Are you using the Bioregistry and want your project/organization on this list? Please let us know on the issue tracker.

To find new users, start with this GitHub search for the Bioregistry. Similarly, downstream users of the Bioregistry often use the curies package. See its usages with this search.

Global Alliance for Genomics and Health

Type Organization
Homepage https://www.ga4gh.org/
Wikidata Q60750423
Usages
  • Gave a tutorial at ISMB 2022 on how to run a local instance of the Bioregistry (ref)

LinkML

Type Project
Homepage https://linkml.io
Wikidata Q108911530
Usages
  • Uses the Bioregistry as a semantic space of other semantic spaces in prefix maps (ref)
  • Caches the Bioregistry data with use case-specific preprocessing (ref)
  • Uses the Bioregistry package for lookup of URI format strings (ref)

Automating Scientific Knowledge Extraction and Modeling

Type Project
Homepage https://indralab.github.io/#askem
Wikidata Q116898517
Usages
  • Deploys a custom instance of the Bioregistry including a subset of prefixes from the main services and additional custom prefixes for epidemiology modeling and space weather use cases

BioClients

Type Package
Homepage https://github.com/jeremyjyang/BioClients
Wikidata Q116898721
Usages
  • Wraps the API of bioregistry.io in a Python package (ref) (ref)

BridgeDb

Type Project
Homepage https://www.bridgedb.org
Wikidata Q55582517
Usages
  • Links prefixes used in BridgeDb's mapping database to Bioregistry prefixes, standardizing when possible (ref) (ref)
  • Standardizes annotations of CURIEs that have been replaced in the TIWID database (ref)

Ontology Lookup Service

Type Project
Homepage https://www.ebi.ac.uk/ols/index
Wikidata Q22230760
Usages
  • Uses the Bioregistry to parse CURIEs in ontologies and generate links (ref)

FAIRsFAIR Research Data Object Assessment Service

Type Project
Homepage https://github.com/pangaea-data-publisher/
Repository https://github.com/pangaea-data-publisher/fuji
Usages
  • Uses the Bioregistry data file directly to implement its own URI parser (ref)

Manubot

Type Project
Homepage https://manubot.org/
Wikidata Q96473455
Usages
  • Uses the Bioregistry python package to parse CURIEs appearing in scholarly articles, generate links, and retrieve metadata (ref)

LOTUS Initiative

Type Project
Homepage https://lotus.naturalproducts.net/
Wikidata Q104225190
Usages
  • Generates Bioregistry links for resolving CURIEs for taxa and natural products (ref)

Text2Term Ontology Mapper

Type Package
Homepage https://github.com/ccb-hms/ontology-mapper
Wikidata Q116924843
Usages
  • Uses the Bioregistry python package for parsing URIs (ref)

Bionty

Type Project
Homepage https://lamin.ai/docs/bionty
Repository https://github.com/laminlabs/bionty
Usages
  • Uses the Bioregistry Python package to normalize prefixes (ref) (ref)
Type Organization
Homepage https://www.related.vc
Wikidata Q116924914
Usages
  • Uses the Bioregistry Python package to normalize prefixes and CURIEs in its ENSEMBL pre-processing pipeline (ref) (ref)

SciBite

Type Organization
Homepage https://scibite.com/
Wikidata Q105080220
Usages
  • Uses the Bioregistry resolver

Gut-brain Axis Knowledge Graph

Type Package
Homepage https://github.com/liwenqingi/GBA-KG
Usages
  • Uses the Bioregistry via BERN2

WikiPathways

Type Project
Homepage https://www.wikipathways.org
Wikidata Q7999828
Usages
  • Standardizes cross-references with the Bioregistry (via BridgeDB) (ref)

Ensmallen / Grape

Type Package
Homepage https://github.com/AnacletoLAB/ensmallen
Wikidata Q116924819
Usages
  • Uses the Bioregistry Python package to standardize CURIEs in knowledge graphs generated from ontologies and other sources (ref)

Advanced Biomedical Entity Recognition and Normalization

Type Package
Homepage https://github.com/dmis-lab/BERN2
Wikidata Q116924884
Usages
  • Uses the Bioregistry web service for expanding CURIEs into URIs (ref)
  • Uses the Bioregistry Python package for normalizing prefixes (ref)

OntoGPT

Description A knowledge extraction tool that uses a large language model to extract semantic information from text.
Type Package
Homepage https://monarch-initiative.github.io/ontogpt/
Repository https://github.com/monarch-initiative/ontogpt
Usages

OBO Foundry

Type Organization
Homepage https://obofoundry.org/
Repository https://github.com/OBOFoundry/OBOFoundry.github.io
Wikidata Q7072326
Usages
  • Uses the Bioregistry in order to identify if proposed ontologies' prefixes collide with existing prefixes (ref) (ref)

Ontology Quality 2022 Analysis

Type Analysis
Homepage https://github.com/Ostrzyciel/ontology-quality-2022
Usages
  • Uses Bioregistry data directly to identify prefixes in ontologies that aren't OBO Foundry prefixes (ref)

iSamples.org

Type Organization
Homepage https://isamplesorg.github.io/
Repository https://github.com/isamplesorg
Usages
  • Uses the Bioregistry as a semantic space for referencing prefixes (in LinkML) (ref)

BioCypher

Type Project
Homepage https://biocypher.org/
Repository https://github.com/saezlab/BioCypher
Usages
  • Uses the Bioregistry Python package for normalizing CURIEs (ref)

Babel Validator

Type Package
Homepage https://github.com/TranslatorSRI/babel-validation
Usages
  • Uses the Bioregistry resolver for creating resolvable links (ref)

National Microbiome Data Collaborative

Type Organization
Homepage https://microbiomedata.org/
Wikidata Q94461838
Usages
  • Uses the Bioregistry Python package to normalize prefixes, look up patterns, etc. (ref)

PheKnowLator

Type Package
Homepage https://github.com/callahantiff/PheKnowLator/wiki
Repository https://github.com/callahantiff/PheKnowLator
Usages
  • Normalizing IRIs and CURIEs during the construction of the knowledge graph

Natural Product Knowledge Graph

Description A graph framework that creates a biomedical knowledge graph to identify and generate mechanistic hypotheses for pharmacokinetic natural product-drug interactions.
Type Package
Homepage https://github.com/sanyabt/np-kg
Usages
  • Normalizing IRIs and CURIEs during the construction of the knowledge graph via PheKnowLator

Ontology Quality Assessment Toolkit

Type Package
Homepage https://cthoyt.github.io/oquat
Repository https://github.com/cthoyt/oquat
Usages
  • Uses the Bioregistry Python package to check the standardization of prefixes in OBO Foundry ontologies
  • Uses the Bioregistry to get a list of ontologies and their download links

PyOBO

Type Package
Homepage https://github.com/pyobo/pyobo
Wikidata Q116738054
Usages
  • Uses the Bioregistry Python package to get a list of ontologies and their download links
  • Uses the Bioregistry Python package to standardize prefixes, CURIEs, and IRIs in ontologies
  • Uses the Bioregistry Python package to validate prefixes, CURIEs, and IRIs in ontologies during the construction of custom ontologies, e.g., from biological databases

SSSOM

Type Project
Homepage https://mapping-commons.github.io/sssom/
Repository https://github.com/mapping-commons/sssom
Wikidata Q108394654
Usages
  • Uses the Bioregistry as a default prefix map

Basic Register of Thesauri, Ontologies & Classifications

Type Project
Homepage https://bartoc.org
Wikidata Q22279816
Usages
  • Included in registry (ref)

DBPedia

Type Project
Homepage https://www.dbpedia.org/
Wikidata Q465
Usages
  • Uses Bioregistry for downloading ontologies and getting URI format strings (ref)

refineGEMs

Type Package
Homepage https://github.com/draeger-lab/refinegems
Usages