: systems-biology-compiler
has prefix: bitbucket

BitterDB Compound
type: Resource
description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.
is part of: bioregistry
has local unique identifier example: 46
has provider formatter: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php
has resource example: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php
has prefix: bitterdb.cpd

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
has local unique identifier example: 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
has resource example: http://bitterdb.agri.huji.ac.il/Receptor.php
has prefix: bitterdb.rec

SBGN Bricks data and ontology
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way.
is part of: bioregistry
keyword: ontology
has local unique identifier example: 0000204
has provider formatter: http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1
has local unique identifier pattern: ^\d+$
has download URL: bko.owl
is deprecated: false
has responsible: Adrien Rougny
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.sbgnbricks.org/BKO/full/entry/all/BKO:
has resource example: BKO:0000204
has prefix: bko

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
has local unique identifier example: 0000006
has provider formatter: http://purl.obolibrary.org/obo/BMONT_$1
has download URL: bmont.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9896-3531
has URI prefix: http://purl.obolibrary.org/obo/BMONT_
has prefix: bmont

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: chemistry
keyword: nmr
keyword: spectrometry
has local unique identifier example: 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
has resource example: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
has prefix: bmrb.restraint

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

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
has local unique identifier example: 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/
has resource example: http://vocab.nerc.ac.uk/collection/L05/current/101
has prefix: bodc.sdn

British Oceanographic Data Centre data storage units
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: terms approved for use by BODC to describe the measurement units for data held in its repositories.
is part of: bioregistry
keyword: unit
keyword: units
has local unique identifier example: UMKS
has provider formatter: http://vocab.nerc.ac.uk/collection/P06/current/$1
is deprecated: false
has alternative prefix: nvs.P06
has URI prefix: http://vocab.nerc.ac.uk/collection/P06/current/
has resource example: UMKS
has prefix: bodc.unit

BOLD Systems taxon
type: Resource
description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.
is part of: bioregistry
keyword: dna
has local unique identifier example: 27267
has provider formatter: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Paul David Neil Hebert
has URI prefix: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage
has resource example: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage
has prefix: bold.taxonomy

Bio-Pesticides DataBase
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Database of biopesticides maintained by the University of Hertfordshire
is part of: bioregistry
keyword: biology
keyword: biopesticides
keyword: pesticides
has local unique identifier example: 2404
has provider formatter: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://bioregistry.io/bpdb:
has resource example: 2404.htm
has prefix: bpdb

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
has local unique identifier example: hasPrimaryUriPattern
has provider formatter: http://vocabularies.bridgedb.org/ops#$1
is deprecated: false
has URI prefix: http://vocabularies.bridgedb.org/ops#
has resource example: hasPrimaryUriPattern
has prefix: bridgedb

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
has local unique identifier example: 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
has resource example: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html
has prefix: broad

Biosapiens Protein Feature Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library.
is part of: bioregistry
git repository: SO-Ontologies
keyword: ontology
has local unique identifier example: 00042
has provider formatter: https://biopragmatics.github.io/providers/bs/$1
has local unique identifier pattern: ^\d+$
has download URL: biosapiens.obo
is deprecated: false
has URI prefix: https://biopragmatics.github.io/providers/bs/
has resource example: https://biopragmatics.github.io/providers/bs/00042
has prefix: bs

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
has local unique identifier example: 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
has resource example: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php
has prefix: bugbase.expt

BugBase Protocol
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 design protocols.
is part of: bioregistry
has local unique identifier example: 67
has provider formatter: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php
has resource example: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php
has prefix: bugbase.protocol

Bacterial Tyrosine Kinase Database
type: Resource
description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information.
is part of: bioregistry
keyword: domain
keyword: life science
keyword: microbial
keyword: sequence
has local unique identifier example: A0A009HB13
has provider formatter: https://bykdb.lyon.inserm.fr/data/html/annotated/$1.html
has local unique identifier pattern: ^[A-Z0-9]+$
provides for: uniprot
is deprecated: false
has responsible: Alain J. Cozzone
has URI prefix: https://bioregistry.io/bykdb:
has resource example: A0A009HB13.html
has prefix: bykdb

CABI Digital Library
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Research and learning in agriculture, the environment and the applied life sciences
is part of: bioregistry
has local unique identifier example: 20000614040
has provider formatter: https://www.cabi.org/cabebooks/ebook/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.cabi.org/cabebooks/ebook/
has resource example: https://www.cabi.org/cabebooks/ebook/20000614040
has prefix: cabi

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: applied microbiology
keyword: medical microbiology
keyword: microbiology
keyword: molecular biology
keyword: molecular microbiology
keyword: virology
has local unique identifier example: 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: Paolo Romano
has URI prefix: https://bioregistry.io/cabri:
has prefix: cabri

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
has local unique identifier example: 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:
has resource example: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML
has prefix: cadsr

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: human
keyword: ontology
keyword: physiology
has local unique identifier example: TS-0001
has provider formatter: https://www.nextprot.org/term/$1
has local unique identifier pattern: ^TS-\d+$
has download URL: caloha.obo
is deprecated: false
has responsible: Paula Duek Roggli
has URI prefix: https://www.nextprot.org/term/
has resource example: TS-0001
has prefix: caloha

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
has local unique identifier example: 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: 0000-0003-2715-335X
has URI prefix: https://www.cameo3d.org/sp/targets/target/
has resource example: 2019-08-03 00000089 1
has prefix: cameo

CAPS-DB
type: Resource
description: CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.
is part of: bioregistry
has local unique identifier example: 434
has provider formatter: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster
has resource example: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster
has prefix: caps

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
has local unique identifier example: 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_
has resource example: Stage 20
has prefix: carnegie.stage

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: physical chemistry
keyword: structure
has local unique identifier example: 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: CASID
has alternative prefix: CAS_RN
has alternative prefix: SECONDARY_CAS_RN
has alternative prefix: cas_id
has URI prefix: https://commonchemistry.cas.org/detail
has resource example: https://commonchemistry.cas.org/detail
has prefix: cas

Eschmeyer's Catalog of Fishes
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
has local unique identifier example: 5359
has provider formatter: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp
has local unique identifier pattern: ^\d+$
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: CASGEN
has URI prefix: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp
has resource example: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp
has prefix: casspc

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
has local unique identifier example: 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/
has resource example: 1cukA01
has prefix: cath.domain

Carbohydrate Active EnZYmes
type: Resource
description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features.
is part of: bioregistry
keyword: classification
keyword: glycomics
keyword: life science
keyword: polysaccharide
has local unique identifier example: GT10
has provider formatter: http://www.cazy.org/$1.html
has local unique identifier pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$
is deprecated: false
has responsible: Nicolas Terrapon
has URI prefix: https://bioregistry.io/cazy:
has resource example: GT10.html
has prefix: cazy

Chinese Biological Abstracts
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.
is part of: bioregistry
keyword: bibliography
has local unique identifier example: 375364
has provider formatter: https://europepmc.org/article/CBA/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://europepmc.org/article/CBA/
has resource example: https://europepmc.org/article/CBA/375364
has prefix: cba

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
has local unique identifier example: License
has provider formatter: http://web.resource.org/cc/$1
is deprecated: true
has URI prefix: http://web.resource.org/cc/
has resource example: License
has prefix: cc.legacy

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
has local unique identifier example: 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:
has resource example: https://www.ccdc.cam.ac.uk/services/structures
has prefix: ccdc

Consensus CDS
type: Resource
description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.
is part of: bioregistry
keyword: gene
keyword: life science
keyword: protein
has local unique identifier example: CCDS12976
has provider formatter: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi
has local unique identifier pattern: ^CCDS\d+(\.\d+)?$
is deprecated: false
has responsible: https://orcid.org/0000-0001-9311-9745
has URI prefix: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi
has resource example: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi
has prefix: ccds

Human Reference Atlas Common Coordinate Framework Ontology
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage—making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA.
is part of: bioregistry
git repository: ccf-ontology
keyword: ontology
has local unique identifier example: extraction_set
has provider formatter: https://bioportal.bioontology.org/ontologies/CCF/
has local unique identifier pattern: ^\S+$
has download URL: ccf.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-3321-6137
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://bioportal.bioontology.org/ontologies/CCF/
has resource example: https://bioportal.bioontology.org/ontologies/CCF/
has prefix: ccf

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
has local unique identifier example: BT20_BREAST
has provider formatter: https://www.cbioportal.org/patient
has download URL: ccle.owl
is deprecated: false
has responsible: William R. Sellers
has alternative prefix: ccle.cell
has URI prefix: https://www.cbioportal.org/patient
has resource example: https://www.cbioportal.org/patient
has prefix: ccle

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: cell
keyword: cell cycle
keyword: functional genomics
keyword: genomics
keyword: life science
keyword: molecular_function
keyword: obo
keyword: ontology
keyword: proteomics
has local unique identifier example: 0000003
has provider formatter: https://www.ebi.ac.uk/ols4/ontologies/cco/terms
has local unique identifier pattern: ^\w+$
has download URL: 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
has resource example: https://www.ebi.ac.uk/ols4/ontologies/cco/terms
has prefix: cco

National Experimental Cell Resource Sharing Platform
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Cell line databases/resources
is part of: bioregistry
has local unique identifier example: 4201PAT-CCTCC00348
has provider formatter: http://www.cellresource.cn/cellsearch.aspx
is deprecated: false
has URI prefix: http://www.cellresource.cn/cellsearch.aspx
has resource example: http://www.cellresource.cn/cellsearch.aspx
has prefix: ccrid

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: bioinformatics
keyword: biomedical science
keyword: evolution
keyword: evolutionary biology
keyword: life science
keyword: molecular biology
keyword: obo
keyword: ontology
keyword: phylogenetics
keyword: taxonomy
has local unique identifier example: 0000072
has provider formatter: http://purl.obolibrary.org/obo/CDAO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: cdao.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-8688-6599
has URI prefix: http://purl.obolibrary.org/obo/CDAO_
has resource example: CDAO_0000072
has prefix: cdao

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
has local unique identifier example: 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
has resource example: https://health-products.canada.ca/dpd-bdpp/info
has prefix: cdpd

Current Dental Terminology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment. Note that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D.
is part of: bioregistry
keyword: ontology
has local unique identifier example: 1000001
has local unique identifier pattern: ^\d{7}$
has download URL: CDTCodes as Classes pruned.owl
is deprecated: false
appears in: ohd
has prefix: cdt

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

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

CellBank Australia
type: Resource
description: CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world.
is part of: bioregistry
has local unique identifier example: ab-1-ha
has provider formatter: https://www.cellbankaustralia.com/$1.html
is deprecated: false
has URI prefix: https://bioregistry.io/cellbank.australia:
has resource example: ab-1-ha.html
has prefix: cellbank.australia

Cellosaurus Publication
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Cellosaurus identifeirs for publications, like Pubmed
is part of: bioregistry
has local unique identifier example: CLPUB00496
has provider formatter: https://web.expasy.org/cellosaurus/cellopub/$1
has local unique identifier pattern: ^CLPUB\d+$
is deprecated: false
has URI prefix: https://web.expasy.org/cellosaurus/cellopub/
has resource example: CLPUB00496
has prefix: cellopub

Cellosaurus Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The set of prefixes used in the Cellosaurus resource
is part of: bioregistry
keyword: cell lines
keyword: cells
keyword: registry
has local unique identifier example: 4DN
has provider formatter: https://bioregistry.io/metaregistry/cellosaurus/$1
is deprecated: false
has URI prefix: https://bioregistry.io/metaregistry/cellosaurus/
has resource example: 4DN
has prefix: cellosaurus.resource

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
has local unique identifier example: 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/
has resource example: https://www.cellrepo.com/repositories/82
has prefix: cellrepo

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/
has prefix: cellxgene.dataset

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
has local unique identifier example: secondary_attack_rate
has provider formatter: https://biopragmatics.github.io/providers/cemo/$1
has local unique identifier pattern: ^[0-9a-z_-]+$
has download URL: 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/
has resource example: secondary attack rate
has prefix: cemo

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

The Cert Ontology
type: Resource
description: Ontology for Certificates and crypto stuff.
is part of: bioregistry
keyword: quality
has local unique identifier example: Certificate
is deprecated: false
has prefix: cert

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: eukaryotic
keyword: genome
keyword: life science
keyword: nucleotide
has local unique identifier example: 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: Gavin Sherlock
has URI prefix: http://www.candidagenome.org/cgi-bin/locus.pl
has resource example: http://www.candidagenome.org/cgi-bin/locus.pl
has prefix: cgd

CGH Data Base
type: Resource
description: Cell line databases/resources
is part of: bioregistry
has local unique identifier example: 300165/p13898_2106T
is deprecated: false
has prefix: cghdb

Chicken Gene Nomenclature Consortium
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)
is part of: bioregistry
keyword: gene
keyword: ontology
has local unique identifier example: 10087
has provider formatter: http://birdgenenames.org/cgnc/GeneReport
has local unique identifier pattern: ^\d+$
has download URL: cgnc.owl
is deprecated: false
has responsible: Fiona M McCarthy
has alternative prefix: BirdBase
has alternative prefix: CGNC
has URI prefix: http://birdgenenames.org/cgnc/GeneReport
has resource example: http://birdgenenames.org/cgnc/GeneReport
has prefix: cgnc

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
has local unique identifier example: 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
has resource example: http://cgsc.biology.yale.edu/Site.php
has prefix: cgsc

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
has local unique identifier example: 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/
has resource example: CH_001923
has prefix: charprot

ChemBank
type: Resource
description: ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG).
is part of: bioregistry
keyword: chemical
keyword: metabolite
has local unique identifier example: 1000000
has provider formatter: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm
has resource example: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm
has prefix: chembank

ChemBioSys Assay
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A assay in the ChemBioSys data platform
is part of: bioregistry
has local unique identifier example: 31
has provider formatter: https://data.chembiosys.de/assays/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.chembiosys.de/assays/
has resource example: https://data.chembiosys.de/assays/31
has prefix: chembiosys.assay

ChemBioSys Dataset
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A dataset in the ChemBioSys data platform
is part of: bioregistry
has local unique identifier example: 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/
has resource example: https://data.chembiosys.de/data_files/103
has prefix: chembiosys.data

ChemBioSys Institution
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An institution in the ChemBioSys data platform
is part of: bioregistry
has local unique identifier example: 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/
has resource example: https://data.chembiosys.de/institutions/13
has prefix: chembiosys.institution

ChemBioSys Investigation
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An investigation in the ChemBioSys data platform
is part of: bioregistry
has local unique identifier example: 27
has provider formatter: https://data.chembiosys.de/investigations/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.chembiosys.de/investigations/
has resource example: https://data.chembiosys.de/investigations/27
has prefix: chembiosys.investigation

ChemBioSys Model
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A model in the ChemBioSys data platform
is part of: bioregistry
has local unique identifier example: 11
has provider formatter: https://data.chembiosys.de/models/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.chembiosys.de/models/
has resource example: https://data.chembiosys.de/models/11
has prefix: chembiosys.model

ChemBioSys Organism
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An organism in the ChemBioSys data platform
is part of: bioregistry
has local unique identifier example: 604090889
has provider formatter: https://data.chembiosys.de/organisms/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.chembiosys.de/organisms/
has resource example: https://data.chembiosys.de/organisms/604090889
has prefix: chembiosys.organism

ChemBioSys Project
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A project in the ChemBioSys data platform
is part of: bioregistry
has local unique identifier example: 15
has provider formatter: https://data.chembiosys.de/projects/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.chembiosys.de/projects/
has resource example: https://data.chembiosys.de/projects/15
has prefix: chembiosys.project

ChemBioSys Publication
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A publication in the ChemBioSys data platform
is part of: bioregistry
has local unique identifier example: 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/
has resource example: https://data.chembiosys.de/publications/157
has prefix: chembiosys.publication

ChemBioSys Strain
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A strain in the ChemBioSys data platform
is part of: bioregistry
has local unique identifier example: 33
has provider formatter: https://data.chembiosys.de/strains/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.chembiosys.de/strains/
has resource example: https://data.chembiosys.de/strains/33
has prefix: chembiosys.strain

ChemBioSys Study
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A study in the ChemBioSys data platform
is part of: bioregistry
has local unique identifier example: 20
has provider formatter: https://data.chembiosys.de/studies/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.chembiosys.de/studies/
has resource example: https://data.chembiosys.de/studies/20
has prefix: chembiosys.study

ChemBioSys Tag
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A tag in the ChemBioSys data platform
is part of: bioregistry
has local unique identifier example: 59
has provider formatter: https://data.chembiosys.de/tags/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.chembiosys.de/tags/
has resource example: https://data.chembiosys.de/tags/59
has prefix: chembiosys.tag

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: bioactivities
keyword: cell lines
has local unique identifier example: 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/
has resource example: CHEMBL3307800
has prefix: chembl.cell

ChEMBL target
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: cell
keyword: cell line
keyword: ontology
keyword: protein
keyword: protein complex
has local unique identifier example: CHEMBL3467
has provider formatter: https://www.ebi.ac.uk/chembl/target/inspect/$1
has local unique identifier pattern: ^CHEMBL\d+$
has download URL: chembl.target.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-0294-5484
has alternative prefix: ChEMBL-Targets
has URI prefix: https://www.ebi.ac.uk/chembl/target/inspect/
has resource example: CHEMBL3467
has prefix: chembl.target

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

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: chemical
keyword: ontology
has local unique identifier example: CFc000239295
has provider formatter: https://www.chemfont.ca/chemicals/$1
has local unique identifier pattern: ^CFc\d{9}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.chemfont.ca/chemicals/
has resource example: https://www.chemfont.ca/chemicals/CFc000239295
has prefix: chemfont.chemical

ChemFOnt Ontology
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 entries in the ChemFOnt ontology that are used to organize individual chemicals. Terms can be looked up using the following URL (https://www.chemfont.ca/ontology_browse/term_info/18), but not directly by ID
is part of: bioregistry
keyword: chemical
keyword: ontology
has local unique identifier example: CFo000000197
has local unique identifier pattern: ^CFo\d{9}$
has download URL: chemfont.owl.zip
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has reviewer: https://orcid.org/0000-0003-4423-4370
has prefix: chemfont.ontology

Chemical Book
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A hybrid chemical enyclopedia and supplier advertizing system for chemicals.
is part of: bioregistry
has local unique identifier example: CB82546919
has provider formatter: https://www.chemicalbook.com/ChemicalProductProperty_IN_$1.htm
is deprecated: false
has alternative prefix: ChemicalBookNo
has URI prefix: https://bioregistry.io/chemicalbook:
has resource example: ChemicalProductProperty IN CB82546919.htm
has prefix: chemicalbook

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
has local unique identifier example: LDCM0160
has provider formatter: https://chemprosquare.idrblab.net/data/competitor/details/$1
has local unique identifier pattern: ^LDCM\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-8069-0053
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://chemprosquare.idrblab.net/data/competitor/details/
has resource example: LDCM0160
has prefix: chempro.competitor

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
has local unique identifier example: LDPC0032
has provider formatter: https://chemprosquare.idrblab.net/data/probe/details/$1
has local unique identifier pattern: ^LDPC\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-8069-0053
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://chemprosquare.idrblab.net/data/probe/details/
has resource example: LDPC0032
has prefix: chempro.probe

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
has local unique identifier example: LDTP03903
has provider formatter: https://chemprosquare.idrblab.net/data/target/details/$1
has local unique identifier pattern: ^LDTP\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-8069-0053
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://chemprosquare.idrblab.net/data/target/details/
has resource example: LDTP03903
has prefix: chempro.target

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
has local unique identifier example: 10090-chr10qC
has provider formatter: http://purl.obolibrary.org/obo/CHR_$1
has download URL: 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_
has resource example: CHR 10090-chr10qC
has prefix: chr

Coronavirus Infectious Disease Ontology
type: Resource
description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.
is part of: bioregistry
git repository: cido
keyword: bioinformatics
keyword: covid-19
keyword: disease
keyword: drug
keyword: drug discovery
keyword: drug interaction
keyword: drug repositioning
keyword: epidemiology
keyword: infection process
keyword: obo
keyword: ontology
keyword: virology
has local unique identifier example: 0000005
has provider formatter: http://purl.obolibrary.org/obo/CIDO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: cido.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9189-9661
has URI prefix: http://purl.obolibrary.org/obo/CIDO_
has resource example: CIDO_0000005
has prefix: cido

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
has local unique identifier example: 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/
has resource example: https://www.cienciavitae.pt/0C1F-DA6C-4B02
has prefix: cienciavitae

Confidence Information Ontology
type: Resource
description: An ontology to capture confidence information about annotations.
is part of: bioregistry
git repository: confidence-information-ontology
keyword: annotation
keyword: biology
keyword: obo
keyword: ontology
has local unique identifier example: 0000040
has provider formatter: http://purl.obolibrary.org/obo/CIO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: cio.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-9415-5104
has URI prefix: http://purl.obolibrary.org/obo/CIO_
has resource example: CIO_0000040
has prefix: cio

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
has local unique identifier example: 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/
has resource example: C6155
has prefix: citexplore

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
has local unique identifier example: 559
has provider formatter: https://civicdb.org/links/molecular_profile/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: 0000-0002-6388-446X
has alternative prefix: civic.molecularprofile
has URI prefix: https://civicdb.org/links/molecular_profile/
has resource example: https://civicdb.org/links/molecular_profile/559
has prefix: civic.mpid

CIViC Variant Group
type: Resource
description: Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance
is part of: bioregistry
has local unique identifier example: 16
has provider formatter: https://civicdb.org/links/variant_group/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: 0000-0002-6388-446X
has alternative prefix: civic.variantgroup
has URI prefix: https://civicdb.org/links/variant_group/
has resource example: https://civicdb.org/links/variant_group/16
has prefix: civic.vgid

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
has local unique identifier example: CDB-00133756-001
has provider formatter: http://cdb.iso.org/lg/$1
is deprecated: false
has URI prefix: http://cdb.iso.org/lg/
has resource example: http://cdb.iso.org/lg/CDB-00133756-001
has prefix: clarin.clavas

CLARIN Concept Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Concepts for encoding bibliometric information
is part of: bioregistry
has provider formatter: http://hdl.handle.net/11459/$1
is deprecated: false
has URI prefix: http://hdl.handle.net/11459/
has prefix: clarin.concept

ClassyFire
type: Resource
description: ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API.
is part of: bioregistry
keyword: ontology
has local unique identifier example: 0004828
has provider formatter: http://classyfire.wishartlab.com/tax_nodes/C$1
has local unique identifier pattern: ^\d{7}$
has download URL: ChemOnt 2 1.obo.zip
is deprecated: false
has alternative prefix: CHEMONTID
has alternative prefix: chemont
has URI prefix: http://classyfire.wishartlab.com/tax_nodes/C
has resource example: http://classyfire.wishartlab.com/tax_nodes/C0004828
has prefix: classyfire

ChecklistBank
type: Resource
description: ChecklistBank is an index and repository for taxonomic and nomenclatural datasets
is part of: bioregistry
has local unique identifier example: 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/
has resource example: https://www.checklistbank.org/dataset/1010
has prefix: clb

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
has local unique identifier example: 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:
has resource example: cl3603.html
has prefix: cldb

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
has local unique identifier example: 40135
has provider formatter: https://clinicalgenome.org/affiliation/$1/
is deprecated: false
has URI prefix: https://bioregistry.io/clingen.affiliation:
has resource example: https://clinicalgenome.org/affiliation/40135/
has prefix: clingen.affiliation

ClinGen Allele Registry
type: Resource
contributor: https://orcid.org/0000-0002-8719-7760
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 and maintains identifiers for alleles.
is part of: bioregistry
keyword: alleles
keyword: genetics
keyword: mutations
has local unique identifier example: 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
has resource example: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid
has prefix: clingen.allele

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
has local unique identifier example: 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:
has resource example: CCID:004126
has prefix: clingen.curation

ClinVar Submission
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 submissions, and is based on SCV accession.
is part of: bioregistry
has local unique identifier example: SCV000151292
has provider formatter: http://www.ncbi.nlm.nih.gov/clinvar
has local unique identifier pattern: ^SCV\d+(\.\d+)?$
is deprecated: false
has URI prefix: http://www.ncbi.nlm.nih.gov/clinvar
has resource example: http://www.ncbi.nlm.nih.gov/clinvar
has prefix: clinvar.submission

ClinVar Submitter
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 (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs).
is part of: bioregistry
has local unique identifier example: 26957
has provider formatter: https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.ncbi.nlm.nih.gov/clinvar/submitters/
has resource example: https://www.ncbi.nlm.nih.gov/clinvar/submitters/26957
has prefix: clinvar.submitter

Cell Markers Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This ontology integrates cell type markers for cells in the Cell Ontology from various sources along with details of marker context (anatomical context, assay), confidence (where available) and provenance. [from repository]
is part of: bioregistry
git repository: CellMark
keyword: ontology
has local unique identifier example: 1000003
has provider formatter: http://purl.obolibrary.org/obo/CLM_$1
has local unique identifier pattern: ^\d{7}$
has download URL: clm.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-7073-9172
has URI prefix: http://purl.obolibrary.org/obo/CLM_
has resource example: CLM_1000003
has prefix: clm

Cell Lines Service
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: 300108/p3934_A-172
has provider formatter: https://www.cytion.com/$1
is deprecated: false
has URI prefix: https://www.cytion.com/
has resource example: p3934 A-172
has prefix: cls

Costal and Marine Ecological Classification Standard
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.
is part of: bioregistry
git repository: cmecs
keyword: ecology
keyword: marine ecology
keyword: ontology
has local unique identifier example: 595
has provider formatter: https://cmecscatalog.org/cmecs/classification/unit/$1.html
has local unique identifier pattern: ^\d+$
has download URL: cmecs.owl
is deprecated: false
has responsible: Kate Rose
has URI prefix: https://bioregistry.io/cmecs:
has resource example: 595.html
has prefix: cmecs

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: Mark Engelstad
has URI prefix: http://purl.obolibrary.org/obo/CMF_
has prefix: cmf

CNCB Genome Warehouse
type: Resource
contributor: 0009-0008-8406-631X
description: The China National Center for Bioinformation's (CNCB) Genome Warehouse (GWH) is a public repository holding genetic information for a wide range of species including humans, plants, animals, and microorganisms. Identifiers in this resource correspond to genomes of various species. The goal of the resource is to make genomic data accessible to researchers in areas like precision medicine and biotechnology.
is part of: bioregistry
has local unique identifier example: 167047
has provider formatter: https://ngdc.cncb.ac.cn/gwh/Genome/$1/show
has local unique identifier pattern: ^\d{6}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9922-9723
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://bioregistry.io/cncb.gwh:
has resource example: show
has prefix: cncb.gwh

French National Center for Scientific Research - Research Group Identifier
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for an academic research group issued by the CNRS
is part of: bioregistry
has local unique identifier example: UMR7315
has provider formatter: https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin
has local unique identifier pattern: ^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY|UPS)\d+$
is deprecated: false
has URI prefix: https://bioregistry.io/cnrs:
has resource example: https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin
has prefix: cnrs

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
has local unique identifier example: Content
has provider formatter: http://www.w3.org/2011/content#$1
is deprecated: false
has URI prefix: http://www.w3.org/2011/content#
has resource example: Content
has prefix: cnt

Rice 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 IBP Rice Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Based on SES, Rice Descriptor and IRIS DB.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: botany
keyword: food
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000618
has provider formatter: https://cropontology.org/rdf/CO_320:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 320.owl
is deprecated: false
has responsible: Jeffrey A. Detras
has URI prefix: https://cropontology.org/rdf/CO_320:
has resource example: CO 320:0000618
has prefix: co_320

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: agriculture
keyword: food
keyword: life science
keyword: ontology
keyword: phenotype
has local unique identifier example: 0000449
has provider formatter: https://cropontology.org/rdf/CO_321:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 321.owl
is deprecated: false
has responsible: Rosemary Shrestha
has URI prefix: https://cropontology.org/rdf/CO_321:
has resource example: CO 321:0000449
has prefix: co_321

Maize Ontology
type: Resource
description: The Maize Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: botany
keyword: food
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000773
has provider formatter: https://cropontology.org/rdf/CO_322:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 322.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_322:
has resource example: CO 322:0000773
has prefix: co_322

Barley 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 Barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Its focus is on traits and variable used in field trials for breeding.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: botany
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000252
has provider formatter: https://cropontology.org/rdf/CO_323:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 323.owl
is deprecated: false
has responsible: Fawzy Nawar
has URI prefix: https://cropontology.org/rdf/CO_323:
has resource example: CO 323:0000252
has prefix: co_323

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: agriculture
keyword: botany
keyword: food
keyword: ontology
keyword: phenotype
has local unique identifier example: 0000111
has provider formatter: https://cropontology.org/rdf/CO_324:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 324.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_324:
has resource example: CO 324:0000111
has prefix: co_324

Banana Ontology
type: Resource
description: The Banana Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: food
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000519
has provider formatter: https://cropontology.org/rdf/CO_325:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 325.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_325:
has resource example: CO 325:0000519
has prefix: co_325

Coconut Ontology
type: Resource
description: Coconut Ontology v1.0 - Coconut trait dictionary started by CIRAD, based on the "Guidelines for collecting coconut germplasm characterisation data during prospecting missions", COGENT (to be published); the "Descriptors for Coconut, (Cocos nucifera L.)", IPGRI (1995); and the "Manual on standardized research techniques in coconut breeding", IPGRI (1996).
is part of: bioregistry
git repository: Crop-Ontology
keyword: ontology
has local unique identifier example: 0000254
has provider formatter: https://cropontology.org/rdf/CO_326:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 326.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_326:
has resource example: CO 326:0000254
has prefix: co_326

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: agriculture
keyword: botany
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000095
has provider formatter: https://cropontology.org/rdf/CO_327:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 327.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_327:
has resource example: CO 327:0000095
has prefix: co_327

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: agriculture
keyword: botany
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000106
has provider formatter: https://cropontology.org/rdf/CO_330:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 330.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_330:
has resource example: CO 330:0000106
has prefix: co_330

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: agriculture
keyword: botany
keyword: food
keyword: life science
keyword: ontology
has local unique identifier example: 0000088
has provider formatter: https://cropontology.org/rdf/CO_331:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 331.owl
is deprecated: false
has responsible: Vilma Hualla Mamani
has URI prefix: https://cropontology.org/rdf/CO_331:
has resource example: CO 331:0000088
has prefix: co_331

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: agriculture
keyword: botany
keyword: food
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant breeding
keyword: plant phenotypes and traits
has local unique identifier example: 3000045
has provider formatter: https://cropontology.org/rdf/CO_333:$1
has local unique identifier pattern: ^\d+$
has download URL: CO 333.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_333:
has resource example: CO 333:3000045
has prefix: co_333

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: botany
keyword: food
keyword: nutritional science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000070
has provider formatter: https://cropontology.org/rdf/CO_334:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 334.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_334:
has resource example: CO 334:0000070
has prefix: co_334

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: agriculture
keyword: botany
keyword: food
keyword: ontology
has local unique identifier example: 0000189
has provider formatter: https://cropontology.org/rdf/CO_335:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 335.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_335:
has resource example: CO 335:0000189
has prefix: co_335

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: food
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000339
has provider formatter: https://cropontology.org/rdf/CO_336:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 336.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_336:
has resource example: CO 336:0000339
has prefix: co_336

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

Chickpea Ontology
type: Resource
description: Development of crop-specific trait ontologies including the Chickpea Ontology began in 2008 as part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: botany
keyword: food
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000138
has provider formatter: https://cropontology.org/rdf/CO_338:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 338.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-0091-7981
has URI prefix: https://cropontology.org/rdf/CO_338:
has resource example: CO 338:0000138
has prefix: co_338

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: agriculture
keyword: botany
keyword: food
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000032
has provider formatter: https://cropontology.org/rdf/CO_339:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 339.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_339:
has resource example: CO 339:0000032
has prefix: co_339

Cowpea Ontology
type: Resource
description: The Cowpea Trait Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: botany
keyword: food
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000639
has provider formatter: https://cropontology.org/rdf/CO_340:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 340.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_340:
has resource example: CO 340:0000639
has prefix: co_340

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: agriculture
keyword: botany
keyword: food
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000140
has provider formatter: https://cropontology.org/rdf/CO_341:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 341.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_341:
has resource example: CO 341:0000140
has prefix: co_341

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: agriculture
keyword: botany
keyword: food
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0100010
has provider formatter: https://cropontology.org/rdf/CO_343:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 343.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_343:
has resource example: CO 343:0100010
has prefix: co_343

Brachiaria 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 Brachiaria Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: botany
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000127
has provider formatter: https://cropontology.org/rdf/CO_345:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 345.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_345:
has resource example: CO 345:0000127
has prefix: co_345

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: agriculture
keyword: food
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000199
has provider formatter: https://cropontology.org/rdf/CO_346:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 346.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_346:
has resource example: CO 346:0000199
has prefix: co_346

Castor Bean Ontology
type: Resource
description: The Castor Bean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: botany
keyword: food
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000108
has provider formatter: https://cropontology.org/rdf/CO_347:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 347.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_347:
has resource example: CO 347:0000108
has prefix: co_347

Brassica Ontology
type: Resource
description: Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Brassica Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: botany
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 1100107
has provider formatter: https://cropontology.org/rdf/CO_348:$1
has local unique identifier pattern: ^\d+$
has download URL: CO 348.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_348:
has resource example: CO 348:1100107
has prefix: co_348

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: agriculture
keyword: botany
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000215
has provider formatter: https://cropontology.org/rdf/CO_350:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 350.owl
is deprecated: false
has responsible: Jean-Luc Jannink
has URI prefix: https://cropontology.org/rdf/CO_350:
has resource example: CO 350:0000215
has prefix: co_350

Vitis 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 Vitis Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
is part of: bioregistry
git repository: Crop-Ontology
keyword: agriculture
keyword: botany
keyword: life science
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 4000027
has provider formatter: https://cropontology.org/rdf/CO_356:$1
has local unique identifier pattern: ^\d+$
has download URL: CO 356.owl
is deprecated: false
has responsible: Eric Duchêne
has URI prefix: https://cropontology.org/rdf/CO_356:
has resource example: CO 356:4000027
has prefix: co_356

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

Cotton Ontology
type: Resource
description: This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.
is part of: bioregistry
git repository: Crop-Ontology
keyword: ontology
has local unique identifier example: 0000139
has provider formatter: https://cropontology.org/rdf/CO_358:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 358.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_358:
has resource example: CO 358:0000139
has prefix: co_358

Sunflower Ontology
type: Resource
description: To add
is part of: bioregistry
git repository: Crop-Ontology
keyword: ontology
has local unique identifier example: 0000947
has provider formatter: https://cropontology.org/rdf/CO_359:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 359.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_359:
has resource example: CO 359:0000947
has prefix: co_359

Sugar Kelp 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 Sugar Kelp Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
is part of: bioregistry
git repository: Crop-Ontology
keyword: botany
keyword: life science
keyword: marine environment
keyword: ontology
keyword: phenotype
keyword: plant phenotypes and traits
has local unique identifier example: 0000071
has provider formatter: https://cropontology.org/rdf/CO_360:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 360.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_360:
has resource example: CO 360:0000071
has prefix: co_360

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

Bambara Groundnut Ontology
type: Resource
description: This ontology is a part of the the Crop Ontology project , as an essential source of traits and variables to support the standardization of the breeding databases.
is part of: bioregistry
git repository: Crop-Ontology
keyword: ontology
has local unique identifier example: 0000072
has provider formatter: https://cropontology.org/rdf/CO_366:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 366.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_366:
has resource example: CO 366:0000072
has prefix: co_366

Quinoa Ontology
type: Resource
description: Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation Challenge Program (GCP) describe traits variables of Quinoa Germinate Database http://germinate.quinoadb.org. Quinoa Phenotyping Consortium Creation Date 23.05.2021
is part of: bioregistry
git repository: Crop-Ontology
keyword: ontology
has local unique identifier example: 0000004
has provider formatter: https://cropontology.org/rdf/CO_367:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 367.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6020-5919
has URI prefix: https://cropontology.org/rdf/CO_367:
has resource example: CO 367:0000004
has prefix: co_367

Apple Ontology
type: Resource
description: Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales. This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 894215.
is part of: bioregistry
git repository: Crop-Ontology
keyword: ontology
has local unique identifier example: 0000890
has provider formatter: https://cropontology.org/rdf/CO_370:$1
has local unique identifier pattern: ^\d{7}$
has download URL: CO 370.owl
is deprecated: false
has responsible: Ekaterina Chuprikova
has URI prefix: https://cropontology.org/rdf/CO_370:
has resource example: CO 370:0000890
has prefix: co_370

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: chemistry
keyword: natural producs
keyword: organic chemistry
has local unique identifier example: 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/
has resource example: CNP0171505
has prefix: coconut

GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).
is part of: bioregistry
keyword: microarray
keyword: transcriptomics
has local unique identifier example: GE86325
has local unique identifier pattern: ^GE\d+$
is deprecated: false
has prefix: codelink

COEXISTENCE
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: COEXISTENCE - Thesaurus of intersectionality and decolonial issues: black studies, gender, sexuality and feminist studies
is part of: bioregistry
has local unique identifier example: 163
has provider formatter: https://mamoura.eci.ufmg.br/tematres/vocab/index.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://mamoura.eci.ufmg.br/tematres/vocab/index.php
has resource example: https://mamoura.eci.ufmg.br/tematres/vocab/index.php
has prefix: coexistence

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
has local unique identifier example: 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/
has resource example: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/K
has prefix: cog.category

Cluster of orthologous genes
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.
is part of: bioregistry
keyword: genome
keyword: life science
keyword: protein
has local unique identifier example: COG0001
has provider formatter: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1
has local unique identifier pattern: ^COG\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-2265-5572
has alternative prefix: COG_Cluster
has alternative prefix: cog
has URI prefix: https://www.ncbi.nlm.nih.gov/research/cog/cog/
has resource example: COG0001
has prefix: cog.cluster

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
has local unique identifier example: 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/
has resource example: NAD biosynthesis
has prefix: cog.pathway

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: clinical data
keyword: clinical trials
keyword: health
keyword: health sciences
is deprecated: false
has prefix: cohd

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: cohesin
keyword: protein
has local unique identifier example: 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/
has resource example: CDBP00415501
has prefix: cohesindb.binding

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
has local unique identifier example: 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/
has resource example: CDBG00009781
has prefix: cohesindb.gene

CohesinDB - cohesin-related chromatin loop
type: Resource
contributor: https://orcid.org/0009-0000-6974-6386
description: Contains identifiers of cohesin-related chromatin loops from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each identifier represents a single cohesin-related chromatin loop. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information.
is part of: bioregistry
keyword: chromatin loop
keyword: cohesin
keyword: interaction
keyword: protein
has local unique identifier example: CDBL00540805
has provider formatter: https://cohesindb.iqb.u-tokyo.ac.jp/browseloop/eachloop/$1
has local unique identifier pattern: ^CDBL00\d{6}$
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/browseloop/eachloop/
has resource example: CDBL00540805
has prefix: cohesindb.loops

COI Catalogue
type: Resource
contributor: https://orcid.org/0009-0001-1912-5132
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
has local unique identifier example: 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
has resource example: https://coicatalogue.uc.pt/index.php
has prefix: coi

Catalogue of Life
type: Resource
description: Identifier of a taxon or synonym in the Catalogue of Life
is part of: bioregistry
has local unique identifier example: 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/
has resource example: 4QHKG
has prefix: col

Catalogue of Life in Taiwan
type: Resource
contributor: https://orcid.org/0000-0003-2699-3066
description: Identifier (name code) for a taxon in the catalogue of life in taiwan
is part of: bioregistry
has local unique identifier example: 431472
has provider formatter: https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php
has local unique identifier pattern: ^[1-9]\d{5}$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php
has resource example: https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php
has prefix: col.taiwan

Collagen Mutation Database
type: Resource
description: This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes.
is part of: bioregistry
keyword: gene
has local unique identifier example: COL3A1
has provider formatter: https://eds.gene.le.ac.uk/home.php
provides for: hgnc.symbol
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://eds.gene.le.ac.uk/home.php
has resource example: https://eds.gene.le.ac.uk/home.php
has prefix: collagenmutdb

Colorectal Cancer Atlas
type: Resource
description: Cell line databases/resources
is part of: bioregistry
has local unique identifier example: ALA
has provider formatter: http://www.coloncanceratlas.org/search_cell_line
is deprecated: false
has URI prefix: http://www.coloncanceratlas.org/search_cell_line
has resource example: http://www.coloncanceratlas.org/search_cell_line
has prefix: colonatlas

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
has local unique identifier example: 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:
has resource example: sed-ml.level-1.version-1.md
has prefix: combine.specifications

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
has local unique identifier example: 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/
has resource example: DTXSID2021028
has prefix: comptox

Compluyeast-2D-DB
type: Resource
description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record.
is part of: bioregistry
keyword: protein
has local unique identifier example: O08709
has provider formatter: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi
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])$
provides for: uniprot
is deprecated: true
has URI prefix: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi
has resource example: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi
has prefix: compulyeast

Conference Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. The conference-ontology adopts best ontology design practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and guarantees interoperability with SWC ontology and all other pertinent vocabularies. (from homepage)
is part of: bioregistry
keyword: ontology
has local unique identifier example: isDocumentRelatedTo
has provider formatter: https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1
has download URL: conference-ontology.owl
is deprecated: false
has URI prefix: https://w3id.org/scholarlydata/ontology/conference-ontology.owl#
has resource example: isDocumentRelatedTo
has prefix: conference

ConfIDent Event
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.
is part of: bioregistry
keyword: conferences
keyword: meetings
keyword: metascience
has provider formatter: https://www.confident-conference.org/index.php/Event:$1
has local unique identifier pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-1595-3213
has URI prefix: https://www.confident-conference.org/index.php/Event:
has prefix: confident.event

ConfIDent Event Series
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.
is part of: bioregistry
keyword: conferences
keyword: grouping
keyword: meetings
keyword: metascience
has local unique identifier example: AAC
has provider formatter: https://www.confident-conference.org/index.php/Event_Series:$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-1595-3213
has URI prefix: https://www.confident-conference.org/index.php/Event_Series:
has resource example: Event Series:AAC
has prefix: confident.series

ConoServer
type: Resource
description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.
is part of: bioregistry
keyword: life science
keyword: neurophysiology
keyword: statistics
keyword: synthetic biology
has local unique identifier example: 2639
has provider formatter: http://www.conoserver.org/
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: David Craik
has URI prefix: http://www.conoserver.org/
has resource example: http://www.conoserver.org/
has prefix: conoserver

Curation of Neurodegeneration Supporting Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases.
is part of: bioregistry
keyword: biology
keyword: life science
keyword: neurodegeneration
keyword: neuroscience
keyword: ontology
has local unique identifier example: CONSO00010
has provider formatter: https://pharmacome.github.io/conso/$1
has local unique identifier pattern: ^CONSO\d{5}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://pharmacome.github.io/conso/
has resource example: CONSO00010
has prefix: conso

Contextual Ontology-based Repository Analysis Library - Context and Measurement Ontology
type: Resource
contributor: https://orcid.org/0000-0002-5153-9079
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
has local unique identifier example: 0000001
has local unique identifier pattern: ^\d+$
has download URL: context measurement ontology.obo
is deprecated: false
has responsible: https://orcid.org/0000-0002-5153-9079
has reviewer: https://orcid.org/0000-0003-4423-4370
has prefix: coral.como

CORDIS Article
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).
is part of: bioregistry
has local unique identifier example: 436605
has provider formatter: https://cordis.europa.eu/article/id/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://cordis.europa.eu/article/id/
has resource example: https://cordis.europa.eu/article/id/436605
has prefix: cordis.article

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
has local unique identifier example: 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/
has resource example: https://cordis.europa.eu/project/id/817732
has prefix: cordis.project

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

Corpus Vitrearum
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A digital photo archive
is part of: bioregistry
has local unique identifier example: F3436
has provider formatter: https://corpusvitrearum.de/id/$1
is deprecated: false
has responsible: Jonatan Jalle Steller
has URI prefix: https://corpusvitrearum.de/id/
has resource example: F3436
has prefix: corpusvitrearum

CorrDB
type: Resource
description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.
is part of: bioregistry
keyword: animal genetics
keyword: genetics
keyword: life science
keyword: systems biology
has local unique identifier example: 37232
has provider formatter: https://www.animalgenome.org/CorrDB/q/
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: Zhiliang Hu
has URI prefix: https://www.animalgenome.org/CorrDB/q/
has resource example: https://www.animalgenome.org/CorrDB/q/
has prefix: corrdb

Comprehensive Resource of Mammalian protein complexes
type: Resource
description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.
is part of: bioregistry
keyword: bioinformatics
keyword: biology
keyword: protein
has local unique identifier example: 100
has provider formatter: https://mips.helmholtz-muenchen.de/corum/
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Andreas Ruepp
has URI prefix: https://mips.helmholtz-muenchen.de/corum/
has resource example: https://mips.helmholtz-muenchen.de/corum/
has prefix: corum

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
has local unique identifier example: SFB_COVID19_MW286762
has provider formatter: https://covid19.sfb.uit.no/api/records/$1
has local unique identifier pattern: ^\w+_COVID19_[-\w]+$
has download URL: covid19.owl
is deprecated: false
has responsible: Dylan McGagh
has URI prefix: https://covid19.sfb.uit.no/api/records/
has resource example: SFB COVID19 MW286762
has prefix: covid19

CoVoc Coronavirus Vocabulary
type: Resource
description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
is part of: bioregistry
git repository: covoc
keyword: ontology
has local unique identifier example: 0010034
has provider formatter: http://purl.obolibrary.org/obo/COVOC_$1
has local unique identifier pattern: ^\d{7}$
has download URL: covoc.owl
is deprecated: false
has responsible: Zoë May Pendlington
has URI prefix: http://purl.obolibrary.org/obo/COVOC_
has resource example: COVOC_0010034
has prefix: covoc

CoyPu Ontology
type: Resource
description: Ontology to describe companies and their supply network, employees, products, production materials, industries, events and relations.
is part of: bioregistry
keyword: coypu
keyword: economics
has local unique identifier example: AbductionOrForcedDisappearance
has provider formatter: https://schema.coypu.org/global#$1
is deprecated: false
has URI prefix: https://schema.coypu.org/global#
has resource example: AbductionOrForcedDisappearance
has prefix: coypu

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: coypu
keyword: earth sciences
keyword: life sciences, biology
has local unique identifier example: Air
has provider formatter: https://schema.coypu.org/em-dat#$1
is deprecated: false
has URI prefix: https://schema.coypu.org/em-dat#
has resource example: Air
has prefix: coypu.emdat

Global Trade Alerts Ontology
type: Resource
description: An ontology for modeling global trade alerts, mainly inspired by the Global Trade Alerts repository.
is part of: bioregistry
keyword: coypu
keyword: economics
has local unique identifier example: AffectedCommercialFlow
has provider formatter: https://schema.coypu.org/gta#$1
is deprecated: false
has URI prefix: https://schema.coypu.org/gta#
has resource example: AffectedCommercialFlow
has prefix: coypu.gta

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

OECD TIVA Ontology
type: Resource
description: An ontology for modeling international trade flows.
is part of: bioregistry
keyword: coypu
keyword: economics
has local unique identifier example: hasExport
has provider formatter: https://schema.coypu.org/vtf#$1
is deprecated: false
has URI prefix: https://schema.coypu.org/vtf#
has resource example: hasExport
has prefix: coypu.tiva

Cellular Phenotypes
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
is deprecated: true
appears in: cl
has prefix: cp

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
has local unique identifier example: 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
has resource example: https://worldwide.espacenet.com/classification
has prefix: cpc

Creative Biolabs antibody
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Creative Biolabs Antigen provides identifiers for antibody-based entities such as recombinant, functional, engineered, and format-specific antibodies as well as antibody processing tools, which are essential for applications in diagnostics, therapeutics, and immunology.
is part of: bioregistry
has local unique identifier example: TAB-884
has local unique identifier pattern: ^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$
is deprecated: false
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: creativebiolabs.antibody

Creative Biolabs protein
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Creative Biolabs Protein provides identifiers for protein-related entities, including therapeutic proteins, proteolytic enzymes, antibody-like scaffold proteins, soluble T cell receptors, and tetramers.
is part of: bioregistry
has local unique identifier example: VS-0724-CJ1
has local unique identifier pattern: ^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$
is deprecated: false
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: creativebiolabs.protein

CRISPRdb
type: Resource
description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data.
is part of: bioregistry
keyword: life science
has local unique identifier example: 551115
has provider formatter: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: Christine Pourcel
has URI prefix: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi
has resource example: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi
has prefix: crisprdb

Contributor Role Ontology
type: Resource
description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability.
is part of: bioregistry
git repository: contributor-role-ontology
keyword: attribution
keyword: contributor roles
keyword: obo
keyword: ontology
has local unique identifier example: 0000038
has provider formatter: http://purl.obolibrary.org/obo/CRO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: cro.owl
is deprecated: false
has responsible: Marijane White
has URI prefix: http://purl.obolibrary.org/obo/CRO_
has resource example: CRO_0000038
has prefix: cro

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
has local unique identifier example: FileObject
has provider formatter: http://mlcommons.org/croissant/$1
is deprecated: false
has URI prefix: http://mlcommons.org/croissant/
has resource example: FileObject
has prefix: croissant

CropMRepository
type: Resource
description: CropMRespository is a database of soil and crop biophysical process models.
is part of: bioregistry
has local unique identifier example: 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/
has resource example: http://www.crop2ml.org/cropmdb/000000001
has prefix: crop2ml

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: bioimaging
keyword: electron microscopy
keyword: ontology
keyword: structural biology
has local unique identifier example: 0000052
has provider formatter: http://scipion.i2pc.es/ontology/CRYOEM_$1
has local unique identifier pattern: ^\d{7}$
has download URL: cryoem.owl
is deprecated: false
has responsible: Carlos Oscar S. Sorzano
has URI prefix: http://scipion.i2pc.es/ontology/CRYOEM_
has resource example: CRYOEM_0000052
has prefix: cryoem

CryptoDB
type: Resource
description: CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
is part of: bioregistry
keyword: functional genomics
keyword: genome
keyword: genomics
keyword: parasitology
has local unique identifier example: cgd7_230
has provider formatter: https://cryptodb.org/cryptodb/app/record/gene/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4446-6200
has URI prefix: https://cryptodb.org/cryptodb/app/record/gene/
has resource example: cgd7 230
has prefix: cryptodb

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: life science
keyword: structure
has local unique identifier example: 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
has resource example: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php
has prefix: csa

Cambridge Structural Database
type: Resource
description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode.
is part of: bioregistry
keyword: biochemistry
keyword: chemistry
keyword: organic chemistry
keyword: organic molecular chemistry
has local unique identifier example: PELNAW
has provider formatter: https://www.ccdc.cam.ac.uk/services/structures
has local unique identifier pattern: ^[A-Z]{6}(\d{2})?$
is deprecated: false
has responsible: Colin Groom
has URI prefix: https://bioregistry.io/csd:
has resource example: https://www.ccdc.cam.ac.uk/services/structures
has prefix: csd

Computer Retrieval of Information on Science Projects Thesaurus
type: Resource
description: CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains. Note that while still available and included in Unified Medical Language System (UMLS), it has not been updated since 2006.
is part of: bioregistry
keyword: anatomy
keyword: biology
keyword: biomedical science
keyword: chemical biology
keyword: disease
keyword: food
keyword: medicine
keyword: ontology
keyword: social science
has local unique identifier example: 2004-2820
has provider formatter: http://purl.bioontology.org/ontology/CSP/$1
is deprecated: true
has responsible: Anita Ghebeles
has alternative prefix: CRISP
has alternative prefix: CRISP Thesaurus
has alternative prefix: CRISP Thesaurus, 2006
has alternative prefix: CSP2005
has URI prefix: http://purl.bioontology.org/ontology/CSP/
has resource example: http://purl.bioontology.org/ontology/CSP/2004-2820
has prefix: csp

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

Cell Signaling Technology Pathways
type: Resource
description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.
is part of: bioregistry
keyword: biomedical science
keyword: life science
has local unique identifier example: Akt_PKB
has provider formatter: http://www.cellsignal.com/reference/pathway/$1.html
has local unique identifier pattern: ^[A-Za-z0-9_-]+$
is deprecated: false
has alternative prefix: cst
has URI prefix: https://bioregistry.io/cst.pathway:
has resource example: Akt PKB.html
has prefix: cst.pathway

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
has local unique identifier example: 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/
has resource example: 31253.11.sciencedb.j00001.00123
has prefix: cstr

CSV on the Web Vocabulary
type: Resource
description: This document describes the RDFS vocabulary description used in the Metadata Vocabulary for Tabular Data along with the default JSON-LD Context.
is part of: bioregistry
keyword: vocabularies
keyword: w3c rec
has local unique identifier example: uriTemplate
is deprecated: false
has prefix: csvw

Common Terminology Criteria for Adverse Events
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI).
is part of: bioregistry
keyword: biomedical science
keyword: cancer
keyword: disease
keyword: ontology
has local unique identifier example: E12768
has provider formatter: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae5.owl#$1
has local unique identifier pattern: ^E\d+$
has download URL: ctcae.owl
is deprecated: false
appears in: oae
has responsible: https://orcid.org/0000-0001-9189-9661
has alternative prefix: CTCAE
has URI prefix: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae5.owl#
has resource example: E12768
has prefix: ctcae

CTD Disease
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
has local unique identifier example: D053716
has provider formatter: http://ctdbase.org/detail.go
has local unique identifier pattern: ^D\d+$
provides for: mesh
is deprecated: false
has URI prefix: http://ctdbase.org/detail.go
has resource example: http://ctdbase.org/detail.go
has prefix: ctd.disease

CTD Gene
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
has local unique identifier example: 101
has provider formatter: http://ctdbase.org/detail.go
has local unique identifier pattern: ^\d+$
provides for: ncbigene
is deprecated: false
has responsible: Allan Peter Davis
has URI prefix: http://ctdbase.org/detail.go
has resource example: http://ctdbase.org/detail.go
has prefix: ctd.gene

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: biomedical science
keyword: disease
keyword: neurobiology
keyword: obo
keyword: ontology
keyword: preclinical studies
has local unique identifier example: 0000022
has provider formatter: http://purl.obolibrary.org/obo/CTO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: cto.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9896-3531
has URI prefix: http://purl.obolibrary.org/obo/CTO_
has resource example: CTO_0000022
has prefix: cto

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
has local unique identifier example: 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:
has resource example: AKR
has prefix: cubedb

Codon Usage Tabulated from GenBank
type: Resource
description: Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank.
is part of: bioregistry
keyword: dna
keyword: gene
has local unique identifier example: 9606
has provider formatter: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi
provides for: ncbitaxon
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi
has resource example: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi
has prefix: cutg

Cardiovascular Disease Ontology
type: Resource
description: An ontology to describe entities related to cardiovascular diseases
is part of: bioregistry
git repository: CVDO
keyword: cardiology
keyword: cardiovascular disease
keyword: obo
keyword: ontology
has local unique identifier example: 0000546
has provider formatter: http://purl.obolibrary.org/obo/CVDO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: cvdo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-3336-2476
has URI prefix: http://purl.obolibrary.org/obo/CVDO_
has resource example: CVDO_0000546
has prefix: cvdo

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

DailyMed
type: Resource
description: DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.
is part of: bioregistry
has provider formatter: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm
has local unique identifier pattern: ^[A-Za-z0-9-]+$
is deprecated: false
has URI prefix: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm
has resource example: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm
has prefix: dailymed

DALIA Community
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A UUID for a community indexed in the Data Liteacy Alliance (DALIA) web application
is part of: bioregistry
has provider formatter: https://search.dalia.education/communities/$1
has local unique identifier pattern: ^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$
is deprecated: false
has URI prefix: https://search.dalia.education/communities/
has prefix: dalia.community

DALIA Open Educational Resource
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A UUID for an open educational resource indexed in the Data Liteacy Alliance (DALIA) web application
is part of: bioregistry
has provider formatter: https://search.dalia.education/items/$1
has local unique identifier pattern: ^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$
is deprecated: false
has URI prefix: https://search.dalia.education/items/
has prefix: dalia.oer

DAML Periodic Table of the Elements
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A representation of the periodic table of the elements in OWL, with both elements and a hierarchical classification. This is from the DARPA Agent Markup Language (DAML) project, which has been inactive since the mid 2000's.
is part of: bioregistry
keyword: ontology
has local unique identifier example: Be
has provider formatter: http://www.daml.org/2003/01/periodictable/PeriodicTable#$1
has download URL: PeriodicTable.owl
is deprecated: false
has URI prefix: http://www.daml.org/2003/01/periodictable/PeriodicTable#
has resource example: Be
has prefix: daml.pt

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
has local unique identifier example: 000017
has provider formatter: https://dandiarchive.org/dandiset/$1
has local unique identifier pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$
is deprecated: false
has responsible: Yaroslav Halchenko
has URI prefix: https://dandiarchive.org/dandiset/
has resource example: https://dandiarchive.org/dandiset/000017
has prefix: dandi

Database of Aligned Ribosomal Complexes
type: Resource
description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.
is part of: bioregistry
keyword: life science
has local unique identifier example: 1250
has provider formatter: http://darcsite.genzentrum.lmu.de/darc/view.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: Daniel N. Wilson
has URI prefix: http://darcsite.genzentrum.lmu.de/darc/view.php
has resource example: http://darcsite.genzentrum.lmu.de/darc/view.php
has prefix: darc

DASHR expression
type: Resource
description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.
is part of: bioregistry
has local unique identifier example: hsa-mir-200a
has provider formatter: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable
has local unique identifier pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
is deprecated: false
has URI prefix: https://bioregistry.io/dashr.expression:
has resource example: exprPerTissueTable
has prefix: dashr.expression

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

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
has local unique identifier example: Gene
has provider formatter: https://datacommons.org/browser/$1
is deprecated: false
has alternative prefix: dcid
has URI prefix: https://datacommons.org/browser/
has resource example: Gene
has prefix: datacommons

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
has local unique identifier example: 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/
has resource example: K00973
has prefix: datanator.gene

Datanator Metabolite
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
has local unique identifier example: OUYCCCASQSFEME-MRVPVSSYSA-N
has provider formatter: https://www.datanator.info/metabolite/$1
has local unique identifier pattern: ^[A-Z\-]+$
is deprecated: false
has URI prefix: https://www.datanator.info/metabolite/
has resource example: OUYCCCASQSFEME-MRVPVSSYSA-N
has prefix: datanator.metabolite

Datanator Reaction
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
has provider formatter: https://datanator.info/reaction/$1
has local unique identifier pattern: ^.*?--%3E.*?$
is deprecated: false
has URI prefix: https://datanator.info/reaction/
has resource example: XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N-->NBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N
has prefix: datanator.reaction

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

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
has local unique identifier example: 28463
has provider formatter: https://awi.cuhk.edu.cn/dbAMP/information.php
has local unique identifier pattern: ^\d{5}$
is deprecated: false
has responsible: Tzong-Yi Lee
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
has resource example: https://awi.cuhk.edu.cn/dbAMP/information.php
has prefix: dbamp

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
has local unique identifier example: 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:
has resource example: http://www.transcriptionfactor.org/index.cgi
has prefix: dbd

DBG2 Introns
type: Resource
description: The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.
is part of: bioregistry
keyword: dna
has local unique identifier example: Cu.me.I1
has provider formatter: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi
has local unique identifier pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$
is deprecated: true
has responsible: Steven John Zimmerly
has URI prefix: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi
has resource example: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi
has prefix: dbg2introns

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
has local unique identifier example: 199/2168
has provider formatter: https://dblp.org/pid/$1
is deprecated: false
has URI prefix: https://dblp.org/pid/
has resource example: https://dblp.org/pid/199/2168
has prefix: dblp.author

Database of human Major Histocompatibility Complex
type: Resource
description: Cell line databases/resources
is part of: bioregistry
has local unique identifier example: 48439
has local unique identifier pattern: ^\d+$
is deprecated: true
appears in: cellosaurus
has prefix: dbmhc

DBPedia Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki.
is part of: bioregistry
keyword: dbpedia
keyword: ontology
has local unique identifier example: careerPrizeMoney
has provider formatter: https://dbpedia.org/ontology/$1
is deprecated: false
has URI prefix: https://dbpedia.org/ontology/
has resource example: careerPrizeMoney
has prefix: dbo

DBPedia Property
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Properties in DBPedia.
is part of: bioregistry
has local unique identifier example: insertion
has provider formatter: http://dbpedia.org/property/$1
is deprecated: false
appears in: fovt
has URI prefix: http://dbpedia.org/property/
has resource example: insertion
has prefix: dbpedia.property

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
has local unique identifier example: 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/
has resource example: https://www.ncbi.nlm.nih.gov/probe/
has prefix: dbprobe

Database of Genomic Structural Variation - Study
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Studies in dbVar.
is part of: bioregistry
has local unique identifier example: 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/
has resource example: nstd102
has prefix: dbvar.study

Database of Genomic Structural Variation - Variant
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Variants in dbVar.
is part of: bioregistry
has local unique identifier example: 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/
has resource example: nsv3875336
has prefix: dbvar.variant

Dendritic cell
type: Resource
is part of: bioregistry
keyword: obo
keyword: ontology
has local unique identifier example: 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_
has resource example: DC CL 0000003
has prefix: dc_cl

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
has local unique identifier example: domainIncludes
has provider formatter: http://purl.org/dc/dcam/$1
is deprecated: false
has URI prefix: http://purl.org/dc/dcam/
has resource example: domainIncludes
has prefix: dcam

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: anatomy
keyword: cell
keyword: life science
keyword: obo
keyword: ontology
keyword: slime-mould
has local unique identifier example: 0000006
has provider formatter: http://purl.obolibrary.org/obo/DDANAT_$1
has local unique identifier pattern: ^\d{7}$
has download URL: ddanat.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-4532-2703
has URI prefix: http://purl.obolibrary.org/obo/DDANAT_
has resource example: DDANAT_0000006
has prefix: ddanat

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
has local unique identifier example: 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:
has resource example: e23
has prefix: ddc

Data Documentation Initiative Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A set of controlled vocabularies in the Data Documentation Initiative, each of which has its own code.
is part of: bioregistry
keyword: biomedical science
keyword: drug discovery
keyword: ontology
keyword: registry
has local unique identifier example: Instrument
has provider formatter: http://rdf-vocabulary.ddialliance.org/lifecycle#$1
has download URL: ddi.owl
is deprecated: false
has responsible: Larisa Soldatova
has URI prefix: http://rdf-vocabulary.ddialliance.org/lifecycle#
has resource example: Instrument
has prefix: ddi

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: chemistry
keyword: drugs
keyword: relationships
has local unique identifier example: DDInter20
has provider formatter: http://ddinter.scbdd.com/ddinter/drug-detail/$1
has local unique identifier pattern: ^DDInter\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-3604-3785
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://ddinter.scbdd.com/ddinter/drug-detail/
has resource example: DDInter20
has prefix: ddinter.drug

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: drug-drug interactions
keyword: drugs
keyword: relationships
has local unique identifier example: 1122888
has provider formatter: http://ddinter.scbdd.com/ddinter/interact/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-3604-3785
has URI prefix: http://ddinter.scbdd.com/ddinter/interact/
has resource example: http://ddinter.scbdd.com/ddinter/interact/1122888
has prefix: ddinter.interaction

Dictyostelium discoideum phenotype ontology
type: Resource
description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.
is part of: bioregistry
git repository: dicty-phenotype-ontology
keyword: anatomy
keyword: developmental biology
keyword: life science
keyword: microbe-host interaction phenotype
keyword: microbial ecology
keyword: obo
keyword: ontology
keyword: phenomics
keyword: phenotype
keyword: soil science
has local unique identifier example: 0001417
has provider formatter: http://purl.obolibrary.org/obo/DDPHENO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: ddpheno.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-4532-2703
has URI prefix: http://purl.obolibrary.org/obo/DDPHENO_
has resource example: DDPHENO_0001417
has prefix: ddpheno

Decentralized Biomedical Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON.
is part of: bioregistry
keyword: ontology
has local unique identifier example: 0000001
has provider formatter: https://biopragmatics.github.io/debio/$1
has local unique identifier pattern: ^\d{7}$
has download URL: debio.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-4423-4370
has alternative prefix: DeBiO
has URI prefix: https://biopragmatics.github.io/debio/
has resource example: https://biopragmatics.github.io/debio/0000001
has prefix: debio

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
has local unique identifier example: 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/
has resource example: Ax1
has prefix: degradome

Dynamic Ecological Information Management System - Site and Dataset Registry - Activity
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Activities in DEIMS SDR
is part of: bioregistry
has provider formatter: https://deims.org/activity/$1
has local unique identifier pattern: ^[0-9a-f\-]+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-0655-3699
has URI prefix: https://deims.org/activity/
has prefix: deims.activity

Dynamic Ecological Information Management System - Site and Dataset Registry - Dataset
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Datasets in DEIMS SDR
is part of: bioregistry
has provider formatter: https://deims.org/dataset/$1
has local unique identifier pattern: ^[0-9a-f\-]+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-0655-3699
has URI prefix: https://deims.org/dataset/
has prefix: deims.dataset

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: https://orcid.org/0000-0002-0655-3699
has URI prefix: https://deims.org/locations/
has prefix: deims.location

Dynamic Ecological Information Management System - Site and Dataset Registry - Network
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Networks in DEIMS SDR
is part of: bioregistry
has provider formatter: https://deims.org/networks/$1
has local unique identifier pattern: ^[0-9a-f\-]+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-0655-3699
has URI prefix: https://deims.org/networks/
has prefix: deims.network

Dynamic Ecological Information Management System - Site and Dataset Registry - Sensor
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Sensors in DEIMS SDR
is part of: bioregistry
has provider formatter: https://deims.org/sensors/$1
has local unique identifier pattern: ^[0-9a-f\-]+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-0655-3699
has URI prefix: https://deims.org/sensors/
has prefix: deims.sensor

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: https://orcid.org/0000-0002-0655-3699
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: deims.id
has URI prefix: https://deims.org/
has prefix: deims.site

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
has local unique identifier example: 21157
has provider formatter: https://deims.org/taxonomy/term/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-0655-3699
has URI prefix: https://deims.org/taxonomy/term/
has resource example: https://deims.org/taxonomy/term/21157
has prefix: deims.taxonomy

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
has local unique identifier example: PTPN1
has provider formatter: http://www.depod.bioss.uni-freiburg.de/showp.php
has local unique identifier pattern: ^[A-Z0-9]+$
provides for: hgnc.symbol
is deprecated: false
has responsible: General Enquiries
has URI prefix: http://www.depod.bioss.uni-freiburg.de/showp.php
has resource example: http://www.depod.bioss.uni-freiburg.de/showp.php
has prefix: depod

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: dermatology
keyword: disease
keyword: ontology
has local unique identifier example: 0000000
has provider formatter: http://purl.obolibrary.org/obo/DERMO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: dermo.obo
is deprecated: false
has responsible: https://orcid.org/0000-0002-5111-7263
has URI prefix: http://purl.obolibrary.org/obo/DERMO_
has resource example: DERMO_0000000
has prefix: dermo

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

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/
has resource example: 2017-03-24T18:43:16.886826-05:00
has prefix: dev.ga4ghdos

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
has local unique identifier example: 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
has resource example: https://www.devtox.org/nomenclature/ml_manus.php
has prefix: devtox

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: drosophila
keyword: genetic resource
keyword: genomics
keyword: organism supplier
has local unique identifier example: 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
has resource example: https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi
has prefix: dggr

Drosophila Genomics Resource Center
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: 215
has provider formatter: https://dgrc.bio.indiana.edu/product/View
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://dgrc.bio.indiana.edu/product/View
has resource example: https://dgrc.bio.indiana.edu/product/View
has prefix: dgrc

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: diabetes
keyword: omics
keyword: sample
has local unique identifier example: 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: Jiang-hua Liu
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://bio.liclab.net/diabetesOmicdb/RNA-seq
has resource example: https://bio.liclab.net/diabetesOmicdb/RNA-seq
has prefix: diabetesomic

Dialnet article ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier of an article in Dialnet
is part of: bioregistry
has local unique identifier example: 262393
has provider formatter: https://dialnet.unirioja.es/servlet/articulo
is deprecated: false
has URI prefix: https://dialnet.unirioja.es/servlet/articulo
has resource example: https://dialnet.unirioja.es/servlet/articulo
has prefix: dialnet.article

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
has local unique identifier example: 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
has resource example: https://dialnet.unirioja.es/servlet/autor
has prefix: dialnet.author

Dialnet book ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier of a book in Dialnet
is part of: bioregistry
has local unique identifier example: 187021
has provider formatter: https://dialnet.unirioja.es/servlet/libro
is deprecated: false
has URI prefix: https://dialnet.unirioja.es/servlet/libro
has resource example: https://dialnet.unirioja.es/servlet/libro
has prefix: dialnet.book

Dialnet journal ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier of a journal in Dialnet
is part of: bioregistry
has local unique identifier example: 1119
has provider formatter: https://dialnet.unirioja.es/servlet/revista
has local unique identifier pattern: ^[1-9]\d{0,6}$
is deprecated: false
has URI prefix: https://dialnet.unirioja.es/servlet/revista
has resource example: https://dialnet.unirioja.es/servlet/revista
has prefix: dialnet.journal

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
has local unique identifier example: 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
has resource example: http://dictybase.org/db/cgi-bin/feature_page.pl
has prefix: dictybase.est

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
has local unique identifier example: 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:
has resource example: did:sov:WRfXPg8dantKVubE3HX8pw
has prefix: did

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: biochemistry
keyword: drug interaction
keyword: evidence
keyword: natural product
keyword: obo
keyword: ontology
has local unique identifier example: 00000180
has provider formatter: http://purl.obolibrary.org/obo/DIDEO_$1
has local unique identifier pattern: ^\d{8}$
has download URL: dideo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-1834-3856
has URI prefix: http://purl.obolibrary.org/obo/DIDEO_
has resource example: DIDEO_00000180
has prefix: dideo

DigitRubber Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology demonstrating rich ontology for rubber extrusion.
is part of: bioregistry
git repository: DIGIT-RUBBER
keyword: ontology
has local unique identifier example: 000040
has provider formatter: https://www.tib.eu/digitrubber#DIGITRUBBER_$1
has download URL: digitrubber.owl
is deprecated: false
has URI prefix: https://www.tib.eu/digitrubber#DIGITRUBBER_
has resource example: DIGITRUBBER_000040
has prefix: digitrubber

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

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: biology
keyword: interaction
keyword: protein
has local unique identifier example: 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: David Eisenberg
has URI prefix: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi
has resource example: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi
has prefix: dip

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

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
has local unique identifier example: 0000000
has provider formatter: http://purl.obolibrary.org/obo/DISDRIV_$1
has local unique identifier pattern: ^\d+$
has download URL: disdriv.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-8910-9851
has URI prefix: http://purl.obolibrary.org/obo/DISDRIV_
has resource example: DISDRIV_0000000
has prefix: disdriv

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
has local unique identifier example: 0000598
has provider formatter: https://biopragmatics.github.io/providers/diseaseclass/$1
has local unique identifier pattern: ^\d{7}$
has download URL: missing-omc.obo
is deprecated: true
appears in: efo
has URI prefix: https://biopragmatics.github.io/providers/diseaseclass/
has resource example: https://biopragmatics.github.io/providers/diseaseclass/0000598
has prefix: diseaseclass

Diseases Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities.
is part of: bioregistry
has local unique identifier example: 1784
has provider formatter: https://www.diseasesdatabase.com/ddb$1.htm
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://bioregistry.io/diseasesdb:
has resource example: ddb1784.htm
has prefix: diseasesdb

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

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

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: bibliometrics
keyword: cultural heritage
keyword: digital humanities
keyword: publishing
has local unique identifier example: 20.500.14351/5a7cdd09d9b65bc39697
has provider formatter: https://docid.africapidalliance.org/docid/$1
is deprecated: false
has responsible: Joy Owango
has alternative prefix: DOCiD
has URI prefix: https://docid.africapidalliance.org/docid/
has identifier space owner: 02y9nww90
has resource example: https://docid.africapidalliance.org/docid/20.500.14351/5a7cdd09d9b65bc39697
has prefix: docid

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

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

DOME Registry
type: Resource
contributor: 0009-0008-8406-631X
description: The DOME registry is a curated set of papers related to machine learning methods in biology, each with its own unique DOME identifier.
is part of: bioregistry
has local unique identifier example: dfyn1yvtz3
has provider formatter: https://registry.dome-ml.org/review/$1
has local unique identifier pattern: ^[a-z0-9]{10}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4525-7793
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://registry.dome-ml.org/review/
has resource example: dfyn1yvtz3
has prefix: dome

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
has local unique identifier example: 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/
has resource example: 2GC4
has prefix: dommino

Database for Prokaryotic Operons
type: Resource
description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes.
is part of: bioregistry
keyword: dna
has local unique identifier example: 1398574
has provider formatter: http://csbl.bmb.uga.edu/DOOR/operon.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: http://csbl.bmb.uga.edu/DOOR/operon.php
has resource example: http://csbl.bmb.uga.edu/DOOR/operon.php
has prefix: door

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
has local unique identifier example: 57
has provider formatter: http://doqcs.ncbs.res.in/template.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-1722-5188
has URI prefix: http://doqcs.ncbs.res.in/template.php
has resource example: http://doqcs.ncbs.res.in/template.php
has prefix: doqcs.model

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
has local unique identifier example: 131
has provider formatter: http://doqcs.ncbs.res.in/template.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-1722-5188
has URI prefix: http://doqcs.ncbs.res.in/template.php
has resource example: http://doqcs.ncbs.res.in/template.php
has prefix: doqcs.pathway

Description of Plant Viruses
type: Resource
contributor: https://orcid.org/0000-0002-2404-1582
contributor: https://orcid.org/0000-0003-4423-4370
description: Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.
is part of: bioregistry
keyword: classification
keyword: gene
has local unique identifier example: 100
has provider formatter: https://www.dpvweb.net/dpv/showdpv/
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Michael J. Adams
has URI prefix: https://www.dpvweb.net/dpv/showdpv/
has resource example: https://www.dpvweb.net/dpv/showdpv/
has prefix: dpv

Data Quality Vocabulary
type: Resource
description: The Data Quality Vocabulary (DQV) is seen as an extension to DCAT to cover the quality of the data, how frequently is it updated, whether it accepts user corrections, persistence commitments etc. When used by publishers, this vocabulary will foster trust in the data amongst developers.
is part of: bioregistry
keyword: quality
has local unique identifier example: QualityAnnotation
is deprecated: false
has prefix: dqv

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
has local unique identifier example: 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:
has resource example: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
has prefix: dragondb.allele

DragonDB DNA
type: Resource
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information.
is part of: bioregistry
has local unique identifier example: 3hB06
has provider formatter: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
has local unique identifier pattern: ^\d\w+$
is deprecated: true
has URI prefix: https://bioregistry.io/dragondb.dna:
has resource example: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
has prefix: dragondb.dna

DragonDB Locus
type: Resource
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.
is part of: bioregistry
has local unique identifier example: DEF
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.locus:
has resource example: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
has prefix: dragondb.locus

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
has local unique identifier example: 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:
has resource example: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB
has prefix: dragondb.protein

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
has local unique identifier example: 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: Heng Zheng
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://dramp.cpu-bioinfor.org/browse/All_Information.php
has resource example: http://dramp.cpu-bioinfor.org/browse/All_Information.php
has prefix: dramp

Domain Resource Application Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A project supporting the DRAO application ontology, a hierarchy of specific research domains and descriptors which imports subsets of terms from over 40 publicly-available terminologies. (from repository)
is part of: bioregistry
git repository: domain-ontology
keyword: agriculture
keyword: biomedical science
keyword: classification
keyword: computer science
keyword: earth science
keyword: environmental science
keyword: fair
keyword: humanities
keyword: life science
keyword: metadata standardization
keyword: natural science
keyword: ontology
keyword: resource metadata
has local unique identifier example: 0000001
has provider formatter: http://www.fairsharing.org/ontology/domain/DRAO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: DRAO.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-7702-4495
has URI prefix: http://www.fairsharing.org/ontology/domain/DRAO_
has resource example: DRAO_0000001
has prefix: drao

Dutch Research Council File Number
type: Resource
contributor: https://orcid.org/0000-0001-7542-0286
description: Dutch Research Council file numbers are used for approved grants.
is part of: bioregistry
has local unique identifier example: 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/
has resource example: osf232097
has prefix: drc.filenumber

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

AnVIL DRS
type: Resource
description: This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research.
is part of: bioregistry
has provider formatter: https://data.terra.bio/ga4gh/drs/v1/objects/$1
has local unique identifier pattern: ^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$
is deprecated: false
has URI prefix: https://data.terra.bio/ga4gh/drs/v1/objects/
has prefix: drsanv0

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
has local unique identifier example: 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
has resource example: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl
has prefix: drsc

DrugBank Target v4
type: Resource
description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.
is part of: bioregistry
has local unique identifier example: BE0000048
has provider formatter: https://go.drugbank.com/bio_entities/$1
has local unique identifier pattern: ^BE\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has alternative prefix: drugbank.target
has alternative prefix: drugbankv4.target
has URI prefix: https://go.drugbank.com/bio_entities/
has resource example: https://go.drugbank.com/bio_entities/BE0000048
has prefix: drugbank.bioentity

DrugBank Drug Category
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Close to 5K Categorizations for drugs, similar to ATCC.
is part of: bioregistry
keyword: chemistry
keyword: drugs
keyword: metascience
keyword: topics
has local unique identifier example: DBCAT000600
has provider formatter: https://www.drugbank.ca/categories/$1
has local unique identifier pattern: ^DBCAT\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has URI prefix: https://www.drugbank.ca/categories/
has resource example: DBCAT000600
has prefix: drugbank.category

DrugBank Condition
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Indications and other conditions in drugbank
is part of: bioregistry
has local unique identifier example: DBCOND0066902
has provider formatter: https://go.drugbank.com/indications/$1
has local unique identifier pattern: ^DBCOND\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has URI prefix: https://go.drugbank.com/indications/
has resource example: DBCOND0066902
has prefix: drugbank.condition

DrugBank Metabolite
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Metabolites in drugbank
is part of: bioregistry
has local unique identifier example: DBMET02292
has provider formatter: https://go.drugbank.com/metabolites/$1
has local unique identifier pattern: ^DBMET\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has URI prefix: https://go.drugbank.com/metabolites/
has resource example: DBMET02292
has prefix: drugbank.metabolite

DrugBank Reaction
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Reactions in drugbank
is part of: bioregistry
has local unique identifier example: 1537
has provider formatter: https://go.drugbank.com/reactions/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has URI prefix: https://go.drugbank.com/reactions/
has resource example: https://go.drugbank.com/reactions/1537
has prefix: drugbank.reaction

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: compound
keyword: salt
keyword: small molecule
has local unique identifier example: DBSALT001211
has provider formatter: https://go.drugbank.com/salts/$1
has local unique identifier pattern: ^DBSALT\d{6}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has URI prefix: https://go.drugbank.com/salts/
has resource example: DBSALT001211
has prefix: drugbank.salt

Diagnostic and Statistical Manual of Mental Disorders (4th 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
has local unique identifier example: 315.1
has local unique identifier pattern: ^\d+\.\d+$
is deprecated: false
has alternative prefix: dsm-iv
has prefix: dsm4

Deutsche Sammlung von Mikroorganismen und Zellkulturen
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers: - `PC`: positive control - `NC`: negative control - `AS`: antiserum - `PV`: plant viruses - `RT`: recommended test - `ACC`: human or animal cell line - `DSM`: microorganism cell line
is part of: bioregistry
has local unique identifier example: ACC-1
has provider formatter: https://www.dsmz.de/collection/catalogue/details/culture/$1
has local unique identifier pattern: ^(ACC|DSM|NC|PC|RT|AS|PV)-\d+$
is deprecated: false
has alternative prefix: DSMZCellDive
has URI prefix: https://www.dsmz.de/collection/catalogue/details/culture/
has resource example: ACC-1
has prefix: dsmz

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: earth sciences
keyword: ess
keyword: fair data spaces
keyword: life sciences, biology
has local unique identifier example: DriedSpecimen
has provider formatter: http://purl.org/dsw/$1
is deprecated: false
has responsible: Steve Baskauf
has URI prefix: http://purl.org/dsw/
has resource example: DriedSpecimen
has prefix: dsw

Drug Target Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.
is part of: bioregistry
git repository: DTO
keyword: biomedical science
keyword: disease
keyword: drug discovery
keyword: drug target
keyword: ontology
keyword: protein
has local unique identifier example: 90000018
has provider formatter: http://www.drugtargetontology.org/dto/DTO_$1
has local unique identifier pattern: ^\d+$
has download URL: dto.owl
is deprecated: false
appears in: pr
has responsible: Stephan Schurer
has URI prefix: http://www.drugtargetontology.org/dto/DTO_
has resource example: DTO_90000018
has prefix: dto

Darwin Core Terms
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Darwin Core is a vocabulary standard for transmitting information about biodiversity. This document lists all terms in namespaces currently used in the vocabulary.
is part of: bioregistry
git repository: dwc
keyword: biodiversity
keyword: geographic location
keyword: life science
keyword: sample annotation
keyword: taxonomic classification
has local unique identifier example: Dataset
has provider formatter: http://rs.tdwg.org/dwc/terms/$1
is deprecated: false
has responsible: John Wieczorek
has URI prefix: http://rs.tdwg.org/dwc/terms/
has resource example: Dataset
has prefix: dwc

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
has local unique identifier example: 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/
has resource example: d001
has prefix: dwc.doe

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
has local unique identifier example: 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/
has resource example: e001
has prefix: dwc.em

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: fair data spaces
keyword: life sciences, biology
has local unique identifier example: 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/
has resource example: p001
has prefix: dwc.pw

eagle-i
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Discovery tool for biomedical research resources available at institutions throughout the U.S.
is part of: bioregistry
has provider formatter: http://hawaii.eagle-i.net/i/$1
is deprecated: true
has URI prefix: http://hawaii.eagle-i.net/i/
has prefix: eaglei

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
has local unique identifier example: Assertion
has provider formatter: http://www.w3.org/ns/earl#$1
is deprecated: false
has URI prefix: http://www.w3.org/ns/earl#
has resource example: Assertion
has prefix: earl

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
has local unique identifier example: 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_
has resource example: AUT_0000001
has prefix: earthcube.aut

Data Model Language Controlled Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Data Model Language Controlled Vocabulary was created for NSF's EarthCube Program's Resource Registry. At this point it merely lists a few of the languages used by data model resources in the registry.
is part of: bioregistry
git repository: mola
keyword: metamodel
has local unique identifier example: 000001
has provider formatter: http://cor.esipfed.org/ont/earthcube/MOLA_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4808-4736
has URI prefix: http://cor.esipfed.org/ont/earthcube/MOLA_
has resource example: MOLA_000001
has prefix: earthcube.mola

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
has local unique identifier example: 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_
has resource example: SFO_0000001
has prefix: earthcube.sfo

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
has local unique identifier example: 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_
has resource example: srt_000001
has prefix: earthcube.srt

Software Licenses Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This mini-ontology contains classes and instances for each version of the licenses that are commonly used in software projects, particularly open source software projects. The URI's for each are the canonical URI's for that license (where they exist).
is part of: bioregistry
git repository: swl
keyword: license
has local unique identifier example: 0000013
has provider formatter: http://cor.esipfed.org/ont/SWL_$1
has local unique identifier pattern: ^\d{7}$
is deprecated: true
has responsible: https://orcid.org/0000-0003-4808-4736
has URI prefix: http://cor.esipfed.org/ont/SWL_
has resource example: SWL_0000013
has prefix: earthcube.swl

EasyChair Call for Paper
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Conferences in EasyChair
is part of: bioregistry
keyword: conferences
keyword: metascience
has local unique identifier example: SysBioCancer2022
has provider formatter: https://easychair.org/cfp/$1
is deprecated: false
has URI prefix: https://easychair.org/cfp/
has resource example: SysBioCancer2022
has prefix: easychair.cfp

EasyChair Topic
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Call for paper topics in EasyChair
is part of: bioregistry
keyword: metascience
keyword: topics
has local unique identifier example: 27106865
has provider formatter: https://easychair.org/cfp/topic.cgi
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://easychair.org/cfp/topic.cgi
has resource example: https://easychair.org/cfp/topic.cgi
has prefix: easychair.topic

European Bank for induced pluripotent Stem Cells
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: ESi007-A
has provider formatter: https://cells.ebisc.org/$1
has local unique identifier pattern: ^E(S|D)i\d+-\w$
is deprecated: false
has URI prefix: https://cells.ebisc.org/
has resource example: ESi007-A
has prefix: ebisc

Electrocardiogram Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.
is part of: bioregistry
keyword: biomedical science
keyword: electrocardiography
keyword: heart
keyword: ontology
has local unique identifier example: 000000159
has provider formatter: http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1
has local unique identifier pattern: ^\d+$
has download URL: ecg.owl
is deprecated: false
has responsible: Raimond Winslow
has alternative prefix: ECGOntology
has URI prefix: http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_
has resource example: ECG_000000159
has prefix: ecg

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
has local unique identifier example: 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
has resource example: https://www.echinobase.org/entry/gene/showgene.do
has prefix: echinobase

EchoBASE post-genomic database for Escherichia coli
type: Resource
description: EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.
is part of: bioregistry
keyword: gene
keyword: gene expression
has local unique identifier example: EB0170
has provider formatter: http://www.york.ac.uk/res/thomas/Gene.cfm
has local unique identifier pattern: ^EB\d+$
is deprecated: false
has responsible: Gavin H. Thomas
has URI prefix: http://www.york.ac.uk/res/thomas/Gene.cfm
has resource example: http://www.york.ac.uk/res/thomas/Gene.cfm
has prefix: echobase

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: educational resources
keyword: literature
has local unique identifier example: 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_
has resource example: notation 004.11.00.0100
has prefix: eclas

EC number
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for a chemical compound per EINECS or ELINCS
is part of: bioregistry
has local unique identifier example: 200-003-9
has provider formatter: https://www.echa.europa.eu/information-on-chemicals/ec-inventory/-/dislist/details/$1
has local unique identifier pattern: ^\d{3}-\d{3}-\d$
is deprecated: false
has URI prefix: https://www.echa.europa.eu/information-on-chemicals/ec-inventory/-/dislist/details/
has resource example: https://www.echa.europa.eu/information-on-chemicals/ec-inventory/-/dislist/details/200-003-9
has prefix: ecn

Evidence and Conclusion Ontology
type: Resource
contributor: Curtis Ross
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: biocuration
keyword: computational biology
keyword: curated information
keyword: digital curation
keyword: evidence
keyword: life science
keyword: literature curation
keyword: obo
keyword: ontology
keyword: resource metadata
keyword: sample annotation
keyword: study design
keyword: text mining
has local unique identifier example: 0007807
has provider formatter: http://purl.obolibrary.org/obo/ECO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: eco.owl
is deprecated: false
has responsible: Michelle Giglio
has URI prefix: http://purl.obolibrary.org/obo/ECO_
has resource example: ECO_0007807
has prefix: eco

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

EcoLexicon
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology.
is part of: bioregistry
keyword: ecology
keyword: environmental science
has local unique identifier example: canal
is deprecated: false
has prefix: ecolexicon

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: bioinformatics
keyword: genomics
keyword: life science
keyword: ontology and terminology
has local unique identifier example: 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: https://orcid.org/0000-0002-5876-6418
has URI prefix: https://bioregistry.io/ecoliwiki:
has resource example: aaeA:Gene
has prefix: ecoliwiki

The Ecosystem Ontology
type: Resource
description: DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases
is part of: bioregistry
git repository: sem-prov-ontologies
keyword: chemical and environmental engineering
keyword: earth science
keyword: earth sciences
keyword: ecosystem
keyword: ecosystem science
keyword: ess
keyword: fair data spaces
keyword: ontology
has local unique identifier example: 00000532
has provider formatter: http://purl.dataone.org/odo/ECSO_$1
has local unique identifier pattern: ^\d+$
has download URL: d1-ECSO.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-0381-3766
has URI prefix: http://purl.dataone.org/odo/ECSO_
has resource example: ECSO_00000532
has prefix: ecso

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
has local unique identifier example: 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/
has resource example: https://www.e-cyanobacterium.org/bcs/entity/23
has prefix: ecyano.entity

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
has local unique identifier example: 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/
has resource example: https://www.e-cyanobacterium.org/experiments-repository/
has prefix: ecyano.experiment

E-cyanobacterium model
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 models.
is part of: bioregistry
has local unique identifier example: 26
has provider formatter: https://e-cyanobacterium.org/models/model/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://e-cyanobacterium.org/models/model/
has resource example: https://e-cyanobacterium.org/models/model/26
has prefix: ecyano.model

E-cyanobacterium rule
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 rules.
is part of: bioregistry
has local unique identifier example: 56
has provider formatter: https://e-cyanobacterium.org/bcs/rule/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://e-cyanobacterium.org/bcs/rule/
has resource example: https://e-cyanobacterium.org/bcs/rule/56
has prefix: ecyano.rule

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
has local unique identifier example: 1664
has provider formatter: http://edamontology.org/data_$1
has local unique identifier pattern: ^\d+$
has download URL: EDAM.obo
is deprecated: false
has responsible: https://orcid.org/0000-0002-1509-4981
has URI prefix: http://edamontology.org/data_
has resource example: data 1664
has prefix: edam.data

EDAM Format
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.
is part of: bioregistry
git repository: edamontology
keyword: ontology
has local unique identifier example: 1915
has provider formatter: http://edamontology.org/format_$1
has local unique identifier pattern: ^\d+$
has download URL: EDAM.obo
is deprecated: false
has responsible: https://orcid.org/0000-0002-1509-4981
has URI prefix: http://edamontology.org/format_
has resource example: format 1915
has prefix: edam.format

EDAM Operation
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.
is part of: bioregistry
git repository: edamontology
keyword: ontology
has local unique identifier example: 0004
has provider formatter: http://edamontology.org/operation_$1
has local unique identifier pattern: ^\d+$
has download URL: EDAM.obo
is deprecated: false
has responsible: https://orcid.org/0000-0002-1509-4981
has URI prefix: http://edamontology.org/operation_
has resource example: operation_0004
has prefix: edam.operation

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
has local unique identifier example: 0003
has provider formatter: http://edamontology.org/topic_$1
has local unique identifier pattern: ^\d+$
has download URL: EDAM.obo
is deprecated: false
has responsible: https://orcid.org/0000-0002-1509-4981
has URI prefix: http://edamontology.org/topic_
has resource example: topic_0003
has prefix: edam.topic

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
has local unique identifier example: 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_
has resource example: c 00098e55
has prefix: edcc

EDDA Study Designs Taxonomy
type: Resource
description: Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries.
is part of: bioregistry
keyword: medicine
keyword: ontology
has local unique identifier example: health_care_quality_assessment
has provider formatter: http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1
has download URL: edda.owl
is deprecated: false
has responsible: Tanja Bekhuis
has URI prefix: http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#
has resource example: health care quality assessment
has prefix: edda

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: coypu
keyword: economics
has local unique identifier example: 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/
has resource example: BEDomain
has prefix: edm.fibo

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
has local unique identifier example: 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#
has resource example: stri
has prefix: educor

European Genome-phenome Archive
type: Resource
description: The European Genome-phenome Archive (EGA) is a global network for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems. Jointly managed by the European Bioinformatics Institute (EMBL-EBI) in Cambridge (UK) and the Centre for Genomic Regulation (CRG) in Barcelona.
is part of: bioregistry
has local unique identifier example: EGAD00001008392
has provider formatter: https://ega-archive.org/identifiers/$1
has local unique identifier pattern: ^EGA[SCPNRXZDBF][0-9]{11}$
is deprecated: false
has URI prefix: https://ega-archive.org/identifiers/
has resource example: EGAD00001008392
has prefix: ega

eggNOG
type: Resource
description: eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).
is part of: bioregistry
keyword: gene
keyword: life science
has local unique identifier example: veNOG12876
has provider formatter: http://eggnog.embl.de/version_3.0/cgi/search.py
has local unique identifier pattern: ^\w+$
is deprecated: true
has responsible: Jaime Huerta-Cepas
has URI prefix: http://eggnog.embl.de/version_3.0/cgi/search.py
has resource example: http://eggnog.embl.de/version_3.0/cgi/search.py
has prefix: eggnog

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: anatomy
keyword: development
keyword: human
keyword: obo
keyword: ontology
has local unique identifier example: 1
has provider formatter: http://purl.obolibrary.org/obo/EHDA_$1
has local unique identifier pattern: ^\d+$
has download URL: ehda.obo
is deprecated: true
has responsible: Jonathan Bard
has URI prefix: http://purl.obolibrary.org/obo/EHDA_
has resource example: EHDA 1
has prefix: ehda

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: anatomy
keyword: development
keyword: human
keyword: obo
keyword: ontology
has local unique identifier example: 1
has provider formatter: http://purl.obolibrary.org/obo/EHDAA_$1
has local unique identifier pattern: ^\d+$
has download URL: ehdaa.obo
is deprecated: true
has responsible: Jonathan Bard
has URI prefix: http://purl.obolibrary.org/obo/EHDAA_
has resource example: EHDAA 1
has prefix: ehdaa

European Joint Programme for Rare Disease Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This ontology is designed to support data search, retrieval and information identification in the EJP-RD catalogs which covers the registries and biobanks for rare diseases. (from repository)
is part of: bioregistry
git repository: EJP-Ontology
keyword: ontology
has local unique identifier example: alternative_term
has provider formatter: http://purl.org/ejp-rd/vocabulary/$1
has download URL: ejp-rd.owl
is deprecated: false
has URI prefix: http://purl.org/ejp-rd/vocabulary/
has resource example: alternative term
has prefix: ejprd

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: contracts
keyword: frbr
has local unique identifier example: InForce
has provider formatter: http://data.europa.eu/eli/ontology#$1
is deprecated: false
has URI prefix: http://data.europa.eu/eli/ontology#
has resource example: InForce
has prefix: eli

Eukaryotic Linear Motif Resource
type: Resource
description: Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances.
is part of: bioregistry
keyword: life science
has local unique identifier example: CLV_MEL_PAP_1
has provider formatter: http://elm.eu.org/elms/elmPages/$1.html
has local unique identifier pattern: ^[A-Za-z_0-9]+$
is deprecated: false
has responsible: Toby J Gibson
has URI prefix: https://bioregistry.io/elm:
has resource example: CLV MEL PAP 1.html
has prefix: elm

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: Alen Vodopijevec
has URI prefix: https://elsst.cessda.eu/id/3/
has prefix: elsst

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

European Medicines Evaluation Agency
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Product number for the European Medicines Agency
is part of: bioregistry
has local unique identifier example: EMEA/H/C/000181
is deprecated: false
has prefix: emea

Reaxys eMolecules
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Catalog of purchasable reagents and building blocks
is part of: bioregistry
keyword: chemistry
keyword: reagents
keyword: vendor
has local unique identifier example: 491187
has provider formatter: https://reaxys.emolecules.com/cgi-bin/more
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://reaxys.emolecules.com/cgi-bin/more
has resource example: https://reaxys.emolecules.com/cgi-bin/more
has prefix: emolecules

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
has local unique identifier example: 00000085
has provider formatter: http://purl.obolibrary.org/obo/EMPTY_$1
has local unique identifier pattern: ^\d+$
has download URL: empty.owl
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/EMPTY_
has resource example: EMPTY_00000085
has prefix: empty

Environmental Molecular Sciences Laboratory Project
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
contributor: Cody O'Donnell
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
has local unique identifier example: 60141
has provider formatter: https://sc-data.emsl.pnnl.gov/
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Montana Smith
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://sc-data.emsl.pnnl.gov/
has resource example: https://sc-data.emsl.pnnl.gov/
has prefix: emsl.project

Encyclopedia of DNA Elements
type: Resource
description: The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.
is part of: bioregistry
keyword: epigenetics
keyword: functional genomics
has local unique identifier example: ENCSR163RYW
has provider formatter: https://www.encodeproject.org/$1
has local unique identifier pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$
is deprecated: false
has responsible: Idan Gabdank
has URI prefix: https://www.encodeproject.org/
has resource example: ENCSR163RYW
has prefix: encode

Ensembl Bacteria
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 bacterial genomes.
is part of: bioregistry
keyword: comparative genomics
keyword: genome
keyword: genomics
has local unique identifier example: MU9_3181
has provider formatter: https://bacteria.ensembl.org/id/$1
has local unique identifier pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3897-7955
has URI prefix: https://bacteria.ensembl.org/id/
has resource example: MU9 3181
has prefix: ensembl.bacteria

Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi.
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 fungal genomes.
is part of: bioregistry
keyword: comparative genomics
keyword: genome
keyword: genomics
has local unique identifier example: CADAFLAT00006211
has provider formatter: https://fungi.ensembl.org/id/$1
has local unique identifier pattern: ^[A-Z-a-z0-9]+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3897-7955
has URI prefix: https://fungi.ensembl.org/id/
has resource example: CADAFLAT00006211
has prefix: ensembl.fungi

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
has local unique identifier example: 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/
has resource example: PF3D7_1328700
has prefix: ensembl.protist

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
has local unique identifier example: 0000198
has provider formatter: http://ensembl.org/glossary/ENSGLOSSARY_$1
has local unique identifier pattern: ^\d{7}$
has download URL: ensembl-glossary.owl
is deprecated: false
has URI prefix: http://ensembl.org/glossary/ENSGLOSSARY_
has resource example: ENSGLOSSARY_0000198
has prefix: ensemblglossary

enviPath
type: Resource
description: enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products.
is part of: bioregistry
keyword: environmental science
has provider formatter: https://envipath.org/package/$1
has local unique identifier pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$
is deprecated: false
has responsible: Jörg Wicker
has URI prefix: https://envipath.org/package/
has prefix: envipath

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: earth sciences
keyword: ecology
keyword: environmental science
keyword: ess
keyword: geochemistry
keyword: geographic location
keyword: monitoring
keyword: natural science
keyword: observations
keyword: ontology
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/
has prefix: envthes

Enzo Life Sciences
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Enzo Life Sciences is an antibody vendor.
is part of: bioregistry
keyword: antibodies
keyword: life sciences
keyword: vendor
has local unique identifier example: ALX-210-175
has provider formatter: https://www.enzolifesciences.com/$1
is deprecated: false
has alternative prefix: Enzo Life Sciences
has URI prefix: https://www.enzolifesciences.com/
has resource example: ALX-210-175
has prefix: enzo

Environment Ontology for Livestock
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems.
is part of: bioregistry
keyword: agriculture
keyword: animal husbandry
keyword: environmental science
keyword: livestock
keyword: ontology
keyword: species-environment interaction
has local unique identifier example: 0001927
has provider formatter: http://purl.org/obo/owlEOL_$1
has local unique identifier pattern: ^\d{7}$
has download URL: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php
is deprecated: false
has responsible: https://orcid.org/0000-0002-8310-5195
has URI prefix: http://purl.org/obo/owlEOL_
has resource example: owlEOL_0001927
has prefix: eol

Encyclopedia of Life Schema
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Predicates in the Encyclopedia of Life data schema for describing animals, plants, and other organisms
is part of: bioregistry
has local unique identifier example: body_symmetry
has provider formatter: http://eol.org/schema/terms/$1
is deprecated: false
has URI prefix: http://eol.org/schema/terms/
has resource example: body symmetry
has prefix: eol.schema

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: biodiversity
keyword: biology
keyword: ecology
keyword: taxonomy
has local unique identifier example: 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/
has resource example: https://eol.org/pages/1044544
has prefix: eolife

EPA Hazardous Wastes
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: This resource provides identifiers for listed hazardous wastes which are substances explicitly identified due to their potential harm to human health and the environment. These are categorized into four groups (F, K, P, and U) based on specific criteria, such as their source or inherent properties.
is part of: bioregistry
has local unique identifier example: F001
has local unique identifier pattern: ^[FKPU]\d{3}$
is deprecated: false
has responsible: Tom Brennan
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: epawaste

European Paediatric Cardiac Codes
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Collection of European paediatric cardiac coding files
is part of: bioregistry
is deprecated: false
has prefix: epcc

Eukaryotic Promoter Database
type: Resource
contributor: 0000-0003-3947-488X
description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.
is part of: bioregistry
keyword: bioinformatics
keyword: biology
has local unique identifier example: TA_H3
has provider formatter: https://epd.expasy.org/cgi-bin/epd/query_result.pl
has local unique identifier pattern: ^[A-Z-_0-9]+$
is deprecated: false
has responsible: Philipp Bucher
has URI prefix: https://epd.expasy.org/cgi-bin/epd/query_result.pl
has resource example: https://epd.expasy.org/cgi-bin/epd/query_result.pl
has prefix: epd

Epidemiology Ontology
type: Resource
contributor: Jeremy Zucker
description: An ontology designed to support the semantic annotation of epidemiology resources
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/EPO_$1
has download URL: epo.owl
is deprecated: true
has URI prefix: http://purl.obolibrary.org/obo/EPO_
has prefix: epo

Epilepsy and Seizure Ontology
type: Resource
description: The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research.
is part of: bioregistry
keyword: epilepsy
keyword: neurology
keyword: ontology
keyword: patient care
has local unique identifier example: 0000400
has provider formatter: http://www.case.edu/EpilepsyOntology.owl#$1
has local unique identifier pattern: ^\d{7}$
has download URL: epso.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9190-4256
has URI prefix: http://www.case.edu/EpilepsyOntology.owl#
has resource example: http://www.case.edu/EpilepsyOntology.owl#0000400
has prefix: epso

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: chemical entity
keyword: materials informatics
keyword: materials science
keyword: nanotechnology
has local unique identifier example: 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: https://orcid.org/0000-0001-7542-0286
has URI prefix: https://nanocommons.github.io/identifiers/registry#
has resource example: ERM00000044
has prefix: erm

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: biomedical science
keyword: biospecimen
keyword: life science
keyword: obo
keyword: ontology
keyword: reagent
keyword: study design
has local unique identifier example: 0001655
has provider formatter: http://purl.obolibrary.org/obo/ERO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: ero.owl
is deprecated: true
has responsible: Marc Ciriello
has URI prefix: http://purl.obolibrary.org/obo/ERO_
has resource example: ERO_0001655
has prefix: ero

Endogenous Regulatory OligoPeptide knowledgebase-Moscow
type: Resource
description: EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.).
is part of: bioregistry
keyword: protein
has local unique identifier example: E00002
has provider formatter: http://erop.inbi.ras.ru/result2.php
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://erop.inbi.ras.ru/result2.php
has resource example: http://erop.inbi.ras.ru/result2.php
has prefix: eropmoscow

Educational Resource Discovery Index Schema
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A metadata stadnard to model data science training materials. Later, was replaced by Bioschemas' [training materials specification](http://bioschemas.org/specifications/TrainingMaterial/specification/).
is part of: bioregistry
keyword: educational resource
keyword: learning material
keyword: open educational resource
keyword: schema
has local unique identifier example: enables
has provider formatter: http://www.bigdatau.org/schema#$1
is deprecated: false
has URI prefix: http://www.bigdatau.org/schema#
has resource example: enables
has prefix: erudite

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
has local unique identifier example: 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/
has resource example: THE1B
has prefix: erv

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
has local unique identifier example: C4
has provider formatter: http://data.europa.eu/esco/isco/$1
is deprecated: false
has URI prefix: http://data.europa.eu/esco/isco/
has resource example: C4
has prefix: esco.isco

ESCO Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The ontology of the taxonomy "European Skills, Competences, qualifications and Occupations". The ontology considers three ESCO pillars (or taxonomy) and 2 registers. The three pillars are: 1) Occupation, 2) Skill (and competences), and 3) Qualification
is part of: bioregistry
has local unique identifier example: Occupation
has provider formatter: https://ec.europa.eu/esco/lod/static/model.html#$1
is deprecated: false
has URI prefix: https://ec.europa.eu/esco/lod/static/model.html#
has resource example: Occupation
has prefix: esco.model

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/
has prefix: esco.occupation

ESCO Skill
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary of knowledge, skills and competences relevant to the European labour market. In ESCO v1.2.0, the skills pillar is structured in a hierarchy which contains the following four sub-classifications: 1) Knowledge, 2) Language skills and knowledge, 3) Skills, and 4) Transversal skills. [adapted from homepage]
is part of: bioregistry
has provider formatter: http://data.europa.eu/esco/skill/$1
is deprecated: false
has URI prefix: http://data.europa.eu/esco/skill/
has prefix: esco.skill

eukaryotic Subcellular Localization database
type: Resource
description: eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.
is part of: bioregistry
keyword: protein
has local unique identifier example: HS000015122
has provider formatter: http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi
has resource example: http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi
has prefix: esldb

European Searchable Tumour Line Database
type: Resource
description: Cell line databases/resources
is part of: bioregistry
has local unique identifier example: 046
has provider formatter: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi
has local unique identifier pattern: ^\d{3}$
is deprecated: true
has URI prefix: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi
has identifier space owner: 02catss52
has resource example: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi
has prefix: estdab

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
has local unique identifier example: euvoc
has provider formatter: http://publications.europa.eu/resource/dataset/$1
is deprecated: false
has URI prefix: http://publications.europa.eu/resource/dataset/
has resource example: euvoc
has prefix: eu.publication

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
has local unique identifier example: 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/
has resource example: jrc-eurl-ecvam-chemagora
has prefix: eu89h

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
has local unique identifier example: EUB0000221
has provider formatter: https://gateway.eubopen.org/compound/$1
has local unique identifier pattern: ^EUB\d{7}$
is deprecated: false
has responsible: Claudia Tredup
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://gateway.eubopen.org/compound/
has resource example: EUB0000221
has prefix: eubopen

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: genome
keyword: life science
keyword: ontology
has local unique identifier example: MGgn0008978
has provider formatter: http://eugenes.org:7072/.bin/fbidq.html
is deprecated: false
has responsible: Don Gilbert
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://eugenes.org:7072/.bin/fbidq.html
has resource example: http://eugenes.org:7072/.bin/fbidq.html
has prefix: eugenes

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: educational resources
keyword: literature
keyword: social sciences
has local unique identifier example: 00b51s9rc5
has provider formatter: http://data.europa.eu/snb/dcf/$1
is deprecated: false
has URI prefix: http://data.europa.eu/snb/dcf/
has resource example: 00b51s9rc5
has prefix: europa.dcf

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
has local unique identifier example: 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/
has resource example: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/org-details/881104060
has prefix: europe.pic

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/
has prefix: euroscivoc

European Science Vocabulary Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Euvoc ontology, published by the Publications Office of the European Union, supports the development of authority tables (Name Authority Lists or NALs), Eurovoc and EU corporate datasets. It contains a set of classes and properties enabling all the information to be expressed in multilingual format. It helps define relationships between terms and concepts across multiple domains, supporting interoperability and standardization across European Union documentation and databases. It also defines a set a commonly use properties (i.e: start date, end dates, status), and supports the reusability on common data (currencies, languages, countries). The Euvoc ontology is maintained by the Publications Office of the European Union and disseminated on the EU Vocabularies website.
is part of: bioregistry
has local unique identifier example: isTextual
is deprecated: false
has prefix: euroscivoc.schema

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: agriculture
keyword: business administration
keyword: economics
keyword: employment
keyword: energy engineering
keyword: environmental science
keyword: fisheries science
keyword: food
keyword: forest management
keyword: geography
keyword: international relations
keyword: linguistics
keyword: political science
keyword: public finance
keyword: social policy
keyword: social science
keyword: trade
keyword: transport
keyword: transportation planning
has local unique identifier example: 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/
has resource example: http://eurovoc.europa.eu/1837
has prefix: eurovoc

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: cell
keyword: development
keyword: experiment
keyword: obo
keyword: ontology
has local unique identifier example: 0100011
has provider formatter: http://purl.obolibrary.org/obo/EV_$1
has local unique identifier pattern: ^\d{7}$
is deprecated: true
appears in: cl
has responsible: eVOC mailing list
has URI prefix: http://purl.obolibrary.org/obo/EV_
has resource example: EV_0100011
has prefix: ev

eVOC mouse development stage
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
is deprecated: true
has prefix: evm

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
has local unique identifier example: AlternateName
has provider formatter: https://w3id.org/evorao/$1
has download URL: evorao.owl
is deprecated: false
has responsible: d3fk
has URI prefix: https://w3id.org/evorao/
has resource example: AlternateName
has prefix: evorao

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
has local unique identifier example: 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/
has resource example: https://cthoyt.com/evr/0000001
has prefix: evr

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
has local unique identifier example: 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/
has resource example: ENSG00000169174
has prefix: exac.gene

ExAC Transcript
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 transcript information.
is part of: bioregistry
has local unique identifier example: ENST00000407236
has provider formatter: http://exac.broadinstitute.org/transcript/$1
has local unique identifier pattern: ^ENST\d{11}$
is deprecated: false
has URI prefix: http://exac.broadinstitute.org/transcript/
has resource example: ENST00000407236
has prefix: exac.transcript

Exif data description vocabulary
type: Resource
description: Vocabulary to describe an Exif format picture data. All Exif 2.2 tags are defined as RDF properties, as well as several terms to help this schema.
is part of: bioregistry
keyword: image
has local unique identifier example: orientation
is deprecated: false
has prefix: exif

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
has local unique identifier example: 0000008
has provider formatter: http://purl.obolibrary.org/obo/EXMO_$1
has download URL: exmo.owl
is deprecated: false
has responsible: Xingyun Liu
has URI prefix: http://purl.obolibrary.org/obo/EXMO_
has prefix: exmo

FaceBase Data Repository
type: Resource
description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.
is part of: bioregistry
keyword: anatomy
keyword: developmental biology
keyword: epigenetics
keyword: genetics
keyword: medicine
has local unique identifier example: FB00000917
has provider formatter: https://www.facebase.org/data/record/
has local unique identifier pattern: ^FB\d{8}$
is deprecated: false
has responsible: Yang Chai
has URI prefix: https://www.facebase.org/data/record/
has resource example: https://www.facebase.org/data/record/
has prefix: facebase

FactGrid
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A wikibase for linguistic knowledge
is part of: bioregistry
has local unique identifier example: Q24708
has provider formatter: https://database.factgrid.de/viewer/item/$1
has local unique identifier pattern: ^Q\d+$
is deprecated: false
has responsible: Olaf Simons
has URI prefix: https://database.factgrid.de/viewer/item/
has resource example: Q24708
has prefix: factgrid

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
has local unique identifier example: 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/
has resource example: https://fairsharing.org/organisations/3851
has prefix: fairsharing.organization

FAIRsharing User
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A user of FAIRsharing
is part of: bioregistry
has local unique identifier example: 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/
has resource example: https://fairsharing.org/users/5112
has prefix: fairsharing.user

Functional Genome Annotations with Transcriptional Activities
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Functional annotations of genomes for studying gene regulation, with a primary focus on cis-regulatory elements (CREs) such as promoters and enhancers.
is part of: bioregistry
has local unique identifier example: FCHS_301358
has provider formatter: https://fanta.bio/cre/$1
has local unique identifier pattern: ^FC(HS|MM)_\d+$
is deprecated: false
has responsible: Takeya Kasukawa
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://fanta.bio/cre/
has resource example: FCHS_301358
has prefix: fanta

Fungal gross anatomy
type: Resource
description: A structured controlled vocabulary for the anatomy of fungi.
is part of: bioregistry
git repository: fungal-anatomy-ontology
keyword: anatomy
keyword: fungi
keyword: life science
keyword: microbiology
keyword: obo
keyword: ontology
has local unique identifier example: 0000001
has provider formatter: http://purl.obolibrary.org/obo/FAO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: fao.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-6330-7526
has URI prefix: http://purl.obolibrary.org/obo/FAO_
has resource example: FAO_0000001
has prefix: fao

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
has local unique identifier example: 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/
has resource example: https://www.fao.org/fishery/en/species/20560
has prefix: fao.asfis

Drosophila gross anatomy
type: Resource
description: An ontology representing the gross anatomy of Drosophila melanogaster.
is part of: bioregistry
git repository: drosophila-anatomy-developmental-ontology
keyword: anatomy
keyword: developmental biology
keyword: fly
keyword: gene expression
keyword: life cycle stage
keyword: life science
keyword: obo
keyword: ontology
keyword: phenotype
has local unique identifier example: 00007294
has provider formatter: http://purl.obolibrary.org/obo/FBbt_$1
has local unique identifier pattern: ^\d{8}$
has download URL: fbbt.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1373-1705
has alternative prefix: FBbt
has alternative prefix: FBbt_root
has URI prefix: http://purl.obolibrary.org/obo/FBbt_
has resource example: FBbt_00007294
has prefix: fbbt

Drosophila development
type: Resource
description: A structured controlled vocabulary of the development of Drosophila melanogaster.
is part of: bioregistry
git repository: drosophila-developmental-ontology
keyword: development
keyword: developmental biology
keyword: fly
keyword: life cycle
keyword: life cycle stage
keyword: life science
keyword: obo
keyword: ontology
has local unique identifier example: 00000000
has provider formatter: http://purl.obolibrary.org/obo/FBdv_$1
has local unique identifier pattern: ^\d{8}$
has download URL: fbdv.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1373-1705
has alternative prefix: FBdv
has URI prefix: http://purl.obolibrary.org/obo/FBdv_
has resource example: FBdv_00000000
has prefix: fbdv

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
has local unique identifier example: 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:
has prefix: fbol

FlyBase Qualifiers
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
has local unique identifier example: 00005254
has local unique identifier pattern: ^\d+$
is deprecated: true
has prefix: fbql

FlyBase Reference Report
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: FlyBase internal citation identifiers
is part of: bioregistry
has local unique identifier example: 0187632
has provider formatter: https://flybase.org/reports/FBrf$1
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has URI prefix: https://flybase.org/reports/FBrf
has resource example: FBrf0187632
has prefix: fbrf

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
has local unique identifier example: 00000000
has provider formatter: http://purl.obolibrary.org/obo/FBSP_$1
has local unique identifier pattern: ^\d{8}$
has download URL: fbsp.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-1373-1705
has URI prefix: http://purl.obolibrary.org/obo/FBSP_
has resource example: FBSP_00000000
has prefix: fbsp

Flybase Cell Line
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The cell line vocabulary inside FlyBase
is part of: bioregistry
has local unique identifier example: 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
has resource example: FBtc0000190
has prefix: fbtc

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

Fetal Calf Serum-Free Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Cell line databases/resources
is part of: bioregistry
has local unique identifier example: 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
has resource example: https://fcs-free.org/fcs-database
has prefix: fcsfree

FDA Application
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: This prefix is for FDA application identifiers. There are multiple types of FDA applications (https://www.fda.gov/drugs/how-drugs-are-developed-and-approved/types-applications), including New Drug Application (NDA). FDA.report provides access to all FDA databases, including applications, in a single portal, and can resolve FDA application identifiers.
is part of: bioregistry
has local unique identifier example: 070886
has provider formatter: https://fda.report/applications/$1
has local unique identifier pattern: ^\d{6}$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-2473-2313
has URI prefix: https://fda.report/applications/
has resource example: https://fda.report/applications/070886
has prefix: fda.application

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
has local unique identifier example: 4667
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Sean Taylor
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: fema

FerroLigandDB
type: Resource
contributor: https://orcid.org/0009-0001-1912-5132
description: FerroLigandDB is a meticulously curated, high-quality database of ferroptosis regulators, including inducers and inhibitors.
is part of: bioregistry
has local unique identifier example: 486
has provider formatter: https://ferr.gulab.org.cn/browse/$1
is deprecated: false
has responsible: Qiong Gu
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://ferr.gulab.org.cn/browse/
has resource example: https://ferr.gulab.org.cn/browse/486
has prefix: ferroliganddb

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
has local unique identifier example: immds
has provider formatter: https://hl7.org/fhir/us/$1
is deprecated: false
has URI prefix: https://hl7.org/fhir/us/
has resource example: immds
has prefix: fhir.implementation

Food Interactions with Drugs Evidence Ontology
type: Resource
description: Food-Drug interactions automatically extracted from scientific literature
is part of: bioregistry
git repository: fideo
keyword: obo
keyword: ontology
has local unique identifier example: 00000021
has provider formatter: http://purl.obolibrary.org/obo/FIDEO_$1
has local unique identifier pattern: ^\d+$
has download URL: fideo.owl
is deprecated: false
has responsible: Georgeta Bordea
has URI prefix: http://purl.obolibrary.org/obo/FIDEO_
has resource example: FIDEO_00000021
has prefix: fideo

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
has local unique identifier example: 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/
has resource example: https://www.fishbase.ca/summary/6472
has prefix: fishbase.species

Five Stars of Online Research Articles Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata.
is part of: bioregistry
git repository: fivestars
keyword: subject agnostic
has local unique identifier example: hasOpenAccessRating
is deprecated: false
has responsible: https://orcid.org/0000-0003-0530-4305
has prefix: fivestars

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: cell biology
keyword: life science
has local unique identifier example: 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: Ryan Brinkman
has URI prefix: http://flowrepository.org/id/
has resource example: FR-FCM-ZYGW
has prefix: flowrepository

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

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
has local unique identifier example: 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:
has resource example: https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=10531&-find=-find.html
has prefix: flybrain.ndb

FlyMine Chromosome Band
type: Resource
description: FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge.
is part of: bioregistry
keyword: gene expression
keyword: genome
keyword: protein
has local unique identifier example: 1047874
has provider formatter: https://www.flymine.org/flymine/report/ChromosomeBand/$1
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.flymine.org/flymine/report/ChromosomeBand/
has resource example: https://www.flymine.org/flymine/report/ChromosomeBand/1047874
has prefix: flymine.chromosome

FooDB compound
type: Resource
description: FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.
is part of: bioregistry
has local unique identifier example: FDB002100
has provider formatter: http://foodb.ca/compounds/$1
has local unique identifier pattern: ^FDB\d+$
is deprecated: false
has alternative prefix: foodb
has URI prefix: http://foodb.ca/compounds/
has resource example: http://foodb.ca/compounds/FDB002100
has prefix: foodb.compound

FooDB Food
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Foods in FooDB
is part of: bioregistry
has local unique identifier example: 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/
has resource example: FOOD00020
has prefix: foodb.food

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
has local unique identifier example: 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/
has resource example: A0TMC
has prefix: foodex2

Fossilworks Journal
type: Resource
contributor: https://orcid.org/0000-0003-2699-3066
description: Identifier for a journal article in the fossilworks website
is part of: bioregistry
has local unique identifier example: 61467
has provider formatter: http://fossilworks.org/
has local unique identifier pattern: ^\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://fossilworks.org/
has resource example: http://fossilworks.org/
has prefix: fossilworks.journal

Fossilworks Taxon
type: Resource
contributor: https://orcid.org/0000-0003-2699-3066
description: Identifier for an animal, plant, or microorganism from the fossilworks website
is part of: bioregistry
has local unique identifier example: 40565
has provider formatter: http://www.fossilworks.org/cgi-bin/bridge.pl
has local unique identifier pattern: ^[1-9]\d{0,5}$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.fossilworks.org/cgi-bin/bridge.pl
has resource example: http://www.fossilworks.org/cgi-bin/bridge.pl
has prefix: fossilworks.taxon

FamPlex
type: Resource
description: FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.
is part of: bioregistry
keyword: ontology
has local unique identifier example: GPIb_IX_V
has provider formatter: https://sorgerlab.github.io/famplex/$1
has local unique identifier pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-9439-5346
has alternative prefix: famplex
has URI prefix: https://sorgerlab.github.io/famplex/
has resource example: GPIb IX V
has prefix: fplx

FAIR* Reviews Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology that enables the description of reviews of scientific articles and other scholarly resources.
is part of: bioregistry
git repository: fr
keyword: subject agnostic
has local unique identifier example: ReviewVersion
is deprecated: false
has responsible: https://orcid.org/0000-0003-0530-4305
has prefix: fr

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: frbr
keyword: subject agnostic
has local unique identifier example: Expression
has provider formatter: http://purl.org/vocab/frbr/core#$1
is deprecated: false
has responsible: https://orcid.org/0000-0003-0530-4305
has URI prefix: http://purl.org/vocab/frbr/core#
has resource example: Expression
has prefix: frbr

Functional Requirements for Bibliographic Records Entity-Relationship Model
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)
is part of: bioregistry
keyword: frbr
has local unique identifier example: 1001
has provider formatter: http://iflastandards.info/ns/fr/frbr/frbrer/$1
is deprecated: false
has URI prefix: http://iflastandards.info/ns/fr/frbr/frbrer/
has resource example: http://iflastandards.info/ns/fr/frbr/frbrer/1001
has prefix: frbrer

F-SNP
type: Resource
description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.
is part of: bioregistry
keyword: dna
keyword: protein
has local unique identifier example: rs17852708
has provider formatter: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi
has local unique identifier pattern: ^rs\d+$
is deprecated: true
has URI prefix: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi
has resource example: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi
has prefix: fsnp

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
has local unique identifier example: 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
has resource example: https://apps.usgs.gov/thesaurus/term-simple.php
has prefix: ftt

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
has local unique identifier example: 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/
has resource example: http://func.mshri.on.ca/fly/genes/list_functional_scores/10194
has prefix: funcbase.fly

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
has local unique identifier example: 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/
has resource example: http://func.mshri.on.ca/human/genes/list_functional_scores/119514
has prefix: funcbase.human

FuncBase Mouse
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 mouse.
is part of: bioregistry
has local unique identifier example: 1351341
has provider formatter: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://func.mshri.on.ca/mouse/genes/list_functional_scores/
has resource example: http://func.mshri.on.ca/mouse/genes/list_functional_scores/1351341
has prefix: funcbase.mouse

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
has local unique identifier example: 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/
has resource example: http://func.mshri.on.ca/yeast/genes/list_functional_scores/2701
has prefix: funcbase.yeast

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: fungi
keyword: growth profiles
keyword: monosaccharides
keyword: plant biomass
keyword: polysaccharides
has local unique identifier example: 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/
has resource example: https://www.fung-growth.org/page/Display%20page%20FG/86
has prefix: funggrowth

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
has local unique identifier example: 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: Jason E. Stajich
has URI prefix: https://fungidb.org/fungidb/app/record/gene/
has resource example: CNBG_0001
has prefix: fungidb

Index Fungorum
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for a fungus taxon in Index Fungorum
is part of: bioregistry
has local unique identifier example: 154022
has provider formatter: http://www.indexfungorum.org/names/NamesRecord.asp
has local unique identifier pattern: ^[1-9]\d{0,5}$
is deprecated: false
has URI prefix: http://www.indexfungorum.org/names/NamesRecord.asp
has resource example: http://www.indexfungorum.org/names/NamesRecord.asp
has prefix: fungorum

Fission Yeast Experimental Conditions Ontology
type: Resource
contributor: https://orcid.org/0000-0001-6330-7526
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
has local unique identifier example: 0000003
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0001-6330-7526
has reviewer: https://orcid.org/0000-0003-4423-4370
has prefix: fyeco

Fyler
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A hierarchical classification of congenital heart disease
is part of: bioregistry
has local unique identifier example: 4447
has local unique identifier pattern: ^\d+$
is deprecated: false
has prefix: fyler

Fission Yeast Phenotype Ontology
type: Resource
description: A formal ontology of phenotypes observed in fission yeast.
is part of: bioregistry
git repository: fypo
keyword: genetics
keyword: go-term enrichment data
keyword: life science
keyword: obo
keyword: ontology
keyword: phenotype
keyword: phylogenetics
has local unique identifier example: 0001707
has provider formatter: http://purl.obolibrary.org/obo/FYPO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: fypo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-6330-7526
has URI prefix: http://purl.obolibrary.org/obo/FYPO_
has resource example: FYPO_0001707
has prefix: fypo

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/
has prefix: ga4ghdos

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: gene
keyword: genome
keyword: plant
has local unique identifier example: 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: Birgit Kersten
has URI prefix: https://bioregistry.io/gabi:
has resource example: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi
has prefix: gabi

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: artificial intelligence
keyword: attribution
keyword: contributor roles
keyword: delegation
keyword: ontology
has local unique identifier example: 0000001
has provider formatter: https://w3id.org/gaidet/$1
has local unique identifier pattern: ^\d{7}$
has download URL: gaidet.owl
is deprecated: false
has responsible: Serhii Nazarovets
has URI prefix: https://w3id.org/gaidet/
has resource example: https://w3id.org/gaidet/0000001
has prefix: gaidet

GALEN
type: Resource
description: A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.
is part of: bioregistry
keyword: ontology
has local unique identifier example: MagnitudeValueType
has provider formatter: http://www.co-ode.org/ontologies/galen#$1
has download URL: galen.owl
is deprecated: true
has responsible: Julian Seidenberg
has URI prefix: http://www.co-ode.org/ontologies/galen#
has resource example: MagnitudeValueType
has prefix: galen

Health Data Research Innovation Gateway
type: Resource
description: The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.
is part of: bioregistry
has provider formatter: https://web.www.healthdatagateway.org/dataset/$1
has local unique identifier pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$
is deprecated: false
has URI prefix: https://web.www.healthdatagateway.org/dataset/
has prefix: gateway

GWAS Catalog
type: Resource
description: The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.
is part of: bioregistry
has local unique identifier example: GCST000035
has provider formatter: https://www.ebi.ac.uk/gwas/studies/$1
has local unique identifier pattern: ^GCST\d{6}\d*$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/gwas/studies/
has identifier space owner: 02catss52
has resource example: GCST000035
has prefix: gcst

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
has local unique identifier example: 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/
has resource example: https://www.cancerrxgene.org/translation/Drug/1242
has prefix: gdsc

Gene Expression Analysis Resource
type: Resource
contributor: https://orcid.org/0000-0002-5705-5710
description: The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains.
is part of: bioregistry
git repository: gEAR
has local unique identifier example: d.a59037e8
has provider formatter: https://umgear.org/p
has local unique identifier pattern: ^[dp]\.[a-z0-9]{8}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5705-5710
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://umgear.org/p
has resource example: https://umgear.org/p
has prefix: gear

Genomics Cohorts Knowledge Ontology
type: Resource
description: An ontology to represent genomics cohort attributes.
is part of: bioregistry
git repository: GECKO
keyword: biospecimen
keyword: experimental measurement
keyword: genomics
keyword: life science
keyword: obo
keyword: ontology
keyword: statistics
has local unique identifier example: 0000044
has provider formatter: http://purl.obolibrary.org/obo/GECKO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: gecko.owl
is deprecated: false
has responsible: Rebecca Jackson
has URI prefix: http://purl.obolibrary.org/obo/GECKO_
has resource example: GECKO_0000044
has prefix: gecko

General Multilingual Environmental Thesaurus Concept
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.
is part of: bioregistry
keyword: biodiversity
keyword: earth sciences
keyword: ecology
keyword: environmental science
keyword: ess
has local unique identifier example: 627
has provider formatter: https://www.eionet.europa.eu/gemet/en/concept/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Eionet Helpdesk
has URI prefix: https://www.eionet.europa.eu/gemet/en/concept/
has resource example: https://www.eionet.europa.eu/gemet/en/concept/627
has prefix: gemet.concept

General Multilingual Environmental Thesaurus Group
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Groups listed in GEMET
is part of: bioregistry
has local unique identifier example: 893
has provider formatter: https://www.eionet.europa.eu/gemet/en/group/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.eionet.europa.eu/gemet/en/group/
has resource example: https://www.eionet.europa.eu/gemet/en/group/893
has prefix: gemet.group

General Multilingual Environmental Thesaurus Relation
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Relations in GEMET
is part of: bioregistry
has local unique identifier example: 6237
has provider formatter: https://www.eionet.europa.eu/gemet/en/relations/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.eionet.europa.eu/gemet/en/relations/
has resource example: https://www.eionet.europa.eu/gemet/en/relations/6237
has prefix: gemet.relation

General Multilingual Environmental Thesaurus Theme
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Themes listed in GEMET
is part of: bioregistry
has local unique identifier example: 4
has provider formatter: https://www.eionet.europa.eu/gemet/en/theme/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.eionet.europa.eu/gemet/en/theme/
has resource example: https://www.eionet.europa.eu/gemet/en/theme/4
has prefix: gemet.theme

Genatlas
type: Resource
description: GenAtlas is a database containing information on human genes, markers and phenotypes.
is part of: bioregistry
keyword: disorder
keyword: gene
keyword: human
keyword: life science
has local unique identifier example: HBB
has provider formatter: http://genatlas.medecine.univ-paris5.fr/fiche.php
has local unique identifier pattern: ^\w+$
is deprecated: false
has URI prefix: http://genatlas.medecine.univ-paris5.fr/fiche.php
has resource example: http://genatlas.medecine.univ-paris5.fr/fiche.php
has prefix: genatlas

GenBase
type: Resource
contributor: https://orcid.org/0009-0001-1912-5132
description: GenBase is a genetic sequence database that accepts user submissions (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids, phages from any organism) and integrates data from INSDC.
is part of: bioregistry
has local unique identifier example: C_AA001108.1
has provider formatter: https://ngdc.cncb.ac.cn/genbase/search/gb/$1
is deprecated: false
has responsible: Xuetong Zhao
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://ngdc.cncb.ac.cn/genbase/search/gb/
has resource example: C AA001108.1
has prefix: genbase

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
has local unique identifier example: 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
has resource example: http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi
has prefix: gendis

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
has local unique identifier example: GSTA1
is deprecated: false
has prefix: genecards.geneannot

Gene Location
type: Resource
description: GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources
is part of: bioregistry
keyword: genome
has local unique identifier example: 17503
has provider formatter: http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl
has resource example: http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl
has prefix: genecards.geneloc

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
has local unique identifier example: 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:
has resource example: http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl
has prefix: genecards.genenote

GeneDB
type: Resource
description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.
is part of: bioregistry
keyword: genome
keyword: life science
keyword: sequence
has local unique identifier example: LinJ.20.0070
has provider formatter: https://www.genedb.org/gene/$1
has local unique identifier pattern: ^[\w\d\.-]*$
is deprecated: true
has URI prefix: https://www.genedb.org/gene/
has resource example: LinJ.20.0070
has prefix: genedb

GeneFarm
type: Resource
description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.
is part of: bioregistry
keyword: expression
keyword: genome
keyword: life science
keyword: nucleotide
keyword: sequence
has local unique identifier example: 4892
has provider formatter: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: sébastien Aubourg
has URI prefix: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl
has resource example: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl
has prefix: genefarm

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: classification
keyword: gene
keyword: protein
has local unique identifier example: 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
has resource example: http://www.ensembl.org/Multi/GeneTree/Image
has prefix: genetree

Gene Wiki
type: Resource
description: The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI.
is part of: bioregistry
keyword: genetics
keyword: life science
has local unique identifier example: 1017
has provider formatter: http://plugins.biogps.org/cgi-bin/wp.cgi
has local unique identifier pattern: ^\d+$
provides for: ncbigene
is deprecated: false
has responsible: Andrew I Su
has URI prefix: http://plugins.biogps.org/cgi-bin/wp.cgi
has resource example: http://plugins.biogps.org/cgi-bin/wp.cgi
has prefix: genewiki

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: genomics
keyword: genotype
keyword: obo
keyword: ontology
has local unique identifier example: 0000632
has provider formatter: http://purl.obolibrary.org/obo/GENO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: geno.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1048-5019
has URI prefix: http://purl.obolibrary.org/obo/GENO_
has resource example: GENO_0000632
has prefix: geno

GenPept
type: Resource
description: The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.
is part of: bioregistry
has local unique identifier example: CAA71118.1
has provider formatter: https://www.ncbi.nlm.nih.gov/protein/$1
has local unique identifier pattern: ^\w{3}\d{5}(\.\d+)?$
is deprecated: false
has URI prefix: https://bioregistry.io/genpept:
has resource example: https://www.ncbi.nlm.nih.gov/protein/CAA71118.1
has prefix: genpept

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: classification
keyword: genome
has local unique identifier example: 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/#
has identifier space owner: 02catss52
has resource example: GenProp0699
has prefix: genprop

Geographical Entity Ontology
type: Resource
description: An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in "The US declared war on Germany" vs. the US in "The plane entered US airspace".
is part of: bioregistry
git repository: geographical-entity-ontology
keyword: geographic location
keyword: human geography
keyword: obo
keyword: ontology
keyword: physical geography
has local unique identifier example: 000000021
has provider formatter: http://purl.obolibrary.org/obo/GEO_$1
has local unique identifier pattern: ^\d{9}$
has download URL: geo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-9881-1017
has URI prefix: http://purl.obolibrary.org/obo/GEO_
has resource example: GEO_000000021
has prefix: geogeo

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: geography
keyword: geoinformatics
keyword: ontology
has local unique identifier example: 3532759
has provider formatter: https://www.geonames.org/$1
has local unique identifier pattern: ^\d+$
has download URL: geonames.owl
is deprecated: false
has responsible: Marc Wick
has alternative prefix: Geomames
has alternative prefix: Geonamaes
has URI prefix: https://www.geonames.org/
has resource example: https://www.geonames.org/3532759
has prefix: geonames

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: geography
keyword: ontology
has local unique identifier example: ADM1
has provider formatter: https://www.geonames.org/recent-changes/featurecode/$1/
has download URL: geonames.feature.owl
is deprecated: false
has responsible: Marc Wick
has URI prefix: https://bioregistry.io/geonames.feature:
has resource example: ADM1
has prefix: geonames.feature

GeoNames Ontology
type: Resource
description: An ontology used to enable annotating geospatial semantic information to entities in GeoNames
is part of: bioregistry
has local unique identifier example: parentFeature
is deprecated: false
has prefix: geonames.ontology

GeoSPARQL Function
type: Resource
description: Functions for GeoSPARQL
is part of: bioregistry
has local unique identifier example: sfEquals
is deprecated: false
has prefix: geosparql.function

GeoSPARQL Rule
type: Resource
description: Rules for GeoSPARQL
is part of: bioregistry
has local unique identifier example: rcc
is deprecated: false
has prefix: geosparql.rule

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: data schema
keyword: nfdi
has local unique identifier example: linkContext
has provider formatter: https://data.gesis.org/gesiskg/schema/$1
is deprecated: false
has URI prefix: https://data.gesis.org/gesiskg/schema/
has resource example: linkContext
has prefix: gesiskg

Gene Expression Ontology
type: Resource
description: Gene Expression Ontology
is part of: bioregistry
keyword: expression data
keyword: gene expression
keyword: life science
keyword: ontology
has download URL: gexo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1171-9876
has prefix: gexo

Ecological Trait-data Standard
type: Resource
description: The Ecological Trait-data Standard defines terms for the use in datasets containing quantitative and qualitative functional traits.
is part of: bioregistry
keyword: earth sciences
keyword: ess
keyword: fair data spaces
keyword: life sciences, biology
has local unique identifier example: BiodiversityExploratories
has provider formatter: http://terminologies.gfbio.org/terms/ETS/$1
is deprecated: false
has URI prefix: http://terminologies.gfbio.org/terms/ETS/
has resource example: BiodiversityExploratories
has prefix: gfbio.ets

General Formal Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas.
is part of: bioregistry
keyword: biomedical science
keyword: engineering
keyword: foundational ontologies
keyword: life science
keyword: ontology
has local unique identifier example: projects_to
has provider formatter: http://www.onto-med.de/ontologies/gfo.owl#$1
has download URL: gfo.owl
is deprecated: false
has responsible: Heinrich Herre
has URI prefix: http://www.onto-med.de/ontologies/gfo.owl#
has resource example: projects to
has prefix: gfo

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
has local unique identifier example: saddan
has provider formatter: https://medlineplus.gov/genetics/condition/$1
is deprecated: false
has URI prefix: https://medlineplus.gov/genetics/condition/
has resource example: saddan
has prefix: ghr

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
has local unique identifier example: GL50803_102438
has provider formatter: https://giardiadb.org/giardiadb/app/record/gene/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4446-6200
has URI prefix: https://giardiadb.org/giardiadb/app/record/gene/
has resource example: GL50803_102438
has prefix: giardiadb

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: software engineering
keyword: subject agnostic
has local unique identifier example: 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/
has resource example: bioregistry
has prefix: github

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: knowledge and information systems
keyword: project management
keyword: software engineering
keyword: version control
has local unique identifier example: 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/
has resource example: https://bioregistry.io/resolve/github/issue/biopragmatics/bioregistry/424
has prefix: github.issue

GitHub Pull Request
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A pull request in any public repository on GitHub.
is part of: bioregistry
keyword: knowledge and information systems
keyword: project management
keyword: software engineering
keyword: version control
has local unique identifier example: biopragmatics/bioregistry/416
has provider formatter: https://bioregistry.io/resolve/github/pull/$1
is deprecated: false
has URI prefix: https://bioregistry.io/resolve/github/pull/
has resource example: https://bioregistry.io/resolve/github/pull/biopragmatics/bioregistry/416
has prefix: github.pull

GitLab
type: Resource
description: GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability.
is part of: bioregistry
keyword: knowledge and information systems
keyword: software engineering
keyword: subject agnostic
has local unique identifier example: morpheus.lab/morpheus
has provider formatter: https://gitlab.com/$1
has local unique identifier pattern: ^.*/.*$
is deprecated: false
has URI prefix: https://gitlab.com/
has resource example: morpheus
has prefix: gitlab

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
has local unique identifier example: 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
has resource example: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php
has prefix: glida.gpcr

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
has local unique identifier example: 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
has resource example: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php
has prefix: glida.ligand

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
has local unique identifier example: nort3314
has provider formatter: https://glottolog.org/resource/languoid/id/$1
is deprecated: false
appears in: gsso
has URI prefix: https://glottolog.org/resource/languoid/id/
has resource example: nort3314
has prefix: glottolog

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
has local unique identifier example: 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/
has resource example: EP0311
has prefix: glycoepitope

GlycoMapsDB
type: Resource
description: A database of GlycoMaps containing 2585 conformational maps.
is part of: bioregistry
keyword: small molecule
has local unique identifier example: 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
has resource example: http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php
has prefix: glycomapsdb

GlycomeDB
type: Resource
description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.
is part of: bioregistry
keyword: life science
keyword: molecules
keyword: small molecules
keyword: structure
has local unique identifier example: G77500AY
has provider formatter: https://glytoucan.org/Structures/Glycans/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has canonical: glytoucan
has responsible: 0000-0003-3147-448X
has URI prefix: https://glytoucan.org/Structures/Glycans/
has resource example: G77500AY
has prefix: glycomedb

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: chemistry
keyword: glycomics
keyword: life science
keyword: organic chemistry
has local unique identifier example: GN_G03681DA
has provider formatter: https://glyconavi.org/hub/
has local unique identifier pattern: ^GN_[A-Za-z0-9_:]+$
is deprecated: false
has responsible: Issaku Yamada
has URI prefix: https://glyconavi.org/hub/
has resource example: https://glyconavi.org/hub/
has prefix: glyconavi

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: glycomics
keyword: life science
has local unique identifier example: 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/
has resource example: GPST000024
has prefix: glycopost

Glycosciences.DB
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
description: A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates.
is part of: bioregistry
has local unique identifier example: 1
has provider formatter: http://www.glycosciences.de/database/start.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Thomas Lütteke
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: glycosciences.db
has URI prefix: http://www.glycosciences.de/database/start.php
has resource example: http://www.glycosciences.de/database/start.php
has prefix: glycosciencesdb

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: life science
keyword: metabolomics
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:
has prefix: gmd

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/
has prefix: gmd.analyte

Golm Metabolome Database GC-MS spectra
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. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.
is part of: bioregistry
has provider formatter: http://gmd.mpimp-golm.mpg.de/Spectrums/$1
has local unique identifier pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
is deprecated: false
has URI prefix: http://gmd.mpimp-golm.mpg.de/Spectrums/
has prefix: gmd.gcms

Golm Metabolome Database Profile
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. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.
is part of: bioregistry
has provider formatter: http://gmd.mpimp-golm.mpg.de/profile/default.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 URI prefix: http://gmd.mpimp-golm.mpg.de/profile/default.aspx
has resource example: http://gmd.mpimp-golm.mpg.de/profile/default.aspx
has prefix: gmd.profile

Golm Metabolome Database Reference Substance
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. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.
is part of: bioregistry
has provider formatter: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1
has local unique identifier pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
is deprecated: false
has URI prefix: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/
has prefix: gmd.ref

Gmelin's Handbook of Inorganic Chemistry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s.
is part of: bioregistry
has local unique identifier example: 1466
has local unique identifier pattern: ^[1-9][0-9]{1,6}$
is deprecated: false
has prefix: gmelin

GND ID
type: Resource
description: The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners.
is part of: bioregistry
keyword: culture
keyword: knowledge and information systems
keyword: social science
has local unique identifier example: 117145750
has provider formatter: https://lobid.org/gnd/$1
has local unique identifier pattern: ^[0-9X\-]+$
is deprecated: false
has URI prefix: https://lobid.org/gnd/
has resource example: https://lobid.org/gnd/117145750
has prefix: gnd

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
has local unique identifier example: 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#
has resource example: AdministrativeUnit
has prefix: gndo

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
has local unique identifier example: 10004892
has provider formatter: http://purl.obolibrary.org/obo/GNO_$1
has local unique identifier pattern: ^(\d{8}|(\w+\d+\w+))$
has download URL: gno.owl
is deprecated: false
has responsible: Nathan Edwards
has alternative prefix: gnome
has URI prefix: http://purl.obolibrary.org/obo/GNO_
has resource example: GNO_10004892
has prefix: gno

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

Global Natural Products Social Molecular Networking Task
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
description: GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS)
is part of: bioregistry
has provider formatter: https://gnps.ucsd.edu/ProteoSAFe/status.jsp
has local unique identifier pattern: ^[a-f0-9]+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-7647-6097
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://gnps.ucsd.edu/ProteoSAFe/status.jsp
has resource example: https://gnps.ucsd.edu/ProteoSAFe/status.jsp
has prefix: gnps.task

Gene Product Information Schema
type: Resource
contributor: https://orcid.org/0000-0002-8719-7760
contributor: https://orcid.org/0000-0003-4423-4370
description: This describes the metadata schema for the Gene Product Information (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier space refer to the columns in GPI files.
is part of: bioregistry
has local unique identifier example: db-object-id
has provider formatter: http://geneontology.org/docs/gene-product-information-gpi-format/#$1
is deprecated: false
has URI prefix: http://geneontology.org/docs/gene-product-information-gpi-format/#
has resource example: db-object-id
has prefix: go.gpi

Gene Ontology Issue Tracker
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An issue on the Gene Ontology GitHub issue tracker
is part of: bioregistry
has local unique identifier example: 23000
has provider formatter: https://github.com/geneontology/go-ontology/issues/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://github.com/geneontology/go-ontology/issues/
has resource example: https://github.com/geneontology/go-ontology/issues/23000
has prefix: go.issue

Gene Ontology Causal Activity Model
type: Resource
description: GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.
is part of: bioregistry
has local unique identifier example: 5fce9b7300001250
has provider formatter: https://model.geneontology.org/$1
is deprecated: false
has URI prefix: https://model.geneontology.org/
has resource example: https://model.geneontology.org/5fce9b7300001250
has prefix: go.model

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
has local unique identifier example: 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/
has resource example: https://geneontology.org/GO_REF/0000041
has prefix: go.ref

Gene Ontology Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A database-specific registry supporting curation in the Gene Ontology
is part of: bioregistry
has local unique identifier example: CHEBI
has provider formatter: https://bioregistry.io/metaregistry/go/$1
is deprecated: false
has URI prefix: https://bioregistry.io/metaregistry/go/
has resource example: CHEBI
has prefix: go.resource

Gene Ontology Rules
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio.
is part of: bioregistry
has local unique identifier example: 0000004
has provider formatter: https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has URI prefix: https://bioregistry.io/go.rule:
has resource example: gorule-0000004.md
has prefix: go.rule

Gene Ontology Annotation Database
type: Resource
description: The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.
is part of: bioregistry
keyword: biology
keyword: gene
keyword: life science
keyword: ontology
keyword: protein
has local unique identifier example: P12345
has provider formatter: https://www.ebi.ac.uk/QuickGO/GProtein
has local unique identifier pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$
provides for: uniprot
is deprecated: false
has responsible: Rachael P. Huntley
has URI prefix: https://www.ebi.ac.uk/QuickGO/GProtein
has resource example: https://www.ebi.ac.uk/QuickGO/GProtein
has prefix: goa

GO Chemicals
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Represent chemical entities having particular CHEBI roles
is part of: bioregistry
git repository: go-ontology
keyword: ontology
has local unique identifier example: 25512
has provider formatter: https://biopragmatics.github.io/providers/goche/$1
has local unique identifier pattern: ^\d+$
has download URL: chebi roles.owl
is deprecated: false
has alternative prefix: go.chebi
has alternative prefix: go.chemical
has alternative prefix: go.chemicals
has URI prefix: https://biopragmatics.github.io/providers/goche/
has resource example: https://biopragmatics.github.io/providers/goche/25512
has prefix: goche

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
has local unique identifier example: IPI
is deprecated: false
has prefix: goeco

GOLD genome
type: Resource
description: - DEPRECATION NOTE - Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.
is part of: bioregistry
has local unique identifier example: Gi07796
has provider formatter: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi
has local unique identifier pattern: ^(Gi|Gc)\d+$
provides for: gold
is deprecated: true
has URI prefix: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi
has resource example: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi
has prefix: gold.genome

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

IUPAC Gold Book Compendium of Chemical Terminology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Compendium is popularly referred to as the "Gold Book", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC "Colour Books" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books. Terminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry. The API can be accessed [here](https://goldbook.iupac.org/pages/api)
is part of: bioregistry
has local unique identifier example: G02681
has provider formatter: https://goldbook.iupac.org/terms/view/$1
has local unique identifier pattern: ^(\wT?)?\d{5}$
is deprecated: false
has responsible: Stuart Chalk
has URI prefix: https://goldbook.iupac.org/terms/view/
has resource example: G02681
has prefix: goldbook

Google Books
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Search the world's most comprehensive index of full-text books.
is part of: bioregistry
has local unique identifier example: qafeQTWIWmcC
has provider formatter: https://books.google.com/books
is deprecated: false
has URI prefix: https://books.google.com/books
has resource example: https://books.google.com/books
has prefix: google.book

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
has local unique identifier example: 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
has resource example: https://scholar.google.com/citations
has prefix: google.scholar

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
has local unique identifier example: 0002005
has provider formatter: http://purl.obolibrary.org/obo/GOREL_$1
has local unique identifier pattern: ^\d{7}$
has download URL: gorel.owl
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/GOREL_
has resource example: GOREL_0002005
has prefix: gorel

G protein-coupled receptor database
type: Resource
description: The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.
is part of: bioregistry
keyword: life science
keyword: molecular biology
keyword: protein
keyword: small molecule
has local unique identifier example: RL3R1_HUMAN
has provider formatter: https://gpcrdb.org/protein/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: David Gloriam
has URI prefix: https://gpcrdb.org/protein/
has resource example: RL3R1 HUMAN
has prefix: gpcrdb

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

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
has local unique identifier example: GPM32310002988
has provider formatter: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1
has local unique identifier pattern: ^GPM\d+$
is deprecated: false
has responsible: Ronald C. Beavis (Ron Beavis)
has URI prefix: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=
has resource example: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002988
has prefix: gpmdb

WikiPathways GPML Vocabulary
type: Resource
contributor: 0000-0001-5608-781X
contributor: https://orcid.org/0000-0001-9439-5346
description: The WikiPatwhays Graphical Pathway Markup Language (GPML) vocabulary.
is part of: bioregistry
git repository: WpVocabularies
keyword: ontology
has local unique identifier example: DataNode
has provider formatter: http://vocabularies.wikipathways.org/gpml#$1
has local unique identifier pattern: ^[A-Za-z]+$
has download URL: gpml.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-7542-0286
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: wikipathways.gpml
has URI prefix: http://vocabularies.wikipathways.org/gpml#
has resource example: DataNode
has prefix: gpml

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

GrainGenes reference
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A database for Triticeae and Avena references.
is part of: bioregistry
has local unique identifier example: 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
has resource example: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi
has prefix: graingenes.reference

GrainGenes symbol
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A database for Triticeae and Avena gene symbols.
is part of: bioregistry
has local unique identifier example: 1-FEH+w3
has provider formatter: http://wheat.pw.usda.gov/report
is deprecated: false
has URI prefix: http://wheat.pw.usda.gov/report
has resource example: http://wheat.pw.usda.gov/report
has prefix: graingenes.symbol

Gramene QTL
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 quantitative trait loci identified in Gramene.
is part of: bioregistry
has local unique identifier example: CQG5
has provider formatter: http://www.gramene.org/db/qtl/qtl_display
has local unique identifier pattern: ^\w+$
is deprecated: false
has alternative prefix: GR_QTL
has URI prefix: http://www.gramene.org/db/qtl/qtl_display
has resource example: http://www.gramene.org/db/qtl/qtl_display
has prefix: gramene.qtl

Gramene Reference
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Literature references in Gramene
is part of: bioregistry
has local unique identifier example: 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
has resource example: http://www.gramene.org/db/literature/pub_search
has prefix: gramene.reference

Gramene Taxonomy
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 taxonomic information in Gramene.
is part of: bioregistry
has local unique identifier example: 013681
has provider formatter: https://archive.gramene.org/db/ontology/search
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://archive.gramene.org/db/ontology/search
has resource example: https://archive.gramene.org/db/ontology/search
has prefix: gramene.taxonomy

GrassBase
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species.
is part of: bioregistry
has local unique identifier example: imp10873
has provider formatter: https://www.kew.org/data/grasses-db/www/$1
has local unique identifier pattern: ^(imp|gen)\d{5}$
is deprecated: false
has URI prefix: https://www.kew.org/data/grasses-db/www/
has resource example: imp10873
has prefix: grassbase

Gleaning Resource Descriptions from Dialects of Languages
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: GRDDL is a mechanism for Gleaning Resource Descriptions from Dialects of Languages. It is a technique for obtaining RDF data from XML documents and in particular XHTML pages. Authors may explicitly associate documents with transformation algorithms, typically represented in XSLT, using a link element in the head of the document. Alternatively, the information needed to obtain the transformation may be held in an associated metadata profile document or namespace document. Clients reading the document can follow links across the Web using techniques described in the GRDDL specification to discover the appropriate transformations. This document uses a number of examples from the GRDDL Use Cases document to illustrate, in detail, the techniques GRDDL provides for associating documents with appropriate instructions for extracting any embedded data. (from homepage)
is part of: bioregistry
keyword: vocabularies
has local unique identifier example: transformation
has provider formatter: http://www.w3.org/2003/g/data-view#$1
is deprecated: false
has URI prefix: http://www.w3.org/2003/g/data-view#
has resource example: transformation
has prefix: grddl

16S rRNA gene database
type: Resource
description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.
is part of: bioregistry
keyword: genetics
keyword: life science
keyword: rna
has local unique identifier example: 100000
has provider formatter: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: Gary L Andersen
has URI prefix: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl
has resource example: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl
has prefix: greengenes

Global Research Identifier Database
type: Resource
description: International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.
is part of: bioregistry
keyword: data management
has local unique identifier example: grid.225360.0
has provider formatter: https://www.grid.ac/institutes/$1
has local unique identifier pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$
is deprecated: false
has URI prefix: https://www.grid.ac/institutes/
has resource example: grid.225360.0
has prefix: grid

Germplasm Resources Information Network
type: Resource
description: GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections.
is part of: bioregistry
keyword: life science
has local unique identifier example: 159787
has provider formatter: http://www.ars.usda.gov/research/publications/publications.htm
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: grin
has URI prefix: http://www.ars.usda.gov/research/publications/publications.htm
has resource example: http://www.ars.usda.gov/research/publications/publications.htm
has prefix: grin.publication

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
has local unique identifier example: 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
has resource example: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail
has prefix: grin.taxonomy

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
has local unique identifier example: Lipid
has provider formatter: http://www.bootstrep.eu/ontology/GRO#$1
has download URL: gro.owl
is deprecated: true
has responsible: Vivian Lee
has alternative prefix: bootstrep
has URI prefix: http://www.bootstrep.eu/ontology/GRO#
has resource example: Lipid
has prefix: gro

G-Rich Sequences Database
type: Resource
description: GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.
is part of: bioregistry
keyword: dna
keyword: rna
has local unique identifier example: 10142
has provider formatter: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php
has resource example: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php
has prefix: grsdb

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

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
has local unique identifier example: 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
has resource example: http://www.fao.org/gsfaonline/additives/details.html
has prefix: gsfa

Genotype-Tissue Expression
type: Resource
description: The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation.
is part of: bioregistry
has local unique identifier example: BRIP1
has provider formatter: https://www.gtexportal.org/home/gene/$1
has local unique identifier pattern: ^\w.+$
is deprecated: false
has URI prefix: https://www.gtexportal.org/home/gene/
has resource example: BRIP1
has prefix: gtex

Galaxy Training Network
type: Resource
contributor: Dilfuza Djamalova
contributor: Jacobo Miranda
description: Identifiers in the GTN correspond to training materials in various formats (markdown, slides, video). The users can apply learned concepts directly within the framework via galaxy workflows.
is part of: bioregistry
git repository: training-material
keyword: galaxy
keyword: learning materials
keyword: learning resources
keyword: training materials
has local unique identifier example: T00148
has provider formatter: https://gxy.io/GTN:$1
has local unique identifier pattern: ^[A-Z]\d+$
is deprecated: false
has responsible: Saskia Hiltemann
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://gxy.io/GTN:
has resource example: GTN:T00148
has prefix: gtn

Genetic Testing Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease
is part of: bioregistry
has local unique identifier example: AN0097748
has provider formatter: https://www.ncbi.nlm.nih.gov/gtr/conditions/$1
is deprecated: false
appears in: mondo
has alternative prefix: gtr
has alternative prefix: medgen.gtr
has URI prefix: https://www.ncbi.nlm.nih.gov/gtr/conditions/
has resource example: AN0097748
has prefix: gtr.condition

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
has local unique identifier example: 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/
has resource example: https://www.ncbi.nlm.nih.gov/gtr/labs/000320401
has prefix: gtr.lab

Genetic Testing Registry Tests
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
has local unique identifier example: 000260236
has provider formatter: https://www.ncbi.nlm.nih.gov/gtr/tests/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.ncbi.nlm.nih.gov/gtr/tests/
has resource example: https://www.ncbi.nlm.nih.gov/gtr/tests/000260236
has prefix: gtr.test

Genitourinary Development Molecular Anatomy Project
type: Resource
description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.
is part of: bioregistry
keyword: cell biology
keyword: developmental biology
keyword: genomics
keyword: molecular biology
has local unique identifier example: Q-2958
has provider formatter: https://gudmap.org/id/$1
has local unique identifier pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9262-8318
has URI prefix: https://gudmap.org/id/
has resource example: Q-2958
has prefix: gudmap

Unified Foundational Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An _gentle_ implementation of the Unified Foundational Ontology (UFO), which is an upper level ontology like BFO that is concerned with e.g. expressing temporal relationships between events.
is part of: bioregistry
git repository: gufo
keyword: events
keyword: general & upper
keyword: ontology
keyword: upper level
has local unique identifier example: Person
has provider formatter: http://purl.org/nemo/gufo#$1
is deprecated: false
has responsible: João Paulo A. Almeida
has URI prefix: http://purl.org/nemo/gufo#
has resource example: Person
has prefix: gufo

GWAS Central Marker
type: Resource
description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.
is part of: bioregistry
has local unique identifier example: HGVM15354
has provider formatter: https://www.gwascentral.org/marker/$1
has local unique identifier pattern: ^HGVM\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-0292-7972
has URI prefix: https://www.gwascentral.org/marker/
has resource example: HGVM15354
has prefix: gwascentral.marker

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

GWAS Central Study
type: Resource
description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.
is part of: bioregistry
keyword: gene
keyword: genome
has local unique identifier example: HGVST1828
has provider formatter: https://www.gwascentral.org/study/$1
has local unique identifier pattern: ^HGVST\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-0292-7972
has URI prefix: https://www.gwascentral.org/study/
has resource example: HGVST1828
has prefix: gwascentral.study

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
has local unique identifier example: 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/
has identifier space owner: 02catss52
has resource example: E-MTAB-2037
has prefix: gxa.expt

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
has local unique identifier example: 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/
has identifier space owner: 02catss52
has resource example: AT4G01080
has prefix: gxa.gene

Habronattus courtship
type: Resource
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/HABRONATTUS_$1
is deprecated: true
has responsible: https://orcid.org/0000-0001-6512-3296
has URI prefix: http://purl.obolibrary.org/obo/HABRONATTUS_
has prefix: habronattus

The Ageing Gene Database
type: Resource
description: GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group.
is part of: bioregistry
keyword: aging
keyword: genes
keyword: longevity
has local unique identifier example: 0001
has provider formatter: http://genomics.senescence.info/genes/details.php
is deprecated: false
has responsible: https://orcid.org/0000-0002-6363-2465
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://genomics.senescence.info/genes/details.php
has resource example: http://genomics.senescence.info/genes/details.php
has prefix: hagr.genage

The Dietary Restriction Gene Database
type: Resource
description: GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals
is part of: bioregistry
keyword: aging
keyword: dietary restriction
keyword: genes
keyword: longevity
has local unique identifier example: 2
has provider formatter: http://genomics.senescence.info/diet/details.php
is deprecated: false
has responsible: https://orcid.org/0000-0002-6363-2465
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://genomics.senescence.info/diet/details.php
has resource example: http://genomics.senescence.info/diet/details.php
has prefix: hagr.gendr

High-quality Automated and Manual Annotation of microbial Proteomes
type: Resource
description: HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.
is part of: bioregistry
keyword: life science
keyword: protein
has local unique identifier example: MF_01400
has provider formatter: https://hamap.expasy.org/unirule/$1
has local unique identifier pattern: ^MF_\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-2148-9135
has URI prefix: https://hamap.expasy.org/unirule/
has resource example: MF_01400
has prefix: hamap

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

Hymenoptera Anatomy Ontology
type: Resource
description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)
is part of: bioregistry
git repository: hao
keyword: anatomy
keyword: life science
keyword: obo
keyword: ontology
has local unique identifier example: 0000187
has provider formatter: http://purl.obolibrary.org/obo/HAO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: hao.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-5640-5491
has URI prefix: http://purl.obolibrary.org/obo/HAO_
has resource example: HAO_0000187
has prefix: hao

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
has local unique identifier example: 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/
has resource example: http://api.hymao.org/api/ref/98127
has prefix: hao.ref

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
has local unique identifier example: 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/
has resource example: https://catalog.hathitrust.org/Record/008893080
has prefix: hathitrust

A Database of Human Hemoglobin Variants and Thalassemias
type: Resource
description: This is a relational database of information about hemoglobin variants and mutations that cause thalassemia.
is part of: bioregistry
keyword: protein
has local unique identifier example: 2526
has provider formatter: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3
has resource example: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3
has prefix: hbvar

Human Cell Atlas Ontology
type: Resource
description: Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.
is part of: bioregistry
keyword: ontology
has download URL: hcao.owl
is deprecated: false
has prefix: hcao

Human Chromosome Ontology
type: Resource
description: The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes.
is part of: bioregistry
has local unique identifier example: MT
has provider formatter: http://biohackathon.org/resource/hco#$1
has local unique identifier pattern: ^.+$
is deprecated: false
has URI prefix: http://biohackathon.org/resource/hco#
has resource example: MT
has prefix: hco

Healthcare Common Procedure Coding System
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers.
is part of: bioregistry
keyword: biomedical science
keyword: business administration
keyword: ontology
has local unique identifier example: G8944
has provider formatter: http://purl.bioontology.org/ontology/HCPCS/$1
is deprecated: false
has responsible: Cynthia Hake
has URI prefix: http://purl.bioontology.org/ontology/HCPCS/
has resource example: G8944
has prefix: hcpcs

Hepatitis C Virus Database Project
type: Resource
description: the European Hepatitis C Virus Database (euHCVdb, euhcvdb.lyon.inserm.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.
is part of: bioregistry
keyword: gene
has local unique identifier example: M58335
has provider formatter: https://euhcvdb.lyon.inserm.fr/euHCVdb/do/displayHCVEntry
has local unique identifier pattern: ^M\d{5}$
is deprecated: false
has URI prefix: https://euhcvdb.lyon.inserm.fr/euHCVdb/do/displayHCVEntry
has resource example: https://euhcvdb.lyon.inserm.fr/euHCVdb/do/displayHCVEntry
has prefix: hcvdb

Handle
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)
is part of: bioregistry
keyword: centrally registered identifier
keyword: subject agnostic
has local unique identifier example: 2381/12775
has provider formatter: http://hdl.handle.net/$1
has local unique identifier pattern: ^\d+/.+$
is deprecated: false
has alternative prefix: handle
has URI prefix: http://hdl.handle.net/
has resource example: http://hdl.handle.net/2381/12775
has prefix: hdl

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
has local unique identifier example: 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
has resource example: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi
has prefix: hdr

HemOnc Terminology
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: HemOnc.org is the largest freely available medical wiki of interventions, regimens, and general information relevant to the fields of hematology and oncology.
is part of: bioregistry
has local unique identifier example: 15543
has local unique identifier pattern: ^\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0002-8169-9049
has prefix: hemonc

Health Procedure Ontology
type: Resource
contributor: https://orcid.org/0000-0002-3336-2476
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
has local unique identifier example: 0000001
has provider formatter: http://purl.obolibrary.org/obo/HEPRO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: HEPRO.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-3336-2476
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://purl.obolibrary.org/obo/HEPRO_
has identifier space owner: 00kybxq39
has resource example: HEPRO_0000001
has prefix: hepro

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
has local unique identifier example: 0154
has local unique identifier pattern: ^\d+$
is deprecated: false
has prefix: hesa

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
has local unique identifier example: 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
has resource example: http://www.hgmd.cf.ac.uk/ac/gene.php
has prefix: hgmd

HGNC gene family
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. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.
is part of: bioregistry
keyword: gene
keyword: gene family
keyword: gene group
has local unique identifier example: 2029
has provider formatter: https://www.genenames.org/cgi-bin/genefamilies/set/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has canonical: hgnc.genegroup
has responsible: https://orcid.org/0000-0002-8380-5247
has alternative prefix: GFAM
has alternative prefix: HGNC_GROUP
has alternative prefix: hgnc.family
has URI prefix: https://www.genenames.org/cgi-bin/genefamilies/set/
has resource example: https://www.genenames.org/cgi-bin/genefamilies/set/2029
has prefix: hgnc.genefamily

Human Genome Variation Society Nomenclature
type: Resource
contributor: Madeline Iseminger
description: The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the [Human Genome Organization (HUGO)](https://hugo-int.org/).
is part of: bioregistry
git repository: hgvs-nomenclature
has local unique identifier example: NP_003997.1:p.Trp24Cys
has provider formatter: http://reg.clinicalgenome.org/allele
is deprecated: false
has responsible: Reece Hart
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://reg.clinicalgenome.org/allele
has resource example: http://reg.clinicalgenome.org/allele
has prefix: hgvs

H-InvDb Locus
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 'Locus' view.
is part of: bioregistry
has local unique identifier example: HIX0004394
has provider formatter: http://h-invitational.jp/hinv/spsoup/locus_view
has local unique identifier pattern: ^HIX\d{7}(\.\d+)?$
is deprecated: true
has URI prefix: http://h-invitational.jp/hinv/spsoup/locus_view
has resource example: http://h-invitational.jp/hinv/spsoup/locus_view
has prefix: hinv.locus

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
has local unique identifier example: 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
has resource example: http://h-invitational.jp/hinv/protein/protein_view.cgi
has prefix: hinv.protein

H-InvDb Transcript
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 'Transcript' view.
is part of: bioregistry
has local unique identifier example: HIT000195363
has provider formatter: http://h-invitational.jp/hinv/spsoup/transcript_view
has local unique identifier pattern: ^HIT\d{9}(\.\d+)?$
is deprecated: true
has URI prefix: http://h-invitational.jp/hinv/spsoup/transcript_view
has resource example: http://h-invitational.jp/hinv/spsoup/transcript_view
has prefix: hinv.transcript

Human Induced Pluripotent Stem Cells Initiative
type: Resource
contributor: Matt Jeffryes
description: Cell line databases/resources
is part of: bioregistry
has local unique identifier example: HPSI0114i-bezi_1
has provider formatter: https://www.hipsci.org/#/lines/$1
is deprecated: false
has URI prefix: https://www.hipsci.org/#/lines/
has resource example: lines/HPSI0114i-bezi 1
has prefix: hipsci

NIH HIV Reagent Program
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: ARP-1513
has provider formatter: https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx
is deprecated: false
has URI prefix: https://bioregistry.io/hivreagentprogram:
has resource example: ARP-1513.aspx
has prefix: hivreagentprogram

HMS Library of Integrated Network-based Cellular Signatures Antibodies
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.
is part of: bioregistry
has local unique identifier example: 80001
has provider formatter: https://lincs.hms.harvard.edu/db/antibodies/$1
has local unique identifier pattern: ^8\d{4}$
is deprecated: false
has URI prefix: https://lincs.hms.harvard.edu/db/antibodies/
has resource example: https://lincs.hms.harvard.edu/db/antibodies/80001
has prefix: hms.lincs.antibody

HMS LINCS Cell
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.
is part of: bioregistry
has local unique identifier example: 50583
has provider formatter: https://lincs.hms.harvard.edu/db/cells/$1
has local unique identifier pattern: ^5\d{4}$
is deprecated: false
has URI prefix: https://lincs.hms.harvard.edu/db/cells/
has resource example: https://lincs.hms.harvard.edu/db/cells/50583
has prefix: hms.lincs.cell

HMS LINCS Compound
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.
is part of: bioregistry
has local unique identifier example: 10001-101
has provider formatter: https://lincs.hms.harvard.edu/db/sm/$1
has local unique identifier pattern: ^1\d{4}-\d{3}$
is deprecated: false
has alternative prefix: HMS-LINCS
has alternative prefix: hmsl_id
has URI prefix: https://lincs.hms.harvard.edu/db/sm/
has resource example: https://lincs.hms.harvard.edu/db/sm/10001-101
has prefix: hms.lincs.compound

HMS Library of Integrated Network-based Cellular Signatures Datasets
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.
is part of: bioregistry
has local unique identifier example: 20003
has provider formatter: https://lincs.hms.harvard.edu/db/datasets/$1
has local unique identifier pattern: ^2\d{4}$
is deprecated: false
has URI prefix: https://lincs.hms.harvard.edu/db/datasets/
has resource example: https://lincs.hms.harvard.edu/db/datasets/20003
has prefix: hms.lincs.dataset

Hölzel Diagnostika
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog.
is part of: bioregistry
keyword: antibodies
keyword: assays
keyword: biologics
keyword: elisa-kits
keyword: inhibitors
keyword: life sciences
keyword: proteins
keyword: vendor
has local unique identifier example: 40592-R001-100
has provider formatter: https://www.hoelzel-biotech.com/de/catalogsearch/result/
is deprecated: false
has responsible: Carsten Linder
has alternative prefix: hölzel
has URI prefix: https://www.hoelzel-biotech.com/de/catalogsearch/result/
has resource example: https://www.hoelzel-biotech.com/de/catalogsearch/result/
has prefix: hoelzel

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
has local unique identifier example: 0000255
has provider formatter: https://biopragmatics.github.io/providers/hog/$1
has local unique identifier pattern: ^\d{7}$
has download URL: HOG.obo
is deprecated: false
has URI prefix: https://biopragmatics.github.io/providers/hog/
has resource example: https://biopragmatics.github.io/providers/hog/0000255
has prefix: hog

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

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
has local unique identifier example: 0040379
has provider formatter: http://purl.bioontology.org/ontology/HOIP/HOIP_$1
has local unique identifier pattern: ^\d{7}$
has download URL: hoip 0308.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-9673-1283
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://purl.bioontology.org/ontology/HOIP/HOIP_
has resource example: HOIP_0040379
has prefix: hoip

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
has local unique identifier example: SAMEA112904733
has provider formatter: https://www.holofooddata.org/animal/$1
has local unique identifier pattern: ^SAMEA\d{9}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5805-7195
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.holofooddata.org/animal/
has resource example: SAMEA112904733
has prefix: holofood.animal

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
has local unique identifier example: SAMEA10104908
has provider formatter: https://www.holofooddata.org/sample/$1
has local unique identifier pattern: ^SAMEA\d{8}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5805-7195
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.holofooddata.org/sample/
has resource example: SAMEA10104908
has prefix: holofood.sample

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: anatomy
keyword: homologous
keyword: life cycle stage
keyword: life science
keyword: molecular entity
keyword: obo
keyword: ontology
has local unique identifier example: 0000049
has provider formatter: http://purl.obolibrary.org/obo/HOM_$1
has local unique identifier pattern: ^\d{7}$
has download URL: hom.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-9415-5104
has URI prefix: http://purl.obolibrary.org/obo/HOM_
has resource example: HOM_0000049
has prefix: hom

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: genome
keyword: microbial
has local unique identifier example: 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
has resource example: https://v31.homd.org/genome/genome_description
has prefix: homd.seq

Human Oral Microbiome Database
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 taxonomic information.
is part of: bioregistry
keyword: microbial
keyword: taxonomy
has local unique identifier example: 811
has provider formatter: http://www.homd.org/modules.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: 0000-0001-6689-317X
has URI prefix: http://www.homd.org/modules.php
has resource example: http://www.homd.org/modules.php
has prefix: homd.taxon

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: gene
keyword: genome
keyword: life science
has local unique identifier example: 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/
has resource example: https://www.ncbi.nlm.nih.gov/homologene/1000
has prefix: homologene

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
has local unique identifier example: queerNewspapers
has provider formatter: http://homosaurus.org/terms/$1
is deprecated: false
appears in: gsso
has responsible: Keahi Kaʻiwalani Adolpho
has URI prefix: http://homosaurus.org/terms/
has resource example: queerNewspapers
has prefix: homosaurus

Horizon Discovery cell line collection
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: HD+118-001
has provider formatter: https://horizondiscovery.com/en/search
is deprecated: false
has URI prefix: https://horizondiscovery.com/en/search
has resource example: https://horizondiscovery.com/en/search
has prefix: horizon_discovery

Healthcare Organizations and Services Ontology
type: Resource
contributor: https://orcid.org/0000-0002-3336-2476
description: HOSO is an ontology of informational entities and processes related to healthcare organizations and services.
is part of: bioregistry
git repository: HOSO
has local unique identifier example: 0000001
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3336-2476
has reviewer: https://orcid.org/0000-0003-4423-4370
has prefix: hoso

Homologous Vertebrate Genes Database
type: Resource
description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.
is part of: bioregistry
keyword: dna
keyword: gene
keyword: life science
keyword: protein
has local unique identifier example: HBG004341
has provider formatter: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl
has local unique identifier pattern: ^HBG\d+$
is deprecated: true
has responsible: Laurent Duret
has URI prefix: https://bioregistry.io/hovergen:
has resource example: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl
has prefix: hovergen

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

Histopathology Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species. The original structure of the histopathology ontology was designed ab initio when the [INHAND](http://www.goreni.org/) manuscripts were not available. However, the ontology has been repetitively reviewed and updated to align with the subsequently published INHAND manuscripts. During this process cross references to INHAND lesion identifiers were added to the ontology. [from GitHub]
is part of: bioregistry
git repository: hpath
keyword: ontology
has local unique identifier example: 2000191
has provider formatter: http://purl.obolibrary.org/obo/MC_$1
has local unique identifier pattern: ^\d+$
has download URL: hpath.obo
is deprecated: false
has responsible: Carlo Ravagli
has alternative prefix: MC
has URI prefix: http://purl.obolibrary.org/obo/MC_
has resource example: MC_2000191
has prefix: hpath

Human Proteome Map Peptide
type: Resource
description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.
is part of: bioregistry
has local unique identifier example: 9606117
has provider formatter: http://www.humanproteomemap.org/spectrum.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://www.humanproteomemap.org/spectrum.php
has resource example: http://www.humanproteomemap.org/spectrum.php
has prefix: hpm.peptide

Human Proteome Map
type: Resource
description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.
is part of: bioregistry
has local unique identifier example: 1968
has provider formatter: http://www.humanproteomemap.org/protein.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: http://www.humanproteomemap.org/protein.php
has resource example: http://www.humanproteomemap.org/protein.php
has prefix: hpm.protein

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
has local unique identifier example: 00001
has provider formatter: http://www.hprd.org/protein/$1
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: Akhilesh Pandey
has URI prefix: http://www.hprd.org/protein/
has resource example: http://www.hprd.org/protein/00001
has prefix: hprd

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: biomedical science
keyword: life science
has local unique identifier example: 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: Stefanie Seltmann
has URI prefix: https://hpscreg.eu/cell-line/
has resource example: BCRTi001-A
has prefix: hpscreg

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
has local unique identifier example: 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/
has resource example: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/5621
has prefix: hsdb

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: clustering
keyword: protein
keyword: sequence
has local unique identifier example: 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:
has resource example: 102l.hssp.bz2
has prefix: hssp

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
has local unique identifier example: 00000014
has provider formatter: http://purl.obolibrary.org/obo/HTN_$1
has local unique identifier pattern: ^\d{8}$
has download URL: htn.owl
is deprecated: false
has responsible: Amanda Hicks
has URI prefix: http://purl.obolibrary.org/obo/HTN_
has resource example: HTN_00000014
has prefix: htn

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/
has prefix: hubmap.collection

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/
has prefix: hubmap.dataset

Human BioMolecular Atlas Program Donor
type: Resource
contributor: 0009-0008-8406-631X
description: The HuBMAP donors dataset contains demographic and clinical metadata for individuals who donated tissue samples. Each donor has a unique identifier used to link them to their associated tissue samples and derived experimental data.
is part of: bioregistry
has provider formatter: https://portal.hubmapconsortium.org/browse/donor/$1
has local unique identifier pattern: ^[a-f0-9]{32}$
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/donor/
has prefix: hubmap.donor

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/
has prefix: hubmap.sample

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

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
has local unique identifier example: 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
has resource example: https://humap3.proteincomplexes.org/displayComplexes
has prefix: humap

The Hydra Core Vocabulary
type: Resource
description: A lightweight vocabulary for hypermedia-driven Web APIs
is part of: bioregistry
keyword: rdf
has local unique identifier example: TemplatedLink
is deprecated: false
has prefix: hydra

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
has local unique identifier example: 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/
has resource example: https://github.com/information-artifact-ontology/IAO/issues/206
has prefix: iao.issue

iCalendar in RDF
type: Resource
description: A vocabulary for calendar events and related objects
is part of: bioregistry
has local unique identifier example: Vevent
is deprecated: false
has prefix: ical

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: biology
keyword: genomics
has local unique identifier example: 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:
has resource example: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php
has prefix: iceberg.cime

ICEberg integrative and conjugative element
type: Resource
description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.
is part of: bioregistry
has local unique identifier example: 100
has provider formatter: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: iceberg.ice
has URI prefix: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php
has resource example: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php
has prefix: iceberg.element

ICEberg family
type: Resource
description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.
is part of: bioregistry
has local unique identifier example: 1
has provider formatter: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-9439-1660
has URI prefix: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php
has resource example: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php
has prefix: iceberg.family

ICEberg 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: biology
keyword: genomics
has local unique identifier example: 1
has provider formatter: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.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.ime:
has resource example: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php
has prefix: iceberg.ime

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
has local unique identifier example: 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
has resource example: https://ice.ntp.niehs.nih.gov/api/v1/search
has prefix: icechem

Integrative and Conjugative Element Ontology
type: Resource
description: A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.
is part of: bioregistry
git repository: ICEO
keyword: obo
keyword: ontology
has local unique identifier example: 0000712_1
has provider formatter: http://purl.obolibrary.org/obo/ICEO_$1
has local unique identifier pattern: ^\d{7}(_\d)?$
has download URL: iceo.owl
is deprecated: false
has responsible: Meng LIU
has URI prefix: http://purl.obolibrary.org/obo/ICEO_
has resource example: ICEO 0000712 1
has prefix: iceo

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
has local unique identifier example: 0000002
has provider formatter: https://biopragmatics.github.io/providers/icepo/$1
has local unique identifier pattern: ^\d{7}$
has download URL: icepo.obo
is deprecated: false
has responsible: Pascale Gaudet
has URI prefix: https://biopragmatics.github.io/providers/icepo/
has resource example: https://biopragmatics.github.io/providers/icepo/0000002
has prefix: icepo

Interlab Cell Line Collection
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: 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
has resource example: http://www.iclc.it/details/det_list.php
has prefix: iclc

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
has local unique identifier example: 64ba
has provider formatter: https://entomology.ca.uky.edu/content/$1
is deprecated: false
has responsible: Surjeet Kumar Arya
has URI prefix: https://entomology.ca.uky.edu/content/
has resource example: 64ba
has prefix: icldb

Indian Crop Phenome Database Project
type: Resource
contributor: https://orcid.org/0000-0003-2136-4519
description: This resource is about projects in the Indian Crop Phenome Database (ICPD). The ICPD is a domain of the Indian Biological Data Center (IBDC), Regional Centre for Biotechnology, Faridabad, developed for the digitization of crop phenome data. Being the global agricultural powerhouse, the bulk of biological data generated in India is associated with agricultural trials. Ironically most of the trial data has been inaccessible to other researchers, and remains unpublished, and is lost as time passes. Therefore, ICPD would act as single-stop user-friendly platform for freely archiving, organizing, analyzing, and sharing the multi-crop phenome data following FAIR (Findable, Accessible, Interoperable and Re-usable) data principles. [from homepage]
is part of: bioregistry
has local unique identifier example: PPJ_100024
has local unique identifier pattern: ^PPJ_\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-2136-4519
has reviewer: https://orcid.org/0000-0003-4423-4370
has prefix: icpd.project

Indian Crop Phenome Database Study
type: Resource
contributor: https://orcid.org/0000-0003-2136-4519
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
has local unique identifier example: 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: https://orcid.org/0000-0003-2136-4519
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://ibdc.dbtindia.gov.in/icpd/study-view-home/
has resource example: PST_100013
has prefix: icpd.study

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
has local unique identifier example: ICTV19990991
has provider formatter: http://ictv.global/id/MSL40/$1
is deprecated: false
has URI prefix: http://ictv.global/id/MSL40/
has resource example: ICTV19990991
has prefix: ictv

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
has local unique identifier example: 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: Satoshi Fukuchi
has URI prefix: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php
has resource example: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php
has prefix: ideal

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
has local unique identifier example: 0001191
has provider formatter: http://purl.obolibrary.org/obo/COVIDO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: ido covid-19
is deprecated: false
has responsible: https://orcid.org/0000-0002-1118-1738
has URI prefix: http://purl.obolibrary.org/obo/COVIDO_
has resource example: COVIDO_0001191
has prefix: idocovid19

Dengue Fever Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology for dengue fever.
is part of: bioregistry
keyword: medicine
keyword: ontology
has local unique identifier example: 0003463
has provider formatter: http://purl.bioontology.org/ontology/IDODEN_$1
has local unique identifier pattern: ^\d{7}$
has download URL: idoden.owl
is deprecated: false
has responsible: Elvira Mitraka
has URI prefix: http://purl.bioontology.org/ontology/IDODEN_
has resource example: IDODEN_0003463
has prefix: idoden

Integrated Resource for Domestic Dog
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses.
is part of: bioregistry
has local unique identifier example: 4
has provider formatter: https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9922-9723
has URI prefix: https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action
has resource example: https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action
has prefix: idog

Identifiers.org Ontology
type: Resource
description: Identifiers.org Ontology
is part of: bioregistry
has local unique identifier example: DataCollection
has provider formatter: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1
has local unique identifier pattern: ^[0-9a-zA-Z]+$
is deprecated: false
has URI prefix: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#
has resource example: DataCollection
has prefix: idoo

Intrinsically Disordered Proteins Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR.
is part of: bioregistry
git repository: idpo
keyword: protein analysis
keyword: protein structure
keyword: proteins
keyword: proteomics
keyword: structural biochemistry
keyword: structural bioinformatics
keyword: structural biology
has local unique identifier example: 00056
has provider formatter: https://www.disprot.org/idpo/IDPO:$1
has local unique identifier pattern: ^\d{5}$
is deprecated: false
has responsible: Federica Quaglia
has URI prefix: https://www.disprot.org/idpo/IDPO:
has resource example: IDPO:00056
has prefix: idpo

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: bioinformatics
keyword: immunology
keyword: life science
has local unique identifier example: 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/
has resource example: https://www.iedb.org/assay/1691753
has prefix: iedb.assay

Immune Epitope Database Epitopes
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for epitopes, which are the specific parts of antigens recognized by the immune system.
is part of: bioregistry
keyword: bioinformatics
keyword: immunology
keyword: life science
keyword: protein
keyword: small molecule
has local unique identifier example: 117395
has provider formatter: https://www.iedb.org/epitope/$1
has local unique identifier pattern: ^\d+$
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/epitope/
has resource example: https://www.iedb.org/epitope/117395
has prefix: iedb.epitope

Immune Epitope Database MHC Restrictions
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for Major Histocompatibility Complex (MHC) restrictions of immune cells, detailing genetic factors that influence immune recognition.
is part of: bioregistry
keyword: bioinformatics
keyword: immunology
keyword: life science
has local unique identifier example: 86
has provider formatter: https://www.iedb.org/mhc/$1
has local unique identifier pattern: ^\d+$
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/mhc/
has resource example: https://www.iedb.org/mhc/86
has prefix: iedb.mhc

Immune Epitope Database Receptors
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for immune receptors, representing receptor complexes or groups studied for their interactions with antigens or epitopes.
is part of: bioregistry
keyword: bioinformatics
keyword: immunology
keyword: life science
has local unique identifier example: 47
has provider formatter: https://www.iedb.org/receptor/$1
has local unique identifier pattern: ^\d+$
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/receptor/
has resource example: https://www.iedb.org/receptor/47
has prefix: iedb.receptor

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: bioinformatics
keyword: immunology
keyword: life science
has local unique identifier example: 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/
has resource example: https://www.iedb.org/reference/1038233
has prefix: iedb.reference

IEEE Xplore author ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for an author in IEEE Xplore
is part of: bioregistry
keyword: person
keyword: researcher
has local unique identifier example: 37271072100
has provider formatter: https://ieeexplore.ieee.org/author/$1
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has URI prefix: https://ieeexplore.ieee.org/author/
has resource example: https://ieeexplore.ieee.org/author/37271072100
has prefix: ieee.author

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
has local unique identifier example: 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/
has resource example: https://ieeexplore.ieee.org/document/1580791
has prefix: ieee.document

Event (INOH pathway ontology)
type: Resource
description: The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.
is part of: bioregistry
keyword: obo
keyword: ontology
keyword: pathway
keyword: structure
has local unique identifier example: 0000000
has provider formatter: http://purl.obolibrary.org/obo/IEV_$1
has local unique identifier pattern: ^\d{7}$
is deprecated: true
has URI prefix: http://purl.obolibrary.org/obo/IEV_
has resource example: IEV_0000000
has prefix: iev

Integrated Genomic Resources of human Cell Lines for Identification
type: Resource
description: Cell line databases/resources
is part of: bioregistry
has local unique identifier example: 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
has resource example: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi
has prefix: igrhcellid

International Generic Sample Number
type: Resource
description: IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents.
is part of: bioregistry
git repository: igsn.github.io
keyword: archaeology
keyword: biospecimen
keyword: centrally registered identifier
keyword: earth science
keyword: environmental material
keyword: environmental science
keyword: geochemistry
keyword: geology
keyword: hydrogeology
keyword: omics
has local unique identifier example: AU124
has provider formatter: http://igsn.org/$1
has local unique identifier pattern: ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$
is deprecated: false
has responsible: Jens Klump
has URI prefix: http://igsn.org/
has resource example: AU124
has prefix: igsn

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: comparative genomics
keyword: genomics
has local unique identifier example: 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/
has resource example: NA06985
has prefix: igsr

International Histocompatibility Workshop cell lines
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics.
is part of: bioregistry
has local unique identifier example: IHW09326
has local unique identifier pattern: ^IHW\d+$
is deprecated: false
has prefix: ihw

Illumina Probe Identifier
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip.
is part of: bioregistry
keyword: transcriptomics
has local unique identifier example: ILMN_129894
has local unique identifier pattern: ^ILMN_\d+$
is deprecated: false
has prefix: illumina.probe

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

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
has prefix: imdrf

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
has local unique identifier example: 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
has identifier space owner: 02catss52
has resource example: https://www.ebi.ac.uk/intact/imex/main.xhtml
has prefix: imex

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
has local unique identifier example: 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
has resource example: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
has prefix: img.gene

Integrated Microbial Genomes Taxon
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 taxon information.
is part of: bioregistry
keyword: genome
keyword: taxonomy
has local unique identifier example: 648028003
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
has resource example: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
has prefix: img.taxon

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

IMGT/PRIMER-DB
type: Resource
description: The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).
is part of: bioregistry
keyword: dna
has local unique identifier example: IPP900099
has provider formatter: http://imgt.org/IMGTPrimerDB/Check_PrDB.pl
is deprecated: false
has URI prefix: https://bioregistry.io/imgt.primerdb:
has resource example: http://imgt.org/IMGTPrimerDB/Check_PrDB.pl
has prefix: imgt.primerdb

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: interaction
keyword: protein
has local unique identifier example: 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
has resource example: http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi
has prefix: imotdb

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: protein
keyword: small molecule
has local unique identifier example: 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_
has resource example: IMR_0000001
has prefix: imr

NHMRC Australian PhenomeBank
type: Resource
description: The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]
is part of: bioregistry
keyword: allele
keyword: alteration
keyword: chromosome
keyword: database
keyword: embryo
keyword: gene
keyword: live mouse
keyword: murine
keyword: mutation
keyword: phenotype
keyword: sperm
keyword: strain
keyword: transgene
keyword: transgenic
has local unique identifier example: 7345
has provider formatter: https://pb.apf.edu.au/phenbank/strain.html
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://pb.apf.edu.au/phenbank/strain.html
has resource example: https://pb.apf.edu.au/phenbank/strain.html
has prefix: imsr.apb

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

Taconic Biosciences
type: Resource
description: Supplier of mice for research purposes. [from RRID]
is part of: bioregistry
keyword: gene
keyword: genetic engineering
keyword: knockout
keyword: mice
keyword: model
keyword: mouse
keyword: repository
keyword: research
keyword: strain
keyword: subject
keyword: supply
keyword: transgenic
has local unique identifier example: 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_
has resource example: RRID:IMSR TAC 1178
has prefix: imsr_tac

iNaturalist Observation
type: Resource
contributor: Pierre-Marie Allard
description: The identifier for an observation in iNaturalist
is part of: bioregistry
has local unique identifier example: 36010371
has provider formatter: https://www.inaturalist.org/observations/$1
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.inaturalist.org/observations/
has resource example: https://www.inaturalist.org/observations/36010371
has prefix: inaturalist.observation

iNaturalist Place
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Identifier for a place in iNaturalist
is part of: bioregistry
has local unique identifier example: 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/
has resource example: https://www.inaturalist.org/places/7207
has prefix: inaturalist.place

iNaturalist Taxonomy
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Identifier for a species in iNaturalist
is part of: bioregistry
has local unique identifier example: 21723
has provider formatter: https://www.inaturalist.org/taxa/$1
has local unique identifier pattern: ^[1-9]\d{0,6}$
is deprecated: false
has URI prefix: https://www.inaturalist.org/taxa/
has resource example: https://www.inaturalist.org/taxa/21723
has prefix: inaturalist.taxon

iNaturalist User
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Identifier for a user in iNaturalist
is part of: bioregistry
keyword: person
has local unique identifier example: 1426686
has provider formatter: https://www.inaturalist.org/users/$1
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has URI prefix: https://www.inaturalist.org/users/
has resource example: https://www.inaturalist.org/users/1426686
has prefix: inaturalist.user

Information Resource Registry
type: Resource
contributor: https://orcid.org/0000-0002-7356-1779
description: The information resource registry is a listing of data sources present in the NCATS Data Translator system. Each information resource has an identifier, a short description, and a URL to more information about that resource.
is part of: bioregistry
git repository: information-resource-registry
has local unique identifier example: agrkb
has provider formatter: https://w3id.org/information-resource-registry/$1
has local unique identifier pattern: ^[a-z0-9-_.]+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8719-7760
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://w3id.org/information-resource-registry/
has resource example: agrkb
has prefix: infores

InformAll Allergenic Food Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The InformAll database was developed to provide a credible source of information on allergenic food materials of both plant and animal origin.
is part of: bioregistry
has local unique identifier example: 410
has provider formatter: http://research.bmh.manchester.ac.uk/informall/allergenic-food/
has local unique identifier pattern: ^\d+$
is deprecated: false
appears in: doid
has URI prefix: http://research.bmh.manchester.ac.uk/informall/allergenic-food/
has resource example: http://research.bmh.manchester.ac.uk/informall/allergenic-food/
has prefix: informall

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: disease
keyword: toxicity
is deprecated: false
has responsible: Jack R Harkema
has prefix: inhand

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
has local unique identifier example: 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
has resource example: https://mednet-communities.net/inn/db/ViewINN.aspx
has prefix: inn

A Knowledge Resource for Innate Immunity Interactions and Pathways
type: Resource
description: InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation.
is part of: bioregistry
keyword: gene
keyword: immunology
keyword: interaction
keyword: life science
keyword: pathway
keyword: protein
has local unique identifier example: 20021
has provider formatter: http://www.innatedb.ca/getGeneCard.do
is deprecated: false
has responsible: David Lynn
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.innatedb.ca/getGeneCard.do
has resource example: http://www.innatedb.ca/getGeneCard.do
has prefix: innatedb

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: life science
keyword: molecular interaction
keyword: obo
keyword: ontology
has local unique identifier example: 0000003
has provider formatter: http://purl.obolibrary.org/obo/INO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: ino.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9189-9661
has URI prefix: http://purl.obolibrary.org/obo/INO_
has resource example: INO_0000003
has prefix: ino

INSDC CDS
type: Resource
description: The coding sequence or protein identifiers as maintained in INSDC.
is part of: bioregistry
has local unique identifier example: AAA35559
has provider formatter: http://getentry.ddbj.nig.ac.jp/getentry/dad/$1
has local unique identifier pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
is deprecated: false
has canonical: ncbiprotein
has URI prefix: http://getentry.ddbj.nig.ac.jp/getentry/dad/
has resource example: http://getentry.ddbj.nig.ac.jp/getentry/dad/AAA35559
has prefix: insdc.cds

Genome assembly database - INSDC accessions
type: Resource
description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.
is part of: bioregistry
has local unique identifier example: GCA_000155495.1
has provider formatter: https://www.ncbi.nlm.nih.gov/datasets/genome/$1
has local unique identifier pattern: ^GCA_[0-9]{9}(\.[0-9]+)?$
is deprecated: false
has canonical: ncbi.assembly
has URI prefix: https://www.ncbi.nlm.nih.gov/datasets/genome/
has resource example: GCA 000155495.1
has prefix: insdc.gca

Genome assembly database - RefSeq accessions
type: Resource
description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database RefSeq accessions does not extend to viroids and bacteriophage.
is part of: bioregistry
has local unique identifier example: GCF_000001405
has provider formatter: https://www.ncbi.nlm.nih.gov/datasets/genome/$1
has local unique identifier pattern: ^GCF_[0-9]{9}(\.[0-9]+)?$
is deprecated: false
has canonical: ncbi.assembly
has alternative prefix: insdc.gcf
has URI prefix: https://www.ncbi.nlm.nih.gov/datasets/genome/
has resource example: GCF_000001405
has prefix: insdc.gcf

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
has local unique identifier example: mr
has provider formatter: https://inspire.ec.europa.eu/theme/$1
is deprecated: false
has URI prefix: https://inspire.ec.europa.eu/theme/
has resource example: mr
has prefix: inspire.theme

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
has local unique identifier example: 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
has resource example: https://www.ebi.ac.uk/intact/search
has prefix: intact.molecule

Integbio
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)
is part of: bioregistry
has local unique identifier example: nbdc01071
has provider formatter: https://catalog.integbio.jp/dbcatalog/en/record/$1
has local unique identifier pattern: ^nbdc\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-7883-3756
has URI prefix: https://catalog.integbio.jp/dbcatalog/en/record/
has resource example: nbdc01071
has prefix: integbio

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
has local unique identifier example: 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
has resource example: http://www.interfil.org/details.php
has prefix: interfil

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: biomedical science
keyword: brain
keyword: imaging
keyword: neurobiology
has local unique identifier example: 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_
has resource example: ilx_0101963
has prefix: interlex

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
has local unique identifier example: 200906038218908385
has provider formatter: http://purl.jp/bio/4/id/$1
has download URL: iobc.owl
is deprecated: false
has responsible: Tatsuya Kushida
has URI prefix: http://purl.jp/bio/4/id/
has resource example: http://purl.jp/bio/4/id/200906038218908385
has prefix: iobc

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
has local unique identifier example: 0000001
has provider formatter: http://purl.obolibrary.org/obo/IOIO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: IOIO.owl
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/IOIO_
has resource example: IOIO_0000001
has prefix: ioio

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

IRD Segment Sequence
type: Resource
description: Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).
is part of: bioregistry
keyword: gene
keyword: protein
has local unique identifier example: CY077097
has provider formatter: http://www.fludb.org/brc/fluSegmentDetails.do
has local unique identifier pattern: ^\w+(\_)?\d+(\.\d+)?$
is deprecated: false
has responsible: 0000-0003-1355-892X
has URI prefix: http://www.fludb.org/brc/fluSegmentDetails.do
has resource example: http://www.fludb.org/brc/fluSegmentDetails.do
has prefix: ird.segment

iRefWeb
type: Resource
description: iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.
is part of: bioregistry
keyword: interaction
keyword: life science
keyword: protein
has local unique identifier example: 617102
has provider formatter: http://wodaklab.org/iRefWeb/interaction/show/$1
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: Shoshana J. Wodak
has URI prefix: http://wodaklab.org/iRefWeb/interaction/show/
has resource example: http://wodaklab.org/iRefWeb/interaction/show/617102
has prefix: irefweb

Database of experimentally verified IRES structures
type: Resource
description: The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.
is part of: bioregistry
keyword: life science
keyword: regulation
keyword: rna
has local unique identifier example: 322
has provider formatter: http://www.iresite.org/IRESite_web.php
is deprecated: false
has responsible: Martin Pospíšek
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.iresite.org/IRESite_web.php
has resource example: http://www.iresite.org/IRESite_web.php
has prefix: iresite

Insect Resistance Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
has local unique identifier example: 0000008
has provider formatter: https://legacy.vectorbase.org/ontology-browser
has local unique identifier pattern: ^\d{7}$
is deprecated: true
has URI prefix: https://legacy.vectorbase.org/ontology-browser
has resource example: https://legacy.vectorbase.org/ontology-browser
has prefix: iro

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

Influenza Sequence and Epitope Database
type: Resource
description: ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea.
is part of: bioregistry
keyword: protein
has local unique identifier example: AY209920
is deprecated: false
has prefix: ised

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
has local unique identifier example: 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
has resource example: https://www-is.biotoul.fr/scripts/ficheIS.php
has prefix: isfinder

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

ISO 639 3-Letter Language Code
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Since the introduction of ISO 639-3 in 2007, access to language information has increased tremendously. The code set initially adopted as ISO639-3:2007 was based on a harmonization of ISO 639-2 with the code set of SIL’s Ethnologue 15th edition and languages from Linguist List to form a comprehensive set of code elements for world languages. SIL International, the Language Coding Agency for 639-3, relies on the contributions of linguists, language coding experts, and language users around the world to maintain and improve the code set through the change request process defined in the ISO 639 standard. [from homepage]
is part of: bioregistry
keyword: computer science
keyword: informatics
keyword: language
keyword: linguistics
has local unique identifier example: spa
has provider formatter: https://iso639-3.sil.org/code/$1
is deprecated: false
has URI prefix: https://iso639-3.sil.org/code/
has resource example: spa
has prefix: iso.639-3

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
has local unique identifier example: 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/
has resource example: https://portal.issn.org/resource/ISSN/0745-4570
has prefix: issn

ISTransbase
type: Resource
contributor: https://orcid.org/0009-0001-1912-5132
description: ISTransbase is a highly reliable and accessible database that focuses on inhibitors and substrates of drug transporters, offering a wealth of vital information encompassing experimental methods, transport parameters, and references.
is part of: bioregistry
has local unique identifier example: IST028
has provider formatter: https://istransbase.scbdd.com/database/trans/$1
is deprecated: false
has responsible: Dongsheng Cao
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://istransbase.scbdd.com/database/trans/
has resource example: IST028
has prefix: istransbase

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: machine learning
keyword: natural language processing
keyword: ontology
has local unique identifier example: 01625
has provider formatter: https://bioportal.bioontology.org/ontologies/ITO/
has local unique identifier pattern: ^\d+$
has download URL: ito.owl
is deprecated: false
has responsible: Matthias Samwald
has URI prefix: https://bioportal.bioontology.org/ontologies/ITO/
has resource example: https://bioportal.bioontology.org/ontologies/ITO/
has prefix: ito

IUPHAR family
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 families of receptors or subunits.
is part of: bioregistry
has local unique identifier example: 78
has provider formatter: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: IUPHARfam
has URI prefix: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward
has resource example: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward
has prefix: iuphar.family

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
has local unique identifier example: 1755
has provider formatter: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: IUPHAR_LIGAND
has alternative prefix: IUPHAR_LIGAND_ID
has URI prefix: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward
has resource example: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward
has prefix: iuphar.ligand

Guide to Pharmacology Target
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 transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits.
is part of: bioregistry
has local unique identifier example: 101
has provider formatter: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9262-8318
has alternative prefix: IUPHAR_GPCR
has alternative prefix: IUPHARobj
has URI prefix: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward
has resource example: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward
has prefix: iuphar.receptor

Influenza Virus Database
type: Resource
description: IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.
is part of: bioregistry
keyword: dna
keyword: gene
keyword: genome
has local unique identifier example: E13035
has provider formatter: http://influenza.psych.ac.cn/search/detail.jsp
is deprecated: false
has URI prefix: http://influenza.psych.ac.cn/search/detail.jsp
has resource example: http://influenza.psych.ac.cn/search/detail.jsp
has prefix: ivdb

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
has local unique identifier example: 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/
has resource example: JCGG-STR008690
has prefix: jcggdb

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: life science
keyword: microbial
keyword: taxonomy
has local unique identifier example: 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
has resource example: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number
has prefix: jcm

JRBC Cell Bank
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: JCRB1355
has provider formatter: https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi
has local unique identifier pattern: ^JCRB\d+$
is deprecated: false
has URI prefix: https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi
has resource example: https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi
has prefix: jcrb

Japan Chemical Substance Dictionary
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).
is part of: bioregistry
keyword: drug
has local unique identifier example: J55.713G
has provider formatter: http://jglobal.jst.go.jp/en/redirect
has local unique identifier pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$
is deprecated: false
has alternative prefix: Nikkaji number
has alternative prefix: nikkaji
has URI prefix: http://jglobal.jst.go.jp/en/redirect
has resource example: http://jglobal.jst.go.jp/en/redirect
has prefix: jcsd

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
has local unique identifier example: 2116
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Kim Petersen
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: jecfa

Joint Genome Institute Proposals
type: Resource
contributor: Alicia Clum
contributor: https://orcid.org/0000-0002-6601-2165
description: Identifiers for proposals/projects at the Joint Genome Institute
is part of: bioregistry
has local unique identifier example: 502930
has provider formatter: https://genome.jgi.doe.gov/portal/lookup
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Steven E. Wilson
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://genome.jgi.doe.gov/portal/lookup
has resource example: https://genome.jgi.doe.gov/portal/lookup
has prefix: jgi.proposal

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

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

Kaggle
type: Resource
description: Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.
is part of: bioregistry
has local unique identifier example: nasa/kepler-exoplanet-search-results
has provider formatter: https://www.kaggle.com/$1
has local unique identifier pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$
is deprecated: false
has URI prefix: https://www.kaggle.com/
has resource example: kepler-exoplanet-search-results
has prefix: kaggle

e-Rad researcher number
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for researchers in Japan used in government-based research funding (from 1980s)
is part of: bioregistry
keyword: person
keyword: researcher
has local unique identifier example: 00011461
has provider formatter: https://nrid.nii.ac.jp/ja/nrid/10000$1
has local unique identifier pattern: ^\d{8}$
is deprecated: false
has URI prefix: https://nrid.nii.ac.jp/ja/nrid/10000
has resource example: https://nrid.nii.ac.jp/ja/nrid/1000000011461
has prefix: kaken

Korean Cell Line Bank
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: 10020.2
has provider formatter: https://cellbank.snu.ac.kr/english/sub/catalog.php
is deprecated: false
has URI prefix: https://cellbank.snu.ac.kr/english/sub/catalog.php
has resource example: https://cellbank.snu.ac.kr/english/sub/catalog.php
has prefix: kclb

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: binding affinity
keyword: kinetics
keyword: rna-protein interactions
has local unique identifier example: 183
has provider formatter: http://www.kdbirp.aiddlab.com/detail/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Xian Zeng
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.kdbirp.aiddlab.com/detail/
has resource example: http://www.kdbirp.aiddlab.com/detail/183
has prefix: kdbirp

KEGG BRITE
type: Resource
description: KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships.
is part of: bioregistry
keyword: classification
keyword: ontology
keyword: pathway
has local unique identifier example: ko00002
has provider formatter: https://www.kegg.jp/brite/$1
is deprecated: false
has URI prefix: https://www.kegg.jp/brite/
has resource example: ko00002
has prefix: kegg.brite

Kerafast cell lines
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: EJH014
has provider formatter: https://www.kerafast.com/Search
is deprecated: false
has URI prefix: https://bioregistry.io/kerafast:
has resource example: https://www.kerafast.com/Search
has prefix: kerafast

KESTREL Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains
is part of: bioregistry
has local unique identifier example: 0000001
has provider formatter: http://purl.obolibrary.org/obo/kestrelo_$1
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-8741-7823
has URI prefix: http://purl.obolibrary.org/obo/kestrelo_
has resource example: kestrelo_0000001
has prefix: kestrelo

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
has local unique identifier example: nonCommercial
has provider formatter: https://w3id.org/kim/license/$1
is deprecated: false
has URI prefix: https://w3id.org/kim/license/
has resource example: nonCommercial
has prefix: kim.license

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

KYinno cell lines
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: KC-0979
has provider formatter: https://www.kyinno.com/
is deprecated: false
has URI prefix: https://www.kyinno.com/
has resource example: https://www.kyinno.com/
has prefix: kyinno

Langua aLimentaria Thesaurus
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Langual stands for "langua alimentaria" or "language of food". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases
is part of: bioregistry
has local unique identifier example: B2067
has provider formatter: https://www.langual.org/langual_thesaurus.asp
has local unique identifier pattern: ^B\d+$
is deprecated: false
has URI prefix: https://www.langual.org/langual_thesaurus.asp
has resource example: https://www.langual.org/langual_thesaurus.asp
has prefix: langual

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
has local unique identifier example: 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/
has resource example: https://lattes.cnpq.br/0061106995455595
has prefix: lattes

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: genetics
keyword: genomics
keyword: ontology
has local unique identifier example: 0000487
has provider formatter: https://bioportal.bioontology.org/ontologies/LBO/
has local unique identifier pattern: ^\d{7}$
has download URL: lbo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-2346-5201
has URI prefix: https://bioportal.bioontology.org/ontologies/LBO/
has resource example: https://bioportal.bioontology.org/ontologies/LBO/
has prefix: lbo

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
has local unique identifier example: 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/
has resource example: https://lccn.loc.gov/2011488555
has prefix: lccn

Linked Data Platform Vocabulary
type: Resource
description: A set of best practices and simple approach for a read-write Linked Data architecture, based on HTTP access to web resources that describe their state using the RDF data model.
is part of: bioregistry
keyword: api
has local unique identifier example: Resource
is deprecated: false
has prefix: ldp

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
has local unique identifier example: Amelanchier laevis
has provider formatter: http://leafsnap.com/species/$1/
is deprecated: false
has URI prefix: https://bioregistry.io/leafsnap:
has prefix: leafsnap

Global LEI Index
type: Resource
description: Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland.
is part of: bioregistry
has local unique identifier example: HWUPKR0MPOU8FGXBT394
has provider formatter: https://www.gleif.org/lei/$1
has local unique identifier pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$
is deprecated: false
has URI prefix: https://www.gleif.org/lei/
has resource example: HWUPKR0MPOU8FGXBT394
has prefix: lei

Lexvo Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The data model underlying lexvo
is part of: bioregistry
keyword: ontology
keyword: vocabularies
has local unique identifier example: Language
has provider formatter: http://lexvo.org/ontology#$1
has download URL: ontology
is deprecated: false
has alternative prefix: lvont
has URI prefix: http://lexvo.org/ontology#
has resource example: Language
has prefix: lexvo.ontology

LG Chemical Entity Detection Dataset (LGCEDe)
type: Resource
description: LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR).
is part of: bioregistry
has local unique identifier example: LGCEDe-S-000002244
has provider formatter: https://s3.us-east-2.amazonaws.com/lg.cede/$1
has local unique identifier pattern: ^LGCEDe-S-\d{9}$
is deprecated: false
has URI prefix: https://s3.us-east-2.amazonaws.com/lg.cede/
has resource example: LGCEDe-S-000002244
has prefix: lgai.cede

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: protein
keyword: sequence
has local unique identifier example: 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:
has resource example: 5HT3Arano.php
has prefix: lgic

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
has local unique identifier example: EMLSAT00000003403
has provider formatter: https://licebase.org/
has local unique identifier pattern: ^[A-Za-z0-9\-\/]+$
is deprecated: false
has responsible: Inge Jonassen
has URI prefix: https://licebase.org/
has resource example: https://licebase.org/
has prefix: licebase

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
has local unique identifier example: 0000015
has provider formatter: http://purl.obolibrary.org/obo/LFID_$1
has download URL: LSFO.owl
is deprecated: false
has responsible: Lars Juhl Jensen
has URI prefix: http://purl.obolibrary.org/obo/LFID_
has resource example: LFID_0000015
has prefix: lifestylefactors

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
has local unique identifier example: 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/
has resource example: https://ligandbook.org/package/785
has prefix: ligandbook

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
has local unique identifier example: 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
has resource example: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi
has prefix: ligandbox

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

Cancer cell LInes GEne fusions portAl
type: Resource
description: Polymorphism and mutation databases
is part of: bioregistry
has local unique identifier example: 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/
has resource example: CCLE 867
has prefix: ligea

Liver Cancer Model Repository
type: Resource
description: Cell line databases/resources
is part of: bioregistry
has local unique identifier example: Li7
has provider formatter: https://www.picb.ac.cn/limore/cellLines/single
is deprecated: false
has URI prefix: https://www.picb.ac.cn/limore/cellLines/single
has resource example: https://www.picb.ac.cn/limore/cellLines/single
has prefix: limore

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
has local unique identifier example: 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/
has resource example: view/LCL-2085
has prefix: lincs.cell

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

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
has local unique identifier example: 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/
has resource example: https://lincs.hms.harvard.edu/db/proteins/200282
has prefix: lincs.protein

Linguist
type: Resource
description: Registry of programming languages for the Linguist program for detecting and highlighting programming languages.
is part of: bioregistry
git repository: linguist
has local unique identifier example: Python
has provider formatter: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1
has local unique identifier pattern: ^[a-zA-Z0-9 +#'*]+$
is deprecated: false
has URI prefix: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#
has resource example: Python
has prefix: linguist

Genderal Ontology for Linguistic Description
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
has local unique identifier example: Term
has provider formatter: https://lambdamusic.github.io/ontospy-examples/gold-2010owl/class-gold$1.html
is deprecated: true
has URI prefix: https://bioregistry.io/linguist.gold:
has resource example: class-goldTerm.html
has prefix: linguist.gold

LinkedIn personal profile ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for a person, on the LinkedIn website
is part of: bioregistry
keyword: person
keyword: researcher
has local unique identifier example: deborahlehr
has provider formatter: https://www.linkedin.com/in/$1
has local unique identifier pattern: ^[\w0-9\-&_'’\.]+$
is deprecated: false
has URI prefix: https://www.linkedin.com/in/
has resource example: deborahlehr
has prefix: linkedin

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: data integration
keyword: ontology and terminology
has local unique identifier example: 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/
has resource example: SchemaDefinition
has prefix: linkml

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

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
has download URL: lipro.owl
is deprecated: true
has responsible: Christopher Baker
has URI prefix: http://purl.obolibrary.org/obo/LIPRO_
has prefix: lipro

LncBook
type: Resource
description: LncBook accommodates a high-quality collection of human lncRNA genes and transcripts, and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional signatures of lncRNAs in human diseases and different biological contexts.
is part of: bioregistry
has local unique identifier example: HSALNG0006197
has provider formatter: https://ngdc.cncb.ac.cn/lncbook/gene
has local unique identifier pattern: ^HSALNG\d{7}$
is deprecated: false
has URI prefix: https://ngdc.cncb.ac.cn/lncbook/gene
has resource example: https://ngdc.cncb.ac.cn/lncbook/gene
has prefix: lncbook

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
has local unique identifier example: SNHG3
is deprecated: false
has responsible: Pieter Mestdagh
has prefix: lncipedia

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
has local unique identifier example: arc
has provider formatter: https://id.loc.gov/vocabulary/relators/$1
is deprecated: false
has URI prefix: https://id.loc.gov/vocabulary/relators/
has resource example: arc
has prefix: loc.relator

Library of Congress Resource Types Scheme
type: Resource
contributor: Petra C. Steiner
contributor: https://orcid.org/0000-0003-4423-4370
description: A controlled vocabulary of media resources, such as audio, cartographic, manuscript, multimedia, etc.
is part of: bioregistry
keyword: data classification
has local unique identifier example: dig
has provider formatter: http://id.loc.gov/vocabulary/resourceTypes/$1
is deprecated: false
has URI prefix: http://id.loc.gov/vocabulary/resourceTypes/
has resource example: dig
has prefix: loc.resourcetype

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
has local unique identifier example: Address
is deprecated: false
has prefix: locn

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
has local unique identifier example: dtlit
is deprecated: false
has prefix: log

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_
has prefix: loggerhead

Lonza
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Contains information about cells and data sheets related to transfection.
is part of: bioregistry
has local unique identifier example: 968
has provider formatter: https://knowledge.lonza.com/cell
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://knowledge.lonza.com/cell
has resource example: https://knowledge.lonza.com/cell
has prefix: lonza

Loop ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for a person, in the Loop database of researcher impact
is part of: bioregistry
keyword: person
keyword: researcher
has local unique identifier example: 1859
has provider formatter: https://loop.frontiersin.org/people/$1
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has URI prefix: https://loop.frontiersin.org/people/
has resource example: https://loop.frontiersin.org/people/1859
has prefix: loop

The localization and quantitation atlas of the yeast proteome
type: Resource
description: The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library
is part of: bioregistry
has local unique identifier example: 1001
has provider formatter: http://www.weizmann.ac.il/molgen/loqate/gene/view/$1
is deprecated: false
has responsible: Maya Schuldiner
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.weizmann.ac.il/molgen/loqate/gene/view/
has resource example: http://www.weizmann.ac.il/molgen/loqate/gene/view/1001
has prefix: loqate

LOTUS Initiative for Open Natural Products Research
type: Resource
contributor: https://orcid.org/0000-0003-0443-9902
description: LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry.
is part of: bioregistry
keyword: chemistry
keyword: drugs
keyword: metabolites
has local unique identifier example: LTS0004651
has provider formatter: https://lotus.naturalproducts.net/compound/lotus_id/$1
has local unique identifier pattern: ^LTS\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-0443-9902
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://lotus.naturalproducts.net/compound/lotus_id/
has resource example: LTS0004651
has prefix: lotus

Livestock Product Trait Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.
is part of: bioregistry
git repository: livestock-product-trait-ontology
keyword: animal husbandry
keyword: ontology
keyword: phenotype
has local unique identifier example: 0000156
has provider formatter: http://purl.obolibrary.org/obo/LPT_$1
has local unique identifier pattern: ^\d+$
has download URL: lpt.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-2346-5201
has URI prefix: http://purl.obolibrary.org/obo/LPT_
has resource example: LPT_0000156
has prefix: lpt

Laboratory of Systems Pharmacology Compound
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)
is part of: bioregistry
keyword: chemistry
keyword: drugs
keyword: metabolites
has local unique identifier example: 1
has provider formatter: https://labsyspharm.github.io/lspci/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://labsyspharm.github.io/lspci/
has resource example: https://labsyspharm.github.io/lspci/1
has prefix: lspci

Long Term Ecological Research Controlled Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Ecological terms
is part of: bioregistry
has local unique identifier example: 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
has resource example: https://vocab.lternet.edu/vocab/vocab/index.php
has prefix: lter

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/
has prefix: lw

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: anatomy
keyword: mouse
keyword: obo
keyword: ontology
keyword: organ
keyword: tissue
has local unique identifier example: 0002502
has provider formatter: http://purl.obolibrary.org/obo/MA_$1
has local unique identifier pattern: ^\d+$
has download URL: ma.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-0956-8634
has URI prefix: http://purl.obolibrary.org/obo/MA_
has resource example: MA_0002502
has prefix: ma

Mechanism, Annotation and Classification in Enzymes
type: Resource
description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.
is part of: bioregistry
keyword: enzyme
keyword: life science
keyword: pathway
has local unique identifier example: M0001
has provider formatter: https://www.ebi.ac.uk/thornton-srv/m-csa/search/
has local unique identifier pattern: ^M\d{4}$
is deprecated: false
has responsible: Gemma L. Holliday
has URI prefix: https://www.ebi.ac.uk/thornton-srv/m-csa/search/
has resource example: https://www.ebi.ac.uk/thornton-srv/m-csa/search/
has prefix: macie

Maggot
type: Resource
description: Sharing descriptive Metadata is the first essential step towards Open Scientific Data. With this in mind, Maggot was specifically designed to annotate datasets by creating a metadata file to attach to the storage space. Indeed, it allows users to easily add descriptive metadata to datasets produced within a collective of people (research unit, platform, multi-partner project, etc.). This approach fits perfectly into a data management plan as it addresses the issues of data organization and documentation, data storage and frictionless metadata sharing within this same collective and beyond.
is part of: bioregistry
has local unique identifier example: frim1
has provider formatter: https://pmb-bordeaux.fr/maggot/metadata/$1
has local unique identifier pattern: ^[A-Za-z0-9]+$
is deprecated: false
has URI prefix: https://pmb-bordeaux.fr/maggot/metadata/
has resource example: frim1
has prefix: maggot

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

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: computational biology
keyword: mathematics
keyword: obo
keyword: ontology
keyword: systems biology
has local unique identifier example: 0000026
has provider formatter: http://bioportal.bioontology.org/ontologies/MAMO/
has local unique identifier pattern: ^\d{7}$
has download URL: mamo.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-6309-7327
has URI prefix: http://bioportal.bioontology.org/ontologies/MAMO/
has resource example: http://bioportal.bioontology.org/ontologies/MAMO/
has prefix: mamo

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
has local unique identifier example: 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
has resource example: http://mampol.uab.es/cgi-bin/MamPol_s2.pl
has prefix: mampol

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

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
has local unique identifier example: MDB00000001
has local unique identifier pattern: ^MDB\d{8}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has reviewer: https://orcid.org/0000-0001-9439-5346
has prefix: markerdb

MassBank
type: Resource
description: MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).
is part of: bioregistry
git repository: MassBank
keyword: chemistry
keyword: life science
keyword: physics
has local unique identifier example: MSBNK-IPB_Halle-PB000166
has provider formatter: https://massbank.jp/MassBank/RecordDisplay
has local unique identifier pattern: ^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$
is deprecated: false
has responsible: Tobias Schulze
has URI prefix: https://massbank.jp/MassBank/RecordDisplay
has resource example: https://massbank.jp/MassBank/RecordDisplay
has prefix: massbank

Mastodon
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: address on the Mastodon decentralized social network (the form is 'user@server.domain' without a leading '@')
is part of: bioregistry
has provider formatter: https://fedirect.toolforge.org/
has local unique identifier pattern: ^[A-Za-z0-9_]+([A-Za-z0-9_\.]+[A-Za-z0-9_]+)?@[\d\w\.\-]+[0-9a-z]+$
is deprecated: false
has URI prefix: https://fedirect.toolforge.org/
has resource example: https://fedirect.toolforge.org/
has prefix: mastodon

Minimal Anatomical Terminology
type: Resource
description: Minimal set of terms for anatomy
is part of: bioregistry
keyword: obo
keyword: ontology
has local unique identifier example: 0000000
has provider formatter: http://purl.obolibrary.org/obo/MAT_$1
has local unique identifier pattern: ^\d{7}$
has download URL: mat.obo
is deprecated: true
has responsible: Jonathan Bard
has URI prefix: http://purl.obolibrary.org/obo/MAT_
has resource example: MAT_0000000
has prefix: mat

MatrixDB
type: Resource
contributor: https://orcid.org/0000-0001-7456-0594
contributor: https://orcid.org/0000-0003-4423-4370
description: MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides
is part of: bioregistry
keyword: biology
keyword: interaction
keyword: protein
keyword: small molecule
has local unique identifier example: MULT_4_VAR1_bovine
has provider formatter: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort
is deprecated: false
appears in: complexportal
has responsible: Sylvie Ricard-Blum
has URI prefix: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort
has resource example: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort
has prefix: matrixdb

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

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
has local unique identifier example: 00000011-a
has provider formatter: https://www.mavedb.org/#/experiments/urn:mavedb:$1
has local unique identifier pattern: ^\S+$
is deprecated: false
has responsible: Alan Rubin
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.mavedb.org/#/experiments/urn:mavedb:
has resource example: experiments/urn:mavedb:00000011-a
has prefix: mavedb

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

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
has local unique identifier example: MFCD00011659
has local unique identifier pattern: ^\w{4}\d{8}$
is deprecated: false
appears in: xlmod
has prefix: mdl

Medical Data Models
type: Resource
description: The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.
is part of: bioregistry
keyword: biomedical science
keyword: medicine
keyword: translational medicine
has local unique identifier example: 4776
has provider formatter: https://medical-data-models.org/forms/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Bernd Müller
has URI prefix: https://medical-data-models.org/forms/
has resource example: https://medical-data-models.org/forms/4776
has prefix: mdm

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: biomedical science
keyword: disease
keyword: medicine
keyword: ontology
keyword: preclinical studies
has local unique identifier example: 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: MEDRA
has alternative prefix: MeDRA
has alternative prefix: MedDRA
has alternative prefix: Medical Dictionary for Regulatory Activities
has URI prefix: https://bioportal.bioontology.org/ontologies/MEDDRA
has resource example: https://bioportal.bioontology.org/ontologies/MEDDRA
has prefix: meddra

Human Medical Genetics
type: Resource
contributor: https://orcid.org/0000-0002-7356-1779
description: MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder.
is part of: bioregistry
has local unique identifier example: 760050
has provider formatter: https://www.ncbi.nlm.nih.gov/medgen/$1
has local unique identifier pattern: ^(CN)?\d{2,7}$
is deprecated: false
has responsible: https://orcid.org/0000-0001-5493-2602
has alternative prefix: medgen.uid
has URI prefix: https://www.ncbi.nlm.nih.gov/medgen/
has resource example: https://www.ncbi.nlm.nih.gov/medgen/760050
has prefix: medgen

MedGen Concept Unique ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This vocabulary is used internally inside MedGen to assign temporary identifiers to terms that will later get put in UMLS. Mappings between MedGen, MedGen CIDs, and UMLS can be found [here](https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.gz).
is part of: bioregistry
has local unique identifier example: CN970821
has local unique identifier pattern: ^CN\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-5493-2602
has prefix: medgen.cid

MediaDive Ingredient
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
has local unique identifier example: 13
has provider formatter: https://mediadive.dsmz.de/ingredients/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-3909-7201
has URI prefix: https://mediadive.dsmz.de/ingredients/
has resource example: https://mediadive.dsmz.de/ingredients/13
has prefix: mediadive.ingredient

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
has local unique identifier example: 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/
has resource example: https://mediadive.dsmz.de/medium/77
has prefix: mediadive.medium

MediaDive Solution
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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
has local unique identifier example: S6
has provider formatter: https://mediadive.dsmz.de/solutions/$1
has local unique identifier pattern: ^S\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-3909-7201
has URI prefix: https://mediadive.dsmz.de/solutions/
has resource example: S6
has prefix: mediadive.solution

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: disease
keyword: health science
keyword: medicine
keyword: ontology
has local unique identifier example: 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:
has resource example: 002804.htm
has prefix: medlineplus

Merck Index Monograph
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A semantic space of small molecules
is part of: bioregistry
has local unique identifier example: M2871
has provider formatter: https://merckindex.rsc.org/monographs/$1
is deprecated: false
has URI prefix: https://merckindex.rsc.org/monographs/
has resource example: M2871
has prefix: merckindex.monograph

Merck Index Reaction
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Chemical reactions in the Merck Index. This website doesn't exist anymore
is part of: bioregistry
has local unique identifier example: r376
has provider formatter: https://www.rsc.org/Merck-Index/reaction/$1
has local unique identifier pattern: ^r\d+$
is deprecated: true
appears in: rxno
has URI prefix: https://www.rsc.org/Merck-Index/reaction/
has resource example: r376
has prefix: merckindex.reaction

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
has local unique identifier example: IA
has provider formatter: https://www.ebi.ac.uk/merops/cgi-bin/clansum
is deprecated: false
has responsible: https://orcid.org/0000-0001-5557-7665
has URI prefix: https://www.ebi.ac.uk/merops/cgi-bin/clansum
has resource example: https://www.ebi.ac.uk/merops/cgi-bin/clansum
has prefix: merops.clan

MEROPS Entry
type: Resource
description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors.
is part of: bioregistry
keyword: biomedical science
keyword: enzyme
keyword: life science
keyword: protein
keyword: structure
has local unique identifier example: I31.952
has provider formatter: https://www.ebi.ac.uk/merops/cgi-bin/pepsum
has local unique identifier pattern: ^[SCTAGMNUIX]{1,2}\d{2}\.([AB]\d{2}|\d{3})$
is deprecated: false
has responsible: https://orcid.org/0000-0001-5557-7665
has alternative prefix: merops.inhibitor
has URI prefix: https://www.ebi.ac.uk/merops/cgi-bin/pepsum
has resource example: https://www.ebi.ac.uk/merops/cgi-bin/pepsum
has prefix: merops.entry

MEROPS Family
type: Resource
description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families.
is part of: bioregistry
has local unique identifier example: S1
has provider formatter: https://www.ebi.ac.uk/merops/cgi-bin/famsum
has local unique identifier pattern: ^[SCTAGMNU]\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-5557-7665
has URI prefix: https://www.ebi.ac.uk/merops/cgi-bin/famsum
has resource example: https://www.ebi.ac.uk/merops/cgi-bin/famsum
has prefix: merops.family

Merriam Webster Dictionary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Online Dictionary
is part of: bioregistry
has local unique identifier example: 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/
has resource example: buccal gland
has prefix: merriamwebster

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
has local unique identifier example: 17186
has provider formatter: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi
has local unique identifier pattern: ^[A-Za-z0-9]+$
provides for: mesh
is deprecated: false
has URI prefix: https://bioregistry.io/mesh.2012:
has resource example: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi
has prefix: mesh.2012

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
has local unique identifier example: 17165
has provider formatter: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi
has local unique identifier pattern: ^[A-Za-z0-9]+$
provides for: mesh
is deprecated: false
has URI prefix: https://bioregistry.io/mesh.2013:
has resource example: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi
has prefix: mesh.2013

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
has local unique identifier example: 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#
has resource example: term
has prefix: mesh.vocab

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
has local unique identifier example: 12DICHLORETHDEG-PWY
has provider formatter: https://metacyc.org/META/NEW-IMAGE
is deprecated: false
has responsible: https://orcid.org/0000-0002-5876-6418
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://metacyc.org/META/NEW-IMAGE
has resource example: https://metacyc.org/META/NEW-IMAGE
has prefix: metacyc.pathway

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
has local unique identifier example: 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: https://orcid.org/0000-0002-5876-6418
has URI prefix: https://metacyc.org/META/NEW-IMAGE
has resource example: https://metacyc.org/META/NEW-IMAGE
has prefix: metacyc.reaction

MetaNetX chemical
type: Resource
description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.
is part of: bioregistry
has local unique identifier example: MNXM1723
has provider formatter: https://www.metanetx.org/chem_info/$1
has local unique identifier pattern: ^(MNXM\d+|BIOMASS|WATER)$
is deprecated: false
has URI prefix: https://www.metanetx.org/chem_info/
has resource example: MNXM1723
has prefix: metanetx.chemical

MetaNetX compartment
type: Resource
description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.
is part of: bioregistry
has local unique identifier example: MNXC15
has provider formatter: https://www.metanetx.org/comp_info/$1
has local unique identifier pattern: ^(MNX[CD]\d+|BOUNDARY|IN|OUT)$
is deprecated: false
has URI prefix: https://www.metanetx.org/comp_info/
has resource example: MNXC15
has prefix: metanetx.compartment

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

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

Metabolic Network Exchange Database
type: Resource
description: The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another.
is part of: bioregistry
keyword: dna
keyword: interaction
keyword: pathway
keyword: protein
keyword: regulation
keyword: rna
keyword: small molecule
has local unique identifier example: 377369
has provider formatter: http://metnetonline.org/browse_pathway2.php
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://metnetonline.org/browse_pathway2.php
has resource example: http://metnetonline.org/browse_pathway2.php
has prefix: metnetdb

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: microbes
keyword: ontology
keyword: phenotypes
has local unique identifier example: 1004005
has provider formatter: https://w3id.org/metpo/$1
has local unique identifier pattern: ^\d+$
has download URL: 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/
has identifier space owner: 02jbv0t02
has resource example: https://w3id.org/metpo/1004005
has prefix: metpo

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

Mental Functioning Ontology
type: Resource
description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.
is part of: bioregistry
git repository: mental-functioning-ontology
keyword: biomedical science
keyword: cognition
keyword: cognitive neuroscience
keyword: mental health
keyword: obo
keyword: ontology
has local unique identifier example: 0000091
has provider formatter: http://purl.obolibrary.org/obo/MF_$1
has local unique identifier pattern: ^\d{7}$
has download URL: mf.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-3469-4923
has URI prefix: http://purl.obolibrary.org/obo/MF_
has resource example: MF_0000091
has prefix: mf

Medaka fish anatomy and development
type: Resource
description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.
is part of: bioregistry
keyword: anatomy
keyword: development
keyword: fish
keyword: obo
keyword: ontology
has local unique identifier example: 0000001
has provider formatter: http://purl.obolibrary.org/obo/MFO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: mfo.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-1548-3290
has URI prefix: http://purl.obolibrary.org/obo/MFO_
has resource example: MFO_0000001
has prefix: mfo

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: biomedical science
keyword: emotion process
keyword: mental health
keyword: obo
keyword: ontology
has local unique identifier example: 000204
has provider formatter: http://purl.obolibrary.org/obo/MFOEM_$1
has local unique identifier pattern: ^\d{6}$
has download URL: mfoem.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-3469-4923
has URI prefix: http://purl.obolibrary.org/obo/MFOEM_
has resource example: MFOEM_000204
has prefix: mfoem

Mental Disease Ontology
type: Resource
description: The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF).
is part of: bioregistry
git repository: mental-functioning-ontology
keyword: disease
keyword: obo
keyword: ontology
keyword: psychiatry
has local unique identifier example: 0000046
has provider formatter: http://purl.obolibrary.org/obo/MFOMD_$1
has local unique identifier pattern: ^\d{7}$
has download URL: mfomd.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-3469-4923
has URI prefix: http://purl.obolibrary.org/obo/MFOMD_
has resource example: MFOMD_0000046
has prefix: mfomd

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: genome
keyword: life science
has local unique identifier example: 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
has resource example: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi
has prefix: mge

MGnify Analysis
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Analyses of microbiome data within MGnify
is part of: bioregistry
has local unique identifier example: MGYA00002270
has provider formatter: https://www.ebi.ac.uk/metagenomics/analyses/$1
has local unique identifier pattern: ^MGYA\d+$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/metagenomics/analyses/
has resource example: MGYA00002270
has prefix: mgnify.analysis

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
has local unique identifier example: 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/
has resource example: ERP004492
has prefix: mgnify.proj

MGnify Sample
type: Resource
description: The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.
is part of: bioregistry
has local unique identifier example: SRS086444
has provider formatter: https://www.ebi.ac.uk/metagenomics/samples/$1
has local unique identifier pattern: ^[A-Z]+[0-9]+$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/metagenomics/samples/
has resource example: SRS086444
has prefix: mgnify.samp

MGnify Genome
type: Resource
description: The free-to-use MGnify platform provides assembly, analysis and archiving of microbiome-derived nucleic acid sequence data from a wide range of biomes, with analysis results providing taxonomic and functional profiles. The platform also includes MGnify Proteins, a database of protein sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes, a resource of biome-specific catalogues of microbial genomes, including extensive functional annotations.
is part of: bioregistry
has local unique identifier example: MGYG000004903
has provider formatter: https://www.ebi.ac.uk/metagenomics/genomes/$1
has local unique identifier pattern: ^MGYG\d{9}(\.\d+)?$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/metagenomics/genomes/
has resource example: MGYG000004903
has prefix: mgnifygenome

MGnify Protein
type: Resource
description: The free-to-use MGnify platform provides assembly, analysis and archiving of microbiome-derived nucleic acid sequence data from a wide range of biomes, with analysis results providing taxonomic and functional profiles. The platform also includes MGnify Proteins, a database of protein sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes, a resource of biome-specific catalogues of microbial genomes, including extensive functional annotations.
is part of: bioregistry
has local unique identifier example: MGYP000261684433
has provider formatter: https://www.ebi.ac.uk/metagenomics/proteins/$1
has local unique identifier pattern: ^MGYP\d{12}$
is deprecated: false
has URI prefix: https://www.ebi.ac.uk/metagenomics/proteins/
has resource example: MGYP000261684433
has prefix: mgnifyprotein

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

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

Minimal Information About Anatomy ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
is deprecated: true
has prefix: miaa

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: life science
keyword: obo
keyword: ontology
keyword: phylogenetics
keyword: phylogeny
has local unique identifier example: 0000010
has provider formatter: http://purl.obolibrary.org/obo/MIAPA_$1
has local unique identifier pattern: ^\d{7}$
has download URL: miapa.owl
is deprecated: false
has responsible: Hilmar Lapp
has URI prefix: http://purl.obolibrary.org/obo/MIAPA_
has resource example: MIAPA_0000010
has prefix: miapa

Minimum Information about a Biosynthetic Gene Cluster data repository
type: Resource
contributor: https://orcid.org/0000-0001-6534-6609
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
has local unique identifier example: 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/
has resource example: BGC0000001
has prefix: mibig

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
has local unique identifier example: 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
has resource example: http://www.genoscope.cns.fr/agc/microscope/mage/info.php
has prefix: microscope

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
has local unique identifier example: ECU03_0820i
has provider formatter: http://microsporidiadb.org/micro/showRecord.do
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4446-6200
has URI prefix: http://microsporidiadb.org/micro/showRecord.do
has resource example: http://microsporidiadb.org/micro/showRecord.do
has prefix: microsporidia

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

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
has local unique identifier example: 1
has provider formatter: http://immunet.cn/bdb/index.php/mimoset/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Jian Huang
has URI prefix: http://immunet.cn/bdb/index.php/mimoset/
has resource example: http://immunet.cn/bdb/index.php/mimoset/1
has prefix: mimodb

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: interaction
keyword: life science
keyword: protein
keyword: proteomics
has local unique identifier example: 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: https://orcid.org/0000-0001-5084-9000
has URI prefix: https://mint.bio.uniroma2.it/index.php/detailed-curation/
has resource example: https://mint.bio.uniroma2.it/index.php/detailed-curation/
has prefix: mint

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

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
has local unique identifier example: MIPF0000002
has provider formatter: http://www.mirbase.org/cgi-bin/mirna_summary.pl
has download URL: 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
has resource example: http://www.mirbase.org/cgi-bin/mirna_summary.pl
has prefix: mirbase.family

miRBase mature miRNA
type: Resource
description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.
is part of: bioregistry
keyword: nucleotide
keyword: ontology
keyword: sequence
has local unique identifier example: MIMAT0046872
has provider formatter: http://mirbase.org/cgi-bin/mature.pl
has local unique identifier pattern: ^MIMAT\d{7}$
has download URL: mirbase.mature.owl
is deprecated: false
has responsible: 0000-0001-6043-807X
has alternative prefix: MIRBASEM
has URI prefix: http://mirbase.org/cgi-bin/mature.pl
has resource example: http://mirbase.org/cgi-bin/mature.pl
has prefix: mirbase.mature

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
has local unique identifier example: 165a
has provider formatter: http://comgen.pl/mirex1/
has local unique identifier pattern: ^\d+(\w+)?$
is deprecated: false
has responsible: Wojciech M. Karlowski
has URI prefix: https://bioregistry.io/mirex:
has resource example: http://comgen.pl/mirex1/
has prefix: mirex

microRNA Gene Database
type: Resource
contributor: 0009-0008-8406-631X
description: mircoRNA Gene Database is a collection of animal microRNA genes. This database allows researchers to analyze mircoRNA properties like secondary structure and features in a phylogenetic context.
is part of: bioregistry
has local unique identifier example: Hsa-Let-7-P2a3
has provider formatter: https://mirgenedb.org/browse
has local unique identifier pattern: ^[a-zA-Z0-9]+(-[a-zA-Z0-9]+)+$
is deprecated: false
has responsible: Bastian Fromm
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://mirgenedb.org/browse
has resource example: https://mirgenedb.org/browse
has prefix: mirgenedb

Identifiers.org namespace
type: Resource
description: Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain.
is part of: bioregistry
keyword: biochemistry
keyword: biomedical science
keyword: life science
has local unique identifier example: pubmed
has provider formatter: https://registry.identifiers.org/registry/$1
has local unique identifier pattern: ^[0-9a-z_:\.-]+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6309-7327
has alternative prefix: identifiers.namespace
has URI prefix: https://registry.identifiers.org/registry/
has resource example: pubmed
has prefix: miriam

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
has local unique identifier example: 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/
has resource example: https://www.ebi.ac.uk/miriam/main/00000008
has prefix: miriam.collection

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
has local unique identifier example: 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/
has resource example: https://resolver.api.identifiers.org/resolveMirId/00100005
has prefix: miriam.resource

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
has download URL: mirnao.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-1635-4810
has URI prefix: http://purl.obolibrary.org/obo/MIRNAO_
has prefix: mirnao

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: genomics
keyword: life science
keyword: prediction
has local unique identifier example: 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: Michael Szcześniak
has URI prefix: http://rhesus.amu.edu.pl/mirnest/copy/details.php
has resource example: http://rhesus.amu.edu.pl/mirnest/copy/details.php
has prefix: mirnest

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

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
has local unique identifier example: 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
has resource example: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php
has prefix: mirtarbase

miRNA Target Prediction at EMBL
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs
is part of: bioregistry
has local unique identifier example: miR-1
is deprecated: false
has prefix: mirte

Minimum Information about a Tailoring Enzyme data repository
type: Resource
contributor: https://orcid.org/0000-0001-6534-6609
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
has local unique identifier example: MITE0000001
has provider formatter: https://mite.bioinformatics.nl/repository/$1
has local unique identifier pattern: ^MITE\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0001-6534-6609
has reviewer: https://orcid.org/0000-0001-9439-5346
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://mite.bioinformatics.nl/repository/
has resource example: MITE0000001
has prefix: mite

Minimum Information about any (x) Sequence
type: Resource
contributor: https://orcid.org/0000-0001-9076-6066
contributor: Chris Hunter
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-8741-7823
description: The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample.
is part of: bioregistry
keyword: ontology
has local unique identifier example: 0001056
has provider formatter: https://w3id.org/mixs/$1
has local unique identifier pattern: ^\d{7}$
has download URL: mixs.owl.ttl
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/mixs/
has resource example: https://w3id.org/mixs/0001056
has prefix: mixs

MLCommons Association
type: Resource
description: MLCommons Association artifacts, including benchmark results, datasets, and saved models.
is part of: bioregistry
has local unique identifier example: 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/
has resource example: https://www.mlcommons.org/mlc-id/0.7-123
has prefix: mlc

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: interaction
keyword: protein
keyword: small molecule
keyword: structure
has local unique identifier example: 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
has resource example: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi
has prefix: mmdb

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
has local unique identifier example: 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
has resource example: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp
has prefix: mmmp.biomaps

MarCat
type: Resource
description: MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.
is part of: bioregistry
has local unique identifier example: MMP743597.11
has provider formatter: https://mmp.sfb.uit.no/databases/marcat/#/records/$1
has local unique identifier pattern: ^MMP\d+.\d+$
is deprecated: false
has URI prefix: https://mmp.sfb.uit.no/databases/marcat/#/records/
has resource example: records/MMP743597.11
has prefix: mmp.cat

MarDB
type: Resource
description: MarDB includes all sequenced marine microbial genomes regardless of level of completeness.
is part of: bioregistry
has local unique identifier example: 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/
has resource example: records/MMP02954345.1
has prefix: mmp.db

MarFun
type: Resource
description: MarFun is manually curated database for marine fungi which is a part of the MAR databases.
is part of: bioregistry
has local unique identifier example: MMP3888430
has provider formatter: https://mmp.sfb.uit.no/databases/marfun/#/records/$1
has local unique identifier pattern: ^MMP\d+.\d+$
is deprecated: false
has URI prefix: https://mmp.sfb.uit.no/databases/marfun/#/records/
has resource example: records/MMP3888430
has prefix: mmp.fun

MarRef
type: Resource
description: MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes.
is part of: bioregistry
has local unique identifier example: MMP3312982.2
has provider formatter: https://mmp.sfb.uit.no/databases/marref/#/records/$1
has local unique identifier pattern: ^MMP\d+.\d+$
is deprecated: false
has URI prefix: https://mmp.sfb.uit.no/databases/marref/#/records/
has resource example: records/MMP3312982.2
has prefix: mmp.ref

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

MMsINC
type: Resource
description: MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats.
is part of: bioregistry
keyword: small molecule
keyword: structure
has local unique identifier example: MMs00000001
has provider formatter: http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php
has resource example: http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php
has prefix: mmsinc

Multum MediSource Lexicon
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included.
is part of: bioregistry
has local unique identifier example: 3355
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: MMSL_CODE
has prefix: mmsl

Microarray experimental conditions
type: Resource
description: The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data.
is part of: bioregistry
keyword: obo
keyword: ontology
has local unique identifier example: ArrayGroup
has provider formatter: https://mged.sourceforge.net/ontologies/MGEDontology.php#$1
has local unique identifier pattern: ^\w+$
has download URL: mo.owl
is deprecated: true
has responsible: Chris Stoeckert
has URI prefix: https://mged.sourceforge.net/ontologies/MGEDontology.php#
has resource example: ArrayGroup
has prefix: mo

MobiDB
type: Resource
description: MobiDB is a database of protein disorder and mobility annotations.
is part of: bioregistry
keyword: biology
keyword: biomedical science
has local unique identifier example: P10636
has provider formatter: https://mobidb.org/$1
has local unique identifier pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$
provides for: uniprot
is deprecated: false
has responsible: https://orcid.org/0000-0003-4525-7793
has URI prefix: https://mobidb.org/
has resource example: P10636
has prefix: mobidb

Mobilome Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Mobilome Ontology describes bacterial mobile genetic elements, their mechanisms, and associated epidemiology.
is part of: bioregistry
git repository: mobio
keyword: ontology
has local unique identifier example: 0000001
has provider formatter: http://purl.obolibrary.org/obo/MOBIO_$1
has local unique identifier pattern: ^\d+$
has download URL: mobio.owl
is deprecated: false
has URI prefix: http://purl.obolibrary.org/obo/MOBIO_
has resource example: MOBIO_0000001
has prefix: mobio

ModelDB
type: Resource
description: ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.
is part of: bioregistry
keyword: computational biology
keyword: life science
keyword: neurobiology
has local unique identifier example: 45539
has provider formatter: https://modeldb.science/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Perry Miller
has URI prefix: https://modeldb.science/
has resource example: https://modeldb.science/45539
has prefix: modeldb

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
has local unique identifier example: 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/
has resource example: https://modeldb.science/modellist/3639
has prefix: modeldb.concept

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
has local unique identifier example: 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/
has resource example: station.6051b2f8b9142a5b8c676342
has prefix: moid

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
has local unique identifier example: 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
has resource example: http://www.molbase.com/en/index.php
has prefix: molbase

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
has local unique identifier example: CL000025
has provider formatter: https://molbic.idrblab.net/data/cellline/details/$1
has local unique identifier pattern: ^CL\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-8069-0053
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://molbic.idrblab.net/data/cellline/details/
has resource example: CL000025
has prefix: molbic.cellline

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
has local unique identifier example: CP0041613
has provider formatter: https://molbic.idrblab.net/data/compound/details/$1
has local unique identifier pattern: ^CP\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-8069-0053
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://molbic.idrblab.net/data/compound/details/
has resource example: CP0041613
has prefix: molbic.compound

MolBiC Protein
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 proteins that serve as molecular targets in cell-based bioactivity measurements.
is part of: bioregistry
has local unique identifier example: PT00819
has provider formatter: https://molbic.idrblab.net/data/protein/details/$1
has local unique identifier pattern: ^PT\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-8069-0053
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://molbic.idrblab.net/data/protein/details/
has resource example: PT00819
has prefix: molbic.protein

MolGlueDB
type: Resource
contributor: https://orcid.org/0009-0009-3402-8013
description: Identifiers correspond to molecular glue compounds in the MolGlueDB which is a free and open-access online database dedicated to the collection and integration of molecular glue compound information.
is part of: bioregistry
keyword: compound
keyword: degraders
keyword: proteolysis
has local unique identifier example: 1
has provider formatter: https://www.molgluedb.com/browseDB/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Chong Qin
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.molgluedb.com/browseDB/
has resource example: https://www.molgluedb.com/browseDB/1
has prefix: molgluedb

MolMeDB
type: Resource
contributor: Dominik Martinat
description: MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations.
is part of: bioregistry
git repository: MolMeDB
keyword: biochemistry
keyword: cheminformatics
keyword: chemistry
keyword: computational chemistry
keyword: molecular biology
keyword: molecular chemistry
keyword: molecular dynamics
keyword: molecular physical chemistry
has local unique identifier example: MM00040
has provider formatter: https://molmedb.upol.cz/mol/$1
has local unique identifier pattern: ^[Mm]{2}[0-9]{5,}(\.[0-9]+)?$
is deprecated: false
has responsible: Karel Berka
has URI prefix: https://molmedb.upol.cz/mol/
has resource example: MM00040
has prefix: molmedb

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: protein
keyword: small molecule
keyword: structure
has local unique identifier example: 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
has resource example: http://www.molmovdb.org/cgi-bin/morph.cgi
has prefix: molmovdb

MONDO Issue Tracker
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An issue on the MONDO GitHub issue tracker
is part of: bioregistry
has local unique identifier example: 832
has provider formatter: https://github.com/monarch-initiative/mondo/issues/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://github.com/monarch-initiative/mondo/issues/
has resource example: https://github.com/monarch-initiative/mondo/issues/832
has prefix: mondo.issue

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
has local unique identifier example: 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/
has resource example: M0001
has prefix: morpheus

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
has local unique identifier example: 00005643
has provider formatter: https://purl.dataone.org/odo/MOSAIC_$1
has local unique identifier pattern: ^\d{8}$
has download URL: MOSAiC.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-0381-3766
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://purl.dataone.org/odo/MOSAIC_
has resource example: MOSAIC_00005643
has prefix: mosaic

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: interaction
keyword: life science
keyword: protein
keyword: small molecule
has local unique identifier example: 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: Johannes B. Goll
has alternative prefix: mpidb
has URI prefix: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-
has resource example: interaction id:MPIDB-INT-1776
has prefix: mpid

Minimum PDDI Information Ontology
type: Resource
description: An ontology of minimum information regarding potential drug-drug interaction information.
is part of: bioregistry
git repository: MPIO
keyword: obo
keyword: ontology
has local unique identifier example: 0000004
has provider formatter: http://purl.obolibrary.org/obo/MPIO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: mpio.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-1834-3856
has URI prefix: http://purl.obolibrary.org/obo/MPIO_
has resource example: MPIO_0000004
has prefix: mpio

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: immune system
keyword: immunology
keyword: major histocompatibility complex
keyword: obo
keyword: ontology
has local unique identifier example: 0000634
has provider formatter: http://purl.obolibrary.org/obo/MRO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: mro.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-8457-6693
has URI prefix: http://purl.obolibrary.org/obo/MRO_
has resource example: MRO_0000634
has prefix: mro

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: gene family
keyword: gene group
keyword: gene set
keyword: ontology
keyword: pathway
keyword: reaction
has local unique identifier example: M1
has provider formatter: https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/$1
has local unique identifier pattern: ^M\d+$
has download URL: msigdb.owl.gz
is deprecated: false
has responsible: Jill P. Mesirov
has alternative prefix: msig
has URI prefix: https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/
has resource example: M1
has prefix: msigdb

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
has local unique identifier example: 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
has resource example: http://tumor.informatics.jax.org/mtbwi/strainDetails.do
has prefix: mtbd

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
has local unique identifier example: U001388
has provider formatter: https://uts.nlm.nih.gov/uts/umls/vocabulary/MTH/$1
has local unique identifier pattern: ^U\d+$
is deprecated: false
appears in: mondo
appears in: umls
has alternative prefix: umls.mth
has URI prefix: https://uts.nlm.nih.gov/uts/umls/vocabulary/MTH/
has resource example: U001388
has prefix: mth

Manufacturers of Vaccines
type: Resource
contributor: https://orcid.org/0000-0002-8741-7823
description: The CDC's National Center for Immunization and Respiratory Diseases ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers of vaccines in the US. Inactive MVX codes allow transmission of historical immunization records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename) (vaccine administered code), the specific trade named vaccine may be indicated.
is part of: bioregistry
has local unique identifier example: ASZ
has provider formatter: https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action
has local unique identifier pattern: ^\w+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action
has resource example: https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action
has prefix: mvx

Metabolomics Workbench Project
type: Resource
description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).
is part of: bioregistry
has local unique identifier example: PR000001
has provider formatter: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php
has local unique identifier pattern: ^PR[0-9]{6}$
is deprecated: false
has URI prefix: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php
has resource example: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php
has prefix: mw.project

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

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
has local unique identifier example: 0001109
has provider formatter: http://purls.helmholtz-metadaten.de/mwo/mwo_$1
has local unique identifier pattern: ^\d{7}$
has download URL: mwo.owl
is deprecated: false
has responsible: Hossein Beygi Nasrabadi
has URI prefix: http://purls.helmholtz-metadaten.de/mwo/mwo_
has resource example: mwo_0001109
has prefix: mwo

Fungal Nomenclature and Species Bank
type: Resource
contributor: Carlos Moreno
description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.
is part of: bioregistry
keyword: biology
keyword: classification
keyword: taxonomy
has local unique identifier example: 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/
has resource example: https://www.mycobank.org/page/Name%20details%20page/349124
has prefix: mycobank

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: data analysis
keyword: data identity and mapping
keyword: data retrieval
keyword: lipidomics
keyword: mass spectrum
keyword: metabolomics
keyword: proteomics
has local unique identifier example: 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: https://orcid.org/0000-0002-1767-2343
has URI prefix: http://proteomecentral.proteomexchange.org/usi/
has resource example: http://proteomecentral.proteomexchange.org/usi/
has prefix: mzspec

Name-to-Thing
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ARK resolver as well as resolver built with common prefixes as in Identifiers.org
is part of: bioregistry
has local unique identifier example: chebi
has provider formatter: https://n2t.net/$1:
is deprecated: false
has URI prefix: https://bioregistry.io/n2t:
has resource example: chebi:
has prefix: n2t

NFDI4Earth Ontology
type: Resource
description: The ontology and metadata schema for the NFDI4Earth Knowledge Hub. See serializations of this schema as an OWL ontology here: - [RDF/XML](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.xml) - [RDF/Turtle](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.ttl) - [RDF/JSON-LD](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.jsonld) - [RDF/N-Triples](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.nt)
is part of: bioregistry
keyword: earth sciences
keyword: ess
has local unique identifier example: API
has provider formatter: http://nfdi4earth.de/ontology/$1
is deprecated: false
has URI prefix: http://nfdi4earth.de/ontology/
has resource example: API
has prefix: n4e

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: chemistry
keyword: reactions
keyword: text mining
has local unique identifier example: 4.2.78
is deprecated: false
has responsible: Gregory Landrum
has prefix: namerxn

Natural Product-Drug Interaction Research Data Repository
type: Resource
description: The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs).
is part of: bioregistry
keyword: biomedical science
keyword: pharmacology
has local unique identifier example: 28
has provider formatter: https://repo.napdi.org/study/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: Richard Boyce
has URI prefix: https://repo.napdi.org/study/
has resource example: https://repo.napdi.org/study/28
has prefix: napdi

Nucleic Acids Phylogenetic Profiling
type: Resource
description: NAPP (Nucleic Acids Phylogenetic Profiling) is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters.
is part of: bioregistry
keyword: clustering
keyword: genomics
keyword: nucleotide
has local unique identifier example: 351
has provider formatter: http://rssf.i2bc.paris-saclay.fr/NAPP/Niveau2.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Daniel Gautheret
has URI prefix: http://rssf.i2bc.paris-saclay.fr/NAPP/Niveau2.php
has resource example: http://rssf.i2bc.paris-saclay.fr/NAPP/Niveau2.php
has prefix: napp

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

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
has local unique identifier example: 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/
has resource example: https://osdr.nasa.gov/bio/repo/data/biospecimens/7943
has prefix: nasaosdr.biospecimen

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
has local unique identifier example: 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/
has resource example: OS-27
has prefix: nasaosdr.experiment

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
has local unique identifier example: 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/
has resource example: https://osdr.nasa.gov/bio/repo/data/hardware/2011
has prefix: nasaosdr.hardware

NASA Open Science Data Repository Mission
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for missions associated with experiments that investigate biological and health responses of terrestrial life to spaceflight
is part of: bioregistry
has local unique identifier example: ARCBedrest
has provider formatter: https://osdr.nasa.gov/bio/repo/data/missions/$1
has local unique identifier pattern: ^.+$
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/missions/
has resource example: ARCBedrest
has prefix: nasaosdr.mission

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
has local unique identifier example: 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/
has resource example: VEG-03D
has prefix: nasaosdr.payload

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
has local unique identifier example: 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/
has resource example: OSD-678
has prefix: nasaosdr.study

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
has local unique identifier example: 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/
has resource example: https://osdr.nasa.gov/bio/repo/data/subjects/58
has prefix: nasaosdr.subject

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

National Bibliography Number
type: Resource
description: The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier.
is part of: bioregistry
has local unique identifier example: urn:nbn:fi:tkk-004781
has provider formatter: http://nbn-resolving.org/$1
has local unique identifier pattern: ^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$
is deprecated: false
has URI prefix: http://nbn-resolving.org/
has resource example: urn:nbn:fi:tkk-004781
has prefix: nbn

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: microbial
keyword: microbiology
keyword: taxonomy
has local unique identifier example: 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
has resource example: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet
has prefix: nbrc

National Center for Advancing Translation Sciences BioPlanet
type: Resource
contributor: https://orcid.org/0000-0002-8719-7760
description: The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays.
is part of: bioregistry
has local unique identifier example: 3
has provider formatter: https://tripod.nih.gov/bioplanet/detail.jsp
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Ruili Huang
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://tripod.nih.gov/bioplanet/detail.jsp
has resource example: https://tripod.nih.gov/bioplanet/detail.jsp
has prefix: ncats.bioplanet

NCATS Drugs
type: Resource
contributor: Vlado Dancik
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-8719-7760
contributor: https://orcid.org/0000-0003-4423-4370
description: The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including: - US Approved Drugs - Marketed Drugs - Investigational Drugs - Other Substances
is part of: bioregistry
has local unique identifier example: 44259
has provider formatter: https://drugs.ncats.io/drug/$1
is deprecated: false
has alternative prefix: inxight
has alternative prefix: inxight-drugs
has URI prefix: https://drugs.ncats.io/drug/
has resource example: https://drugs.ncats.io/drug/44259
has prefix: ncats.drug

NCBI Genetic Code
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.
is part of: bioregistry
keyword: genetic code
keyword: genome
keyword: ontology
has local unique identifier example: 11
has provider formatter: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi#SG$1
has local unique identifier pattern: ^\d+$
has download URL: ncbi.gc.owl
is deprecated: false
has responsible: Andrzej Elzanowski
has alternative prefix: gc
has alternative prefix: gc_id
has URI prefix: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi#SG
has resource example: SG11
has prefix: ncbi.gc

NCBI Genome
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.
is part of: bioregistry
has local unique identifier example: 51
has provider formatter: https://www.ncbi.nlm.nih.gov/genome/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.ncbi.nlm.nih.gov/genome/
has resource example: https://www.ncbi.nlm.nih.gov/genome/51
has prefix: ncbi.genome

NCBI Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources
is part of: bioregistry
has local unique identifier example: ECOCYC
has provider formatter: https://bioregistry.io/metaregistry/ncbi/$1
is deprecated: false
has URI prefix: https://bioregistry.io/metaregistry/ncbi/
has resource example: ECOCYC
has prefix: ncbi.resource

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
has local unique identifier example: 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/
has resource example: NBK331
has prefix: ncbibook

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/
has prefix: ncbidrs

GenInfo Identifier
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number.
is part of: bioregistry
has local unique identifier example: 568815597
has provider formatter: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
has local unique identifier pattern: ^\d+$
is deprecated: false
has canonical: genbank
has alternative prefix: NCBI_gi
has alternative prefix: ncbi.gi
has URI prefix: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
has identifier space owner: 02meqm098
has resource example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
has prefix: ncbigi

NCBI Orthologs
type: Resource
contributor: https://orcid.org/0000-0001-9311-9745
description: Database of one-to-one ortholog information provided by the NCBI as a subset of their Gene resource. Used for users to access ortholog information for over 1000 species of vertebrates and arthropods.
is part of: bioregistry
has local unique identifier example: 2
has provider formatter: https://www.ncbi.nlm.nih.gov/gene/$1/ortholog
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-9311-9745
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://bioregistry.io/ncbiortholog:
has resource example: ortholog
has prefix: ncbiortholog

NCI Drug Dictionary ID
type: Resource
description: identifier of an entry in the NCI Drug Dictionary
is part of: bioregistry
has local unique identifier example: 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/
has resource example: beta-carotene
has prefix: nci.drug

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
has local unique identifier example: 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
has identifier space owner: 040gcmg81
has resource example: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp
has prefix: ncim

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

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: biomedical science
keyword: chemical entity
keyword: drug
keyword: medicinal chemistry
keyword: ontology
has local unique identifier example: 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/
has resource example: http://purl.bioontology.org/ontology/NDDF/002678
has prefix: nddf

Network Data Exchange
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge.
is part of: bioregistry
git repository: ndexbio
keyword: epidemiology
keyword: life science
keyword: microbiology
has provider formatter: https://www.ndexbio.org/viewer/networks/$1
is deprecated: false
has responsible: Rudolf T. Pillich
has URI prefix: https://www.ndexbio.org/viewer/networks/
has prefix: ndex

Nematode & Neglected Genomics
type: Resource
description: NEMBASE is a comprehensive Nematode Transcriptome Database. NEMBASE4 includes robust protein predictions (NemPep4), and protein families for 63 nematode species, over 600,000 ESTs and over 250,000 proteins.
is part of: bioregistry
keyword: dna
keyword: protein
keyword: rna
has local unique identifier example: NBC00001
has provider formatter: http://www.nematodes.org/nembase4/cluster.php
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.nematodes.org/nembase4/cluster.php
has resource example: http://www.nematodes.org/nembase4/cluster.php
has prefix: nembase

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
has local unique identifier example: 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/
has resource example: smp-m3w9hbe
has prefix: nemo

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: competence
keyword: ontology
keyword: skills
has local unique identifier example: 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#
has resource example: CognitiveCompetence
has prefix: nemo.competence

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

NEPOMUK Annotation Ontology Specification
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The annotation ontology provides vocabulary that enables users to attach custom descriptions, identifiers, tags and ratings to resources on their desktop. Via other properties, the user is also able to make generic relationships between related resources explicit. Some relationships between resources are too general to be included at the domain ontology level. Instead, these properties are also defined in the annotation ontology. Given the high-level status of this ontology, these propreties can be used to link any related resources on the user's desktop, as well as provide custom human-readable textual annotations. (from homepage)
is part of: bioregistry
has local unique identifier example: created
has provider formatter: http://www.semanticdesktop.org/ontologies/2007/08/15/nao#$1
is deprecated: false
has URI prefix: http://www.semanticdesktop.org/ontologies/2007/08/15/nao#
has resource example: created
has prefix: nepomuk.nao

NEPOMUK Contact Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: NEPOMUK Contact Ontology describes contact information, common in many places on the desktop. It evolved from the VCARD specification (RFC 2426) and has been inspired by the Vcard Ontology by Renato Ianella. The scope of NCO is much broader though. This document gives an overview of the classes, properties and intended use cases of the NCO ontology. (from homepage)
is part of: bioregistry
has local unique identifier example: fullname
has provider formatter: http://www.semanticdesktop.org/ontologies/2007/03/22/nco#$1
is deprecated: false
has URI prefix: http://www.semanticdesktop.org/ontologies/2007/03/22/nco#
has resource example: fullname
has prefix: nepomuk.nco

Personal Information Model
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The PIMO Ontology can be used to express Personal Information Models of individuals. It is based on RDF and NRL, the NEPOMUK Representational Language and other Semantic Web ontologies. This document describes the principle elements of the language and how to use them. (from homepage)
is part of: bioregistry
has local unique identifier example: Note
has provider formatter: http://www.semanticdesktop.org/ontologies/2007/11/01/pimo#$1
is deprecated: false
has URI prefix: http://www.semanticdesktop.org/ontologies/2007/11/01/pimo#
has resource example: Note
has prefix: nepomuk.pimo

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

NeuroNames
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it.
is part of: bioregistry
has local unique identifier example: 268
has provider formatter: http://braininfo.rprc.washington.edu/centraldirectory.aspx
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: neuroname
has URI prefix: http://braininfo.rprc.washington.edu/centraldirectory.aspx
has resource example: http://braininfo.rprc.washington.edu/centraldirectory.aspx
has prefix: neuronames

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: cellular neuroscience
keyword: comparative neurobiology
keyword: computational neuroscience
keyword: molecular neuroscience
keyword: neurobiology
keyword: neurophysiology
keyword: structure
has local unique identifier example: 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
has resource example: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx
has prefix: neurondb

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
has local unique identifier example: 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/
has resource example: https://neurovault.org/collections/3304
has prefix: neurovault.collection

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

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: dna
keyword: gene expression
keyword: genome
keyword: life science
has local unique identifier example: 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
has resource example: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php
has prefix: nextdb

neXtProt family
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. (Developed by the SIB Swiss Institute of Bioinformatics)
is part of: bioregistry
has local unique identifier example: 01406
has provider formatter: https://www.nextprot.org/term/FA-$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: NXPFA
has URI prefix: https://www.nextprot.org/term/FA-
has resource example: https://www.nextprot.org/term/FA-01406
has prefix: nextprot.family

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
has local unique identifier example: 0000106
has provider formatter: https://nfdi.fiz-karlsruhe.de/ontology/NFDI_$1
has local unique identifier pattern: ^\d+$
has download URL: nfdicore.owl
is deprecated: false
has responsible: Jörg Waitelonis
has URI prefix: https://nfdi.fiz-karlsruhe.de/ontology/NFDI_
has resource example: NFDI_0000106
has prefix: nfdi.core

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
has local unique identifier example: KGR1
has provider formatter: http://kgi.services.base4nfdi.de/entity/$1
has local unique identifier pattern: ^KGR\d+$
is deprecated: false
has responsible: Lozana Rossenova
has URI prefix: http://kgi.services.base4nfdi.de/entity/
has resource example: KGR1
has prefix: nfdi.kgi

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: generic
keyword: organization
has local unique identifier example: E4330
has provider formatter: https://nfdi4culture.de/id/$1
is deprecated: false
has URI prefix: https://nfdi4culture.de/id/
has resource example: E4330
has prefix: nfdi4culture.id

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: experimental tools
keyword: neurofibromatosis
keyword: research resources
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: https://orcid.org/0000-0003-3573-3565
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://nf.synapse.org/Explore/Tools/DetailsPage
has resource example: https://nf.synapse.org/Explore/Tools/DetailsPage
has prefix: nfportal.tool

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
has local unique identifier example: 6000122
has provider formatter: http://purl.obolibrary.org/obo/NGBO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: ngbo.owl
is deprecated: false
has responsible: Dalia Alghamdi
has URI prefix: http://purl.obolibrary.org/obo/NGBO_
has resource example: NGBO_6000122
has prefix: ngbo

NASA GeneLab
type: Resource
description: NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.
is part of: bioregistry
has local unique identifier example: GLDS-141
has provider formatter: https://genelab-data.ndc.nasa.gov/genelab/accession/$1
has local unique identifier pattern: ^GLDS-\d+$
is deprecated: false
has URI prefix: https://genelab-data.ndc.nasa.gov/genelab/accession/
has resource example: GLDS-141
has prefix: ngl

NINDS Human Cell and Data Repository
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: ND50028
has provider formatter: https://stemcells.nindsgenetics.org
is deprecated: false
has URI prefix: https://stemcells.nindsgenetics.org
has resource example: https://stemcells.nindsgenetics.org
has prefix: nhcdr

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: dna
keyword: life science
has local unique identifier example: 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
has resource example: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3
has prefix: niaest

NIAID ChemDB ID
type: Resource
description: ID in NIAID ChemDB
is part of: bioregistry
has local unique identifier example: 059486
has provider formatter: http://chemdb.niaid.nih.gov/CompoundDetails.aspx
is deprecated: false
has URI prefix: http://chemdb.niaid.nih.gov/CompoundDetails.aspx
has resource example: http://chemdb.niaid.nih.gov/CompoundDetails.aspx
has prefix: niaid.chemdb

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
has download URL: nifcell.owl
is deprecated: true
has responsible: 0000-0003-4752-543X
has URI prefix: http://purl.obolibrary.org/obo/NIF_CELL_
has prefix: nif.cell

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_
has prefix: nif.dysfunction

NIF Standard Ontology: External
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
description: NIFEXT covers IRIs that were "external" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed.
is part of: bioregistry
git repository: NIF-Ontology
has local unique identifier example: 7123
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nifext_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NIFEXT
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nifext_
has resource example: nifext 7123
has prefix: nif.ext

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

NIF Standard Ontology
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
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: brain
keyword: disease
keyword: neuroscience
keyword: ontology
has local unique identifier example: BAMSC981
has provider formatter: http://uri.neuinfo.org/nif/nifstd/$1
has local unique identifier pattern: ^BAMSC\d+$
has download URL: nifstd.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NIFSTD
has URI prefix: http://uri.neuinfo.org/nif/nifstd/
has resource example: BAMSC981
has prefix: nif.std

NIH Human Embryonic Stem Cell Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage)
is part of: bioregistry
has local unique identifier example: NIHhESC-10-0083
has provider formatter: https://grants.nih.gov/stem_cells/registry/current.htm
is deprecated: false
has URI prefix: https://grants.nih.gov/stem_cells/registry/current.htm
has resource example: https://grants.nih.gov/stem_cells/registry/current.htm
has prefix: nihhesc

NIST Chemistry WebBook
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species.
is part of: bioregistry
is deprecated: false
has alternative prefix: NIST
has alternative prefix: NIST Chemistry WebBook
has prefix: nist

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

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
has local unique identifier example: alignedWith
has provider formatter: http://w3id.org/nkos/$1
is deprecated: false
has URI prefix: http://w3id.org/nkos/
has resource example: alignedWith
has prefix: nkos

United States Geological Survey - National Land Cover Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary for describing the usage of land cover (e.g., pasture, wetlands, barren, forest, water) extended from the original 16 land cover classes proposed by the [Anderson Level II classification system](https://doi.org/10.3133/pp964) in 1976
is part of: bioregistry
keyword: environment
keyword: forestry
has local unique identifier example: 12
has local unique identifier pattern: ^\d+$
is deprecated: false
appears in: envo
has prefix: nlcd

NLFFF Database
type: Resource
description: Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database
is part of: bioregistry
has local unique identifier example: 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/
has resource example: http://database.deepsolar.space:18080/dbs/nlfff/345201101230312003
has prefix: nlfff

NLM Publisher Codes
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Publisher short codes appearin in the NLM Catalog.
is part of: bioregistry
keyword: bibliometrics
keyword: ontology
keyword: publisher
has local unique identifier example: wiley
has download URL: nlm.publisher.owl
is deprecated: false
appears in: nlm
has responsible: NLM Customer Service
has prefix: nlm.publisher

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
has local unique identifier example: 090201
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_anat_
has resource example: nlx anat 090201
has prefix: nlx.anat

NIF Standard Ontology: Brain Regions
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
description: NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999).
is part of: bioregistry
git repository: NIF-Ontology
keyword: anatomy
keyword: brain regions
keyword: neuroscience
has local unique identifier example: 145
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_br_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXBR
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_br_
has resource example: nlx br 145
has prefix: nlx.br

NIF Standard Ontology: Cell Types
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
description: NLXCELL conatins cell types with a focus on neuron types.
is part of: bioregistry
git repository: NIF-Ontology
keyword: cell lines
keyword: cell types
keyword: cells
keyword: neuroscience
has local unique identifier example: 091005
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXCELL
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_cell_
has resource example: nlx cell 091005
has prefix: nlx.cell

NIF Standard Ontology: Chemical
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
description: NLXCHEM covers chemicals. Most classes are also in ChEBI.
is part of: bioregistry
git repository: NIF-Ontology
keyword: chemistry
has local unique identifier example: 090801
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXCHEM
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_chem_
has resource example: nlx chem 090801
has prefix: nlx.chem

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: disease
keyword: disorders
keyword: phenotypes
has local unique identifier example: 20090602
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
appears in: mondo
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_dys_
has resource example: nlx dys 20090602
has prefix: nlx.dys

NIF Standard Ontology: Cognitive Function
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
description: NLXFUNC covers terms for cognitive function.
is part of: bioregistry
git repository: NIF-Ontology
keyword: neuroscience
has local unique identifier example: 90801
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_func_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXFUNC
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_func_
has resource example: nlx func 90801
has prefix: nlx.func

NIF Standard Ontology: Investigations
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
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
has local unique identifier example: 90901
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXINV
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_inv_
has resource example: nlx inv 90901
has prefix: nlx.inv

NIF Standard Ontology: Molecules
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
description: NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system.
is part of: bioregistry
git repository: NIF-Ontology
keyword: biology
keyword: chemistry
keyword: neuroscience
keyword: proteins
has local unique identifier example: 90806
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXMOL
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_mol_
has resource example: nlx mol 90806
has prefix: nlx.mol

NIF Standard Ontology: OEN Terms in Neurolex
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
description: NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results).
is part of: bioregistry
git repository: NIF-Ontology
keyword: neuroscience
has local unique identifier example: 0001000
has provider formatter: http://uri.neuinfo.org/nif/nifstd/oen_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXOEN
has URI prefix: http://uri.neuinfo.org/nif/nifstd/oen_
has resource example: oen_0001000
has prefix: nlx.oen

NIF Standard Ontology: Organisms
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
description: NLXORG covers organisms.
is part of: bioregistry
git repository: NIF-Ontology
keyword: taxonomy
has local unique identifier example: 090701
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXORG
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_organ_
has resource example: nlx organ 090701
has prefix: nlx.org

NIF Standard Ontology: Qualities
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
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
has local unique identifier example: 100810
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXQUAL
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_qual_
has resource example: nlx qual 100810
has prefix: nlx.qual

NIF Standard Ontology: Digital Resources
type: Resource
contributor: https://orcid.org/0000-0002-7509-4801
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
has local unique identifier example: 090924
has provider formatter: http://uri.neuinfo.org/nif/nifstd/nlx_res_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7509-4801
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: NLXRES
has URI prefix: http://uri.neuinfo.org/nif/nifstd/nlx_res_
has resource example: nlx res 090924
has prefix: nlx.res

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
has local unique identifier example: 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/
has resource example: y3ax-8bq3-60
has prefix: nmdc

National Microbial Pathogen Data Resource
type: Resource
description: The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.
is part of: bioregistry
keyword: genome
has local unique identifier example: fig|306254.1.peg.183
has provider formatter: http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer
has prefix: nmpdr

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
has local unique identifier example: 234
has provider formatter: https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1
has local unique identifier pattern: ^[0-9]+$
is deprecated: false
has responsible: Stefan Kuhn
has alternative prefix: NMRShiftDB
has URI prefix: https://nmrshiftdb.nmr.uni-koeln.de/molecule/
has resource example: https://nmrshiftdb.nmr.uni-koeln.de/molecule/234
has prefix: nmrshiftdb2

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
has local unique identifier example: 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
has resource example: https://nmrxiv.org/spectra
has prefix: nmrxiv.compound

nmrXiv project
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A project in the nmrXiv
is part of: bioregistry
keyword: datasets
keyword: project
has local unique identifier example: 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/
has resource example: P136
has prefix: nmrxiv.project

nmrXiv sample
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: spectra (samples) in the nmrXiv database
is part of: bioregistry
keyword: nmr
keyword: sample
keyword: spectra
keyword: spectrum
has local unique identifier example: 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/
has resource example: S1295
has prefix: nmrxiv.sample

CAMEO Chemicals ID
type: Resource
description: CAMEO Chemicals is a database of hazardous chemical datasheets that emergency responders and planners can use to get response recommendations and predict hazards—such as explosions or toxic fumes.
is part of: bioregistry
has local unique identifier example: 19757
has provider formatter: https://cameochemicals.noaa.gov/chemical/$1
has local unique identifier pattern: ^\d*$
is deprecated: false
has URI prefix: https://cameochemicals.noaa.gov/chemical/
has resource example: https://cameochemicals.noaa.gov/chemical/19757
has prefix: noaa.cameo

NOAA Fisheries Species Directory
type: Resource
contributor: https://orcid.org/0000-0003-2699-3066
description: Identifier for a species on the noaa fisheries website
is part of: bioregistry
has local unique identifier example: long-finned-pilot-whale
has provider formatter: https://www.fisheries.noaa.gov/species/$1
has local unique identifier pattern: ^[a-z]+(\-[a-z]+)*$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: noaa
has URI prefix: https://www.fisheries.noaa.gov/species/
has resource example: long-finned-pilot-whale
has prefix: noaa.species

A nomenclatural ontology for biological names
type: Resource
description: NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.
is part of: bioregistry
git repository: nomen
keyword: obo
keyword: ontology
has local unique identifier example: 0000295
has provider formatter: http://purl.obolibrary.org/obo/NOMEN_$1
has local unique identifier pattern: ^\d{7}$
has download URL: nomen.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-5640-5491
has URI prefix: http://purl.obolibrary.org/obo/NOMEN_
has resource example: NOMEN_0000295
has prefix: nomen

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
has local unique identifier example: 377550
has provider formatter: http://www.noncode.org/NONCODERv3/ncrna.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: Yi Zhao
has URI prefix: http://www.noncode.org/NONCODERv3/ncrna.php
has resource example: http://www.noncode.org/NONCODERv3/ncrna.php
has prefix: noncodev3

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

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
has local unique identifier example: 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
has resource example: http://www.bioinfo.org/NONCODEv4/show_rna.php
has prefix: noncodev4.rna

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
has local unique identifier example: 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: Maude Pupin
has URI prefix: https://bioinfo.cristal.univ-lille.fr/norine/result.jsp
has resource example: https://bioinfo.cristal.univ-lille.fr/norine/result.jsp
has prefix: norine

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

Natural Product Activity and Species Source Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.
is part of: bioregistry
keyword: chemical
keyword: compound
keyword: natural product
keyword: ontology
keyword: small molecule
has local unique identifier example: NPC139585
has provider formatter: https://bidd.group/NPASS/compound.php
has local unique identifier pattern: ^NPC\d+$
has download URL: npass.owl
is deprecated: false
has responsible: Yu Zong Chen
has URI prefix: https://bidd.group/NPASS/compound.php
has resource example: https://bidd.group/NPASS/compound.php
has prefix: npass

The Natural Products Atlas
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for microbially derived natural products that contains compound structures, producing organism taxonomy, biosynthetic and chemical properties.
is part of: bioregistry
has local unique identifier example: NPA000001
has provider formatter: https://www.npatlas.org/explore/compounds/$1
has local unique identifier pattern: ^NPA\d{6}$
is deprecated: false
has responsible: Roger Linington
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.npatlas.org/explore/compounds/
has resource example: NPA000001
has prefix: npatlas

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: life science
keyword: molecular entity
keyword: nanoparticle
keyword: ontology
keyword: structure
has local unique identifier example: 1731
has provider formatter: http://purl.bioontology.org/ontology/npo#NPO_$1
has local unique identifier pattern: ^\d+$
has download URL: npo.owl
is deprecated: false
has responsible: Nathan Baker
has URI prefix: http://purl.bioontology.org/ontology/npo#NPO_
has resource example: NPO 1731
has prefix: npo

National Repository of Fish Cell Lines
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)
is part of: bioregistry
has local unique identifier example: NRFC051
has local unique identifier pattern: ^NRFC\d+$
is deprecated: false
has prefix: nrfc

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
has local unique identifier example: 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
has resource example: https://dtp.cancer.gov/dtpstandard/servlet/ChemData
has prefix: nsc

National Science Foundation Award
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research.
is part of: bioregistry
has local unique identifier example: 1458400
has provider formatter: https://www.nsf.gov/awardsearch/showAward
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.nsf.gov/awardsearch/showAward
has resource example: https://www.nsf.gov/awardsearch/showAward
has prefix: nsf.award

National Swine Resource and Research Center
type: Resource
description: Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. [from RRID]
is part of: bioregistry
keyword: biomaterial manufacture
keyword: breeding
keyword: consulting
keyword: cryopreservation
keyword: fetal fibroblast
keyword: fetus
keyword: fibroblast
keyword: genetically modified pig
keyword: genetics
keyword: genome
keyword: genotyping
keyword: health monitoring
keyword: live animal
keyword: phenotyping
keyword: pig
keyword: reproduction
keyword: tissue
has local unique identifier example: 0005
has provider formatter: https://nsrrc.missouri.edu/nsrrc$1info/
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://bioregistry.io/nsrrc:
has resource example: nsrrc0005info
has prefix: nsrrc

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
has local unique identifier example: 2A
has local unique identifier pattern: ^\d(\d|\w)$
is deprecated: false
has prefix: nucc.characteristic

NucleaRDB
type: Resource
description: NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.
is part of: bioregistry
keyword: classification
has local unique identifier example: prgr_human
has provider formatter: http://www.receptors.org/nucleardb/proteins/$1
has local unique identifier pattern: ^\w+\_\w+$
is deprecated: false
has responsible: Gert Vriend
has alternative prefix: nuclearbd
has URI prefix: http://www.receptors.org/nucleardb/proteins/
has resource example: prgr human
has prefix: nucleardb

Nucleotide
type: Resource
description: The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
is part of: bioregistry
has local unique identifier example: 880798137
has provider formatter: https://www.ncbi.nlm.nih.gov/nuccore/$1
has local unique identifier pattern: ^[a-zA-Z0-9_\.]+$
is deprecated: false
has canonical: insdc
has URI prefix: https://www.ncbi.nlm.nih.gov/nuccore/
has resource example: https://www.ncbi.nlm.nih.gov/nuccore/880798137
has prefix: nucleotide

NERC Vocabulary Server
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: SKOS concept collections held in the NERC Vocabulary Server. A concept collection is useful where a group of concepts shares something in common, and it is convenient to group them under a common label. In the NVS, concept collections are synonymous with controlled vocabularies or code lists. Each collection is associated with its governance body. An external website link is displayed when applicable.
is part of: bioregistry
has local unique identifier example: P06
has provider formatter: https://vocab.nerc.ac.uk/collection/$1
is deprecated: false
has URI prefix: https://vocab.nerc.ac.uk/collection/
has resource example: P06
has prefix: nvs

National Xenopus Resource
type: Resource
description: National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID]
is part of: bioregistry
keyword: laevis
keyword: tropicalis
keyword: xenopus
has local unique identifier example: 0024
has provider formatter: https://scicrunch.org/resolver/RRID:NXR_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://scicrunch.org/resolver/RRID:NXR_
has resource example: RRID:NXR 0024
has prefix: nxr

New Zealand Threat Classification System
type: Resource
contributor: https://orcid.org/0000-0002-1216-4761
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for species classified under the New Zealand Threat Classification System
is part of: bioregistry
keyword: taxon
keyword: taxonomy
has local unique identifier example: 11061
has provider formatter: https://nztcs.org.nz/nztcs-species/$1
has local unique identifier pattern: ^[1-9]\d{2,6}$
is deprecated: false
has URI prefix: https://nztcs.org.nz/nztcs-species/
has resource example: https://nztcs.org.nz/nztcs-species/11061
has prefix: nztcs

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: anatomy
keyword: angiology
keyword: obo
keyword: ontology
has local unique identifier example: 0000029
has provider formatter: http://purl.obolibrary.org/obo/OARCS_$1
has local unique identifier pattern: ^\d{7}$
has download URL: oarcs.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-5640-5491
has URI prefix: http://purl.obolibrary.org/obo/OARCS_
has resource example: OARCS_0000029
has prefix: oarcs

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
has local unique identifier example: provenance
has provider formatter: http://purl.org/oban/$1
has local unique identifier pattern: ^\w+$
has download URL: oban core.owl
is deprecated: false
has URI prefix: http://purl.org/oban/
has resource example: provenance
has prefix: oban

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

Ontology of Biological and Clinical Statistics
type: Resource
description: OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)
is part of: bioregistry
git repository: obcs
keyword: biology
keyword: biomedical science
keyword: medical informatics
keyword: medicine
keyword: obo
keyword: ontology
keyword: statistics
keyword: vaccine
has local unique identifier example: 0000121
has provider formatter: http://purl.obolibrary.org/obo/OBCS_$1
has local unique identifier pattern: ^\d{7}$
has download URL: obcs.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-2999-0103
has URI prefix: http://purl.obolibrary.org/obo/OBCS_
has resource example: OBCS_0000121
has prefix: obcs

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

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

OBOE Standard
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Units in OBOE
is part of: bioregistry
keyword: ontology
keyword: unit
keyword: units
has local unique identifier example: 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
has resource example: oboe-standards.owlAcre
has prefix: oboe.standard

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
has local unique identifier example: 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/
has resource example: https://permalink.obvsg.at/AC00963334
has prefix: obv

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
has local unique identifier example: 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/
has resource example: https://w3id.org/oc/corpus/br/1
has prefix: occ

Occupation Ontology
type: Resource
description: This Occupaton Ontology (OccO) is an ontology in the domain of human occupaitons. Current OccO version is developed based on the US Bureau of Labor Statistics Standard Occupation Classification (SOC) and the related O*Net System. The OccO development follows the principles of the Open Biological and Biomedical (OBO) Foundry.
is part of: bioregistry
git repository: OccO
keyword: obo
keyword: ontology
has local unique identifier example: 00000001
has provider formatter: http://purl.obolibrary.org/obo/OCCO_$1
has local unique identifier pattern: ^\d+$
has download URL: occo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-2999-0103
has URI prefix: http://purl.obolibrary.org/obo/OCCO_
has prefix: occo

Crystallographic Defect Core Ontology
type: Resource
contributor: https://orcid.org/0000-0002-1595-3213
description: The Crystallographic Defect Core Ontology (CDCO) defines the common terminology shared across all types of crystallographic defects, providing a unified framework for data integration in materials science.
is part of: bioregistry
git repository: cdco
keyword: ontology
has local unique identifier example: hasDefectComplex
has provider formatter: http://purls.helmholtz-metadaten.de/cdos/cdco/$1
has download URL: cdco.owl
is deprecated: false
has responsible: Abril Azocar Guzman
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://purls.helmholtz-metadaten.de/cdos/cdco/
has resource example: hasDefectComplex
has prefix: ocdo

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
has local unique identifier example: 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/
has resource example: https://opencitations.net/index/ci/01027931310-01022252312
has prefix: oci

Ontology Concept Identifiers
type: Resource
description: 'ocid' stands for "Ontology Concept Identifiers" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology.
is part of: bioregistry
has local unique identifier example: 190000021540
has provider formatter: https://ocid.ontochem.com/prefname
has local unique identifier pattern: ^[0-9]{12}$
is deprecated: false
has URI prefix: https://ocid.ontochem.com/prefname
has resource example: https://ocid.ontochem.com/prefname
has prefix: ocid

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

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

ODAM Data explorer
type: Resource
description: ODAM (Open Data for Access and Mining) is an Experimental data table management software (EDTMS) to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines. ODAM allows datasets to be explored and then extracted in whole or in part as needed. For more information/explanation, see ODAM User's Guide : https://inrae.github.io/ODAM/
is part of: bioregistry
has local unique identifier example: frim1
has provider formatter: https://pmb-bordeaux.fr/dataexplorer/
has local unique identifier pattern: ^[A-Za-z][A-Za-z0-9]+$
is deprecated: false
has URI prefix: https://pmb-bordeaux.fr/dataexplorer/
has resource example: https://pmb-bordeaux.fr/dataexplorer/
has prefix: odamexplorer

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: biomedical science
keyword: neurobiology
keyword: neurology
keyword: neuroscience
has local unique identifier example: 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/
has resource example: https://odc-sci.org/data/602
has prefix: odc.sci

Open Data Commons for Traumatic Brain Injury
type: Resource
description: The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data.
is part of: bioregistry
has local unique identifier example: 408
has provider formatter: https://odc-tbi.org/data/$1
has local unique identifier pattern: ^[0-9]*$
is deprecated: false
has URI prefix: https://odc-tbi.org/data/
has resource example: https://odc-tbi.org/data/408
has prefix: odc.tbi

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
has local unique identifier example: 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/
has resource example: https://ordb.biotech.ttu.edu/OdorDB/Data/74
has prefix: odor

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
has local unique identifier example: 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/
has resource example: assetConcepts
has prefix: odrl

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
has local unique identifier example: 74.186
has local unique identifier pattern: ^\d+\.\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has prefix: oecd.template

Austrian Fields of Science and Technology Classification
type: Resource
description: The Austrian Fields of Science and Technology Classification (ÖFOS 2012) is the Austrian version of the revised international Fields of Science and Technology Classification of the OECD (FOS) published in the Frascati Manual 2015 as Fields of Research and Development (FORD). These fields are adjusted to national needs, whose application for international comparisons is binding, particularly within the European Statistical System. The six major Fields of Science: Natural Sciences; Technical Sciences; Human Medicine, Health Sciences; Agricultural Sciences, Veterinary Medicine; Social Sciences and Humanities remained unchanged in comparison to ÖFOS 2002. In order to ensure international comparability, the previous 2-digit levels from 2002, which are no longer applicable, were replaced by new 3-digit levels (groups) according to the international FOS respectively FORD. These 3-digit levels were provided with further sub-groups (4-digits) taking into account the comments of the international classification. It is therefore feasible that the new Austrian Fields of Science adapt to national peculiarities of the Austrian research activities. The research area with the corresponding 6-digits in alphabetical order serves as a description of the fields of activities and research projects and/or for the coverage of the main scientific activities of a statistical unit in the research and development surveys. (Current revision status: August 2017)
is part of: bioregistry
keyword: educational resources
keyword: educational science
has local unique identifier example: 509015
has provider formatter: https://vocabs.acdh.oeaw.ac.at/oefosdisciplines/$1
is deprecated: false
has URI prefix: https://vocabs.acdh.oeaw.ac.at/oefosdisciplines/
has resource example: https://vocabs.acdh.oeaw.ac.at/oefosdisciplines/509015
has prefix: oefos

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: api
keyword: data schema
keyword: linked open data
keyword: semantic web
has local unique identifier example: title
has provider formatter: https://ogp.me/ns#$1
is deprecated: false
has URI prefix: https://ogp.me/ns#
has resource example: title
has prefix: og

Open Geospatial Consortium Simple Features Vocabulary
type: Resource
description: An RDF/OWL vocabulary for defining SimpleFeature geometry types
is part of: bioregistry
has local unique identifier example: Triangle
has provider formatter: http://www.opengis.net/ont/sf#$1
is deprecated: false
has URI prefix: http://www.opengis.net/ont/sf#
has resource example: Triangle
has prefix: ogc.sf

The Ontology of Genes and Genomes
type: Resource
description: OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.
is part of: bioregistry
git repository: ogg
keyword: biology
keyword: gene
keyword: gene name
keyword: genome
keyword: life science
keyword: obo
keyword: ontology
has local unique identifier example: 3000887619
has provider formatter: http://purl.obolibrary.org/obo/OGG_$1
has local unique identifier pattern: ^\d+$
has download URL: ogg.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9189-9661
has URI prefix: http://purl.obolibrary.org/obo/OGG_
has resource example: OGG_3000887619
has prefix: ogg

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

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: adverse reaction
keyword: biomedical science
keyword: disease
keyword: epidemiology
keyword: genetic disorder
keyword: genetics
keyword: obo
keyword: ontology
has local unique identifier example: 0000025
has provider formatter: http://purl.obolibrary.org/obo/OGSF_$1
has local unique identifier pattern: ^\d{7}$
has download URL: ogsf.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-5379-5359
has URI prefix: http://purl.obolibrary.org/obo/OGSF_
has resource example: OGSF_0000025
has prefix: ogsf

Ontology of Host-Microbiome Interactions
type: Resource
description: OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.
is part of: bioregistry
git repository: ohmi
keyword: host
keyword: life science
keyword: microbiome
keyword: obo
keyword: ontology
has local unique identifier example: 0000460
has provider formatter: http://purl.obolibrary.org/obo/OHMI_$1
has local unique identifier pattern: ^\d{7}$
has download URL: ohmi.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9189-9661
has URI prefix: http://purl.obolibrary.org/obo/OHMI_
has resource example: OHMI_0000460
has prefix: ohmi

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: bioinformatics
keyword: biomedical science
keyword: host
keyword: infection process
keyword: obo
keyword: ontology
keyword: pathogen
has local unique identifier example: 9001411
has provider formatter: http://purl.obolibrary.org/obo/OHPI_$1
has local unique identifier pattern: ^\d+$
has download URL: ohpi.owl
is deprecated: false
has responsible: Edison Ong
has URI prefix: http://purl.obolibrary.org/obo/OHPI_
has resource example: OHPI_9001411
has prefix: ohpi

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
has local unique identifier example: 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/
has resource example: https://oid-base.com/get/2.16.840
has prefix: oid

Solid OpenID Connect vocabulary
type: Resource
description: The OpenID Connect vocabulary used by the Solid-OIDC authentication specification
is part of: bioregistry
has local unique identifier example: client_name
is deprecated: false
has prefix: oidc

Medaka Developmental Stages
type: Resource
description: Life cycle stages for Medaka
is part of: bioregistry
git repository: developmental-stage-ontologies
keyword: aquaculture
keyword: developmental biology
keyword: life cycle stage
keyword: life science
keyword: obo
keyword: ontology
has local unique identifier example: 0000210
has provider formatter: http://purl.obolibrary.org/obo/OlatDv_$1
has local unique identifier pattern: ^\d{7}$
has download URL: olatdv.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-9415-5104
has URI prefix: http://purl.obolibrary.org/obo/OlatDv_
has resource example: OlatDv_0000210
has prefix: olatdv

OMA Group
type: Resource
description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.
is part of: bioregistry
has local unique identifier example: LCSCCPN
has provider formatter: https://omabrowser.org/cgi-bin/gateway.pl
has local unique identifier pattern: ^[A-Z]+$
is deprecated: false
has URI prefix: https://omabrowser.org/cgi-bin/gateway.pl
has resource example: https://omabrowser.org/cgi-bin/gateway.pl
has prefix: oma.grp

OMA HOGs
type: Resource
description: Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference.
is part of: bioregistry
has local unique identifier example: 0459895
has provider formatter: https://omabrowser.org/oma/hog/HOG:$1
has local unique identifier pattern: ^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$
is deprecated: false
has URI prefix: https://omabrowser.org/oma/hog/HOG:
has resource example: HOG:0459895
has prefix: oma.hog

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
has local unique identifier example: 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/
has resource example: HUMAN16963
has prefix: oma.protein

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: classification
keyword: disorders
keyword: gene
keyword: model organism database
keyword: traits
has local unique identifier example: 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:
has resource example: omia:001000
has prefix: omia

OMIA variants
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.variant' prefix is used for genetic variants associated with phenes listed in OMIA
is part of: bioregistry
keyword: disorders
keyword: model organism database
keyword: traits
has local unique identifier example: 1710
has provider formatter: https://omia.org/variant/omia.variant:$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5520-6597
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://omia.org/variant/omia.variant:
has resource example: omia.variant:1710
has prefix: omia.variant

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
has local unique identifier example: 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/
has resource example: https://w3id.org/oc/meta/br/0601
has prefix: omid

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

Overview of Medical Research in the Netherlands
type: Resource
contributor: Tomohiro Oga
description: The new national clinical trials registry of the Netherlands
is part of: bioregistry
has local unique identifier example: 53367
has provider formatter: https://onderzoekmetmensen.nl/en/trial/$1
has local unique identifier pattern: ^\d{5}$
is deprecated: false
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://onderzoekmetmensen.nl/en/trial/
has resource example: https://onderzoekmetmensen.nl/en/trial/53367
has prefix: omon

OncoMX Dataset
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX.
is part of: bioregistry
has local unique identifier example: 000059
has provider formatter: https://data.oncomx.org/OMX_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://data.oncomx.org/OMX_
has resource example: OMX_000059
has prefix: omx.dataset

OncoTree
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.
is part of: bioregistry
keyword: cancer
keyword: clinical decision support systems
keyword: oncology
has local unique identifier example: BLL
has provider formatter: http://oncotree.mskcc.org/api/tumorTypes/search/code/$1
is deprecated: false
appears in: efo
has responsible: Nikolaus Schultz
has URI prefix: http://oncotree.mskcc.org/api/tumorTypes/search/code/
has resource example: BLL
has prefix: oncotree

Ontology for Immune Epitopes
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes.
is part of: bioregistry
git repository: ONTIE
keyword: immunology
keyword: infection process
keyword: life science
keyword: major histocompatibility complex
keyword: ontology
has local unique identifier example: 0000001
has provider formatter: https://ontology.iedb.org/ontology/ONTIE_$1
has local unique identifier pattern: ^\d{7}$
has download URL: ontie.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-8457-6693
has URI prefix: https://ontology.iedb.org/ontology/ONTIE_
has resource example: ONTIE_0000001
has prefix: ontie

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
has local unique identifier example: 000072
has provider formatter: http://www.ontodm.com/OntoDM-core/OntoDM_$1
has local unique identifier pattern: ^\d+$
has download URL: OntoDM.owl
is deprecated: false
appears in: efo
has responsible: Pance Panov
has URI prefix: http://www.ontodm.com/OntoDM-core/OntoDM_
has resource example: OntoDM_000072
has prefix: ontodm

Obstetric and Neonatal Ontology
type: Resource
description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.
is part of: bioregistry
git repository: Ontoneo
keyword: electronic health record
keyword: obo
keyword: obstetrics
keyword: ontology
has local unique identifier example: 00000098
has provider formatter: http://purl.obolibrary.org/obo/ONTONEO_$1
has local unique identifier pattern: ^\d{8}$
has download URL: ontoneo.owl
is deprecated: false
has responsible: Fernanda Farinelli
has URI prefix: http://purl.obolibrary.org/obo/ONTONEO_
has resource example: ONTONEO_00000098
has prefix: ontoneo

Ontology of Organizational Structures of Trauma centers and Trauma systems
type: Resource
description: The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2).
is part of: bioregistry
git repository: OOSTT
keyword: obo
keyword: ontology
keyword: traumatology
has local unique identifier example: 00000099
has provider formatter: http://purl.obolibrary.org/obo/OOSTT_$1
has local unique identifier pattern: ^\d{8}$
has download URL: oostt.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-1834-3856
has URI prefix: http://purl.obolibrary.org/obo/OOSTT_
has resource example: OOSTT_00000099
has prefix: oostt

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: concentration
keyword: life science
keyword: ontology
keyword: physics
keyword: structure
has local unique identifier example: 00573
has provider formatter: https://bioportal.bioontology.org/ontologies/OPB/
has local unique identifier pattern: ^\d+$
has download URL: opb.owl
is deprecated: false
has responsible: Maxwell L. Neal
has URI prefix: https://bioportal.bioontology.org/ontologies/OPB/
has resource example: https://bioportal.bioontology.org/ontologies/OPB/
has prefix: opb

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: knowledge graph
keyword: wikidata
has local unique identifier example: W2741809807
has provider formatter: https://openalex.org/$1
has local unique identifier pattern: ^[WAICV]\d{2,}$
is deprecated: false
has responsible: Heather Piwowar
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://openalex.org/
has resource example: W2741809807
has prefix: openalex

openWEMI Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item.
is part of: bioregistry
git repository: openwemi
has local unique identifier example: Endeavor
has provider formatter: https://dcmi.github.io/openwemi/ns#$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: Karen Coyle
has URI prefix: https://dcmi.github.io/openwemi/ns#
has resource example: Endeavor
has prefix: openwemi

Ontology for Parasite LifeCycle
type: Resource
description: The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc.
is part of: bioregistry
git repository: OPL
keyword: anatomy
keyword: developmental biology
keyword: host
keyword: life cycle
keyword: life cycle stage
keyword: life science
keyword: obo
keyword: ontology
has local unique identifier example: 0000319
has provider formatter: http://purl.obolibrary.org/obo/OPL_$1
has local unique identifier pattern: ^\d{7}$
has download URL: opl.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-2999-0103
has URI prefix: http://purl.obolibrary.org/obo/OPL_
has resource example: OPL_0000319
has prefix: opl

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
has local unique identifier example: 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
has resource example: http://opm.phar.umich.edu/protein.php
has prefix: opm

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
has local unique identifier example: 6782
has provider formatter: https://oprlm.org/proteins/$1
has local unique identifier pattern: ^\d*$
is deprecated: false
has responsible: Wonpil Im
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://oprlm.org/proteins/
has resource example: https://oprlm.org/proteins/6782
has prefix: oprlm

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
has local unique identifier example: 10.2.1.1.3
is deprecated: false
has prefix: orangebook

Olfactory Receptor Database
type: Resource
description: The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs).
is part of: bioregistry
keyword: gene
keyword: life science
keyword: protein
has local unique identifier example: 8497
has provider formatter: https://ordb.biotech.ttu.edu/ORDB/Data/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://ordb.biotech.ttu.edu/ORDB/Data/
has resource example: https://ordb.biotech.ttu.edu/ORDB/Data/8497
has prefix: ordb

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

OriDB Saccharomyces
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 Saccharomyces cerevisiae.
is part of: bioregistry
has local unique identifier example: 1
has provider formatter: http://cerevisiae.oridb.org/details.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://cerevisiae.oridb.org/details.php
has resource example: http://cerevisiae.oridb.org/details.php
has prefix: oridb.sacch

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
has local unique identifier example: 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
has resource example: http://pombe.oridb.org/details.php
has prefix: oridb.schizo

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

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: gene
keyword: homologous
keyword: ontology
keyword: orthologous
keyword: paralogous
keyword: protein
keyword: region
has local unique identifier example: HomologyRelation
has provider formatter: http://purl.org/net/orth#$1
has download URL: orthOntology RC v2 A.owl
is deprecated: false
has responsible: Jesualdo Tomás Fernández-Breis
has URI prefix: http://purl.org/net/orth#
has resource example: HomologyRelation
has prefix: orth

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: eukaryotic
keyword: life science
keyword: protein
has local unique identifier example: Q9P0K8
has provider formatter: http://cegg.unige.ch/orthodb/results
has local unique identifier pattern: ^\w+$
provides for: uniprot
is deprecated: false
has responsible: Evgeny M Zdobnov
has URI prefix: http://cegg.unige.ch/orthodb/results
has resource example: http://cegg.unige.ch/orthodb/results
has prefix: orthodb

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
has local unique identifier example: 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/
has resource example: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/117
has prefix: oryzabase.gene

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
has local unique identifier example: 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/
has resource example: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/21393
has prefix: oryzabase.mutant

Oryzabase Reference
type: Resource
description: The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan.
is part of: bioregistry
has local unique identifier example: 42840
has provider formatter: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/
has resource example: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/42840
has prefix: oryzabase.reference

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
has local unique identifier example: 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/
has resource example: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/34
has prefix: oryzabase.stage

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
has local unique identifier example: 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/
has resource example: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/1
has prefix: oryzabase.strain

Office of Scientific and Technical Information (OSTI)
type: Resource
contributor: https://orcid.org/0000-0002-8741-7823
description: The U.S. Department of Energy (DOE) Office of Scientific and Technical Information (OSTI) is the main metadata archive for permanent storage of registered [DOE DOI products](https://www.osti.gov/pids/doi-services/doe-data-id-service) (datasets, code, articles, patents, multimedia, etc.). When a DOI is minted a unique OSTI identifier for each record [{osti_id}](https://www.osti.gov/api/v1/docs#endpoints-singlerecord) is provided as the suffix in the DOI schema ([{site-specific-prefix}/{user-supplied-doi-infix}/{osti_id}](https://www.osti.gov/pids/doi-services)) and can be alternatively used as the main product identifier endpoint when [searching OSTI.GOV](https://www.osti.gov/search-tools) registry archive (see example below). OSTI.GOV is the primary registry and search tool for all Department of Energy (DOE) funded science, technology, and engineering research and development (R&D) results and the organizational hub for information about the DOE Office of Scientific and Technical Information (OSTI. **Data Product Type Example:** - https://www.osti.gov/biblio/1668761 - https://www.osti.gov/search/semantic:1668761 - https://www.osti.gov/dataexplorer/biblio/dataset/1668761 - https://www.osti.gov/api/v1/records/1668761 - https://doi.org/10.11578/1668761 **Other Core Product Registry Examples:** - Journal Articles: https://www.osti.gov/pages/biblio - Datasets: https://www.osti.gov/dataexplorer/biblio/dataset/ - Software: https://www.osti.gov/doecode/biblio/ - Patents: https://www.osti.gov/doepatents/biblio/ - Multimedia: https://www.osti.gov/sciencecinema/biblio/
is part of: bioregistry
keyword: article
keyword: articles
keyword: publication
keyword: publications
has local unique identifier example: 1668761
has provider formatter: https://www.osti.gov/biblio/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.osti.gov/biblio/
has resource example: https://www.osti.gov/biblio/1668761
has prefix: osti.article

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

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
has local unique identifier example: 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
has resource example: https://tree.opentreeoflife.org/taxonomy/browse
has prefix: otol

Ontological Interpretations for Web Property Graphs
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]
is part of: bioregistry
git repository: owlstar
has local unique identifier example: AllSomeInterpretation
has provider formatter: http://w3id.org/owlstar/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6601-2165
has URI prefix: http://w3id.org/owlstar/
has resource example: AllSomeInterpretation
has prefix: owlstar

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

P3DB Site
type: Resource
description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.
is part of: bioregistry
has local unique identifier example: 65
has provider formatter: http://www.p3db.org/phosphosite.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://bioregistry.io/p3db.site:
has resource example: http://www.p3db.org/phosphosite.php
has prefix: p3db.site

Phylogenomic Analysis of Human Genome
type: Resource
contributor: https://orcid.org/0009-0009-3402-8013
description: Identifiers correspond to curated multigene families in the human genome from the Phylogenomic Analysis of Human Genome (PAHG) database, focusing on evolutionary relationships and gene duplication events across vertebrates.
is part of: bioregistry
keyword: gene duplication
keyword: human genome
keyword: multigene families
keyword: paralogons
keyword: phylogenomics
keyword: vertebrate evolution
has local unique identifier example: 92
has provider formatter: https://www.pahgncb.com/genomedb/public/genefamily/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9922-9723
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.pahgncb.com/genomedb/public/genefamily/
has resource example: https://www.pahgncb.com/genomedb/public/genefamily/92
has prefix: pahg

Paleobiology Database
type: Resource
description: The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.
is part of: bioregistry
keyword: taxonomy
has local unique identifier example: 83088
has provider formatter: http://fossilworks.org/
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://fossilworks.org/
has resource example: http://fossilworks.org/
has prefix: paleodb

Protein and Associated NucleotideDomains with Inferred Trees
type: Resource
description: PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.
is part of: bioregistry
keyword: dna
keyword: protein
keyword: structure
has local unique identifier example: PF00004
has provider formatter: http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi
provides for: pfam
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi
has resource example: http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi
has prefix: pandit

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_
has prefix: pao

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: dna
keyword: genome
keyword: structure
has local unique identifier example: 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/
has resource example: https://caps.ncbs.res.in/pass2.8/
has prefix: pass2

PathBank
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana.
is part of: bioregistry
keyword: animal genetics
keyword: bioinformatics
keyword: biology
keyword: cell biology
keyword: cheminformatics
keyword: database management
keyword: drug metabolism
keyword: endocrinology
keyword: genetics
keyword: human genetics
keyword: medical informatics
keyword: metabolomics
keyword: microbiology
keyword: molecular biology
keyword: molecular microbiology
keyword: ontology
keyword: plant genetics
keyword: proteomics
keyword: systems biology
keyword: transcriptomics
has local unique identifier example: SMP0000219
has provider formatter: https://pathbank.org/view/$1
has local unique identifier pattern: ^(SMP|PW)\d+$
has download URL: pathbank.owl.gz
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has URI prefix: https://pathbank.org/view/
has resource example: SMP0000219
has prefix: pathbank

Pathguide
type: Resource
description: Pathguide contains information about 325 biological related resources and molecular interaction related resources.
is part of: bioregistry
keyword: gene
keyword: interaction
keyword: pathway
keyword: protein
keyword: small molecule
has local unique identifier example: 49
has provider formatter: http://www.pathguide.org/fullrecord.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-0185-8861
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.pathguide.org/fullrecord.php
has resource example: http://www.pathguide.org/fullrecord.php
has prefix: pathguide

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: gene expression
keyword: interaction
keyword: pathway
keyword: protein
keyword: small molecule
has local unique identifier example: 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
has resource example: http://www.pathoplant.de/detail.php
has prefix: pathoplant

Pathway Commons
type: Resource
description: Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.
is part of: bioregistry
keyword: pathway
has local unique identifier example: 485991
has provider formatter: http://www.pathwaycommons.org/pc/record2.do
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0001-6059-6270
has URI prefix: http://www.pathwaycommons.org/pc/record2.do
has resource example: http://www.pathwaycommons.org/pc/record2.do
has prefix: pathwaycommons

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
has local unique identifier example: 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/
has resource example: !species/9606
has prefix: paxdb.organism

PaxDb Protein
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 individual protein abundance levels.
is part of: bioregistry
has local unique identifier example: 977869
has provider formatter: http://pax-db.org/#!protein/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://pax-db.org/#!protein/
has resource example: !protein/977869
has prefix: paxdb.protein

Pazar Transcription Factor
type: Resource
description: The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.
is part of: bioregistry
keyword: dna
keyword: life science
keyword: regulation
keyword: rna
has local unique identifier example: TF0001053
has provider formatter: http://www.pazar.info/cgi-bin/tf_search.cgi
has local unique identifier pattern: ^TF\w+$
is deprecated: true
has responsible: Wyeth W. Wasserman
has URI prefix: http://www.pazar.info/cgi-bin/tf_search.cgi
has resource example: http://www.pazar.info/cgi-bin/tf_search.cgi
has prefix: pazar

Physiologically-Based Pharmacokinetic Ontology
type: Resource
description: An ontology for modeling and understanding of pharmacokinetics in biological systems.
is part of: bioregistry
git repository: pbpko
keyword: obo
keyword: ontology
has local unique identifier example: 10008
has provider formatter: http://purl.obolibrary.org/obo/PBPKO_$1
has download URL: pbpko.owl
is deprecated: false
has responsible: Saurav Kumar
has URI prefix: http://purl.obolibrary.org/obo/PBPKO_
has prefix: pbpko

Platynereis stage ontology
type: Resource
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/PD_ST_$1
is deprecated: true
has responsible: https://orcid.org/0000-0002-1548-3290
has URI prefix: http://purl.obolibrary.org/obo/PD_ST_
has prefix: pd_st

PDBsum; at-a-glance overview of macromolecular structures
type: Resource
description: PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
is part of: bioregistry
keyword: interaction
keyword: protein
keyword: structural biology
keyword: structure
has local unique identifier example: 1kfv
has provider formatter: https://www.ebi.ac.uk/pdbsum/$1
provides for: pdb
is deprecated: false
has responsible: Roman Laskowski
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.ebi.ac.uk/pdbsum/
has resource example: 1kfv
has prefix: pdbsum

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
has local unique identifier example: 0010039
has provider formatter: http://purl.obolibrary.org/obo/PDRO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: pdro.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-3336-2476
has URI prefix: http://purl.obolibrary.org/obo/PDRO_
has resource example: PDRO_0010039
has prefix: pdro

Platynereis Developmental Stages
type: Resource
description: Life cycle stages for Platynereis dumerilii
is part of: bioregistry
git repository: developmental-stage-ontologies
keyword: developmental biology
keyword: life cycle stage
keyword: life science
keyword: obo
keyword: ontology
has local unique identifier example: 0001410
has provider formatter: http://purl.obolibrary.org/obo/PdumDv_$1
has local unique identifier pattern: ^\d{7}$
has download URL: pdumdv.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-9415-5104
has alternative prefix: PdumDv
has URI prefix: http://purl.obolibrary.org/obo/PdumDv_
has resource example: PdumDv_0001410
has prefix: pdumdv

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

Pennsieve
type: Resource
description: Pennsieve is a publicly accessible Scientific Data Management and publication platform. The platform supports data curation, sharing and publishing complex scientific datasets with a focus on integration between graph-based metadata and file-archival. The platform provides a "peer"-reviewed publication mechanism and public datasets are available through its Discover Web Application and APIs.
is part of: bioregistry
has provider formatter: https://discover.pennsieve.io/package/$1
has local unique identifier pattern: ^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$
is deprecated: false
has URI prefix: https://discover.pennsieve.io/package/
has prefix: pennsieve

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
has local unique identifier example: 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/
has resource example: http://pepbank.mgh.harvard.edu/interactions/details/21877
has prefix: pepbank

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
has local unique identifier example: 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: Nathan Sheffield
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://pephub.databio.org/
has resource example: geo
has prefix: pephub

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

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
has local unique identifier example: SCC111
has provider formatter: https://www.perkinelmer.com/searchresult
is deprecated: false
has URI prefix: https://www.perkinelmer.com/searchresult
has resource example: https://www.perkinelmer.com/searchresult
has prefix: perkinelmer

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

PesticideInfo chemical ID
type: Resource
description: chemical in the database supplied by Pesticide Action Network North America
is part of: bioregistry
has local unique identifier example: PRI10
has provider formatter: https://www.pesticideinfo.org/chemical/$1
has local unique identifier pattern: ^PRI\d*$
is deprecated: false
has URI prefix: https://www.pesticideinfo.org/chemical/
has resource example: PRI10
has prefix: pesticideinfo

Proteoform Atlas
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets.
is part of: bioregistry
has local unique identifier example: 1001
has provider formatter: http://repository.topdownproteomics.org/proteoforms/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: TDR
has URI prefix: http://repository.topdownproteomics.org/proteoforms/
has resource example: http://repository.topdownproteomics.org/proteoforms/1001
has prefix: pfr

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

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
has local unique identifier example: 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/
has resource example: PGS000018
has prefix: pgs

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: biomedical science
keyword: genomics
has local unique identifier example: 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: https://orcid.org/0000-0002-9903-4248
has alternative prefix: Progenetix
has URI prefix: https://progenetix.org/services/ids/
has resource example: pgxbs-kftva5zv
has prefix: pgx

PhageDive
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: PhageDive is a database for bacteriophages and archaeal viruses. It provides information regarding taxonomy, host strain, phage morphology, life cycle, origin and genomic data.
is part of: bioregistry
has local unique identifier example: 3
has provider formatter: https://phagedive.dsmz.de/strain/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Johannes Wittmann
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://phagedive.dsmz.de/strain/
has resource example: https://phagedive.dsmz.de/strain/3
has prefix: phagedive

PharmacoDB Cells
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line.
is part of: bioregistry
has local unique identifier example: 22RV1_12_2019
has provider formatter: https://pharmacodb.ca/cell_lines/$1
is deprecated: false
has URI prefix: https://pharmacodb.ca/cell_lines/
has resource example: 22RV1 12 2019
has prefix: pharmacodb.cell

PharmacoDB Datasets
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset.
is part of: bioregistry
has local unique identifier example: 1
has provider formatter: https://pharmacodb.ca/datasets/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://pharmacodb.ca/datasets/
has resource example: https://pharmacodb.ca/datasets/1
has prefix: pharmacodb.dataset

PharmacoDB Tissues
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue.
is part of: bioregistry
has local unique identifier example: 13
has provider formatter: https://pharmacodb.ca/tissues/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://pharmacodb.ca/tissues/
has resource example: https://pharmacodb.ca/tissues/13
has prefix: pharmacodb.tissue

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: genetic variant
keyword: genetic variation
keyword: ontology
keyword: snp
has local unique identifier example: PA166156302
has provider formatter: https://www.pharmgkb.org/variant/$1
has local unique identifier pattern: ^PA\d+$
has download URL: pharmgkb.variant.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-5527-6475
has URI prefix: https://www.pharmgkb.org/variant/
has resource example: PA166156302
has prefix: pharmgkb.variant

Pharmacogene Variation Consortium
type: Resource
description: The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium.
is part of: bioregistry
keyword: gene
keyword: pharmacogenomics
keyword: variant
has local unique identifier example: CYP2A6
has provider formatter: https://www.pharmvar.org/gene/$1
provides for: hgnc.symbol
is deprecated: false
has responsible: Andrea Gaedigk
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.pharmvar.org/gene/
has resource example: CYP2A6
has prefix: pharmvar

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

PhenX Toolkit
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants.
is part of: bioregistry
keyword: biomedical science
keyword: disease
keyword: environmental science
keyword: exposure
keyword: life science
keyword: ontology
keyword: phenotype
has local unique identifier example: 130502
has provider formatter: https://www.phenxtoolkit.org/protocols/view/$1
has local unique identifier pattern: ^\d+$
has download URL: phenx.owl
is deprecated: false
has responsible: PhenX Admin
has alternative prefix: phenxtoolkit
has URI prefix: https://www.phenxtoolkit.org/protocols/view/
has resource example: https://www.phenxtoolkit.org/protocols/view/130502
has prefix: phenx

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

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

PhosphoSite Curation
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to curation records that collect information extracted from specific publications.
is part of: bioregistry
has local unique identifier example: 34665743
has provider formatter: https://www.phosphosite.org/curatedInfoAction.action
has local unique identifier pattern: ^\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.phosphosite.org/curatedInfoAction.action
has resource example: https://www.phosphosite.org/curatedInfoAction.action
has prefix: phosphosite.curation

PhosphoSite Protein
type: Resource
description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.
is part of: bioregistry
has local unique identifier example: 12300
has provider formatter: http://www.phosphosite.org/proteinAction.do
has local unique identifier pattern: ^\d{5}$
is deprecated: false
has URI prefix: http://www.phosphosite.org/proteinAction.do
has resource example: http://www.phosphosite.org/proteinAction.do
has prefix: phosphosite.protein

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
has local unique identifier example: 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
has resource example: http://www.phosphosite.org/siteAction.do
has prefix: phosphosite.residue

PhosphoSite Site Group
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur.
is part of: bioregistry
keyword: biochemistry
keyword: grouping
keyword: post-translational modification
has local unique identifier example: 447860
has local unique identifier pattern: ^\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has prefix: phosphosite.sitegroup

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

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
has local unique identifier example: 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
has resource example: http://www.phytozome.net/genePage.php
has prefix: phytozome.locus

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: protein
keyword: structure
has local unique identifier example: 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
has resource example: http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl
has prefix: pibase

PicTar
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
has local unique identifier example: hsa-let-7a
is deprecated: true
has alternative prefix: pictar-vert
has prefix: pictar

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: protein
keyword: small molecule
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$
has download URL: pid.pathway.owl
is deprecated: true
has responsible: Carl F. Schaefer
has alternative prefix: pid
has URI prefix: http://pid.nci.nih.gov/search/pathway_landing.shtml
has resource example: http://pid.nci.nih.gov/search/pathway_landing.shtml
has prefix: pid.pathway

Publisher Item Identifier
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A combination of an ISBN and local unique identifier for articles and other published works. Please see the [Wikipedia page](https://en.wikipedia.org/wiki/Publisher_Item_Identifier) for a detailed explanation. Some PIIs are used as the local identifiers in DOIs, such as https://doi.org/10.1136/S0003-4967(24)38620-0.
is part of: bioregistry
has local unique identifier example: S0960-9822(11)01319-4
has local unique identifier pattern: ^((S\d{4}-\d{4}\(\d{2}\)\d{5})|(B\d-\d{3}-\d{5}-\d/\d{5}))-[\d|X]$
is deprecated: false
appears in: pubmed
has prefix: pii

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: data visualization
keyword: life science
has local unique identifier example: 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])$
provides for: uniprot
is deprecated: false
has responsible: Jianmin Wu
has URI prefix: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do
has resource example: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do
has prefix: pina

PiroplasmaDB
type: Resource
description: PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
is part of: bioregistry
has local unique identifier example: TA14985
has provider formatter: http://piroplasmadb.org/piro/showRecord.do
has local unique identifier pattern: ^TA\d+$
is deprecated: false
has URI prefix: http://piroplasmadb.org/piro/showRecord.do
has resource example: http://piroplasmadb.org/piro/showRecord.do
has prefix: piroplasma

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: life science
keyword: protein
keyword: proteomics
keyword: structure
has local unique identifier example: 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
has resource example: https://pir.georgetown.edu/cgi-bin/ipcSF
has prefix: pirsf

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: clinical studies
keyword: clinical veterinary medicine
keyword: life science
keyword: personalized medicine
keyword: pharmacogenomics
keyword: pharmacology
keyword: preclinical studies
has local unique identifier example: 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/
has resource example: PKDB00198
has prefix: pkdb

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
has local unique identifier example: 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/
has resource example: R-ACH-1120024
has prefix: plant_reactome

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

PlasmoDB
type: Resource
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: genome
keyword: genomics
keyword: infectious disease medicine
has local unique identifier example: PF11_0344
has provider formatter: http://plasmodb.org/plasmo/showRecord.do
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4446-6200
has alternative prefix: ApiDB_PlasmoDB
has URI prefix: http://plasmodb.org/plasmo/showRecord.do
has resource example: http://plasmodb.org/plasmo/showRecord.do
has prefix: plasmodb

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
has local unique identifier example: 1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Martin Wagner
has prefix: plastchem

Plasmodium Life Cycle
type: Resource
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/PLO_$1
is deprecated: true
has responsible: Matt Berriman
has URI prefix: http://purl.obolibrary.org/obo/PLO_
has prefix: plo

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: ontology
keyword: subject agnostic
has local unique identifier example: 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#
has resource example: http://localhost/plosthes.2017-1#1443
has prefix: plos

PMADS
type: Resource
contributor: https://orcid.org/0009-0009-3402-8013
description: Identifiers correspond to curated and proteomics-inferred associations between protein post-translational modifications (PTM) and drug sensitivity.
is part of: bioregistry
keyword: drug sensitivity
keyword: modification
keyword: proteomics
has local unique identifier example: acc0079
has provider formatter: https://pmads-db.org/result/
has local unique identifier pattern: ^acc\d{4}$
is deprecated: false
has responsible: Haiyun Wang
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://pmads-db.org/result/
has resource example: https://pmads-db.org/result/
has prefix: pmads

CutDB
type: Resource
description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).
is part of: bioregistry
keyword: enzyme
keyword: pathway
keyword: protein
has local unique identifier example: 25782
has provider formatter: http://cutdb.burnham.org/relation/show/$1
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: Adam Godzik
has URI prefix: http://cutdb.burnham.org/relation/show/
has resource example: http://cutdb.burnham.org/relation/show/25782
has prefix: pmap.cutdb

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

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

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: prediction
keyword: protein
keyword: structure
has local unique identifier example: Q0VCA6
has provider formatter: http://www.proteinmodelportal.org/query/uniprot/$1
has local unique identifier pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$
provides for: uniprot
is deprecated: true
has responsible: 0000-0003-2715-335X
has URI prefix: http://www.proteinmodelportal.org/query/uniprot/
has resource example: Q0VCA6
has prefix: pmp

Physical Medicine and Rehabilitation
type: Resource
description: Resource for the community to store, retrieve, search, reference, and reuse CellML models.
is part of: bioregistry
keyword: biomedical science
keyword: life science
keyword: mathematics
keyword: ontology
keyword: physiology
keyword: systems biology
has provider formatter: https://models.physiomeproject.org/exposure/$1
has local unique identifier pattern: ^[a-z0-9]{32,32}$
has download URL: pmr.owl
is deprecated: false
has responsible: Laia Subirats
has alternative prefix: pmr
has URI prefix: https://models.physiomeproject.org/exposure/
has prefix: pmr.exposure

Physiome Model Repository workspace
type: Resource
description: Workspace (Git repository) for modeling projects managed by the Physiome Model Repository
is part of: bioregistry
has local unique identifier example: modularmassactionprimer
has provider formatter: https://models.physiomeproject.org/workspace/$1
has local unique identifier pattern: ^[a-zA-Z0-9_\-]+(/.*?)?$
is deprecated: false
has URI prefix: https://models.physiomeproject.org/workspace/
has resource example: modularmassactionprimer
has prefix: pmr.workspace

Pocketome
type: Resource
description: Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries.
is part of: bioregistry
keyword: life science
has local unique identifier example: 1433C_TOBAC_1_252
has provider formatter: http://www.pocketome.org/files/$1.html
has local unique identifier pattern: ^[A-Za-z_0-9]+$
is deprecated: false
has responsible: Ruben Abagyan
has URI prefix: https://bioregistry.io/pocketome:
has resource example: 1433C TOBAC 1 252.html
has prefix: pocketome

PolBase
type: Resource
description: Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity.
is part of: bioregistry
keyword: biochemistry
keyword: genetics
has local unique identifier example: 19-T4
has provider formatter: https://polbase.neb.com/polymerases/$1#sequences
has local unique identifier pattern: ^[A-Za-z-0-9]+$
is deprecated: false
has responsible: Linda Reha-Krantz
has URI prefix: https://bioregistry.io/polbase:
has resource example: sequences
has prefix: polbase

Polytraits Trait Definitions
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Reproductive and behavioural traits of both adult and larval stages, as well as information on environmental preferences and a few morphological traits.
is part of: bioregistry
has local unique identifier example: PRED
has provider formatter: http://polytraits.lifewatchgreece.eu/traitspublic_traitdefinitions.php#$1
is deprecated: false
has URI prefix: http://polytraits.lifewatchgreece.eu/traitspublic_traitdefinitions.php#
has resource example: PRED
has prefix: polytraits.trait

Pesticide Properties DataBase
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties.
is part of: bioregistry
has local unique identifier example: 1484
has provider formatter: https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://bioregistry.io/ppdb:
has resource example: 1484.htm
has prefix: ppdb

Europe PMC Preprints
type: Resource
contributor: https://orcid.org/0000-0001-7542-0286
contributor: Javier Millán Acosta
contributor: https://orcid.org/0000-0003-4423-4370
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
has local unique identifier example: 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/
has resource example: PPR103739
has prefix: ppr

PREFER Ontology
type: Resource
description: An ontology for PREcision FERmentation.
is part of: bioregistry
keyword: ontology
has local unique identifier example: 0000020
has download URL: prefer.owl
is deprecated: false
has responsible: Shawn Zheng Kai Tan
has prefix: prefer

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

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

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
has local unique identifier example: 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/
has resource example: PD000596
has prefix: probesanddrugs

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: computational biology
keyword: mathematics
keyword: statistics
keyword: systems biology
has local unique identifier example: 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_
has resource example: PROB c0000005
has prefix: probonto

ProDom
type: Resource
description: ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.
is part of: bioregistry
keyword: classification
keyword: life science
keyword: protein
has local unique identifier example: PD10000
has provider formatter: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl
has local unique identifier pattern: ^PD\d+$
is deprecated: true
has responsible: Daniel Kahn
has URI prefix: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl
has resource example: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl
has prefix: prodom

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
has local unique identifier example: 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
has resource example: http://www.proglycprot.org/detail.aspx
has prefix: proglyc

Proteomics data and process provenance
type: Resource
description: A comprehensive proteomics data and process provenance ontology.
is part of: bioregistry
keyword: obo
keyword: ontology
keyword: owl
keyword: proteomics
has local unique identifier example: protein
has provider formatter: http://purl.obolibrary.org/obo/PROPREO_$1
has download URL: propreo.owl
is deprecated: true
has responsible: https://orcid.org/0000-0001-9190-4256
has URI prefix: http://purl.obolibrary.org/obo/PROPREO_
has resource example: PROPREO protein
has prefix: propreo

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

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

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: life science
keyword: protein
keyword: structure
has local unique identifier example: 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
has resource example: https://www.ncbi.nlm.nih.gov/sites/entrez
has prefix: protclustdb

Database of protein-protein complexes
type: Resource
description: This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures).
is part of: bioregistry
keyword: protein
keyword: structure
has local unique identifier example: 12e8LH
has provider formatter: http://www.ces.clemson.edu/compbio/protcom/print_file.cgi
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.ces.clemson.edu/compbio/protcom/print_file.cgi
has resource example: http://www.ces.clemson.edu/compbio/protcom/print_file.cgi
has prefix: protcom

Protege Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology of metadata from protege
is part of: bioregistry
has local unique identifier example: 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#
has resource example: defaultLanguage
has prefix: protege

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

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

ProtoNet Cluster
type: Resource
description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.
is part of: bioregistry
keyword: classification
keyword: clustering
keyword: protein
has local unique identifier example: 4349895
has provider formatter: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: https://orcid.org/0000-0002-9357-4526
has URI prefix: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php
has resource example: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php
has prefix: protonet.cluster

ProtoNet ProteinCard
type: Resource
description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.
is part of: bioregistry
keyword: protein
has local unique identifier example: 16941567
has provider formatter: http://www.protonet.cs.huji.ac.il/requested/protein_card.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: https://orcid.org/0000-0002-9357-4526
has URI prefix: http://www.protonet.cs.huji.ac.il/requested/protein_card.php
has resource example: http://www.protonet.cs.huji.ac.il/requested/protein_card.php
has prefix: protonet.proteincard

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
has local unique identifier example: 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: Motonori Ota
has URI prefix: https://bioregistry.io/pscdb:
has resource example: 051.html
has prefix: pscdb

PseudoGene
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.
is part of: bioregistry
keyword: gene
keyword: ontology
has local unique identifier example: PGOHUM00000289843
has provider formatter: https://bioregistry.io/pseudogene:$1
is deprecated: true
has responsible: Mark Gerstein
has alternative prefix: pseudogene.org
has URI prefix: https://bioregistry.io/pseudogene:
has resource example: pseudogene:PGOHUM00000289843
has prefix: pseudogene

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
has local unique identifier example: 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/
has resource example: http://www.pseudomonas.com/feature/show/
has prefix: pseudomonas

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
has local unique identifier example: 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/
has resource example: https://www.ebi.ac.uk/ontology-lookup/
has prefix: psipar

Phenoscape Publication
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Documentation of the Phenoscape Curation Workflow
is part of: bioregistry
is deprecated: false
has prefix: pspub

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
has local unique identifier example: 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: Anna L. Kaysheva
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://psskb.org/motif/card/
has resource example: 2VM6 A55 A135
has prefix: psskb

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
has local unique identifier example: Atlas
has provider formatter: http://www.productontology.org/id/$1
is deprecated: false
has URI prefix: http://www.productontology.org/id/
has resource example: Atlas
has prefix: pto

Pointer Methods in RDF
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This specification contains a framework for representing pointers - entities that permit identifying a portion or segment of a piece of content - making use of the Resource Description Framework (RDF). It also describes a number of specific types of pointers that permit portions of a document to be referred to in different ways. When referring to a specific part of, say, a piece of web content, it is useful to be able to have a consistent manner by which to refer to a particular segment of a web document, to have a variety of ways by which to refer to that same segment, and to make the reference robust in the face of changes to that document. This specification is part of the Evaluation And Report Language (EARL) but can be reused in other contexts too. [from homepage]
is part of: bioregistry
has local unique identifier example: Pointer
has provider formatter: https://www.w3.org/2009/pointers#$1
is deprecated: false
has URI prefix: https://www.w3.org/2009/pointers#
has resource example: Pointer
has prefix: ptr

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
has local unique identifier example: 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/
has resource example: https://pubchem.ncbi.nlm.nih.gov/bioassay/1018
has prefix: pubchem.bioassay

PubChem Cell Line
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Cell Lines in PubChem
is part of: bioregistry
keyword: bioactivities
keyword: cell lines
keyword: chemistry
has local unique identifier example: 31
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/cell/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/cell/
has resource example: https://pubchem.ncbi.nlm.nih.gov/cell/31
has prefix: pubchem.cell

PubChem Classification
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records.
is part of: bioregistry
keyword: chemistry
has local unique identifier example: 87
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/classification/
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/classification/
has resource example: https://pubchem.ncbi.nlm.nih.gov/classification/
has prefix: pubchem.classification

PubChem Element
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number.
is part of: bioregistry
keyword: chemistry
has local unique identifier example: 1
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/element/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/element/
has resource example: https://pubchem.ncbi.nlm.nih.gov/element/1
has prefix: pubchem.element

PubChem Substance ID (SID)
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 Substance archives chemical substance records.
is part of: bioregistry
keyword: protein
keyword: small molecule
keyword: structure
has local unique identifier example: 100101
has provider formatter: https://pubchem.ncbi.nlm.nih.gov/substance/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: DSSTox_Generic_SID
has URI prefix: https://pubchem.ncbi.nlm.nih.gov/substance/
has resource example: https://pubchem.ncbi.nlm.nih.gov/substance/100101
has prefix: pubchem.substance

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
has local unique identifier example: 18466622
has provider formatter: https://publons.com/publon/$1
is deprecated: false
has URI prefix: https://publons.com/publon/
has resource example: https://publons.com/publon/18466622
has prefix: publons.publication

Publons Researcher
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Database of researchers to track publications, citation metrics, peer reviews, and journal editing work.
is part of: bioregistry
has local unique identifier example: 1981638
has provider formatter: https://publons.com/researcher/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://publons.com/researcher/
has resource example: https://publons.com/researcher/1981638
has prefix: publons.researcher

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: biological regulation
keyword: disease
keyword: drug
keyword: drug metabolism
keyword: enzymatic reaction
keyword: human
keyword: life science
keyword: molecular entity
keyword: obo
keyword: ontology
keyword: pathway
keyword: signaling
has local unique identifier example: 0000423
has provider formatter: http://purl.obolibrary.org/obo/PW_$1
has local unique identifier pattern: ^\d{7}$
has download URL: pw.owl
is deprecated: false
has responsible: G. Thomas Hayman
has URI prefix: http://purl.obolibrary.org/obo/PW_
has resource example: PW_0000423
has prefix: pw

Qualification Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology of qualifications, distinctions, and certifications that uses the Phenotype And Trait Ontology term quality (PATO:0000001) as a root term.
is part of: bioregistry
git repository: qualo
has local unique identifier example: 0000001
has provider formatter: https://w3id.org/qualo/id/$1
has local unique identifier pattern: ^\d{7}$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://w3id.org/qualo/id/
has resource example: https://w3id.org/qualo/id/0000001
has prefix: qualo

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
has local unique identifier example: LK99
has provider formatter: http://www.radiomics.org/RO/$1
is deprecated: false
has responsible: Alberto Traverso
has URI prefix: http://www.radiomics.org/RO/
has resource example: LK99
has prefix: radiomics

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

RAP-DB Locus
type: Resource
description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB.
is part of: bioregistry
has local unique identifier example: Os01g0883800
has provider formatter: https://rapdb.dna.affrc.go.jp/locus/
has local unique identifier pattern: ^Os\S+g\d{7}$
is deprecated: false
has alternative prefix: irgsp
has URI prefix: https://rapdb.dna.affrc.go.jp/locus/
has resource example: https://rapdb.dna.affrc.go.jp/locus/
has prefix: rapdb.locus

Rice annotation Project database
type: Resource
description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB.
is part of: bioregistry
keyword: dna
keyword: genome
has local unique identifier example: Os01t0883800-02
has provider formatter: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1
has local unique identifier pattern: ^Os\S+t\d{7}-\d{2}$
is deprecated: false
has URI prefix: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1
has resource example: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1
has prefix: rapdb.transcript

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: dna
keyword: gene
keyword: genome
has local unique identifier example: 5
has provider formatter: http://ratmap.org/Showgene.php
provides for: ensembl
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://ratmap.org/Showgene.php
has resource example: http://ratmap.org/Showgene.php
has prefix: ratmap

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
has local unique identifier example: 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: Leif Oxburgh
has URI prefix: https://www.rebuildingakidney.org/id/
has resource example: Q-2958
has prefix: rbk

RIKEN Bioresource Center Cell Bank
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center.
is part of: bioregistry
keyword: animal
keyword: bioresource
keyword: cell
keyword: cell line
keyword: cultured cell
keyword: cultured cell line
keyword: dna
keyword: embryo
keyword: experimental animal
keyword: experimental plant
keyword: faseb list
keyword: gene
keyword: genetic material
keyword: organ
keyword: plant
keyword: recombinant host
keyword: seed
keyword: sperm
keyword: tissue
keyword: virus
has local unique identifier example: RCB0002
has provider formatter: https://cellbank.brc.riken.jp/cell_bank/CellInfo/
has local unique identifier pattern: ^RCB\d+$
is deprecated: false
has responsible: Atsushi Yoshiki
has URI prefix: https://cellbank.brc.riken.jp/cell_bank/CellInfo/
has resource example: https://cellbank.brc.riken.jp/cell_bank/CellInfo/
has prefix: rcb

Registry and database of bioparts for synthetic biology
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: This database provides identifiers for catalytic bioparts which are fundamental to the design, construction, and optimization of biological systems for specific metabolic pathways. It provides basic information, function information (including catalytic functions, qualitative and quantitative parameters, and biopart expression), and sequence information (nucleotide sequence and amino acid sequence)
is part of: bioregistry
has local unique identifier example: OENC205
has provider formatter: https://www.biosino.org/rdbsb/bioparts_detail/$1
has local unique identifier pattern: ^OENC\d+$
is deprecated: false
has responsible: Guoqing Zhang
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.biosino.org/rdbsb/bioparts_detail/
has resource example: OENC205
has prefix: rdbsb

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
has local unique identifier example: 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#
has resource example: PrefixOrTermMapping
has prefix: rdfa

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
has local unique identifier example: 9002859
has provider formatter: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1
has local unique identifier pattern: ^\d{7}$
has download URL: RDO.owl
is deprecated: false
has URI prefix: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#
has resource example: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#9002859
has prefix: rdo

re3data
type: Resource
description: Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines.
is part of: bioregistry
has local unique identifier example: r3d100010772
has provider formatter: https://www.re3data.org/repository/$1
has local unique identifier pattern: ^r3d\d{9,9}$
is deprecated: false
has URI prefix: https://www.re3data.org/repository/
has resource example: r3d100010772
has prefix: re3data

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
has local unique identifier example: 1257009
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: Beilstein
has alternative prefix: Reaxys
has prefix: reaxys

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

Recommendation Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Recommendation Ontology specification provides basic concepts and properties for describing recommendations on/for the Semantic Web.
is part of: bioregistry
keyword: ontology
keyword: rec
has local unique identifier example: Recommendation
has provider formatter: http://purl.org/ontology/rec/core#$1
has download URL: recommendationontology.owl
is deprecated: false
has URI prefix: http://purl.org/ontology/rec/core#
has resource example: Recommendation
has prefix: rec

Human Plasma Membrane Receptome Families
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database.
is part of: bioregistry
keyword: protein
has local unique identifier example: 5.1
has provider formatter: http://www.receptome.org/families/Frameset_family.asp
is deprecated: false
has URI prefix: http://www.receptome.org/families/Frameset_family.asp
has resource example: http://www.receptome.org/families/Frameset_family.asp
has prefix: receptome.family

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
has local unique identifier example: 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/
has resource example: http://redfly.ccr.buffalo.edu/
has prefix: redfly

Reagent Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.
is part of: bioregistry
git repository: reagent-ontology
keyword: ontology
has local unique identifier example: 0000079
has provider formatter: http://purl.obolibrary.org/obo/REO_$11
has local unique identifier pattern: ^\d{7}$
has download URL: reo reasoned 9-6-12.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1048-5019
has URI prefix: https://bioregistry.io/reo:
has resource example: REO_00000791
has prefix: reo

RepeatsDB Protein
type: Resource
description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database.
is part of: bioregistry
has local unique identifier example: P29894
has provider formatter: https://repeatsdb.org/protein/$1
has local unique identifier pattern: ^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$
provides for: uniprot
is deprecated: false
has URI prefix: https://repeatsdb.org/protein/
has resource example: P29894
has prefix: repeatsdb.protein

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

ResearchGate profile ID
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for a person, used by ResearchGate profiles
is part of: bioregistry
keyword: person
keyword: researcher
has local unique identifier example: Rita-Heuser
has provider formatter: https://www.researchgate.net/profile/$1
has local unique identifier pattern: ^[0-9A-Za-z_-]+$
is deprecated: false
has URI prefix: https://www.researchgate.net/profile/
has resource example: Rita-Heuser
has prefix: researchgate.profile

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: transcript
keyword: transcriptomics
has download URL: reto.owl
is deprecated: false
has responsible: Vladimir Mironov
has prefix: reto

Regulation of Gene Expression Ontology
type: Resource
description: Regulation of Gene Expression
is part of: bioregistry
keyword: expression data
keyword: life science
keyword: ontology
keyword: orthologous
keyword: regulation of gene expression
has download URL: rexo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1171-9876
has prefix: rexo

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
has local unique identifier example: 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
has resource example: http://rgd.mcw.edu/rgdweb/report/qtl/main.html
has prefix: rgd.qtl

Rat Genome Database strain
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 strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology.
is part of: bioregistry
has local unique identifier example: 5688061
has provider formatter: http://rgd.mcw.edu/rgdweb/report/strain/main.html
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://rgd.mcw.edu/rgdweb/report/strain/main.html
has resource example: http://rgd.mcw.edu/rgdweb/report/strain/main.html
has prefix: rgd.strain

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
has local unique identifier example: hammer
has provider formatter: https://www.ribocentre.org/docs/$1
has local unique identifier pattern: ^[a-zA-Z0-9-]+$
is deprecated: false
has responsible: Lin Huang
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: ribocenter
has URI prefix: https://www.ribocentre.org/docs/
has resource example: hammer
has prefix: ribocentre

riboCIRC
type: Resource
contributor: https://orcid.org/0009-0009-3402-8013
description: Identifiers represent computationally predicted and experimentally verified translatable circular RNAs (circRNAs) across six model species (human, mouse, rat, worm, fly, and zebrafish), including ribosome-associated circRNAs and their encoded peptides with systematic annotation of sequence, structure, and function.
is part of: bioregistry
keyword: circrna
keyword: peptides
keyword: ribosome profiling
keyword: translation
has local unique identifier example: hsa_ribocircSCD_001
has provider formatter: http://www.ribocirc.com/rna_detail.php
has local unique identifier pattern: ^(hsa|mmu|rno|cel|dme|dre)_ribocirc[A-Za-z0-9.:]+_\d{3}$
is deprecated: false
has responsible: Zhi Xie
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: http://www.ribocirc.com/rna_detail.php
has resource example: http://www.ribocirc.com/rna_detail.php
has prefix: ribocirc

Rice Metabolic Pathways
type: Resource
description: RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project
is part of: bioregistry
keyword: gene
keyword: pathway
has local unique identifier example: PWY-1042
has provider formatter: http://pathway.gramene.org/RICE/NEW-IMAGE
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://pathway.gramene.org/RICE/NEW-IMAGE
has resource example: http://pathway.gramene.org/RICE/NEW-IMAGE
has prefix: ricecyc

Rice Genome Annotation Project
type: Resource
description: The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.
is part of: bioregistry
keyword: dna
keyword: genome
has local unique identifier example: LOC_Os02g13300
has provider formatter: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi
has local unique identifier pattern: ^LOC\_Os\d{1,2}g\d{5}$
is deprecated: false
has responsible: C. Robin Buell
has alternative prefix: rgap
has URI prefix: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi
has resource example: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi
has prefix: ricegap

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
has local unique identifier example: 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
has resource example: http://bis.zju.edu.cn/ricenetdb/compounddetails.php
has prefix: ricenetdb.compound

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
has local unique identifier example: 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
has resource example: http://bis.zju.edu.cn/ricenetdb/genedetails.php
has prefix: ricenetdb.gene

RiceNetDB miRNA
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
has local unique identifier example: osa-miR446
has provider formatter: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php
has local unique identifier pattern: ^osa-miR\d{3,5}[a-z]{0,1}$
is deprecated: false
has URI prefix: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php
has resource example: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php
has prefix: ricenetdb.mirna

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
has local unique identifier example: 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
has resource example: http://bis.zju.edu.cn/ricenetdb/proteindetails.php
has prefix: ricenetdb.protein

RiceNetDB Reaction
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
has local unique identifier example: OSR0818
has provider formatter: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php
has local unique identifier pattern: ^OSR\d{4}$
is deprecated: false
has URI prefix: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php
has resource example: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php
has prefix: ricenetdb.reaction

RISM Online
type: Resource
description: RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project.
is part of: bioregistry
has local unique identifier example: people/11035
has provider formatter: https://rism.online/$1
has local unique identifier pattern: ^[a-z]+/[0-9]+$
is deprecated: false
has URI prefix: https://rism.online/
has resource example: https://rism.online/people/11035
has prefix: rism

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
has local unique identifier example: 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
has resource example: http://www.rnasoft.ca/sstrand/show_results.php
has prefix: rna_sstrand

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: rna
keyword: structural biology
keyword: structure
has local unique identifier example: 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
has resource example: https://rnajunction.ncifcrf.gov/JunctionPage.php
has prefix: rnajunction

RNAloops
type: Resource
contributor: https://orcid.org/0000-0001-9439-5346
description: Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank.
is part of: bioregistry
keyword: rna
keyword: structural bioinformatcs
has local unique identifier example: 91792
has provider formatter: https://rnaloops.cs.put.poznan.pl/search/details/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Maciej Antczak
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://rnaloops.cs.put.poznan.pl/search/details/
has resource example: https://rnaloops.cs.put.poznan.pl/search/details/91792
has prefix: rnaloops

The RNA Modification Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A comprehensive listing of post-transcriptionally modified nucleosides from RNA -
is part of: bioregistry
keyword: post-transcriptional modification
keyword: rna
keyword: structural bioinformatcs
has local unique identifier example: 051
has provider formatter: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl
has local unique identifier pattern: ^\d{3}$
is deprecated: false
has URI prefix: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl
has resource example: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl
has prefix: rnamod

RNA Modification Database
type: Resource
description: The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA.
is part of: bioregistry
keyword: rna
keyword: structure
has local unique identifier example: 101
has provider formatter: http://rna.rega.kuleuven.be/rnamods/rnashow.pl
has local unique identifier pattern: ^\d{3}$
is deprecated: false
has URI prefix: http://rna.rega.kuleuven.be/rnamods/rnashow.pl
has resource example: http://rna.rega.kuleuven.be/rnamods/rnashow.pl
has prefix: rnamods

RNA ontology
type: Resource
description: Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.
is part of: bioregistry
git repository: rnao
keyword: biochemistry
keyword: life science
keyword: obo
keyword: ontology
keyword: ribonucleic acid
keyword: rna secondary structure
keyword: sequence motif
keyword: structure
has local unique identifier example: 0000128
has provider formatter: http://purl.obolibrary.org/obo/RNAO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: rnao.owl
is deprecated: true
has responsible: https://orcid.org/0000-0001-5985-7429
has URI prefix: http://purl.obolibrary.org/obo/RNAO_
has resource example: RNAO_0000128
has prefix: rnao

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: genome
keyword: rna
has local unique identifier example: 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
has resource example: http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php
has prefix: rnavdb

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
has local unique identifier example: 0000002
has provider formatter: http://purl.obolibrary.org/obo/RoleO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: 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_
has resource example: RoleO_0000002
has prefix: roleo

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: dna
keyword: life science
keyword: protein
has local unique identifier example: 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/
has resource example: mKIAA4200
has prefix: rouge

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

Registry of Toxic Effects of Chemical Substances
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments.
is part of: bioregistry
has local unique identifier example: AB1925000
has local unique identifier pattern: ^AB\d+$
is deprecated: false
has responsible: Vernon Putz-Anderson
has prefix: rtecs

runBioSimulations
type: Resource
description: runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive.
is part of: bioregistry
has local unique identifier example: 5fde96bdc5f1aa9ff0cce18a
has provider formatter: https://run.biosimulations.org/simulations/$1
has local unique identifier pattern: ^[0-9a-z]{24,24}$
is deprecated: false
has URI prefix: https://run.biosimulations.org/simulations/
has resource example: https://run.biosimulations.org/simulations/5fde96bdc5f1aa9ff0cce18a
has prefix: runbiosimulations

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
has local unique identifier example: 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
has resource example: http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi
has prefix: s_mart_db

SABIO-RK Compound
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 compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information.
is part of: bioregistry
has local unique identifier example: 75
has provider formatter: http://sabiork.h-its.org/newSearch
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://sabiork.h-its.org/newSearch
has resource example: http://sabiork.h-its.org/newSearch
has prefix: sabiork.compound

SABIO-RK EC Record
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 EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data.
is part of: bioregistry
keyword: reaction
has local unique identifier example: 2.7.1.1
has provider formatter: http://sabiork.h-its.org/newSearch
has local unique identifier pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$
provides for: ec
is deprecated: false
has responsible: https://orcid.org/0000-0002-9077-5664
has URI prefix: http://sabiork.h-its.org/newSearch
has resource example: http://sabiork.h-its.org/newSearch
has prefix: sabiork.ec

SABIO Reaction Kinetics
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 kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information.
is part of: bioregistry
keyword: classification
keyword: enzyme
keyword: kinetics
has local unique identifier example: 5046
has provider formatter: http://sabiork.h-its.org/kineticLawEntry.jsp
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9077-5664
has URI prefix: http://sabiork.h-its.org/kineticLawEntry.jsp
has resource example: http://sabiork.h-its.org/kineticLawEntry.jsp
has prefix: sabiork.kineticrecord

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: biochemistry
keyword: kinetics
keyword: life science
keyword: pathway
keyword: reaction
has local unique identifier example: 75
has provider formatter: http://sabiork.h-its.org/reacdetails.jsp
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-9077-5664
has alternative prefix: SABIO-RK
has URI prefix: http://sabiork.h-its.org/reacdetails.jsp
has resource example: http://sabiork.h-its.org/reacdetails.jsp
has prefix: sabiork.reaction

Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
is deprecated: true
has prefix: sael

Salk Institute for Biological Studies
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Scientific research institute for neuroscience, genetics, immunology, plant biology and more.
is part of: bioregistry
has local unique identifier example: 037727
has provider formatter: https://abrc.osu.edu/stocks/number/SALK_$1
has local unique identifier pattern: ^\d{6}$
is deprecated: false
appears in: efo
has URI prefix: https://abrc.osu.edu/stocks/number/SALK_
has resource example: SALK_037727
has prefix: salk

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
has local unique identifier example: 00000674
has provider formatter: https://purl.dataone.org/odo/SALMON_$1
has local unique identifier pattern: ^\d+$
has download URL: salmon.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-0381-3766
has URI prefix: https://purl.dataone.org/odo/SALMON_
has resource example: SALMON_00000674
has prefix: salmon

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: biochemistry
keyword: obo
keyword: ontology
keyword: owl
has local unique identifier example: 5277619
has provider formatter: http://uri.neuinfo.org/nif/nifstd/sao$1
has local unique identifier pattern: ^\d+$
has download URL: sao.owl
is deprecated: true
has responsible: Stephen Larson
has URI prefix: http://uri.neuinfo.org/nif/nifstd/sao
has resource example: sao5277619
has prefix: sao

SAREF extension for Agriculture
type: Resource
description: This ontology extends the SAREF ontology for the Agricultural domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Agricultural domain.
is part of: bioregistry
keyword: agriculture
keyword: food
keyword: iot
keyword: miscellaneous
has local unique identifier example: Animal
has provider formatter: https://saref.etsi.org/saref4agri/$1
is deprecated: false
has alternative prefix: s4agri
has URI prefix: https://saref.etsi.org/saref4agri/
has resource example: Animal
has prefix: saref.agri

SAREF extension for Smart City
type: Resource
description: This ontology extends the SAREF ontology for the Smart City domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Smart City domain.
is part of: bioregistry
keyword: civil engineering
keyword: computer science
keyword: digital planning and construction
keyword: fid move
keyword: government
keyword: iot
keyword: traffic engineering
has local unique identifier example: AccessibilityConcept
has provider formatter: https://saref.etsi.org/saref4city/$1
is deprecated: false
has alternative prefix: s4city
has URI prefix: https://saref.etsi.org/saref4city/
has resource example: AccessibilityConcept
has prefix: saref.city

SAREF4MARI: an extension of SAREF for the maritime domain
type: Resource
description: SAREF4MARI is an extension of SAREF for the maritime domain.
is part of: bioregistry
keyword: fid move
keyword: traffic engineering
has local unique identifier example: AISDevice
has provider formatter: https://saref.etsi.org/saref4mari/$1
is deprecated: false
has alternative prefix: s4mari
has URI prefix: https://saref.etsi.org/saref4mari/
has resource example: AISDevice
has prefix: saref.maritime

The State of Alaska's Salmon and People Ontology
type: Resource
description: An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities.
is part of: bioregistry
keyword: ontology
has local unique identifier example: 00000101
has provider formatter: https://purl.dataone.org/odo/SASAP_$1
has local unique identifier pattern: ^\d+$
has download URL: sasap.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-0381-3766
has URI prefix: https://purl.dataone.org/odo/SASAP_
has resource example: SASAP_00000101
has prefix: sasap

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: life science
keyword: molecular biology
has local unique identifier example: 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: Al Kikhney
has URI prefix: http://www.sasbdb.org/data/
has resource example: SASDAX8
has prefix: sasbdb

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
has local unique identifier example: 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
has resource example: http://www.scancerrna.com/toDetail
has prefix: scancerrna

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: bel
keyword: chemistry
keyword: selventa
has local unique identifier example: 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/
has resource example: A0001
has prefix: schem

Scholia Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A frontend to Wikidata
is part of: bioregistry
keyword: registry
keyword: wikidata
has local unique identifier example: doi
has provider formatter: https://bioregistry.io/metaregistry/scholia/$1
is deprecated: false
has URI prefix: https://bioregistry.io/metaregistry/scholia/
has resource example: doi
has prefix: scholia.resource

Sciflection
type: Resource
description: Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions
is part of: bioregistry
has provider formatter: https://sciflection.com/$1
has local unique identifier pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
is deprecated: false
has URI prefix: https://sciflection.com/
has prefix: sciflection

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
has local unique identifier example: 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/
has resource example: https://sciprofiles.com/profile/118021
has prefix: sciprofiles

Selventa Complexes
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Selventa legacy complex namespace used with the Biological Expression Language
is part of: bioregistry
keyword: bel
keyword: protein complexes
keyword: selventa
has local unique identifier example: C0001
has provider formatter: https://biopragmatics.github.io/providers/scomp/$1
has local unique identifier pattern: ^C\d{4}$
is deprecated: false
has responsible: Natalie L Catlett
has URI prefix: https://biopragmatics.github.io/providers/scomp/
has resource example: C0001
has prefix: scomp

SCOP(e) concise classification string
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents the superfamily, and the last '1' represents the family.
is part of: bioregistry
has local unique identifier example: a.39.1.1
has provider formatter: http://scop.berkeley.edu/sccs=$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-5153-9079
has URI prefix: http://scop.berkeley.edu/sccs=
has resource example: http://scop.berkeley.edu/sccs=a.39.1.1
has prefix: scop.sccs

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
has local unique identifier example: d4akea1
has provider formatter: http://scop.berkeley.edu/sid=$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-5153-9079
has URI prefix: http://scop.berkeley.edu/sid=
has resource example: http://scop.berkeley.edu/sid=d4akea1
has prefix: scop.sid

Scopus Researcher
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. Delivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts and humanities, Scopus features smart tools to track, analyze and visualize research.
is part of: bioregistry
keyword: subject agnostic
has local unique identifier example: 56305849200
has provider formatter: https://www.scopus.com/authid/detail.uri
has local unique identifier pattern: ^\d+$
is deprecated: false
has alternative prefix: scopus.author
has URI prefix: https://www.scopus.com/authid/detail.uri
has resource example: https://www.scopus.com/authid/detail.uri
has prefix: scopus

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

Scopus Publication
type: Resource
description: identifier for a source/publication venue (journal, conference, etc) in Scopus
is part of: bioregistry
has local unique identifier example: 16129
has provider formatter: https://www.scopus.com/sourceid/$1
has local unique identifier pattern: ^[1-9]\d{0,11}$
is deprecated: false
has URI prefix: https://www.scopus.com/sourceid/
has resource example: https://www.scopus.com/sourceid/16129
has prefix: scopus.publication

Scopus Work
type: Resource
description: unique academic work identifier assigned in Scopus bibliographic database
is part of: bioregistry
has local unique identifier example: 2-s2.0-0030770923
has provider formatter: http://www.scopus.com/record/display.url
has local unique identifier pattern: ^2-s2\.0-\d+$
is deprecated: false
has alternative prefix: scopus.eid
has URI prefix: http://www.scopus.com/record/display.url
has resource example: http://www.scopus.com/record/display.url
has prefix: scopus.work

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
has local unique identifier example: ActiviateOrArchiveContract
has provider formatter: http://purl.org/eis/vocab/scor#$1
is deprecated: false
has URI prefix: http://purl.org/eis/vocab/scor#
has resource example: ActiviateOrArchiveContract
has prefix: scor

Saccharomyces cerevisiae promoter database
type: Resource
description: Database containing promotor sequences found in Saccharomyces cerevisiae.
is part of: bioregistry
keyword: dna
keyword: rna
has local unique identifier example: CDC2
has provider formatter: http://rulai.cshl.edu/cgi-bin/SCPD/getgene2
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://rulai.cshl.edu/cgi-bin/SCPD/getgene2
has resource example: http://rulai.cshl.edu/cgi-bin/SCPD/getgene2
has prefix: scpd

SciCrunch Registry
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources.
is part of: bioregistry
keyword: interactive portal
keyword: life science
keyword: neurobiology
keyword: nih initiative
keyword: rrid
has local unique identifier example: 022586
has provider formatter: http://scicrunch.org/resolver/SCR_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-5497-0243
has alternative prefix: scicrunch
has URI prefix: http://scicrunch.org/resolver/SCR_
has resource example: SCR_022586
has prefix: scr

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
has local unique identifier example: 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/
has resource example: RSC3
has prefix: scretf

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
has local unique identifier example: endpoint
is deprecated: false
has prefix: sd

Structural Database of Allergenic Proteins
type: Resource
description: SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes.
is part of: bioregistry
keyword: protein
keyword: structure
has local unique identifier example: 610
has provider formatter: http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02
has resource example: http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02
has prefix: sdap

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

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
has local unique identifier example: 3000001
has provider formatter: http://purl.obolibrary.org/obo/SDDO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: sddo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-4312-9552
has URI prefix: http://purl.obolibrary.org/obo/SDDO_
has resource example: SDDO_3000001
has prefix: sddo

Sustainable Development Goals Interface Ontology
type: Resource
description: The Sustainable Development Goals Interface Ontology (SDGIO) aims to provide a semantic bridge between 1) the Sustainable Development Goals, their targets, and indicators and 2) the large array of entities they refer to. SDGIO will reuse existing ontologies where appropriate.
is part of: bioregistry
git repository: sdgio
keyword: environmental science
keyword: ontology
keyword: sustainability
has local unique identifier example: 00020134
has provider formatter: http://purl.unep.org/sdg/SDGIO_$1
has local unique identifier pattern: ^\d{8}$
has download URL: sdgio.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-4366-3088
has URI prefix: http://purl.unep.org/sdg/SDGIO_
has resource example: SDGIO_00020134
has prefix: sdgio

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
has local unique identifier example: 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/
has resource example: D0001
has prefix: sdis

SDMX-RDF vocabulary
type: Resource
description: This vocabulary extends the data cube vocabulary to support publication of statistical data in RDF, using an information model based on SDMX
is part of: bioregistry
keyword: methods
has local unique identifier example: EntityRole
is deprecated: false
has prefix: sdmx

Immunology Database and Analysis Portal (ImmPort)
type: Resource
description: ImmPort is a scientific data resource funded by the National Institutes of Health (NIH) to preserve and share immunology research and clinical trials data generated by NIH researchers and external organizations. ImmPort uses FAIR principles to maximize reuse of deposited data for advancement of biomedical sciences.
is part of: bioregistry
has local unique identifier example: sdy998
has provider formatter: https://immport.org/shared/study/$1
has local unique identifier pattern: ^[sS][dD][yY]\d+$
is deprecated: false
has URI prefix: https://immport.org/shared/study/
has resource example: sdy998
has prefix: sdy

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
has local unique identifier example: 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:
has resource example: format:csv
has prefix: sedml.format

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
has local unique identifier example: 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:
has resource example: language:sbml.level-3.version-2
has prefix: sedml.language

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
has local unique identifier example: 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/
has resource example: cpd15380
has prefix: seed.compound

SEED Reactions
type: Resource
description: ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.
is part of: bioregistry
has local unique identifier example: rxn00001
has provider formatter: http://modelseed.org/biochem/reactions/$1
has local unique identifier pattern: ^rxn\d+$
is deprecated: false
has URI prefix: http://modelseed.org/biochem/reactions/
has resource example: rxn00001
has prefix: seed.reaction

The SEED
type: Resource
contributor: https://orcid.org/0000-0002-7674-5194
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
has local unique identifier example: Histidinol dehydrogenase (EC 1.1.1.23)
has provider formatter: https://pubseed.theseed.org/SubsysEditor.cgi
is deprecated: false
has reviewer: https://orcid.org/0000-0001-9439-5346
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://pubseed.theseed.org/SubsysEditor.cgi
has prefix: seed.role

SEED Subsystem
type: Resource
contributor: https://orcid.org/0000-0002-7674-5194
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
has local unique identifier example: 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
has resource example: https://pubseed.theseed.org/SubsysEditor.cgi
has prefix: seed.subsystem

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
has local unique identifier example: 762
has provider formatter: https://swbiodiversity.org/seinet/taxa/index.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0002-8169-9049
has URI prefix: https://swbiodiversity.org/seinet/taxa/index.php
has resource example: https://swbiodiversity.org/seinet/taxa/index.php
has prefix: seinet

Semantic Mapping Vocabulary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata.
is part of: bioregistry
git repository: semantic-mapping-vocabulary
keyword: ontology
has local unique identifier example: LexicalMatching
has provider formatter: https://w3id.org/semapv/vocab/$1
has download URL: semapv.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-7356-1779
has alternative prefix: semapv_voc
has alternative prefix: sempav_voc
has URI prefix: https://w3id.org/semapv/vocab/
has identifier space owner: Q115518213
has resource example: LexicalMatching
has prefix: semapv

Semion author ID (archived)
type: Resource
description: identifier of an author or reviewer, in Semion
is part of: bioregistry
has local unique identifier example: 22132778
has provider formatter: https://web.archive.org/web/1/https://www.semion.io/Author/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://web.archive.org/web/1/https://www.semion.io/Author/
has resource example: https://web.archive.org/web/1/https://www.semion.io/Author/22132778
has prefix: semion

Sensitive Data Ontology
type: Resource
description: The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing.
is part of: bioregistry
keyword: ontology
has local unique identifier example: 00000003
has provider formatter: http://purl.dataone.org/odo/SENSO_$1
has local unique identifier pattern: ^\d+$
has download URL: senso.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-0381-3766
has URI prefix: http://purl.dataone.org/odo/SENSO_
has resource example: SENSO_00000003
has prefix: senso

Scientific Event Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Scientific Event Ontology (SEO) is a reference ontology for modeling data about scientific events such as conferences, symposioums, and workshops.
is part of: bioregistry
keyword: academy
keyword: events
has local unique identifier example: Symposium
has provider formatter: https://w3id.org/seo#$1
is deprecated: false
has URI prefix: https://w3id.org/seo#
has resource example: Symposium
has prefix: seo

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
has local unique identifier example: 00073
has provider formatter: http://purl.obolibrary.org/obo/SEP_$1
has local unique identifier pattern: ^\d{5,6}$
has download URL: 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_
has resource example: SEP_00073
has prefix: sep

Selventa Families
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Selventa legacy protein family namespace used with the Biological Expression Language
is part of: bioregistry
keyword: bel
keyword: protein families
keyword: selventa
has local unique identifier example: F0001
has provider formatter: https://biopragmatics.github.io/providers/sfam/$1
has local unique identifier pattern: ^F\d{4}$
is deprecated: false
has responsible: Natalie L Catlett
has URI prefix: https://biopragmatics.github.io/providers/sfam/
has resource example: F0001
has prefix: sfam

Saccharomyces genome database pathways
type: Resource
description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD).
is part of: bioregistry
keyword: genome
keyword: pathway
keyword: sequence
has local unique identifier example: PWY3O-214
has provider formatter: http://pathway.yeastgenome.org/YEAST/new-image
has local unique identifier pattern: ^PWY\w{2}\-\d{3}$
is deprecated: false
has responsible: Karen R. Christie
has URI prefix: http://pathway.yeastgenome.org/YEAST/new-image
has resource example: http://pathway.yeastgenome.org/YEAST/new-image
has prefix: sgd.pathways

Sol Genomics Network
type: Resource
description: The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.
is part of: bioregistry
keyword: agriculture
keyword: botany
keyword: comparative genomics
keyword: genome
keyword: genomics
keyword: pathway
keyword: plant
keyword: small molecule
has local unique identifier example: 0001
has provider formatter: http://solgenomics.net/phenome/locus_display.pl
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Lukas A. Mueller
has URI prefix: http://solgenomics.net/phenome/locus_display.pl
has resource example: http://solgenomics.net/phenome/locus_display.pl
has prefix: sgn

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
has local unique identifier example: 000004
has provider formatter: https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1
has local unique identifier pattern: ^\d{6}$
has download URL: shareloc.owl
is deprecated: false
has URI prefix: https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_
has resource example: ontology/vocabulary/SHARELOC 000004
has prefix: shareloc

Sharkipedia Species
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
has local unique identifier example: 983
has provider formatter: https://www.sharkipedia.org/species/$1
has local unique identifier pattern: ^\d+$
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/species/
has resource example: https://www.sharkipedia.org/species/983
has prefix: sharkipedia.species

Sharkipedia Trait
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
has local unique identifier example: 13
has provider formatter: https://www.sharkipedia.org/traits/$1
has local unique identifier pattern: ^\d+$
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/traits/
has resource example: https://www.sharkipedia.org/traits/13
has prefix: sharkipedia.trait

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
has local unique identifier example: 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/
has resource example: https://www.sharkipedia.org/trends/3447
has prefix: sharkipedia.trend

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
has local unique identifier example: 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
has resource example: http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi
has prefix: shibase

SHACL Node Expression
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A vocabulary used in tandem with SHACL for representing node shapes
is part of: bioregistry
git repository: data-shapes
has local unique identifier example: instancesOf
has provider formatter: http://www.w3.org/ns/shacl-node-expr#$1
is deprecated: false
has URI prefix: http://www.w3.org/ns/shacl-node-expr#
has resource example: instancesOf
has prefix: shnex

SHACL in SHACL
type: Resource
description: This shapes graph can be used to validate SHACL shapes graphs against a subset of the syntax rules.
is part of: bioregistry
has local unique identifier example: ListShape
is deprecated: false
has prefix: shsh

Social Insect Behavior Ontology
type: Resource
description: Social Behavior in insects
is part of: bioregistry
git repository: sibo
keyword: biology
keyword: obo
keyword: ontology
has local unique identifier example: 0000509
has provider formatter: http://purl.obolibrary.org/obo/SIBO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: sibo.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-6601-2165
has URI prefix: http://purl.obolibrary.org/obo/SIBO_
has resource example: SIBO_0000509
has prefix: sibo

SIDER Drug
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 drugs in SIDER.
is part of: bioregistry
has local unique identifier example: 2244
has provider formatter: http://sideeffects.embl.de/drugs/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://sideeffects.embl.de/drugs/
has resource example: http://sideeffects.embl.de/drugs/2244
has prefix: sider.drug

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
has local unique identifier example: C0017565
has provider formatter: http://sideeffects.embl.de/se/$1
has local unique identifier pattern: ^C\d+$
provides for: umls
is deprecated: false
has URI prefix: http://sideeffects.embl.de/se/
has resource example: http://sideeffects.embl.de/se/C0017565
has prefix: sider.effect

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: biology
keyword: chemistry
keyword: life sciences
keyword: vendor
has local unique identifier example: 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/
has resource example: HPA000698
has prefix: sigmaaldrich

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

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
has local unique identifier example: SIGNOR-252737
has local unique identifier pattern: ^SIGNOR-\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has prefix: signor.relation

SILVA Taxon
type: Resource
contributor: Jose P. Faria
description: SILVA is a resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes. It assigns internal, auto-incremented integer identifiers to taxa. However, these identifiers are not persistent nor unique - if the label for a taxon is changed, it assigned a new identifier and the old identifier is removed.
is part of: bioregistry
has local unique identifier example: 11084
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-7805-0660
has reviewer: https://orcid.org/0000-0003-4423-4370
has prefix: silva.taxon

Semantically-Interlinked Online Communities Access Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining basic information on permissions and access rights.
is part of: bioregistry
has local unique identifier example: Permission
has provider formatter: http://rdfs.org/sioc/access#$1
is deprecated: false
has URI prefix: http://rdfs.org/sioc/access#
has resource example: Permission
has prefix: sioc.access

Semantically-Interlinked Online Communities Actions Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An ontology of predicates for actions in SIOC
is part of: bioregistry
has local unique identifier example: DigitalArtifact
has provider formatter: http://rdfs.org/sioc/actions#$1
is deprecated: false
has URI prefix: http://rdfs.org/sioc/actions#
has resource example: DigitalArtifact
has prefix: sioc.actions

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
has local unique identifier example: decides
has provider formatter: http://rdfs.org/sioc/argument#$1
is deprecated: false
has URI prefix: http://rdfs.org/sioc/argument#
has resource example: decides
has prefix: sioc.argument

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
has local unique identifier example: 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#
has resource example: Item
has prefix: sioc.core

Semantically-Interlinked Online Communities Services Ontology - Quote Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining basic information on community-related web services.
is part of: bioregistry
has local unique identifier example: has_service
has provider formatter: http://rdfs.org/sioc/services#$1
is deprecated: false
has URI prefix: http://rdfs.org/sioc/services#
has resource example: has service
has prefix: sioc.quote

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
has local unique identifier example: OnlineJournal
has provider formatter: http://rdfs.org/sioc/swan#$1
is deprecated: false
has URI prefix: http://rdfs.org/sioc/swan#
has resource example: OnlineJournal
has prefix: sioc.swan

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
has local unique identifier example: AddressBook
has provider formatter: http://rdfs.org/sioc/types#$1
is deprecated: false
has URI prefix: http://rdfs.org/sioc/types#
has resource example: AddressBook
has prefix: sioc.types

Scientific Information Retrieval and Exchange Network
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods
is part of: bioregistry
has local unique identifier example: F11903
has local unique identifier pattern: ^F\d+$
is deprecated: false
has responsible: Patrice Buche
has alternative prefix: SUBSET_SIREN
has prefix: siren

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

SitEx
type: Resource
description: SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.
is part of: bioregistry
keyword: domain
keyword: eukaryotic
keyword: life science
keyword: sequence
keyword: structure
has local unique identifier example: 1000
has provider formatter: http://www-bionet.sscc.ru/sitex/index.php
has local unique identifier pattern: ^\d+$
is deprecated: true
has responsible: Irina Medvedeva
has URI prefix: http://www-bionet.sscc.ru/sitex/index.php
has resource example: http://www-bionet.sscc.ru/sitex/index.php
has prefix: sitex

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
has local unique identifier example: 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
has resource example: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail
has prefix: skip

Stress Knowledge Map
type: Resource
description: Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors.
is part of: bioregistry
has local unique identifier example: rx00408
has provider formatter: https://skm.nib.si/api/pss/reactions
has local unique identifier pattern: ^rx[0-9]{5}$
is deprecated: false
has URI prefix: https://bioregistry.io/skm:
has resource example: https://skm.nib.si/api/pss/reactions
has prefix: skm

SKOS Thesaurus Extension
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: SKOS-Thes: An extension to SKOS based on the ISO 25964 data model. The ISO 25964 standard, published in 2011, covers all aspects of developing thesauri and setting up mappings across vocabularies to encourage high quality information retrieval across networked resources. [from https://www.dublincore.org/specifications/skos-thes/]
is part of: bioregistry
has local unique identifier example: CompoundEquivalence
has provider formatter: https://www.dublincore.org/specifications/skos-thes/ns/#$1
is deprecated: false
has alternative prefix: skos-thes
has alternative prefix: skosthes
has URI prefix: https://www.dublincore.org/specifications/skos-thes/ns/#
has resource example: CompoundEquivalence
has prefix: skos.thes

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

SwissLipid
type: Resource
description: SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.
is part of: bioregistry
keyword: life science
keyword: metabolomics
keyword: ontology
has local unique identifier example: 000000341
has provider formatter: https://www.swisslipids.org/#/entity/SLM:$1
has local unique identifier pattern: ^\d+$
has download URL: slm.owl.gz
is deprecated: false
has responsible: https://orcid.org/0000-0003-2148-9135
has alternative prefix: swisslipid
has alternative prefix: swisslipids
has URI prefix: https://www.swisslipids.org/#/entity/SLM:
has resource example: entity/SLM:000000341
has prefix: slm

Space Life Sciences Ontology
type: Resource
description: The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data.
is part of: bioregistry
git repository: LSDAO
keyword: obo
keyword: ontology
has local unique identifier example: 0000000
has provider formatter: http://purl.obolibrary.org/obo/SLSO_$1
has download URL: slso.owl
is deprecated: false
has responsible: https://orcid.org/0000-0003-4312-9552
has URI prefix: http://purl.obolibrary.org/obo/SLSO_
has prefix: slso

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: domain
keyword: life science
keyword: protein
keyword: structure
has local unique identifier example: 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
has resource example: http://smart.embl-heidelberg.de/smart/do_annotation.pl
has prefix: smart

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
has local unique identifier example: 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/
has resource example: https://smc.jgi.doe.gov/bgc/12039302
has prefix: smc.bgc

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
has local unique identifier example: 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/
has resource example: https://smc.jgi.doe.gov/sources/1
has prefix: smc.source

Simplified molecular-input line-entry system
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
contributor: Nisha Sharma
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: bioinformatics
keyword: chemistry
keyword: data analysis
keyword: life science
keyword: lipidomics
keyword: metabolomics
keyword: molecular entity
keyword: structure
has local unique identifier example: 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: https://orcid.org/0000-0001-7542-0286
has URI prefix: https://bioregistry.io/smiles:
has prefix: smiles

Small Molecule Pathway Database
type: Resource
description: The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.
is part of: bioregistry
keyword: chemical
keyword: human
keyword: life science
keyword: metabolite
keyword: pathway
has local unique identifier example: SMP0000219
has provider formatter: https://smpdb.ca/view/$1
has local unique identifier pattern: ^SMP\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has alternative prefix: SMP
has URI prefix: https://smpdb.ca/view/
has resource example: SMP0000219
has prefix: smpdb

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
has local unique identifier example: 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#
has resource example: Quality
has prefix: snap

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: human nucleolar rna
keyword: rna
keyword: snorna-protein
has local unique identifier example: 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/
has resource example: snoDB0001
has prefix: snodb

snoRNABase
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A comprehensive database of human H/ACA and C/D box snoRNAs.
is part of: bioregistry
keyword: rna
has local unique identifier example: SR0000178
has provider formatter: http://www-snorna.biotoul.fr/plus.php
is deprecated: false
has URI prefix: http://www-snorna.biotoul.fr/plus.php
has resource example: http://www-snorna.biotoul.fr/plus.php
has prefix: snornabase

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
has local unique identifier example: rs11603840
has provider formatter: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi
has local unique identifier pattern: ^rs[0-9]+$
provides for: dbsnp
is deprecated: false
has URI prefix: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi
has resource example: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi
has prefix: snp2tfbs

SNP500Cancer
type: Resource
description: The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer.
is part of: bioregistry
keyword: dna
has local unique identifier example: TP53-47
has provider formatter: http://snp500cancer.nci.nih.gov/snp.cfm
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://snp500cancer.nci.nih.gov/snp.cfm
has resource example: http://snp500cancer.nci.nih.gov/snp.cfm
has prefix: snp500cancer

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
has download URL: sopharm.owl
is deprecated: true
has responsible: Adrien Coulet
has URI prefix: http://purl.obolibrary.org/obo/SOPHARM_
has prefix: sopharm

SoyBase
type: Resource
description: SoyBase is a repository for curated genetics, genomics and related data resources for soybean.
is part of: bioregistry
keyword: agriculture
keyword: comparative genomics
keyword: development
keyword: life science
keyword: obo
keyword: phenotype
keyword: plant breeding
keyword: spider
has local unique identifier example: 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: Jacqueline Campbell
has URI prefix: https://legacy.soybase.org/sbt/search/search_results.php
has resource example: https://legacy.soybase.org/sbt/search/search_results.php
has prefix: soybase

Span
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality.
is part of: bioregistry
keyword: ontology
keyword: upper-level ontology
is deprecated: false
has alternative prefix: bfo11span
has prefix: span

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

SPARQL Operation
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Used for operations in SPARQL, such as ceil() and bound().
is part of: bioregistry
has local unique identifier example: ceil
has provider formatter: http://www.w3.org/ns/sparql#$1
is deprecated: false
has URI prefix: http://www.w3.org/ns/sparql#
has resource example: ceil
has prefix: sparql

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: dna
keyword: genome
keyword: rna
has local unique identifier example: 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
has resource example: http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php
has prefix: spbase

Spider Ontology
type: Resource
description: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).
is part of: bioregistry
git repository: spider-ontology
keyword: anatomy
keyword: behavior
keyword: life science
keyword: obo
keyword: ontology
keyword: spider
has local unique identifier example: 0000001
has provider formatter: http://purl.obolibrary.org/obo/SPD_$1
has local unique identifier pattern: ^\d{7}$
has download URL: spd.owl
is deprecated: false
has responsible: Martin Ramirez
has URI prefix: http://purl.obolibrary.org/obo/SPD_
has resource example: SPD_0000001
has prefix: spd

Swiss Personalized Health Network Schema
type: Resource
contributor: https://orcid.org/0000-0002-3583-7340
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
has local unique identifier example: Allergy
has provider formatter: https://biomedit.ch/rdf/sphn-ontology/sphn#$1
has local unique identifier pattern: ^\S+$
has download URL: 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#
has resource example: Allergy
has prefix: sphn

SPIKE Map
type: Resource
description: SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.
is part of: bioregistry
keyword: dna
keyword: gene expression
keyword: pathway
has local unique identifier example: spike00001
has provider formatter: http://www.cs.tau.ac.il/~spike/maps/$1.html
has local unique identifier pattern: ^spike\d{5}$
is deprecated: false
has responsible: Yosef Shiloh
has URI prefix: https://bioregistry.io/spike.map:
has resource example: spike00001.html
has prefix: spike.map

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

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: dna
keyword: gene
keyword: genome
has local unique identifier example: 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
has resource example: http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi
has prefix: splicenest

Signaling Pathways Project
type: Resource
description: The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways.
is part of: bioregistry
keyword: omics
keyword: transcriptomics
has local unique identifier example: 10.1621/vwN2g2HaX3
has provider formatter: https://www.signalingpathways.org/datasets/dataset.jsf
has local unique identifier pattern: ^10.\w{4}/\w{10}$
is deprecated: false
has responsible: Neil McKenna
has URI prefix: https://www.signalingpathways.org/datasets/dataset.jsf
has resource example: https://www.signalingpathways.org/datasets/dataset.jsf
has prefix: spp

FAIRsharing Subject Ontology
type: Resource
description: The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies.
is part of: bioregistry
git repository: subject-ontology
keyword: agriculture
keyword: biomedical science
keyword: classification
keyword: computer science
keyword: earth science
keyword: environmental science
keyword: fair
keyword: humanities
keyword: life science
keyword: metadata standardization
keyword: metascience
keyword: natural science
keyword: ontology
keyword: resource metadata
keyword: topics
has local unique identifier example: 0000400
has provider formatter: http://www.fairsharing.org/ontology/subject/SRAO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: SRAO.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-7702-4495
has URI prefix: http://www.fairsharing.org/ontology/subject/SRAO_
has resource example: SRAO_0000400
has prefix: srao

Social Science Research Network Article
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for an article/paper at the SSRN
is part of: bioregistry
has local unique identifier example: 1667659
has provider formatter: https://ssrn.com/abstract=$1
is deprecated: false
has URI prefix: https://ssrn.com/abstract=
has resource example: https://ssrn.com/abstract=1667659
has prefix: ssrn.article

Social Science Research Network Author
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for an author at the Social Science Research Network
is part of: bioregistry
keyword: person
keyword: researcher
has local unique identifier example: 112517
has provider formatter: https://ssrn.com/author=$1
has local unique identifier pattern: ^[1-9]\d{0,6}$
is deprecated: false
has URI prefix: https://ssrn.com/author=
has resource example: https://ssrn.com/author=112517
has prefix: ssrn.author

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
has local unique identifier example: 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/
has resource example: mapping justification
has prefix: sssom

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
has local unique identifier example: 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
has resource example: http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi
has prefix: sstoss

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

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
has local unique identifier example: 125768
is deprecated: false
has prefix: stn

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: biomedical science
keyword: ecology
keyword: epidemiology
keyword: life science
keyword: preclinical studies
has local unique identifier example: 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/
has resource example: https://www.storedb.org/
has prefix: storedb

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

StoreDB File
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: File inside StoreDB at University of Cambridge
is part of: bioregistry
has local unique identifier example: 12929
has provider formatter: https://www.storedb.org/store_v3/download.jsp
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.storedb.org/store_v3/download.jsp
has resource example: https://www.storedb.org/store_v3/download.jsp
has prefix: storedb.file

StoreDB Study
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Study inside StoreDB at University of Cambridge
is part of: bioregistry
has local unique identifier example: 1174
has provider formatter: https://www.storedb.org/store_v3/study.jsp
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.storedb.org/store_v3/study.jsp
has resource example: https://www.storedb.org/store_v3/study.jsp
has prefix: storedb.study

StreptomeDB
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifers for natural products isolated or mutasynthesized by bacteria of the genus Streptomyces.
is part of: bioregistry
has local unique identifier example: 15753
has provider formatter: http://streptomedb.vm.uni-freiburg.de/streptomedb/get_drugcard/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Stefan Günther
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: http://streptomedb.vm.uni-freiburg.de/streptomedb/get_drugcard/
has resource example: http://streptomedb.vm.uni-freiburg.de/streptomedb/get_drugcard/15753
has prefix: streptomedb

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

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: dna
keyword: genome
keyword: protein
has local unique identifier example: 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
has resource example: http://genolist.pasteur.fr/SubtiList/genome.cgi
has prefix: subtilist

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: dna
keyword: gene
keyword: life science
keyword: protein
keyword: rna
has local unique identifier example: 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: Jörg Stülke
has URI prefix: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/
has resource example: BSU29180
has prefix: subtiwiki

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

Simplified Upper Level Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Simplified Upper Level Ontology (SULO) is ontology with a minimal set of classes and relations to guide the development of a personal health knowledge graph. [from homepage]
is part of: bioregistry
git repository: sulo
keyword: health
has local unique identifier example: Capability
has provider formatter: https://w3id.org/sulo/$1
is deprecated: false
has responsible: https://orcid.org/0000-0003-4727-9435
has URI prefix: https://w3id.org/sulo/
has resource example: Capability
has prefix: sulo

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
has local unique identifier example: SSF57615
has provider formatter: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: Arun Prasad Pandurangan
has URI prefix: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi
has resource example: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi
has prefix: supfam

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
has local unique identifier example: 6T
has provider formatter: https://netmode.gitlab.io/sustaingraph/$1
is deprecated: false
has URI prefix: https://netmode.gitlab.io/sustaingraph/
has resource example: 6T
has prefix: sustaingraph

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
has download URL: swan.owl
is deprecated: true
has prefix: swan

Software Heritage
type: Resource
description: Software Heritage is the universal archive of software source code.
is part of: bioregistry
has provider formatter: https://archive.softwareheritage.org/browse/swh:$1
has local unique identifier pattern: ^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$
is deprecated: false
has URI prefix: https://archive.softwareheritage.org/browse/swh:
has prefix: swh

SWISS-MODEL Repository
type: Resource
description: The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences.
is part of: bioregistry
keyword: life science
keyword: protein
keyword: proteomics
keyword: structure
has local unique identifier example: P23298
has provider formatter: https://swissmodel.expasy.org/repository/uniprot/$1
has local unique identifier pattern: ^\w+$
provides for: uniprot
is deprecated: false
has responsible: 0000-0003-2715-335X
has URI prefix: https://swissmodel.expasy.org/repository/uniprot/
has resource example: P23298
has prefix: swiss-model

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

Synapse Data Repository
type: Resource
description: Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate.
is part of: bioregistry
has local unique identifier example: 41455251.1
has provider formatter: https://www.synapse.org/Synapse:syn$1
has local unique identifier pattern: ^[0-9]*\.*[0-9]*$
is deprecated: false
has responsible: Kevin Boske
has alternative prefix: syn
has URI prefix: https://www.synapse.org/Synapse:syn
has resource example: Synapse:syn41455251.1
has prefix: synapse

Synthetic Binding Proteins Binding Target
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for the binding targets of synthetic binding proteins (SBP), describing the specific molecules or complexes that SBPs interact with for their intended applications
is part of: bioregistry
has local unique identifier example: st00576
has provider formatter: http://synbip.idrblab.net/data/bts/details/$1
has local unique identifier pattern: ^st\d+$
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/bts/details/
has resource example: st00576
has prefix: synbip.bts

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
has local unique identifier example: 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/
has resource example: mt002305
has prefix: synbip.epitope

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
has local unique identifier example: 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/
has resource example: ps048
has prefix: synbip.pss

Synthetic Binding Protein
type: Resource
contributor: https://orcid.org/0009-0009-5240-7463
description: Identifiers for synthetic binding proteins, providing detailed information on their sequences, structures, targets, and functional properties for research, diagnostic, and therapeutic applications.
is part of: bioregistry
has local unique identifier example: sbp000002
has provider formatter: http://synbip.idrblab.net/data/sbp/details/$1
has local unique identifier pattern: ^sbp\d+$
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/details/
has resource example: sbp000002
has prefix: synbip.sbp

Gemina Symptom Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
is deprecated: true
has prefix: syoid

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: life science
keyword: molecule
keyword: protein
has local unique identifier example: T3D0001
has provider formatter: http://www.t3db.org/toxins/$1
has local unique identifier pattern: ^T3D\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-3207-2434
has URI prefix: http://www.t3db.org/toxins/
has resource example: T3D0001
has prefix: t3db

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

Terminology of Anatomy of Human Embryology
type: Resource
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/TAHE_$1
is deprecated: true
has responsible: Pierre Sprumont
has URI prefix: http://purl.obolibrary.org/obo/TAHE_
has prefix: tahe

Terminology of Anatomy of Human Histology
type: Resource
is part of: bioregistry
keyword: obo
keyword: ontology
has provider formatter: http://purl.obolibrary.org/obo/TAHH_$1
is deprecated: true
has responsible: Pierre Sprumont
has URI prefix: http://purl.obolibrary.org/obo/TAHH_
has prefix: tahh

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
has local unique identifier example: 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
has resource example: http://arabidopsis.org/servlets/TairObject
has prefix: tair.gene

The Arabidopsis Information Resource
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. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.
is part of: bioregistry
keyword: genome
has local unique identifier example: 2200950
has provider formatter: https://www.arabidopsis.org/locus
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: 0000-0003-3871-858X
has URI prefix: https://www.arabidopsis.org/locus
has resource example: https://www.arabidopsis.org/locus
has prefix: tair.locus

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
has local unique identifier example: 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
has resource example: https://www.arabidopsis.org/protein
has prefix: tair.protein

TarBase
type: Resource
description: TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used.
is part of: bioregistry
keyword: biomedical science
keyword: life science
has local unique identifier example: hsa-let-7a-2-3p
has provider formatter: http://diana.imis.athena-innovation.gr/DianaTools/index.php
has local unique identifier pattern: ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)?$
is deprecated: false
has URI prefix: http://diana.imis.athena-innovation.gr/DianaTools/index.php
has resource example: http://diana.imis.athena-innovation.gr/DianaTools/index.php
has prefix: tarbase

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

Tick Cell Biobank
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A cell line collection
is part of: bioregistry
has local unique identifier example: 2966
has provider formatter: https://www.pirbright.ac.uk/node/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://www.pirbright.ac.uk/node/
has resource example: https://www.pirbright.ac.uk/node/2966
has prefix: tcb

The Cell Cycle DB
type: Resource
description: Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle
is part of: bioregistry
keyword: gene
keyword: pathway
keyword: protein
has local unique identifier example: TP53
has provider formatter: http://www.itb.cnr.it/cellcycle/gene_rep.php
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.itb.cnr.it/cellcycle/gene_rep.php
has resource example: http://www.itb.cnr.it/cellcycle/gene_rep.php
has prefix: tccd

Access to Biological Collection Data Schema
type: Resource
description: The base ontology of the ABCD Standard.
is part of: bioregistry
keyword: ess
keyword: fair data spaces
keyword: life sciences, biology
has local unique identifier example: Accession
is deprecated: false
has prefix: tdwg.abcd

format controlled vocabulary
type: Resource
description: Controlled vocabulary for the Dublin Core term format
is part of: bioregistry
keyword: fair data spaces
keyword: life sciences, biology
has local unique identifier example: e001
has provider formatter: http://rs.tdwg.org/format/$1
is deprecated: false
has URI prefix: http://rs.tdwg.org/format/
has resource example: e001
has prefix: tdwg.format

TDWG Taxon Rank LSID Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Ontology describing a controlled vocabulary for taxon ranks.
is part of: bioregistry
git repository: ontology
keyword: ontology
has local unique identifier example: InfragenericTaxon
has provider formatter: http://rs.tdwg.org/ontology/voc/TaxonRank#$1
has download URL: TaxonRank.rdf
is deprecated: false
has responsible: Roger Hyam
has URI prefix: http://rs.tdwg.org/ontology/voc/TaxonRank#
has resource example: InfragenericTaxon
has prefix: tdwg.taxonrank

Vocabulary Maintenance Standard
type: Resource
description: The TDWG Vocabulary Maintenance Standard consists of a single document: the Vocabulary Maintenance Specification.
is part of: bioregistry
keyword: fair data spaces
keyword: life sciences, biology
has provider formatter: http://www.tdwg.org/standards/642$1
is deprecated: false
has URI prefix: http://www.tdwg.org/standards/642
has prefix: tdwg.vms

Terminologia Embryologica
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]
is part of: bioregistry
has local unique identifier example: E5.11.2.0.0.0.4
is deprecated: false
has prefix: te

Classification of Transcription Factors in Mammalia
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here..
is part of: bioregistry
keyword: binding
keyword: binding site
keyword: bioinformatics
keyword: expression data
keyword: phylogenetics
keyword: transcription factor
keyword: transcription factor binding site prediction
keyword: transcriptomics
has local unique identifier example: 2.1.1
has provider formatter: http://tfclass.bioinf.med.uni-goettingen.de/
is deprecated: false
has responsible: Edgar Wingender
has URI prefix: http://tfclass.bioinf.med.uni-goettingen.de/
has resource example: http://tfclass.bioinf.med.uni-goettingen.de/
has prefix: tfclass

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

Mosquito gross anatomy ontology
type: Resource
description: A structured controlled vocabulary of the anatomy of mosquitoes.
is part of: bioregistry
git repository: TGMA
keyword: anatomy
keyword: life science
keyword: mosquito
keyword: obo
keyword: ontology
has local unique identifier example: 0000984
has provider formatter: http://purl.obolibrary.org/obo/TGMA_$1
has local unique identifier pattern: ^\d{7}$
has download URL: tgma.owl
is deprecated: true
has responsible: https://orcid.org/0000-0002-1635-4810
has URI prefix: http://purl.obolibrary.org/obo/TGMA_
has resource example: TGMA_0000984
has prefix: tgma

Terminologia Histologica
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]
is part of: bioregistry
keyword: biology
keyword: cytology
keyword: histology
keyword: life sciences
has local unique identifier example: H3.03.00.0.00007
has local unique identifier pattern: ^H\d\.\d{2}\.\d{2}\.\d\.\d{5}$
is deprecated: false
has prefix: th

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
has local unique identifier example: 23
has provider formatter: https://www.emouseatlas.org/emap/ema/DAOAnatomyJSP/anatomy.html
has local unique identifier pattern: ^\d+[a-d]?$
is deprecated: false
appears in: emaps
appears in: mmusdv
has responsible: https://orcid.org/0000-0002-0956-8634
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
has resource example: https://www.emouseatlas.org/emap/ema/DAOAnatomyJSP/anatomy.html
has prefix: theiler

Thermo Fisher Scientific
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: ThermoFisher is a life sciences supply vendor.
is part of: bioregistry
keyword: biology
keyword: chemistry
keyword: life sciences
keyword: vendor
has local unique identifier example: OSR00185W
has provider formatter: https://www.thermofisher.com/antibody/product/$1
has local unique identifier pattern: ^\w+$
is deprecated: false
has URI prefix: https://www.thermofisher.com/antibody/product/
has resource example: OSR00185W
has prefix: thermofisher

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: chemical and environmental engineering
keyword: earth sciences
keyword: ess
keyword: horticulture
has local unique identifier example: 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#
has resource example: AbioticStressTrait
has prefix: tib.cgo

Modular Ontology Modeling for Food Supply Chains
type: Resource
description: Modular Ontology Modeling for Food Supply Chains.
is part of: bioregistry
keyword: coypu
keyword: economics
has local unique identifier example: Agent
has provider formatter: http://dase.cs.ksu.edu/ontology/food-traceability#$1
is deprecated: false
has URI prefix: http://dase.cs.ksu.edu/ontology/food-traceability#
has resource example: Agent
has prefix: tib.fto

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
has local unique identifier example: arc
has provider formatter: https://purl.org/linsearch/$1
is deprecated: false
has URI prefix: https://purl.org/linsearch/
has resource example: arc
has prefix: tib.linsearch

Analytical methods for geochemistry
type: Resource
description: This concept scheme contains skos concepts for analysis methods used to produce observation results with information about the physical properties, chemical or isotopic composition, crystallography, or molecular structure of material samples. Based on spreadsheet compilation of method vocabularies from Geo.X, GEOROC, PetDB and OSIRIS-REx. Definitions added and updated based on web research, and SKOS serialization by S.M. Richard. Note that although there are high-level method categories for 'Physical property measurements' and the 'Bioanalytical method', these are placeholders and only include a few examples that are relevant to analytical methods in geo- or cosmochemistry.
is part of: bioregistry
keyword: earth sciences
keyword: ess
has local unique identifier example: acceleratormassspectrometry
has provider formatter: https://w3id.org/geochem/1.0/analyticalmethod/$1
is deprecated: false
has URI prefix: https://w3id.org/geochem/1.0/analyticalmethod/
has resource example: acceleratormassspectrometry
has prefix: tib.meth

TIB Terminology Service
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An instance of the EBI Lookup Service deployed by TIB
is part of: bioregistry
has local unique identifier example: abcd
has provider formatter: https://terminology.tib.eu/ts/ontologies/$1
is deprecated: false
has responsible: https://orcid.org/0000-0001-5246-9351
has URI prefix: https://terminology.tib.eu/ts/ontologies/
has resource example: abcd
has prefix: tib.ts

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
has local unique identifier example: 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
has resource example: https://www.ncbi.nlm.nih.gov/cdd
has prefix: tigrfam

Tohoku University cell line catalog
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells.
is part of: bioregistry
has local unique identifier example: 0221
has provider formatter: http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://bioregistry.io/tkg:
has resource example: 0221.html
has prefix: tkg

Telethon Network of Genetic Biobanks
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: 67035
has provider formatter: https://biobanknetwork.telethon.it/Sample/View
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://biobanknetwork.telethon.it/Sample/View
has resource example: https://biobanknetwork.telethon.it/Sample/View
has prefix: tngb

TogoID Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
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/)
is part of: bioregistry
git repository: togoid-config
keyword: ontology
has local unique identifier example: AffyProbeset
has provider formatter: https://togoid.dbcls.jp/#$1
has download URL: togoid-ontology.ttl
is deprecated: false
has responsible: https://orcid.org/0000-0003-2391-0384
has URI prefix: https://togoid.dbcls.jp/#
has resource example: AffyProbeset
has prefix: togoid

TogoVar
type: Resource
description: TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them.
is part of: bioregistry
has local unique identifier example: tgv139393198
has provider formatter: https://grch38.togovar.org/variant/$1
has local unique identifier pattern: ^tgv[0-9]+$
is deprecated: false
has URI prefix: https://grch38.togovar.org/variant/
has resource example: tgv139393198
has prefix: togovar

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:
has prefix: tokue

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

Topology Data Bank of Transmembrane Proteins
type: Resource
description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases.
is part of: bioregistry
keyword: protein
has local unique identifier example: AP00378
has provider formatter: http://topdb.enzim.hu/
has local unique identifier pattern: ^[A-Z0-9]+$
is deprecated: false
has URI prefix: http://topdb.enzim.hu/
has resource example: http://topdb.enzim.hu/
has prefix: topdb

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

ToxoDB
type: Resource
description: ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
is part of: bioregistry
has local unique identifier example: TGME49_053730
has provider formatter: http://toxodb.org/toxo/showRecord.do
has local unique identifier pattern: ^\w+$
is deprecated: false
has URI prefix: http://toxodb.org/toxo/showRecord.do
has resource example: http://toxodb.org/toxo/showRecord.do
has prefix: toxoplasma

TransportDB
type: Resource
description: TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.
is part of: bioregistry
keyword: protein
has local unique identifier example: MMP0523
has provider formatter: http://www.membranetransport.org/protein.php
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.membranetransport.org/protein.php
has resource example: http://www.membranetransport.org/protein.php
has prefix: transportdb

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
has local unique identifier example: 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/
has resource example: TR0000001
has prefix: transyt

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
has local unique identifier example: 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
has resource example: http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi
has prefix: tred

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: classification
keyword: phylogenetics
keyword: phylogenomics
has local unique identifier example: 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: Rutger Vos
has URI prefix: https://bioregistry.io/treebase:
has resource example: http://purl.org/phylo/treebase/phylows/study/TB2:S1000
has prefix: treebase

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
has local unique identifier example: 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/
has resource example: TF101014
has prefix: treefam

TreeHub
type: Resource
contributor: https://orcid.org/0009-0000-6974-6386
description: TreeHub is a taxonomical database for trees. TreeHub contains extracted phylogenetic data and integrates relevant species information for each identifier.
is part of: bioregistry
keyword: dendrology
keyword: taxonomy
keyword: tree
has local unique identifier example: T00232742
has provider formatter: https://www.plantplus.cn/treehub/tree/$1
has local unique identifier pattern: ^T\d{8}$
is deprecated: false
has responsible: Hui Wu
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://www.plantplus.cn/treehub/tree/
has resource example: T00232742
has prefix: treehub

tricdb
type: Resource
description: Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of Tri©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine.
is part of: bioregistry
has provider formatter: http://biomeddb.org/Disease/Details
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 URI prefix: http://biomeddb.org/Disease/Details
has resource example: http://biomeddb.org/Disease/Details
has prefix: tricdb

TrichDB
type: Resource
description: TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
is part of: bioregistry
keyword: genomics
has local unique identifier example: TVAG_386080
has provider formatter: http://trichdb.org/trichdb/showRecord.do
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4446-6200
has URI prefix: http://trichdb.org/trichdb/showRecord.do
has resource example: http://trichdb.org/trichdb/showRecord.do
has prefix: trichdb

TriTrypDB
type: Resource
description: TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
is part of: bioregistry
keyword: comparative genomics
keyword: genomics
keyword: infectious disease medicine
has local unique identifier example: Tb927.8.620
has provider formatter: http://tritrypdb.org/tritrypdb/showRecord.do
has local unique identifier pattern: ^\w+(\.)?\w+(\.)?\w+$
is deprecated: false
has responsible: https://orcid.org/0000-0003-4446-6200
has URI prefix: http://tritrypdb.org/tritrypdb/showRecord.do
has resource example: http://tritrypdb.org/tritrypdb/showRecord.do
has prefix: tritrypdb

tRNA Gene Database
type: Resource
description: The tRNA Gene DataBase Curated by Experts "tRNADB-CE" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones.
is part of: bioregistry
keyword: dna
keyword: gene
keyword: genome
keyword: rna
has local unique identifier example: 265912
has provider formatter: http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi
has resource example: http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi
has prefix: trnadbce

Tetrahymena Stock Center
type: Resource
description: Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID]
is part of: bioregistry
keyword: biology
keyword: cell
keyword: cellular
keyword: culture
keyword: eukaryota
keyword: genetics
keyword: model
keyword: molecular
keyword: protozoan
keyword: repository
keyword: research
keyword: tetrahymena thermophila
has local unique identifier example: SD00043
has provider formatter: https://tetrahymena.vet.cornell.edu/display.php
has local unique identifier pattern: ^SD\d+$
is deprecated: false
has URI prefix: https://tetrahymena.vet.cornell.edu/display.php
has resource example: https://tetrahymena.vet.cornell.edu/display.php
has prefix: tsc

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
has local unique identifier example: 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: Zhen Yang
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: http://118.178.132.53/tsRNADisease/detail.php
has resource example: http://118.178.132.53/tsRNADisease/detail.php
has prefix: tsrnadisease

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
has local unique identifier example: 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/
has resource example: D0N5OV
has prefix: ttd.drug

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
has local unique identifier example: 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/
has resource example: t59328
has prefix: ttd.target

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

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: obo
keyword: ontology
has local unique identifier example: 0002066
has provider formatter: http://purl.obolibrary.org/obo/TXPO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: txpo.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-9673-1283
has URI prefix: http://purl.obolibrary.org/obo/TXPO_
has resource example: TXPO_0002066
has prefix: txpo

UBERON Issue Tracker
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An issue on the UBERON GitHub Issue tracker
is part of: bioregistry
has local unique identifier example: 530
has provider formatter: https://github.com/obophenotype/uberon/issues/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://github.com/obophenotype/uberon/issues/
has resource example: https://github.com/obophenotype/uberon/issues/530
has prefix: uberon.issue

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
has local unique identifier example: 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
has resource example: http://www.ubio.org/browser/details.php
has prefix: ubio.namebank

Uberon Property
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
is deprecated: true
has alternative prefix: UBPROP
has alternative prefix: UBREL
has prefix: ubprop

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
has local unique identifier example: N21
has local unique identifier pattern: ^\w\d+$
is deprecated: false
has prefix: ucas

UK Provider Reference Number
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for an educational organization issued by the UK Register of Learning Providers
is part of: bioregistry
has local unique identifier example: 10007835
has provider formatter: https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails
has local unique identifier pattern: ^[1-9]\d*$
is deprecated: false
has alternative prefix: ukprns
has URI prefix: https://bioregistry.io/ukprn:
has resource example: https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails
has prefix: ukprn

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
has local unique identifier example: 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
has resource example: http://eawag-bbd.ethz.ch/servlets/pageservlet
has prefix: umbbd.enzyme

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
has local unique identifier example: 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
has resource example: http://umbbd.ethz.ch/servlets/pageservlet
has prefix: umbbd.pathway

EAWAG Biocatalysis/Biodegradation Database reaction
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 reaction information.
is part of: bioregistry
has local unique identifier example: r0001
has provider formatter: http://eawag-bbd.ethz.ch/servlets/pageservlet
has local unique identifier pattern: ^r\d+$
is deprecated: false
has alternative prefix: UM-BBD_reactionID
has URI prefix: http://eawag-bbd.ethz.ch/servlets/pageservlet
has resource example: http://eawag-bbd.ethz.ch/servlets/pageservlet
has prefix: umbbd.reaction

EAWAG Biocatalysis/Biodegradation Database rule
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 UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules.
is part of: bioregistry
has local unique identifier example: bt0001
has provider formatter: http://www.umbbd.ethz.ch/servlets/rule.jsp
has local unique identifier pattern: ^bt\d+$
is deprecated: false
has alternative prefix: UM-BBD_ruleID
has URI prefix: http://www.umbbd.ethz.ch/servlets/rule.jsp
has resource example: http://www.umbbd.ethz.ch/servlets/rule.jsp
has prefix: umbbd.rule

Unified Medical Language System Atomic Unique Identifier
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus.
is part of: bioregistry
has local unique identifier example: A0118748
has local unique identifier pattern: ^A\d+$
is deprecated: false
has alternative prefix: UMLS_ICD9CM_2005_AUI
has prefix: umls.aui

UniCarb-DB
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: UniCarb-DB stores structural and mass spectrometry (MS) glycomic data, and has now grown to be one of the largest experimental glycomic MS databases. Identifiers correspond to individual glycan structures and corresponding MS spectra.
is part of: bioregistry
has local unique identifier example: 91
has provider formatter: https://unicarb-db.expasy.org/msData/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Niclas Karlsson
has reviewer: https://orcid.org/0000-0001-9439-5346
has URI prefix: https://unicarb-db.expasy.org/msData/
has resource example: https://unicarb-db.expasy.org/msData/91
has prefix: unicarbdb

UniChem compound
type: Resource
description: identifier of a compound in the UniChem database
is part of: bioregistry
has local unique identifier example: 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
has resource example: https://www.ebi.ac.uk/unichem/compoundsources
has prefix: unichem

UniGene
type: Resource
description: A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
is part of: bioregistry
keyword: dna
keyword: gene
keyword: gene expression
keyword: life science
keyword: protein
has local unique identifier example: 4900
has provider formatter: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi
has resource example: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi
has prefix: unigene

Unimod protein modification database for mass spectrometry
type: Resource
description: Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).
is part of: bioregistry
keyword: bioinformatics
keyword: ontology
has local unique identifier example: 1200
has provider formatter: http://www.unimod.org/modifications_view.php
has local unique identifier pattern: ^\d+$
has download URL: unimod.owl
is deprecated: false
has responsible: John Cottrell
has URI prefix: http://www.unimod.org/modifications_view.php
has resource example: http://www.unimod.org/modifications_view.php
has prefix: unimod

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
has local unique identifier example: 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
has resource example: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc
has prefix: unipathway.compound

UniPathway Reaction
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 individual reactions.
is part of: bioregistry
has local unique identifier example: UCR00226
has provider formatter: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr
has local unique identifier pattern: ^UCR\d{5}$
is deprecated: false
has URI prefix: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr
has resource example: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr
has prefix: unipathway.reaction

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
has local unique identifier example: ARBA00000001
has provider formatter: https://www.uniprot.org/arba/$1
has local unique identifier pattern: ^ARBA\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6982-4660
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: arba
has URI prefix: https://www.uniprot.org/arba/
has resource example: ARBA00000001
has prefix: uniprot.arba

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
has local unique identifier example: 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: https://orcid.org/0000-0002-6982-4660
has alternative prefix: UPPRO
has URI prefix: http://purl.uniprot.org/annotation/
has resource example: PRO_0000016681
has prefix: uniprot.chain

Uniprot Core Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Properties and classes used for protein annotation
is part of: bioregistry
keyword: biology
keyword: ontology
has local unique identifier example: certain
has provider formatter: http://purl.uniprot.org/core/$1
has download URL: core.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6982-4660
has URI prefix: http://purl.uniprot.org/core/
has resource example: certain
has prefix: uniprot.core

UniProt Diseases
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary.
is part of: bioregistry
keyword: ontology
has local unique identifier example: DI-04240
has provider formatter: https://www.uniprot.org/diseases/$1
has local unique identifier pattern: ^DI-\d{5}$
has download URL: https://rest.uniprot.org/diseases/stream
is deprecated: false
has responsible: https://orcid.org/0000-0002-6982-4660
has alternative prefix: DI
has alternative prefix: SP_DI
has URI prefix: https://www.uniprot.org/diseases/
has resource example: DI-04240
has prefix: uniprot.disease

UniProt journal
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: identifier for a scientific journal, in the UniProt database
is part of: bioregistry
keyword: journal
keyword: publication
has local unique identifier example: 3546
has provider formatter: https://www.uniprot.org/journals/$1
has local unique identifier pattern: ^\d{4}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6982-4660
has URI prefix: https://www.uniprot.org/journals/
has resource example: https://www.uniprot.org/journals/3546
has prefix: uniprot.journal

UniProt Keywords
type: Resource
description: UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries.
is part of: bioregistry
keyword: classification
keyword: ontology
has local unique identifier example: KW-1273
has provider formatter: https://www.uniprot.org/keywords/$1
has local unique identifier pattern: ^KW-\d{4}$
has download URL: https://rest.uniprot.org/keywords/stream
is deprecated: false
has responsible: https://orcid.org/0000-0002-6982-4660
has alternative prefix: SP_KW
has alternative prefix: UniProtKB-KW
has alternative prefix: uniprot.keyword
has alternative prefix: uniprot.kw
has URI prefix: https://www.uniprot.org/keywords/
has resource example: KW-1273
has prefix: uniprot.keyword

UniProt Subcellular Locations
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms.
is part of: bioregistry
keyword: ontology
has local unique identifier example: SL-0002
has provider formatter: https://www.uniprot.org/locations/$1
has local unique identifier pattern: ^SL-\d+$
has download URL: https://rest.uniprot.org/locations/stream
is deprecated: false
has responsible: https://orcid.org/0000-0002-6982-4660
has alternative prefix: SP_SL
has alternative prefix: UPLOC
has alternative prefix: UniProtKB-SubCell
has URI prefix: https://www.uniprot.org/locations/
has resource example: SL-0002
has prefix: uniprot.location

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
has local unique identifier example: 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: https://orcid.org/0000-0002-6982-4660
has reviewer: https://orcid.org/0000-0003-2473-2313
has URI prefix: https://www.uniprot.org/uniprotkb/
has resource example: BRAF HUMAN
has prefix: uniprot.mnemonic

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: biochemistry
keyword: ontology
keyword: post-translational modification
keyword: structural biology
has local unique identifier example: PTM-0450
has provider formatter: https://biopragmatics.github.io/providers/uniprot.ptm/$1
has local unique identifier pattern: ^PTM-\d{4}$
has download URL: uniprot.ptm.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-6982-4660
has alternative prefix: PTM
has URI prefix: https://biopragmatics.github.io/providers/uniprot.ptm/
has resource example: PTM-0450
has prefix: uniprot.ptm

UniProt Resource
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources.
is part of: bioregistry
has local unique identifier example: DB-0174
has provider formatter: https://www.uniprot.org/database/$1
has local unique identifier pattern: ^DB-\d{4}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6982-4660
has alternative prefix: uniprot.database
has alternative prefix: uniprot.db
has URI prefix: https://www.uniprot.org/database/
has resource example: DB-0174
has prefix: uniprot.resource

Tissue List
type: Resource
description: The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified.
is part of: bioregistry
has local unique identifier example: TS-0285
has provider formatter: https://www.uniprot.org/tissues/$1
has local unique identifier pattern: ^TS-\d{4}$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6982-4660
has URI prefix: https://www.uniprot.org/tissues/
has resource example: TS-0285
has prefix: uniprot.tissue

UniProt Variants
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species.
is part of: bioregistry
has local unique identifier example: 068078
has provider formatter: http://purl.uniprot.org/annotation/VAR_$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: https://orcid.org/0000-0002-6982-4660
has alternative prefix: SP_VAR
has alternative prefix: UPVAR
has alternative prefix: UniProtKB_VAR
has URI prefix: http://purl.uniprot.org/annotation/VAR_
has resource example: VAR_068078
has prefix: uniprot.var

UniRule
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites.
is part of: bioregistry
has local unique identifier example: UR000124451
has provider formatter: https://www.uniprot.org/unirule/$1
is deprecated: false
has responsible: https://orcid.org/0000-0002-6982-4660
has URI prefix: https://www.uniprot.org/unirule/
has resource example: UR000124451
has prefix: unirule

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: gene
keyword: protein
has local unique identifier example: 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
has resource example: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi
has prefix: unists

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

Universal Natural Products Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
keyword: compound
keyword: natural product
keyword: small molecule
is deprecated: true
has prefix: unpd

Unified Phenotype Ontology
type: Resource
description: The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
is part of: bioregistry
git repository: upheno
keyword: data analysis
keyword: evolutionary biology
keyword: expression data
keyword: obo
keyword: omics
keyword: ontology
keyword: phenomics
keyword: phenotype
has provider formatter: http://purl.obolibrary.org/obo/UPHENO_$1
has download URL: upheno.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-8361-2795
has URI prefix: http://purl.obolibrary.org/obo/UPHENO_
has prefix: upheno

UR-DBMS Syndrome Finder
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
has local unique identifier example: 3567
has provider formatter: http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php
has local unique identifier pattern: ^\d+$
is deprecated: true
appears in: nando
has responsible: Kenji Naritomi
has URI prefix: http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php
has resource example: http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php
has prefix: urdbms.syndromefinder

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: antitoxin
keyword: bacterin
keyword: bacterin-toxoid
keyword: diagnostic product
keyword: toxoid
keyword: vaccine
has local unique identifier example: 1011.00
has local unique identifier pattern: ^[A-Z0-9]{4}\.[A-Z0-9]{2}$
is deprecated: false
appears in: vo
has identifier space owner: 0599wfz09
has prefix: usda.cvb.pcn

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
has local unique identifier example: 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
has resource example: http://patft.uspto.gov/netacgi/nph-Parser
has prefix: uspto

UTRdb
type: Resource
description: A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets.
is part of: bioregistry
has local unique identifier example: 5UTR_107_ENST00000517291.2
has provider formatter: https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb
has local unique identifier pattern: ^([3-5][A-Z])\w+[^A-Z][0-9]$
is deprecated: false
has URI prefix: https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb
has resource example: https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb
has prefix: utrdb

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: biology
keyword: immunology
keyword: vaccines
has local unique identifier example: 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
has resource example: https://vac.niaid.nih.gov/view
has prefix: vac

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
has local unique identifier example: 2h6o
has provider formatter: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1
has local unique identifier pattern: ^[A-Za-z0-9\/]+$
provides for: pdb
is deprecated: false
has responsible: David Sehnal
has URI prefix: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/
has resource example: 2h6o
has prefix: validatordb

Veterans Administration National Drug File
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.
is part of: bioregistry
keyword: biomedical science
keyword: drug
keyword: drug interaction
keyword: ontology
keyword: pharmacology
has local unique identifier example: 4019477
has provider formatter: http://purl.bioontology.org/ontology/VANDF/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Michael Lincoln
has URI prefix: http://purl.bioontology.org/ontology/VANDF/
has resource example: http://purl.bioontology.org/ontology/VANDF/4019477
has prefix: vandf

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

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
has local unique identifier example: humIGHV025
has provider formatter: http://www.vbase2.org/vgene.php
has local unique identifier pattern: ^\w+$
is deprecated: false
has responsible: Werner Müller
has URI prefix: http://www.vbase2.org/vgene.php
has resource example: http://www.vbase2.org/vgene.php
has prefix: vbase2

Vertebrate Breed Ontology Issue Tracker
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: An issue on the Vertebrate Breed Ontology GitHub issue tracker
is part of: bioregistry
has local unique identifier example: 126
has provider formatter: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/
has resource example: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126
has prefix: vbo.issue

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
has local unique identifier example: 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
has resource example: http://vbrc.org/gene_detail.asp
has prefix: vbrc

Virtual Contact File
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: vCard is a specification developed by the Internet Engineering Task Force (IETF) for the description of people and organisations
is part of: bioregistry
keyword: ontology
keyword: people
has local unique identifier example: Agent
has provider formatter: http://www.w3.org/2006/vcard/ns#$1
has download URL: ns
is deprecated: false
has responsible: Renato Iannella
has URI prefix: http://www.w3.org/2006/vcard/ns#
has resource example: Agent
has prefix: vcard

VCell Published Models
type: Resource
description: Models developed with the Virtual Cell (VCell) software prorgam.
is part of: bioregistry
has local unique identifier example: 201022999
has provider formatter: https://vcell.org/biomodel-$1
has local unique identifier pattern: ^\d{5,}$
is deprecated: false
has URI prefix: https://vcell.org/biomodel-
has resource example: biomodel-201022999
has prefix: vcell

Vienna Drosophila Resource Center
type: Resource
description: Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID]
is part of: bioregistry
keyword: biomaterial supply resource
keyword: drosophila
keyword: fly lines
has local unique identifier example: 100291
has provider formatter: https://shop.vbc.ac.at/vdrc_store/$1.html
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://bioregistry.io/vdrc:
has resource example: 100291.html
has prefix: vdrc

Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens
type: Resource
description: VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host.
is part of: bioregistry
keyword: comparative genomics
keyword: functional genomics
keyword: gene
keyword: genome
keyword: genomics
keyword: population dynamics
keyword: population genetics
keyword: protein
has local unique identifier example: ISCW007415
has provider formatter: https://vectorbase.org/gene/$1
has local unique identifier pattern: ^\D{4}\d{6}(\-\D{2})?$
is deprecated: false
has responsible: David Starns
has URI prefix: https://vectorbase.org/gene/
has resource example: ISCW007415
has prefix: vectorbase

Vertebrate Genome Annotation Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A repository for high-quality gene models produced by the manual annotation of vertebrate genomes.
is part of: bioregistry
keyword: genome
keyword: life science
has local unique identifier example: OTTHUMG00000169812
has provider formatter: https://bioregistry.io/vega:$1
is deprecated: true
has responsible: Jennifer L Harrow
has alternative prefix: VEGA
has URI prefix: https://bioregistry.io/vega:
has resource example: vega:OTTHUMG00000169812
has prefix: vega

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
has local unique identifier example: 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/
has resource example: VB.Ob.3736.GRSM125
has prefix: vegbank

Veterinary Nomenclature
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems.
is part of: bioregistry
has local unique identifier example: 12969
has local unique identifier pattern: ^\d+$
is deprecated: false
appears in: vbo
has responsible: David Brodbelt
has prefix: venom

Virtual Fly Brain
type: Resource
description: An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.
is part of: bioregistry
keyword: life science
keyword: neurobiology
has local unique identifier example: 00000001
has provider formatter: http://virtualflybrain.org/reports/$1
has local unique identifier pattern: ^[0-9a-zA-Z]{8}$
is deprecated: false
has responsible: Robert Court
has URI prefix: http://virtualflybrain.org/reports/
has resource example: http://virtualflybrain.org/reports/00000001
has prefix: vfb

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

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

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
has local unique identifier example: 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: https://orcid.org/0000-0003-1818-8243
has URI prefix: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/
has resource example: !/vgnc id/3792
has prefix: vgnc

Vertebrate Homologous Organ Group Ontology
type: Resource
description: vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 "historical homology". Each mapping has been manually reviewed, and we provide confidence codes and references when available.
is part of: bioregistry
keyword: anatomy
keyword: development
keyword: obo
keyword: ontology
has local unique identifier example: 0000411
has provider formatter: http://purl.obolibrary.org/obo/VHOG_$1
has local unique identifier pattern: ^\d{7}$
has download URL: vhog.owl
is deprecated: true
has responsible: Bgee team
has alternative prefix: VHOG_RETIRED
has URI prefix: http://purl.obolibrary.org/obo/VHOG_
has resource example: VHOG_0000411
has prefix: vhog

VIAF cluster ID
type: Resource
description: The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.
is part of: bioregistry
keyword: centrally registered identifier
keyword: subject agnostic
has local unique identifier example: 75121530
has provider formatter: http://viaf.org/viaf/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: http://viaf.org/viaf/
has resource example: http://viaf.org/viaf/75121530
has prefix: viaf

Virus Infectious Disease Ontology
type: Resource
description: The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.
is part of: bioregistry
git repository: ido-virus
keyword: ontology
has local unique identifier example: 0001114
has provider formatter: http://purl.obolibrary.org/obo/VIDO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: vido.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-1118-1738
has URI prefix: http://purl.obolibrary.org/obo/VIDO_
has resource example: VIDO_0001114
has prefix: vido

ViolinNet
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Defunct vaccine information source from the He Lab
is part of: bioregistry
has local unique identifier example: 4140
has provider formatter: http://www.violinet.org/vaxquery/vaccine_detail.php
has local unique identifier pattern: ^\d+$
is deprecated: true
appears in: oae
has alternative prefix: violinID
has alternative prefix: violinId
has URI prefix: http://www.violinet.org/vaxquery/vaccine_detail.php
has resource example: http://www.violinet.org/vaxquery/vaccine_detail.php
has prefix: violinnet

VIPERdb
type: Resource
description: VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration.
is part of: bioregistry
keyword: small molecule
keyword: structure
has local unique identifier example: 2c6s
has provider formatter: https://viperdb.org/Info_Page.php
provides for: pdb
is deprecated: false
has URI prefix: https://viperdb.org/Info_Page.php
has resource example: https://viperdb.org/Info_Page.php
has prefix: viperdb

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: biomedical science
keyword: epidemiology
keyword: genomics
keyword: immunology
keyword: life science
keyword: proteomics
keyword: virology
has local unique identifier example: 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:
has prefix: vipr

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: epidemiology
keyword: life science
keyword: molecular biology
keyword: virology
keyword: virus
has local unique identifier example: 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/
has resource example: https://viralzone.expasy.org/992
has prefix: viralzone

VirGen
type: Resource
description: VirGen a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences.
is part of: bioregistry
keyword: genome
has local unique identifier example: AY321118
is deprecated: false
has prefix: virgen

Vir-Mir db
type: Resource
description: A database containing predicted viral miRNA candidate hairpins.
is part of: bioregistry
keyword: rna
keyword: structure
has local unique identifier example: 11002
has provider formatter: http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi
provides for: ncbitaxon
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi
has resource example: http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi
has prefix: virmirdb

VirOligo
type: Resource
description: The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place.
is part of: bioregistry
keyword: small molecule
has local unique identifier example: BM0456
has provider formatter: http://viroligo.okstate.edu/main.php
is deprecated: false
has URI prefix: http://viroligo.okstate.edu/main.php
has resource example: http://viroligo.okstate.edu/main.php
has prefix: viroligo

VIRsiRNA
type: Resource
description: The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.
is part of: bioregistry
has local unique identifier example: virsi1909
has provider formatter: http://crdd.osdd.net/servers/virsirnadb/record.php
has local unique identifier pattern: ^virsi\d+$
is deprecated: false
has URI prefix: http://crdd.osdd.net/servers/virsirnadb/record.php
has resource example: http://crdd.osdd.net/servers/virsirnadb/record.php
has prefix: virsirna

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
has local unique identifier example: 438782
has provider formatter: https://www.genome.jp/virushostdb/$1
provides for: ncbitaxon
is deprecated: false
has responsible: Hiroyuki Ogata
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: https://www.genome.jp/virushostdb/
has resource example: https://www.genome.jp/virushostdb/438782
has prefix: virushostdb

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

Vitro Application Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Vitro is a full stack framework for building semantic web applications. It is not domain specific.
is part of: bioregistry
git repository: Vitro
keyword: ontology
has local unique identifier example: descriptionAnnot
has provider formatter: http://vitro.mannlib.cornell.edu/ns/vitro/0.7#$1
has download URL: vitro-0.7.owl
is deprecated: false
appears in: fabio
appears in: foaf
has URI prefix: http://vitro.mannlib.cornell.edu/ns/vitro/0.7#
has resource example: descriptionAnnot
has prefix: vitro

Variation Modelling Collaboration
type: Resource
is part of: bioregistry
is deprecated: true
has prefix: vmc

VMH Gene
type: Resource
description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.
is part of: bioregistry
has local unique identifier example: 8639.1
has provider formatter: https://www.vmh.life/#gene/$1
has local unique identifier pattern: ^[0-9]+\.[0-9]+$
is deprecated: false
has URI prefix: https://www.vmh.life/#gene/
has resource example: gene/8639.1
has prefix: vmhgene

VMH metabolite
type: Resource
description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.
is part of: bioregistry
has local unique identifier example: h2o
has provider formatter: https://www.vmh.life/#metabolite/$1
has local unique identifier pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$
is deprecated: false
has URI prefix: https://www.vmh.life/#metabolite/
has resource example: metabolite/h2o
has prefix: vmhmetabolite

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

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: metadata
keyword: ontology
keyword: semantic web
has local unique identifier example: term_status
has provider formatter: http://www.w3.org/2003/06/sw-vocab-status/ns#$1
has download URL: ns
is deprecated: false
has URI prefix: http://www.w3.org/2003/06/sw-vocab-status/ns#
has resource example: term status
has prefix: vs

Vertebrate Skeletal Anatomy Ontology
type: Resource
description: Vertebrate skeletal anatomy ontology.
is part of: bioregistry
keyword: anatomy
keyword: obo
keyword: ontology
keyword: vertebrate
has local unique identifier example: 0000183
has provider formatter: http://purl.obolibrary.org/obo/VSAO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: 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_
has resource example: VSAO_0000183
has prefix: vsao

Veterinary Substances DataBase
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source.
is part of: bioregistry
has local unique identifier example: 1868
has provider formatter: https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://bioregistry.io/vsdb:
has resource example: 1868.htm
has prefix: vsdb

Ontology for vector surveillance and management
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems.
is part of: bioregistry
keyword: ontology
has local unique identifier example: 0000000
has provider formatter: http://purl.obolibrary.org/obo/VSMO_$1
has download URL: vsmo.owl
is deprecated: false
has responsible: Lars Eisen
has URI prefix: http://purl.obolibrary.org/obo/VSMO_
has resource example: VSMO_0000000
has prefix: vsmo

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: biomedical science
keyword: blood
keyword: experimental measurement
keyword: health
keyword: health science
keyword: ontology
keyword: owl
has local unique identifier example: 0000041
has provider formatter: https://bioportal.bioontology.org/ontologies/VSO/
has local unique identifier pattern: ^\d{7}$
has download URL: vso.owl
is deprecated: false
has responsible: Albert Goldfain
has URI prefix: https://bioportal.bioontology.org/ontologies/VSO/
has resource example: https://bioportal.bioontology.org/ontologies/VSO/
has prefix: vso

Vertebrate Taxonomy Ontology
type: Resource
description: Comprehensive hierarchy of extinct and extant vertebrate taxa.
is part of: bioregistry
git repository: vertebrate-taxonomy-ontology
keyword: bone element
keyword: obo
keyword: ontology
keyword: taxonomy
has local unique identifier example: 9008500
has provider formatter: http://purl.obolibrary.org/obo/VTO_$1
has local unique identifier pattern: ^\d{7}$
has download URL: vto.owl
is deprecated: false
has responsible: https://orcid.org/0000-0002-8688-6599
has URI prefix: http://purl.obolibrary.org/obo/VTO_
has resource example: VTO_9008500
has prefix: vto

Veterans Health Administration (VHA) unique identifier
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year.
is part of: bioregistry
has local unique identifier example: 4007166
has local unique identifier pattern: ^\d+$
is deprecated: false
has prefix: vuid

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
has local unique identifier example: 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/
has resource example: WBRNAi00086878
has prefix: wb.rnai

C. elegans Gross Anatomy Ontology
type: Resource
description: Ontology about the gross anatomy of the C. elegans
is part of: bioregistry
git repository: c-elegans-gross-anatomy-ontology
keyword: anatomy
keyword: cell
keyword: life science
keyword: obo
keyword: ontology
keyword: worm
has local unique identifier example: 0001290
has provider formatter: http://purl.obolibrary.org/obo/WBbt_$1
has local unique identifier pattern: ^\d{7}$
has download URL: wbbt.owl
is deprecated: false
has responsible: Raymond Lee
has alternative prefix: WBbt
has URI prefix: http://purl.obolibrary.org/obo/WBbt_
has resource example: WBbt_0001290
has prefix: wbbt

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

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: anatomy
keyword: life science
keyword: obo
keyword: omics
keyword: ontology
keyword: phenomics
keyword: phenotype
keyword: worm
has local unique identifier example: 0000983
has provider formatter: http://purl.obolibrary.org/obo/WBPhenotype_$1
has local unique identifier pattern: ^\d{7}$
has download URL: wbphenotype.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-9076-6015
has alternative prefix: WBPhenotype
has URI prefix: http://purl.obolibrary.org/obo/WBPhenotype_
has resource example: WBPhenotype_0000983
has prefix: wbphenotype

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
has local unique identifier example: 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#
has resource example: tag
has prefix: wdr

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
has local unique identifier example: 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#
has resource example: latitude
has prefix: wgs84

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
has local unique identifier example: 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
has prefix: who.va

WiCell Research Institute Cell Collection
type: Resource
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: 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:
has resource example: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/ai10e-kctd13b.cmsx
has prefix: wicell

WikiPathways Types
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Types used in WikiPathways RDF
is part of: bioregistry
git repository: WpVocabularies
keyword: ontology
has local unique identifier example: Arrow
has provider formatter: http://vocabularies.wikipathways.org/wpTypes#$1
has download URL: wpTypes.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-7542-0286
has alternative prefix: wikipathways.types
has alternative prefix: wptypes
has URI prefix: http://vocabularies.wikipathways.org/wpTypes#
has resource example: Arrow
has prefix: wikipathways.type

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
has local unique identifier example: DataNode
has provider formatter: https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/
has download URL: wp.owl
is deprecated: false
has responsible: https://orcid.org/0000-0001-7542-0286
has URI prefix: https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/
has resource example: https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/
has prefix: wikipathways.vocab

Wikipedia
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
description: Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.
is part of: bioregistry
has local unique identifier example: SM_UB-81
has provider formatter: http://en.wikipedia.org/wiki/$1
has local unique identifier pattern: ^\S+$
is deprecated: false
has alternative prefix: Wikipedia
has alternative prefix: wikipedia
has URI prefix: http://en.wikipedia.org/wiki/
has resource example: SM UB-81
has prefix: wikipedia.en

Wiktionary
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: A free dictionary
is part of: bioregistry
has local unique identifier example: pharmacist
has provider formatter: https://en.wiktionary.org/wiki/$1
is deprecated: false
has URI prefix: https://en.wiktionary.org/wiki/
has resource example: pharmacist
has prefix: wiktionary

Wildlife Monitoring Ontology
type: Resource
description: This semantic artifact describes the semantic relationships between entities which model the setup of a biodiversity monitoring project based on capturing audiovisual digital recordings. It encodes the semantics of the Wildlife Monitoring Ontology and at the same time provides the datamodel behind the wildlive.senckenberg.de platform.
is part of: bioregistry
keyword: earth sciences
keyword: ess
has local unique identifier example: Annotation
has provider formatter: https://wildlive.senckenberg.de/wlmo/$1
is deprecated: false
has responsible: Alexander Wolodkin
has URI prefix: https://wildlive.senckenberg.de/wlmo/
has resource example: Annotation
has prefix: wlmo

C. elegans ORFeome cloning project
type: Resource
description: WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends).
is part of: bioregistry
keyword: dna
has local unique identifier example: T01B6.1
has provider formatter: http://worfdb.dfci.harvard.edu/html/index.php
has local unique identifier pattern: ^\w+(\.\d+)?$
is deprecated: false
has URI prefix: http://worfdb.dfci.harvard.edu/html/index.php
has resource example: http://worfdb.dfci.harvard.edu/html/index.php
has prefix: worfdb

The World-2DPAGE database
type: Resource
description: A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots.
is part of: bioregistry
keyword: 2d-page
keyword: protein
keyword: structure
has local unique identifier example: 0020
has provider formatter: http://world-2dpage.expasy.org/repository/database=$1
is deprecated: true
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://world-2dpage.expasy.org/repository/database=
has resource example: http://world-2dpage.expasy.org/repository/database=0020
has prefix: world2dpage

Wormpep
type: Resource
description: Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.
is part of: bioregistry
keyword: protein
keyword: structure
has local unique identifier example: CE28239
has provider formatter: https://www.wormbase.org/db/seq/protein
has local unique identifier pattern: ^CE\d{5}$
is deprecated: false
has URI prefix: https://www.wormbase.org/db/seq/protein
has resource example: https://www.wormbase.org/db/seq/protein
has prefix: wormpep

WoRMS-ID for taxa
type: Resource
contributor: https://orcid.org/0000-0003-2699-3066
description: The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts.
is part of: bioregistry
keyword: biodiversity
keyword: environmental science
keyword: taxonomy
has local unique identifier example: 146421
has provider formatter: http://www.marinespecies.org/aphia.php
has local unique identifier pattern: ^\d+$
is deprecated: false
has responsible: Leen Vandepitte
has URI prefix: http://www.marinespecies.org/aphia.php
has resource example: http://www.marinespecies.org/aphia.php
has prefix: worms

ResearcherID
type: Resource
description: identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829
is part of: bioregistry
has local unique identifier example: B-5720-2018
has provider formatter: https://www.webofscience.com/wos/author/record/$1
has local unique identifier pattern: ^[A-Z]{1,3}-\d{4}-(19|20)\d\d$
is deprecated: false
has URI prefix: https://www.webofscience.com/wos/author/record/
has resource example: https://www.webofscience.com/wos/author/record/B-5720-2018
has prefix: wos.researcher

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
has local unique identifier example: 000177759000002
has provider formatter: https://www.webofscience.com/wos/woscc/full-record/WOS:$1
is deprecated: false
has alternative prefix: wos
has alternative prefix: wosid
has alternative prefix: wosuid
has URI prefix: https://www.webofscience.com/wos/woscc/full-record/WOS:
has resource example: WOS:000177759000002
has prefix: wos.work

XML Web of Trust Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: he WOT, or Web Of Trust, schema is designed to facilitate the use of Public Key Cryptography tools such as PGP or GPG to sign RDF documents and document these signatures.
is part of: bioregistry
keyword: quality
keyword: security
has local unique identifier example: EncryptedDocument
has provider formatter: http://xmlns.com/wot/0.1/$1
is deprecated: false
has URI prefix: http://xmlns.com/wot/0.1/
has resource example: EncryptedDocument
has prefix: wot

Web of Things Hypermedia Controls Ontology
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: an ontology for links and forms, the main hypermedia controls in use on the Web. This ontology offers, among others, a means to reify RDF statements interpreted as links between Web resources. It also provides a versatile exchange format for links and forms in RESTful Web applications. [from homepage]
is part of: bioregistry
has local unique identifier example: AdditionalExpectedResponse
has provider formatter: https://www.w3.org/2019/wot/hypermedia#$1
is deprecated: false
has URI prefix: https://www.w3.org/2019/wot/hypermedia#
has resource example: AdditionalExpectedResponse
has prefix: wot.hypermedia

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
has local unique identifier example: 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#
has resource example: APIKeySecurityScheme
has prefix: wot.security

Web of Things Thing Model
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: The Thing Model (TM) ontology is an RDF axiomatization of the TM concepts, one of the building blocks of the Web of Things (WoT). Besides providing an alternative to the standard JSON representation format for TM documents, the TM ontology can also be used to process contextual information on Things and for alignments with other WoT-related ontologies. [from homepage]
is part of: bioregistry
has local unique identifier example: model
has provider formatter: https://www.w3.org/2022/wot/tm#$1
is deprecated: false
has URI prefix: https://www.w3.org/2022/wot/tm#
has resource example: model
has prefix: wot.tm

World Wildlife Fund Ecoregion
type: Resource
contributor: https://orcid.org/0000-0002-6601-2165
description: WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
is part of: bioregistry
has local unique identifier example: AT1402
has provider formatter: https://www.worldwildlife.org/ecoregions/$1
has local unique identifier pattern: ^AT\d+$
is deprecated: false
has reviewer: https://orcid.org/0000-0003-4423-4370
has alternative prefix: WWF
has URI prefix: https://www.worldwildlife.org/ecoregions/
has resource example: AT1402
has prefix: wwf.ecoregion

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
has local unique identifier example: 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#
has resource example: alternate
has prefix: xhv

Ximbio
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Cell line collections (Providers)
is part of: bioregistry
has local unique identifier example: 151022
has provider formatter: https://ximbio.com/reagent/$1
has local unique identifier pattern: ^\d+$
is deprecated: false
has URI prefix: https://ximbio.com/reagent/
has resource example: https://ximbio.com/reagent/151022
has prefix: ximbio

An SKOS extension for representing statistical classifications
type: Resource
description: An extension of SKOS for representaion of nomenclatures
is part of: bioregistry
keyword: vocabularies
has local unique identifier example: belongsTo
is deprecated: false
has prefix: xkos

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

Xenobiotics Metabolism Database
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
description: Metabolites in the Xenobiotics Metabolism Database.
is part of: bioregistry
has local unique identifier example: 171
has provider formatter: http://www.xmetdb.org/xmetdb/protocol/$1
has local unique identifier pattern: ^\d+$
is deprecated: true
has URI prefix: http://www.xmetdb.org/xmetdb/protocol/
has resource example: http://www.xmetdb.org/xmetdb/protocol/171
has prefix: xmetdb

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
has local unique identifier example: 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#
has resource example: lang
has prefix: xml

XUO
type: Resource
contributor: https://orcid.org/0000-0003-4423-4370
is part of: bioregistry
is deprecated: true
appears in: hsapdv
has prefix: xuo

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
has local unique identifier example: 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
has resource example: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi
has prefix: ydpm

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
has local unique identifier example: 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
has resource example: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl
has prefix: yeastintron

Yeast Searching for Transcriptional Regulators and Consensus Tracking
type: Resource
description: YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.
is part of: bioregistry
keyword: dna
keyword: gene
keyword: life science
keyword: regulation
keyword: small molecule
has local unique identifier example: YBR125c
has provider formatter: http://www.yeastract.com/view.php
is deprecated: false
has responsible: Isabel Sá-Correia
has reviewer: https://orcid.org/0000-0003-4423-4370
has URI prefix: http://www.yeastract.com/view.php
has resource example: http://www.yeastract.com/view.php
has prefix: yeastract

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
has local unique identifier example: 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
has resource example: http://yetfasco.ccbr.utoronto.ca/showPFM.php
has prefix: yetfasco

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
has local unique identifier example: ADH1
has provider formatter: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl
provides for: 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
has resource example: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl
has prefix: ygob

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
has local unique identifier example: 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
has resource example: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb
has prefix: yid

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: https://orcid.org/0000-0001-9163-5180
has URI prefix: http://purl.obolibrary.org/obo/YPO_
has prefix: ypo

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: life science
keyword: protein
has local unique identifier example: 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
has resource example: http://yeastrc.org/pdr/viewProtein.do
has prefix: yrcpdr

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
has local unique identifier example: frbr
has provider formatter: https://prefix.zazuko.com/prefix/$1:
is deprecated: false
has responsible: https://orcid.org/0000-0002-2079-9636
has URI prefix: https://bioregistry.io/zazuko:
has resource example: frbr:
has prefix: zazuko

Maize gross anatomy
type: Resource
description: Maize gross anatomy
is part of: bioregistry
keyword: anatomy
keyword: maize
keyword: obo
keyword: ontology
has local unique identifier example: 0015177
has provider formatter: http://purl.obolibrary.org/obo/ZEA_$1
has local unique identifier pattern: ^\d{7}$
has download URL: zea.obo
is deprecated: true
has responsible: Leszek Vincent
has URI prefix: http://purl.obolibrary.org/obo/ZEA_
has resource example: ZEA_0015177
has prefix: zea

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

Nicole Vasilevsky

Marilyn Safran

Milton H. Saier, Jr.

Doug Howe

Alvis Brazma

Tim Robertson

Pol Castellano Escuder

Yasset Perez-Riverol

Zhang Zhang

Donovan Parks

Haruki Nakamura

Suzi Aleksander

Henriette Harmse

Anton I Petrov

Donna R. Maglott

Thomas Keane

Hector Escriva

David N. Orloff

Eric Sid

Leigh Carmody

Guy Cochrane

Monique Zahn

Samuel Friedman

Daniel Schober

Lars Holm Nielsen

Robert Hoehndorf

Clair Kronk

Henning Hermjakob

Fernanda Dorea

Maximilian Haeussler

Alayne Cuzick

James C. Hu

Alistair Miles

Adrian Pohl

Melissa Haendel

Christian-Alexander Dudek

Francesco Vitali

Chen Yang

Ugis Sarkans

Mark Jensen

Andrea Perego

Jonathan Clark

Bill Duncan

Stian Soiland-Reyes

Pierre-Alain Binz

Citlalli Mejía-Almonte

Jawahar Swaminathan

Harry E. Pence

Hannah Dörpholz

Andreas Ledl

Simon Jupp

Karen Eilbeck

TBK Reddy

Andrew G. McArthur

Victoria K. Jenkins

Robert Druzinsky

Michael Feolo

Carrine Blank

Andy Deans

Jade Hotchkiss

Giacomo Lanza

Troy Pells

David Clunie

Eric P. Nawrocki

Antony Williams

Francisca Vazquez

Joe Flack

Maria Gould

Tarcisio Mendes de Farias

Helen Berman

Dietmar Schomburg

Trish Whetzel

Stuart A. Sutton

Charles Ettensohn

John Garavelli

Gerald Guala

Harshvardhan J. Pandit

Ali Syed

Sebastian Koehler

Peter D'Eustachio

Stephen R. Heller

Jianjiong Gao

David Linke

Evan E Bolton

Heidi L. Rehm

Tudor Oprea

Nikolaos Moustakas

Laurel Cooper

Dan Brickley

Blake A Sweeney

Anita Caron

Christine Orengo

Lucas Leclere

JervenBolleman

Liliana Andres Hernandez

Sheeba Samuel

Angela Kranz

Shuichi Onami

John G Tate

Miguel A. Fortuna

Marie-Angélique Laporte

Dorothea Iglezakis

Evan Patterson

Wes Schafer

Willy Wong

Paul D Thomas

Zach Landis-Lewis

Liz Allen

Tanya Barrett

Gianni Cesareni

Brendan MacLean

Rhiannon Cameron

Denny Vrandečić

Bob Thacker

Arthit Suriyawongkul

Kathryn Dumschott

Daniel Garijo

Oonagh Brendike-Mannix

Pierre-Yves Vandenbussche

Rahuman Sheriff

Joshua Klein

Brian Aevermann

Hugh P Shanahan

Barry Smith

Stewart Thomas Cole

John L. Markley

Conrad L Schoch

Abdelmoneim Amer Desouki

Ian Foster

Christian Hauschke

Kalpana Panneerselvam

Steven G. E. Marsh

Colleen Xu

Todd M Lowe

Joel Richardson

Sebastian Lobentanzer

Todd W Harris

Edward A Dennis

Kristian Axelsen

Josh Moore

Birgit Meldal

Michael Witt

Tuan Amith

Xeni Kechagioglou

Sue Bello

Will Simpson

Muhammad Arsalan

Matteo Guenci

Yohann Paris