{"0000001":{"identifier":"0000001","name":"Resources mentioned in \"Sharing biological data: why, when, and how\"","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.","resources":["biostudies","bmrb.entry","cellimage","ega.dataset","ega.study","emdb","empiar","genbank","geo","idr","insdc.sra","massive","panorama","pdb","peptideatlas.dataset","pride","ssbd.dataset","ssbd.project"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000002":{"identifier":"0000002","name":"Semantic Web Context","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.","resources":["ac","bibo","dc","dcat","dcmitype","dcterms","doap","faldo","foaf","idot","oa","oboinowl","oslc","owl","pav","prov","qb","qudt","rdf","rdfs","schema","sh","shex","skos","skosxl","swrl","vann","void","xsd"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":"semweb","references":null,"keywords":null,"mappings":null,"tags":null},"0000003":{"identifier":"0000003","name":"ChEBI Data Sources","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).","resources":["chebi","chemidplus","come","drugbank","ecmdb","eurofir","google.patent","hmdb","kegg.compound","kegg.drug","kegg.glycan","knapsack","lincs.smallmolecule","lipidmaps","metacyc.compound","molbase.sheffield","pdb","pdb-ccd","pesticides","resid","smid","umbbd.compound","webelements","ymdb"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000004":{"identifier":"0000004","name":"International Classifications of Diseases","description":"This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions.","resources":["icd10","icd10cm","icd10pcs","icd11","icd11.code","icd9","icd9cm","icdo"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000005":{"identifier":"0000005","name":"Allen Institute Ontologies","description":"This collection contains various brain atlases from the Allen Institute.","resources":["dhba","dmba","hba","mba","pba"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000006":{"identifier":"0000006","name":"SPAR Ontologies","description":"The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF.","resources":["bido","biro","c4o","cito","datacite","deo","doco","fabio","frapo","mito","pso","puro","pwo","scoro"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":"spar","references":null,"keywords":null,"mappings":null,"tags":null},"0000007":{"identifier":"0000007","name":"Publication Provenance Prefixes","description":"Prefixes useful in annotating documentation provenance.","resources":["arxiv","doi","pmc","pubmed"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000008":{"identifier":"0000008","name":"ASKEM Epidemiology Prefixes","description":"Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project.","resources":["bfo","caro","doi","doid","dso","hp","ido","oae","oboinowl","ovae","owl","pmc","pubmed","rdfs","ro","symp","trans","vo"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000009":{"identifier":"0000009","name":"FHIR External Terminologies","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:\n\n- HGVS (see discussion at [#460](https://github.com/biopragmatics/bioregistry/issues/460))\n- [NUBC](http://www.nubc.org) (National Uniform Billing Committee) - could not find information about the terminology or its entries\n- [ICPC](http://www.ph3c.org/) (International Classification of Primary Care) _same_\n- [GTIN](https://www.gs1.org/standards/id-keys/gtin) (Global Trade Item Number) _same_\n- [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","resources":["atcc","clinicaltrials","clinvar.variation","cosmic.gene","cpt","cvx","dbsnp","dicom","dsm5","ensembl","hc.din","hc.npn","hgnc","hl7.v2codesystem","hl7.v3codesystem","icd10","icd9","icf","ietf.language","imgt.hla","iso.3166","loinc","lrg","ncit","ndc","ndfrt","nucc.taxonomy","omim","pharmgkb.gene","pubmed","radlex","refseq","rxnorm","snomedct","so","ucum","unii"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000010":{"identifier":"0000010","name":"Global Biodata Coalition - Global Core Biodata Resources","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)).\n\nWhile 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:\n\n- [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.)\n- [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC)\n- [GENCODE](https://www.gencodegenes.org/) (uses GenBank)\n- [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc)\n- [STRING](https://string-db.org/) (uses UniProt)","resources":["agrkb","bacdive","brenda","brenda.ligand","brenda.ligandgroup","bto","chebi","chembl","civic.aid","civic.did","civic.eid","civic.gid","civic.sid","civic.tid","civic.vid","ecocyc","ena.embl","ensembl","eupath","flybase","gbif","gnomad","go","hgnc","interpro","mgi","orpha","orphanet.ordo","panther.family","panther.node","panther.pathway","panther.pthcmp","pdb","pharmgkb.disease","pharmgkb.drug","pharmgkb.gene","pharmgkb.pathways","pmc","pombase","px","reactome","rgd","rhea","sgd","ucsc","uniprot","wormbase","zfin"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000011":{"identifier":"0000011","name":"NFDI4Cat Collection","description":"A collection of ontologies, controlled vocabularies, and schemas relevant for the NDFI4Cat Consortium.\n\nThis collection was originally based on the metadata landscape of the ontologies in this list can be found [here](https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat).\n\nOntoCompChem 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.","resources":["afo","bao","bfo","cao","chebi","cheminf","chmo","dolce","edam","emmo","emmo.cif","envo","iso15926","m4i","mop","ms","obi","om","ontocape","osmo","rex","rxno","sbo","voc4cat","worldavatar.compchem","worldavatar.kin"],"contributors":[{"name":" Hendrik Borgelt","orcid":"0000-0001-5886-7860","email":"hendrik.borgelt@tu-dortmund.de","github":"HendrikBorgelt","wikidata":null},{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":[{"name":" Hendrik Borgelt","orcid":"0000-0001-5886-7860","email":"hendrik.borgelt@tu-dortmund.de","github":"HendrikBorgelt","wikidata":null},{"name":"Alexander Behr","orcid":"0000-0003-4620-8248","email":"alexander.behr@tu-dortmund.de","github":"AleSteB","wikidata":null},{"name":"David Linke","orcid":"0000-0002-5898-1820","email":"david.linke@catalysis.de","github":"dalito","wikidata":null}],"logo":"https://www.nfdi.de/wp-content/uploads/2021/06/Logo_Ohne-BG.png","organizations":[{"ror":"01k9z4a50","wikidata":"Q98380342","gnd":null,"name":"NFDI4Cat","partnered":false},{"ror":"05qj6w324","wikidata":"Q61658497","gnd":null,"name":"NFDI","partnered":false}],"context":null,"references":["https://nfdi4cat.org/services/ontologie-sammlung/","https://terminology.tib.eu/ts/ontologies?collection=NFDI4CAT&and=false&page=1","https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat"],"keywords":null,"mappings":[{"prefix":"tib.collection","identifier":"nfdi4cat"}],"tags":null},"0000012":{"identifier":"0000012","name":"Clinical Trial Registries","description":"A collection of clinical trial registries appearing in the World Health Organization's [International Clinical Trials Registry Platform (ICTRP)](https://trialsearch.who.int/)","resources":["anzctr","chictr","clinicaltrials","ctis","ctri","drks","euclinicaltrials","hc.trial","irct","isrctn","itmctr","jrct","kcris","lbctr","pactr","phrr","rebec","repec","rpcec","slctr","snctp","tctr","uminctr"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000013":{"identifier":"0000013","name":"Software Package Repositories","description":"These resources represent software repositories","resources":["cran","crates","npm","packagist","pypi","rubygems"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000014":{"identifier":"0000014","name":"NFDI4Chem Collection","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).\n\nNFDI4Chem 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).","resources":["afo",{"prefix":"bfo","comment":null,"tags":["production"]},"bto",{"prefix":"chebi","comment":"Used in YMDB, HMDB, PubChem, MassBank, KNApSAcK, UM-BBD, GMD, SMID-DB","tags":null},{"prefix":"cheminf","comment":null,"tags":["production"]},"chemrof","chiro",{"prefix":"chmo","comment":null,"tags":["collaborative","production"]},{"prefix":"dcat","comment":null,"tags":["production"]},"duo","edam","efo","enm","envo","fair",{"prefix":"fix","comment":null,"tags":["research"]},{"prefix":"gainesville.core","comment":null,"tags":["research"]},"iao","mod","mop","ms","ncit","nmr","obi","oboe","oboe.standard","om","ontorxn","pato","proco",{"prefix":"prov","comment":null,"tags":["production"]},"reproduceme",{"prefix":"rex","comment":null,"tags":["research"]},"ro",{"prefix":"rxno","comment":null,"tags":["collaborative"]},"sepio","sio","sosa","ssn","ssn.system","swo","time","uo",{"prefix":"vibso","comment":null,"tags":["collaborative"]},"voc4cat","worldavatar.compchem","worldavatar.kin","worldavatar.species"],"contributors":[{"name":" Philip Strömert","orcid":"0000-0002-1595-3213","email":"philip.stroemert@tib.eu","github":"StroemPhi","wikidata":null},{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":[{"name":" Philip Strömert","orcid":"0000-0002-1595-3213","email":"philip.stroemert@tib.eu","github":"StroemPhi","wikidata":null}],"logo":"https://nfdi4chem.de/wp-content/themes/wptheme/assets/img/logo.svg","organizations":[{"ror":"05wwzbv21","wikidata":"Q96678459","gnd":null,"name":"NFDI4Chem","partnered":false},{"ror":"05qj6w324","wikidata":"Q61658497","gnd":null,"name":"NFDI","partnered":false}],"context":null,"references":["https://terminology.nfdi4chem.de/ts/","https://doi.org/10.1515/pac-2021-2007"],"keywords":["chemistry"],"mappings":[{"prefix":"tib.collection","identifier":"nfdi4chem"}],"tags":[{"code":"collaborative","name":"Collaborative","description":"External, but curated by the consortium"},{"code":"production","name":"In Production","description":"Used in production within services of the consortium"},{"code":"research","name":"Research","description":"not in any associated services of the consortium of the collection, but indexed to compare with the ones used, or to learn from, or to maybe build mappings"}]},"0000015":{"identifier":"0000015","name":"Biocuration Conference 2025 Collection","description":"A collection of resources added during Biocuration 2025 in Kansas City, MO, USA.","resources":["antifam","biomarkerkb.biomarker","biomarkerkb.canonical","blastrule","emi","endlessforms.collection","endlessforms.element","endlessforms.graphic","endlessforms.image","endlessforms.library","endlessforms.unit","gdo"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000016":{"identifier":"0000016","name":"Synapse.org external links","description":"A curated list by Sage Bionetworks of external resources that are automatically linked on Synapse.org and affiliated data portals","resources":["ado","agrkb","anzctr","arrayexpress","arxiv","atc","atcc","bacdive","bfo","bgee.gene","biocyc","biogrid","bioportal","bioproject","biorxiv","biosample","biostudies","bmrb.entry","brenda","brenda.ligand","brenda.ligandgroup","bto","cath","cbioportal","cdd","cellimage","cellxgene.collection","chebi","chembl","chembl.compound","chemspider","civic.aid","civic.did","civic.eid","civic.gid","civic.sid","civic.tid","civic.vid","clinicaltrials","clinvar.record","clinvar.variation","complexportal","cosmic.cell","cosmic.gene","cpt","ctd.chemical","ctri","cvx","dbgap","dbsnp","decipher","depmap","dhba","disprot","dmba","doi","doid","drks","drugbank","drugcentral","duo","ec","ecacc","edam","ega.dataset","ega.study","emdb","empiar","ena.embl","ensembl","ensembl.metazoa","ensembl.plant","euclinicaltrials","eupath","exac.variant","fairsharing","flybase","fma","funderregistry","gard","gbif","gdc","genecards.gene","geo","go","gramene.gene","gramene.growthstage","gramene.protein","gtdb","hba","hc.trial","hgnc","hl7.v2codesystem","hmdb","icd10","icd9","icdc","icf","idr","imgt.hla","inchi","inchikey","insdc","insdc.sra","intact","interpro","iso.3166","isrctn","itis","jaxmice","kegg","kegg.compound","kegg.disease","kegg.drug","kegg.glycan","kegg.pathway","kegg.reaction","loinc","massive","mba","mesh","metabolights","metacyc.compound","mgi","mir","mirbase","mondo","ncbigene","ncbiprotein","ncbitaxon","ncit","ndc","ndfrt","nextprot","nihreporter.project","nord","omim","omop","orcid","orpha","orphanet.ordo","osf","panther.family","panther.pathway","panther.pthcmp","pba","pdb","pdb-ccd","pdb.ligand","pdc.study","peco","peptideatlas.dataset","pfam","pfam.clan","pharmgkb.disease","pharmgkb.drug","pharmgkb.gene","pharmgkb.pathways","pmc","pombase","pride.project","pubchem.compound","pubmed","px","radlex","reactome","rebec","refseq","rfam","rfc","rgd","rhea","rnacentral","ror","rrid","rrrc","rxnorm","scop","sgd","signor","snomedct","so","ssbd.dataset","ssbd.project","stitch","string","tao","tcdb","uberon","unii","uniparc","uniprot","uniprot.isoform","uniprot.proteome","uniref","wikidata","wikigenes","wikipathways","wormbase","xenbase","zenodo.record","zfin","zinc"],"contributors":[{"name":"Robert Allaway","orcid":"0000-0003-3573-3565","email":"robert.j.allaway@gmail.com","github":"allaway","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000017":{"identifier":"0000017","name":"DALIA Resources","description":"Prefixes relevant for the [Data Literacy Alliance (DALIA)](https://dalia.education/en) project","resources":["ans.educationlevel","bibframe","bibo","bmbf.glossary","ceds.element","citedcat","codata.rdmt","dai.thesauri","datacite","dbpedia.resource","dcterms","emmo","fabio","iana.mediatype","isced1997","isced2011","loc.fdd","m4i","marc21","modalia","nfdi4dso","owl","prov","sage.socialsciencethesaurus","schema","sio","spdx","spdx.term","t4fs","unesco.thesaurus","wdrs","wikidata"],"contributors":[{"name":"Charles Tapley 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The working group is in the process of identifying NFDI4Memory Consortium members appropriate for maintaining this collection.","resources":["cidoc.crm","edm","factgrid","geonames","getty.att","getty.cona","getty.ia","getty.tgn","getty.ulan","gnd","gov.object","hisco","iconclass","kldb","lido","nfdi.core","nfdi4culture.cto","ohdab","ontome","tadirah","wikidata"],"contributors":[{"name":"NFDI Section Metadata WG Ontology Harmonization and Mapping","orcid":null,"email":null,"github":null,"wikidata":"Q139055838"}],"maintainers":[{"name":"Tabea Tietz","orcid":"0000-0002-1648-1684","email":"tabea.tietz@fiz-karlsruhe.de","github":"tabeatietz","wikidata":null}],"logo":"https://www.nfdi.de/wp-content/uploads/2023/08/Logo_for_memory_RGB.png","organizations":[{"ror":"0310v3480","wikidata":"Q98231721","gnd":null,"name":"NFDI4Memory","partnered":false},{"ror":"05qj6w324","wikidata":"Q61658497","gnd":null,"name":"NFDI","partnered":false}],"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000038":{"identifier":"0000038","name":"Text+ Collection","description":"A placeholder collection of ontologies, controlled vocabularies, and schemas relevant for the Text+ Consortium created by the [NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). The working group is in the process of identifying Text+ Consortium members appropriate for maintaining this collection.","resources":["bibframe","cessda.topicclassification","cidoc.crm","geonames","getty.att","getty.cona","getty.ia","getty.tgn","getty.ulan","gnd","iconclass","lido","ontolex","ontome","tadirah"],"contributors":[{"name":"NFDI Section Metadata WG Ontology Harmonization and Mapping","orcid":null,"email":null,"github":null,"wikidata":"Q139055838"}],"maintainers":[{"name":"Thorsten Trippel","orcid":"0000-0002-7211-7393","email":null,"github":"ttrippel","wikidata":null}],"logo":"https://www.nfdi.de/wp-content/uploads/2023/12/textplus_logo_RGB.png","organizations":[{"ror":"04dy2xw62","wikidata":"Q98271443","gnd":null,"name":"Text+","partnered":false},{"ror":"05qj6w324","wikidata":"Q61658497","gnd":null,"name":"NFDI","partnered":false}],"context":null,"references":["https://go.rocket.chat/invite?host=all-chat.nfdi.de&path=invite%2FaKbtMN"],"keywords":null,"mappings":null,"tags":null},"0000039":{"identifier":"0000039","name":"GHGA Collection","description":"A placeholder collection of ontologies, controlled vocabularies, and schemas relevant for the GHGA Consortium created by the [NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). The working group is in the process of identifying GHGA Consortium members appropriate for maintaining this collection.","resources":["biolink","cob","duo","edam","efo","genepio","ghga","gsso","hancestro","linkml","ncit","sio"],"contributors":[{"name":"NFDI Section Metadata WG Ontology Harmonization and Mapping","orcid":null,"email":null,"github":null,"wikidata":"Q139055838"}],"maintainers":[{"name":"Karoline Mauer","orcid":"0000-0002-9454-7941","email":null,"github":"mauerk","wikidata":null}],"logo":"https://www.nfdi.de/wp-content/uploads/2022/10/Logo-GHGA.png","organizations":[{"ror":"05nfk7108","wikidata":"Q98380337","gnd":null,"name":"GHGA","partnered":false},{"ror":"05qj6w324","wikidata":"Q61658497","gnd":null,"name":"NFDI","partnered":false}],"context":null,"references":["https://go.rocket.chat/invite?host=all-chat.nfdi.de&path=invite%2FCHzcLh"],"keywords":null,"mappings":null,"tags":null},"0000040":{"identifier":"0000040","name":"NFDI4Biodiversity Collection","description":"A placeholder collection of ontologies, controlled vocabularies, and schemas relevant for the NFDI4Biodiversity Consortium created by the [NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). 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The working group is in the process of identifying NFDI4Immuno Consortium members appropriate for maintaining this collection.","resources":[{"prefix":"clo","comment":"Recommended for entities of type: cell_lin_name","tags":null},{"prefix":"doid","comment":"Disease ontology used to describe patients disease / disease of research focus. Recommended for entities of type: disease","tags":null},{"prefix":"hancestro","comment":"Recommended for entities of type: ancestry","tags":null},{"prefix":"ncit","comment":"Only a subclass of NCIT is used to describe the medication used within the study / individual patient. Recommended for entities of type: medication","tags":null},{"prefix":"obi","comment":"Only a subclass of OBI is used to describe the data processing steps before the analysis part. Recommended for entities of type: data_processing_steps","tags":null},{"prefix":"snomedct","comment":"Only a subclass of SNOMED CT is used to describe the Ethnicity of human patients. 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This collection reflects their [PID Providers](https://pid.services.base4nfdi.de/get-pid/providers/) page. This comes with the following caveats:\n\n- Crossref and DataCite are services that mint DOIs. Since DOIs are the identifier space, only `doi` appears in this collection.\n- ePIC is a service that mints Handle system. Since Handles are the identifier space, only `hdl` appears in this collection\n- PIDINST is an abstraction on top of DataCite / ePIC, which is covered by `doi` and `hdl` as described above","resources":["ark","doi","factgrid","gnd","hdl","igsn","orcid","pida","raid","ror","swh","wikidata"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000045":{"identifier":"0000045","name":"Earth System Sciences Collection","description":"The Earth System Sciences (ESS) collection contains terminologies (ontologies and vocabularies) for describing Earth System Sciences (e.g., `bodc.cf`, `envo`), data and structures (e.g., `prov-o`), physical units (e.g., `time`), as well as measurements and observations (e.g., `tib.meth`).\n\nIt was developed by the [BITS project](https://projects.tib.eu/bits/home) (BluePrints for the Integration of Terminology Services in Earth System Sciences), which was funded by the Deutsche Forschungsgemeinschaft ([project number 508107981](https://gepris.dfg.de/gepris/projekt/508107981), July 2023 – June 2026). The ESS collection's terminologies were firstly chosen by the three project partners [TIB – Leibniz Information Centre for Science and Technology](https://www.tib.eu/en/), the [German Climate Computing Center (DKRZ)](https://www.dkrz.de/en/dkrz-partner-for-climate-research?set_language=en), and the [Senckenberg - Leibniz Institution for Biodiversity and Earth System Research (SGN)](https://www.senckenberg.de/en/about-us/senckenberg-society-nature-research/) in close cooperation with [NFDI4Earth](https://www.nfdi4earth.de/) and the [Helmholtz Metadata Collaboration](https://helmholtz-metadaten.de/).","resources":["bco","bodc.cf","bodc.sdn","cgo","chebi","dcat","dcterms","dfg.fo","dpvocab","dsw","duo","ecso","edam","efo","envo","envthes","flopo","gemet.concept","geosparql","gfbio.ets","gndo","n4e","oboe","om","pato","po","prov","sbo","schema","sio","sosa","ssn","stato","sweet","t4fs","tdwg.abcd","tib.bk","tib.meth","time","to","uat","uo","wlmo"],"contributors":[{"name":"Anette Ganske","orcid":"0000-0003-1043-4964","email":null,"github":"anganske","wikidata":null},{"name":"Angelina Kraft","orcid":"0000-0002-6454-335X","email":null,"github":"kraftalin","wikidata":null},{"name":"Markus Stocker","orcid":"0000-0001-5492-3212","email":"markus.stocker@tib.eu","github":"markusstocker","wikidata":null}],"maintainers":null,"logo":"https://private-user-images.githubusercontent.com/58422600/595255823-95fb77d4-c775-4d1f-8d1d-aacbda324bb7.png?jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.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.9V4j3O3ppguT7s4TmyLNAJQwULkh2oGzIrRcP7N0SYg","organizations":null,"context":null,"references":null,"keywords":null,"mappings":[{"prefix":"tib.collection","identifier":"ess"}],"tags":null},"0000046":{"identifier":"0000046","name":"Ontologies used by European Synchrotron Radiation Facility","description":"Physics ontologies used by the European Synchrotron Radiation Facility (ESRF) and listed in <https://github.com/pan-ontologies/esrf-ontologies>. Overlaps with the interests of DAPHNE4NFDI, NFDI-MatWerk, and FAIRmat.","resources":["esrfet","nexus","panet"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":[{"ror":"02550n020","wikidata":null,"gnd":null,"name":"European Synchrotron Radiation Facility","partnered":false}],"context":null,"references":null,"keywords":null,"mappings":null,"tags":null},"0000047":{"identifier":"0000047","name":"Ontologies4Chem 2026","description":"The [5<sup>th</sup> Ontologies4Chem Workshop](https://nfdi4chem.de/event/5th-ontologies4chem-workshop/) took place between November 2-4<sup>th</sup>, 2026 in Limburg an der Lahn at the Dom Limburg Hotel. This collection covers records for ontologies, controlled vocabularies, and other relevant semantic spaces that were presented directly, used by work that was presented, or otherwise discussed at the workshop.\n\nThe contributors list reflects the union of the presenters of the talks, maintainers of the ontologies/resources listed who were in attendance, and other contributions to the construction of the conference/list. Note: this collection isn't meant to be a complete summary of the Ontologies4Chem Workshop, but rather it's meant to contextualize the discussion topics from different parts of the workshop based on the resources they were about.","resources":[{"prefix":"asmo","comment":"Mentioned during the computational chemistry hackathon as a potential ontology for reuse or extension","tags":["computational-chemistry"]},{"prefix":"bioregistry","comment":"The Semantic Farm/Bioregistry was a recurring topic of conversation on the indexing of ontologies such that they are easier to find and reuse.","tags":null},{"prefix":"chebi","comment":"ChEBI was the primary topic of the morning session of Day 3 entitled *Chemical Entities – Classification and Design Patterns*. Noel O'Boyle presented general updates, Simon Flügel presented [Rule-based ChEBI extension](https://drive.google.com/file/d/1JUms-SGC8qUJhCNy9eosOPSIq3jubrhU/view?usp=drive_link), Charlotte Tumescheit presented [Explainability of chemical language models](https://drive.google.com/file/d/1_-lO7eK3znepyWPvqYfI75yMTB1vblZM/view?usp=sharing), and Miranda Carlsson presented [ChEBI-N – An Updated Ontology-Based Chemical Enrichment Analysis Tool](https://drive.google.com/open?id=1K-XuLOGsuAoxdD6tiOWDXCESuVSa1_bB).","tags":["presented"]},{"prefix":"cheminf","comment":"CHEMINF was mentioned in several contexs, including in the computational chemistry modeling hackathon and in Philip Strömert's presentation [Design Patterns for Chemical Composition of Substances and Materials](https://docs.google.com/presentation/d/1ER8eNIuptmyi_QM4S6fZak0TjA-vw3q6imIJCfQguks/edit?slide=id.p#slide=id.p) in the context of ChemDCAT-AP.","tags":["computational-chemistry"]},{"prefix":"chmo","comment":"Noura Rayya presented [NFDI4Chem’s Ontology Curation Status Updates: CHMO, RXNO & MOP](https://docs.google.com/presentation/d/1zyXHNBURO1mjZqVhUGzTqClNIttspihEEnSKVZ6vG50/edit?slide=id.h6509b6cc4dfea78a_0_284) on Day 1 of the workshop which outlined the maturing ODK-ization of CHMO.","tags":["presented"]},{"prefix":"climoo.picco","comment":null,"tags":["presented"]},{"prefix":"climoo.piccomela","comment":null,"tags":["presented"]},{"prefix":"climoo.plastico","comment":"PlasticO was presented by Giorgio A. Ubbiali on Day 2 as part of a suite of ontologies describing plastics, their lifecycles, debris, their environment and ecological impacts, and effects on climate change ([slides](https://docs.google.com/presentation/d/1uvbEEk8nAXnagbRCkWpda4M5VizHLf2a/edit?usp=sharing&ouid=102267574585791126574&rtpof=true&sd=true)).","tags":["presented"]},{"prefix":"climoo.sdc2","comment":null,"tags":["presented"]},{"prefix":"emmo","comment":"Mentioned during the computational chemistry hackathon as a potential ontology for reuse or extension. EMMO is an upper-level ontology framework often used in the natural sciences and engineering (but not so much in the life sciences, which typically use BFO)","tags":["computational-chemistry"]},{"prefix":"goldbook","comment":"Leah McEwen and Stuart Chalk hosted a hackathon for the serialization of the IUPAC Goldbook to SKOS","tags":["presented"]},{"prefix":"mlips","comment":"Mentioned during the computational chemistry hackathon as a potential ontology for reuse or extension","tags":["computational-chemistry"]},{"prefix":"molsim","comment":"Fathoni Musyaffa presented [MOLSIM: an OBO-aligned ontology for describing molecular simulation data](https://docs.google.com/presentation/d/1GxCXMAeNbpo3LsTUyuWIACm1LpBj9ckx2vdKkJh4NO8/edit?slide=id.p1#slide=id.p1) on Day 1","tags":["computational-chemistry"]},{"prefix":"mop","comment":"Noura Rayya presented [NFDI4Chem’s Ontology Curation Status Updates: CHMO, RXNO & MOP](https://docs.google.com/presentation/d/1zyXHNBURO1mjZqVhUGzTqClNIttspihEEnSKVZ6vG50/edit?slide=id.h6509b6cc4dfea78a_0_284) on Day 1 of the workshop which outlined the plan for the ODK-ization of MOP.","tags":["presented"]},{"prefix":"ontmm","comment":"Darren Rhodes has been constructing the Molecular Modelling Project Ontology from a chemist's perspective and joined the workshop to share the competency questions that were encoded in this application ontology.","tags":["computational-chemistry"]},{"prefix":"ontoiochem","comment":"Presented by Gabi Dias during Day 1 of the computational chemistry ontology hackathon.","tags":["computational-chemistry","presented"]},{"prefix":"pmdco","comment":"Philipp von Hartrott presented *Description of compositions of metallic materials using PMDco* on Day 3.","tags":["presented"]},{"prefix":"psdi.voc","comment":"Samantha Pearman-Kanza and Aileen Day presented the Physical Science Data Infrastructure (PSDI), an organization in the UK with similar goals as the NFDI, on Day 1. Their presentation included the metadata strategy and controlled vocabularies under development ([slides](https://doi.org/10.5281/zenodo.23921526)).","tags":["presented"]},{"prefix":"pubchem.vocabulary","comment":"Evan Bolton presented _PubChem & ChemRef_ on Day 3","tags":["presented"]},{"prefix":"qudt","comment":null,"tags":["computational-chemistry"]},{"prefix":"rhea","comment":"Jerven Bolleman and Alex Sommer-Behr lead the discussion following Day 2's long talk on Alexei Lapkin and Laura Fadler's high level *context* ontology proposal, in which we discussed the needs for modeling reactions, experiments, instruments, and related concepts. Rhea was a natural suggestion from Jerven's work at SIB as an existing resource to take inspiration from.","tags":["presented"]},{"prefix":"rxno","comment":"Noura Rayya presented [NFDI4Chem’s Ontology Curation Status Updates: CHMO, RXNO & MOP](https://docs.google.com/presentation/d/1zyXHNBURO1mjZqVhUGzTqClNIttspihEEnSKVZ6vG50/edit?slide=id.h6509b6cc4dfea78a_0_284) on Day 1 of the workshop which outlined the plan for the ODK-ization of RXNO.","tags":["presented"]},{"prefix":"sre.cpo","comment":"Laura Fadler and Alexei Lapkin presented [A high-level ‘Context’ ontology - providing more context for reactions](https://drive.google.com/file/d/1ntDJi81oMZb7uMErb5sweXuI22Wl13Hb/view?usp=sharing) which showcased two ontologies - the Chemical Process Ontology (CPO) was the domain-specific application of their high-level ontology (HLO).","tags":["presented"]},{"prefix":"sre.hlo","comment":"Laura Fadler and Alexei Lapkin presented [A high-level ‘Context’ ontology - providing more context for reactions](https://drive.google.com/file/d/1ntDJi81oMZb7uMErb5sweXuI22Wl13Hb/view?usp=sharing) which showcased two ontologies - the Chemical Process Ontology (CPO) was the domain-specific application of their high-level ontology (HLO).","tags":["presented"]},{"prefix":"sssom","comment":"SSSOM was presented by Charles Tapley Hoyt on Day 1 ([slides](https://zenodo.org/records/23892214)).","tags":["presented"]},{"prefix":"tib.mdo","comment":"Mentioned during the computational chemistry hackathon as a potential ontology for reuse or extension","tags":["computational-chemistry"]},{"prefix":"voc4cat","comment":"David Linke presented *Terms are the easy part: Editorial rules, tooling and review in Voc4Cat* on Day 1.","tags":["presented"]},{"prefix":"worldavatar.compchem","comment":"Mentioned during the computational chemistry hackathon as a potential ontology for reuse or extension","tags":["computational-chemistry"]}],"contributors":[{"name":"Shashank S. 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