The content of the Bioregistry's database is split into three sections. See the JSON schema page for further documentation on their format.
The registry contains information about prefixes and their associated metadata. It can be downloaded as:
The manually curated portions of these data are available under the CC0 1.0 Universal License. Aggregated data are redistributed under their original licenses as described here. More information about these resources can be found here.
The metaregistry contains information about registries and their associated metadata. It can be downloaded as:
The entirety of the metaregistry is manually curated and is available under the CC0 1.0 Universal License. More information about these resources can be found here.
Mappings between registries (i.e., Identifiers.org uses taxonomy and OBO Foundry uses
NCBITaxon for the same thing) are exported in the
Simple Standard for Sharing Ontology Mappings (SSSOM)
format.
The entirety of the cross-registry mappings is semi-automatically curated and is available under the CC0 1.0 Universal License. More information about these resources can be found here.
The collections contain curated lists of prefixes. They can be downloaded in bulk from:
The entirety of the collections is manually curated and is available under the CC0 1.0 Universal License. More information about these resources can be found here.
The Bioregistry exports a unified knowledge graph encoded in the Resource Description Framework (RDF) for integration in triple stores and linked open data settings. See the RDF schema page for documentation on schema elements. The schema is provided in the following formats:
The combine registry, metaregistry, and collections can be downloaded as RDF in the following formats:
The manually curated portions of these data are available under the CC0 1.0 Universal License. Aggregated data are redistributed under their original licenses as described here. More information about these resources can be found here.
A network-based view over the full knowledge graph is generated and uploaded to the Network Data Exchange (NDEx) for exploration using Cytoscape.
Semantic web applications often require mappings between prefixes and URI prefixes to locally handle CURIE/URI conversion. The Bioregistry generates context files for the full registry for reuse:
All context exports are available under the CC0 1.0 Universal License. In addition to the full export, the Bioregistry generates contexts for all collections as well as has more powerful utilities for curating prescriptive contexts. A full list of semantic web contexts generated from both collections and prescriptive contexts can be found here.
The Bioregistry Regular Expression Report uses PyOBO to check how consistent all of the regular expression patterns are with the actual identifiers from databases that are parsed by PyOBO. This contains most entries from the OBO Foundry that are still accessible as well as several additional resources such as HGNC, UniProt, etc. The automatically generated/updated report is available here.