Bioregistry - Collections

Collections

Collections are curated lists of prefixes along with a description of what the list is for. For example, there's a collection that lists all of the resources from the review article Sharing biological data: why, when, and how. There's also a collection comprising semantic web prefixes.

New collections can be added in one of the following ways:

Edit the collections.json file with the GitHub editor.
Make a pull request to biopragmatics/bioregistry.

Name	Size	Description
Resources mentioned in "Sharing biological data: why, when, and how"	18	These resources were listed in Sharing biological data: why, when, and how, 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.
Semantic Web Context	28	Resources used in the semantic web, inspired by this list in BioContext.
ChEBI Data Sources	24	The data sources used in xrefs in the ChEBI ontology. More information in the "Data Sources" section of this document.
International Classifications of Diseases	7	This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions.
Allen Institute Ontologies	5	This collection contains various brain atlases from the Allen Institute.
SPAR Ontologies	13	The Semantic Publishing and Referencing (SPAR) 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.
Publication Provenance Prefixes	4	Prefixes useful in annotating documentation provenance.
ASKEM Epidemiology Prefixes	18	Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project.
FHIR External Terminologies	37	Prefixes mentioned on the external list on the FHIR Code Systems page. This list is mostly complete. Notably, some entries that have not been curated: HGVS (see discussion at #460) NUBC (National Uniform Billing Committee) - could not find information about the terminology or its entries ICPC (International Classification of Primary Care) same GTIN (Global Trade Item Number) same MDC (Medical Device Codes) since that appears to be part of a larger ISO standard vocabulary that needs further investigation
Global Biodata Coalition - Global Core Biodata Resources	48	The Global Biodata Coalition released a curated list of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria here). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and FAIRsharing 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 (uses HGNC, MONDO, PharmGKB, etc.) DNA Data Bank of Japan (uses INSDC) GENCODE (uses GenBank) GWAS Catalog (uses dbSNP, EFO, etc) STRING (uses UniProt)
NDFI4Chem Collection	15	A collection of ontologies relevant for chemistry. Skipped: - DOLCE (dead links)
Clinical Trial Registries	20	A collection of clinical trial registries appearing in the World Health Organization's International Clinical Trials Registry Platform (ICTRP)