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 contains information about prefixes and their associated metadata. It 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 about these resources can be found here.

Metaregistry

The metaregistry contains information about registries and their associated metadata. It 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 about these resources can be found here.

Cross-Registry Mappings

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.

  • SSSOM TSV (auto-generated by GitHub Actions)

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.

Collections

The collections contain curated lists of prefixes. They can be downloaded in bulk from:

  • 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 about these resources can be found here.

Bioregistry Knowledge Graph

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 Contexts

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.

Related Downloads

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.