An overview on registries covering biomedical ontologies, controlled vocabularies, and databases.
A 🟢 means the field is required. A 🟡 means it is part of the schema, but not required or incomplete on some entries. A 🔴 means that it is not part of the metadata schema. For lookup services like the OLS, some fields (i.e., Example ID, Default Provider, Alternate Providers) are omitted because inclusion would be redundant.
Caveats: Several of Wikidata's fields can be accessed indirectly with alternative SPARQL queries. BioPortal's data is locked behind an API that requires a key and has rate limited access. The Crop Ontology Curation Tool does not list homepages because it is the homepage itself. Non-english language registries in the OntoPortal Alliance were not included.
Registry | Score | Name | Homepage | Description | Example | Pattern | Provider | Alternate Providers | Alternate Prefixes | License | Version | Contact |
---|---|---|---|---|---|---|---|---|---|---|---|---|
AberOWL | 13 | 🟢 | 🟢 | 🟢 | ⚪ | 🔴 | ⚪ | ⚪ | 🔴 | 🔴 | 🟡 | 🔴 |
AgroPortal | 12 | 🟢 | 🟢 | 🟢 | ⚪ | 🔴 | ⚪ | ⚪ | 🔴 | 🟡 | 🟡 | 🟡 |
BioContext | -4 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🟡 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 |
BioPortal | 12 | 🟢 | 🟢 | 🟢 | ⚪ | 🔴 | ⚪ | ⚪ | 🔴 | 🔴 | 🟢 | 🟡 |
Biolink | 3 | 🟢 | 🔴 | 🔴 | 🔴 | 🔴 | 🟢 | 🔴 | 🔴 | 🟡 | 🔴 | 🔴 |
Bioregistry | 25 | 🟢 | 🟢 | 🟢 | 🟢 | 🟡 | 🟡 | 🟡 | 🟡 | 🟡 | 🟡 | 🟡 |
Cellosaurus | 4 | 🟢 | 🟢 | 🔴 | 🔴 | 🔴 | 🟢 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 |
CHEMINF | -5 | 🟢 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 |
Crop OCT | 3 | 🟢 | ⚪* | 🔴 | ⚪ | 🔴 | ⚪ | ⚪ | 🔴 | 🔴 | 🔴 | 🔴 |
EcoPortal | 10 | 🟢 | 🟡 | 🟢 | ⚪ | 🔴 | ⚪ | ⚪ | 🔴 | 🟡 | 🟡 | 🟡 |
FAIRSharing | 8 | 🟢 | 🟢 | 🟢 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🟢 |
GO | 9 | 🟢 | 🟡 | 🟡 | 🟡 | 🟡 | 🟡 | 🟡 | 🔴 | 🔴 | 🔴 | 🔴 |
Identifiers.org | 22 | 🟢 | 🟢 | 🟢 | 🟢 | 🟢 | 🟢 | 🟡 | 🔴 | 🔴 | 🔴 | 🔴 |
Name-to-Thing | 23 | 🟢 | 🟢 | 🟢 | 🟢 | 🟢 | 🟢 | 🟡 | 🟡 | 🔴 | 🔴 | 🔴 |
NCBI | 2 | 🟢 | 🟢 | 🔴 | 🟢 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 |
OBO Foundry | 15 | 🟢 | 🟢 | 🟢 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🟢 | 🔴 | 🟢 |
OntoBee | 11 | 🟢 | 🟢 | 🟢 | ⚪ | 🔴 | ⚪ | ⚪ | 🔴 | 🔴 | 🔴 | 🟢 |
OLS | 15 | 🟢 | 🟡 | 🟢 | ⚪ | 🔴 | ⚪ | ⚪ | 🔴 | 🟢 | 🟡 | 🟡 |
Prefix Commons | 15 | 🟢 | 🟡 | 🟡 | 🟡 | 🟡 | 🟡 | 🟢 | 🟡 | 🔴 | 🔴 | 🔴 |
Prefix.cc | 0 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🟢 | 🟡 | 🔴 | 🔴 | 🔴 | 🔴 |
Scholia | -9 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 |
UniProt | 7 | 🟢 | 🟢 | 🔴 | 🔴 | 🔴 | 🟢 | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 |
Wikidata | 21 | 🟢 | 🟡 | 🟢 | 🟡 | 🟡 | 🟡 | 🟡 | 🔴 | 🟡* | 🟡* | 🟡* |
This section provides a systematic evaluation and comparison of the capabilities of each registry.
Registry | FAIR | Search | Provider | Resolver | Lookup |
---|---|---|---|---|---|
AberOWL | 🟢 | 🟢 | 🟢 | 🔴 | 🟢 |
AgroPortal | 🔴 | 🔴 | 🟢 | 🔴 | 🔴 |
BioContext | 🟢 | 🔴 | 🟢 | 🔴 | 🔴 |
BioPortal | 🔴 | 🔴 | 🟢 | 🔴 | 🔴 |
Biolink | 🟢 | 🔴 | 🔴 | 🔴 | 🔴 |
Bioregistry | 🟢 | 🔴 | 🟢 | 🟢 | 🔴 |
Cellosaurus | 🟢 | 🔴 | 🔴 | 🔴 | 🔴 |
CHEMINF | 🔴 | 🔴 | 🟢 | 🔴 | 🔴 |
Crop OCT | 🟢 | 🟢 | 🟢 | 🔴 | 🔴 |
EcoPortal | 🔴 | 🔴 | 🟢 | 🔴 | 🔴 |
FAIRSharing | 🔴 | 🟢 | 🟢 | 🔴 | 🔴 |
GO | 🟢 | 🔴 | 🔴 | 🔴 | 🔴 |
Identifiers.org | 🟢 | 🟢 | 🟢 | 🟢 | 🔴 |
Name-to-Thing | 🟢 | 🔴 | 🟢 | 🟢 | 🔴 |
NCBI | 🔴 | 🔴 | 🔴 | 🔴 | 🔴 |
OBO Foundry | 🟢 | 🔴 | 🟢 | 🟢 | 🔴 |
OntoBee | 🔴 | 🔴 | 🟢 | 🔴 | 🟢 |
OLS | 🟢 | 🟢 | 🟢 | 🔴 | 🔴 |
Prefix Commons | 🟢 | 🟢 | 🟢 | 🔴 | 🔴 |
Prefix.cc | 🟢 | 🔴 | 🟢 | 🔴 | 🔴 |
Scholia | 🔴 | 🔴 | 🔴 | 🔴 | 🟢 |
UniProt | 🟢 | 🟢 | 🟢 | 🔴 | 🔴 |
Wikidata | 🟢 | 🟢 | 🟢 | 🔴 | 🔴 |
This section provides a systematic evaluation and comparison of the governance and standard operating procedures for each registry.
Registry | Accepts External Contributions | Public Version Control | Review Team | Scope | Status |
---|---|---|---|---|---|
AberOWL | 🔴 | 🔴 | n/a | bio-ontologies | active |
AgroPortal | 🟢 | 🔴 | private | agro-ontologies | active |
BioContext | 🟢 | 🟢 | inferrable | internal | active |
BioPortal | 🟢 | 🔴 | private | bio-ontologies | active |
Biolink | 🟢 | 🟢 | inferrable | internal | active |
Bioregistry | 🟢 | 🟢 | public | life sciences | active |
Cellosaurus | 🔴 | 🔴 | n/a | internal | active |
CHEMINF | 🟢 | 🟢 | inferrable | chemistry | unresponsive |
Crop OCT | 🟢 | 🔴 | public | agro-ontologies | active |
EcoPortal | 🟢 | 🔴 | private | eco-ontologies | active |
FAIRSharing | 🟢 | 🔴 | private | life sciences | active |
GO | 🟢 | 🟢 | inferrable | internal | inactive |
Identifiers.org | 🟢 | 🔴 | private | life sciences | unresponsive |
Name-to-Thing | 🔴 | 🔴 | n/a | life sciences | active |
NCBI | 🔴 | 🔴 | n/a | internal | inactive |
OBO Foundry | 🟢 | 🟢 | public | bio-ontologies | active |
OntoBee | 🔴 | 🔴 | n/a | bio-ontologies | active |
OLS | 🟢 | 🔴 | inferrable | bio-ontologies | active |
Prefix Commons | 🟢 | 🔴 | public | life sciences | active |
Prefix.cc | 🟢 | 🟢 | n/a | general | active |
Scholia | 🟢 | 🟢 | inferrable | life sciences | active |
UniProt | 🔴 | 🔴 | n/a | internal | active |
Wikidata | 🟢 | 🔴 | inferrable | general | active |
The semantic web and ontology communities are bound to the use of IRIs as identifiers and therefore are very interested in the interconversion between compact identifiers (i.e., CURIEs) and IRIs. While the Bioregistry provides many tools for one way conversion from CURIEs to IRIs, there are several related packages that help parse CURIEs from IRIs: