Downloads

The content of the Bioregistry's database is split into three sections. See the JSON schema page for further documentation on their format.

Registry

The registry can be downloaded as:

  • JSON (reference file)
  • JSON (consensus file, auto-generated by GitHub Actions)
  • YAML (consensus file, auto-generated by GitHub Actions)
  • TSV (consensus file, auto-generated by GitHub Actions)

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 can be found here.

Metaregistry

The metaregistry can be downloaded as:

  • JSON (reference file)
  • YAML (auto-generated by GitHub Actions)
  • TSV (auto-generated by GitHub Actions)

The entirety of the metaregistry is manually curated and is available under the CC0 1.0 Universal License.

More information can be found here.

Collections

The collections can be downloaded as:

  • JSON (reference file)
  • YAML (auto-generated by GitHub Actions)
  • TSV (auto-generated by GitHub Actions)

The entirety of the collections is manually curated and is available under the CC0 1.0 Universal License.

More information can be found here.

Derived and Related Resources

RDF

The Bioregisty provides an RDF dump 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 can be found here.

Bioregistry Regular Expression Report

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.

Bioregistry SSSOM

Mappings between registries are exported in the Simple Standard for Sharing Ontology Mappings (SSSOM) format.

More information can be found here.

Bioregistry Knowledge Graph

Related to the RDF dump, there is preliminary work in generating a knowledge graph around the information in the Bioregistry, including the relations between resources, providers, and registries. It can be viewed on the Network Data Exchange (NDEx).