Repositories list

• ols4

  Public
  The EMBL-EBI Ontology Lookup Service (OLS)

  mcpowlembeddings+ 7

  mcpowlembeddingsknowledge-graphontologiessemantic-searchknowledge-managementknowledge-representationfair-datamcp-server

  Java

  •

  Apache License 2.0

  •4545 forks•9898 stars•7272 issues•1313 pull requests•Updated Aug 14, 2026Aug 14, 2026

• efo

  Public
  Github repo for the Experimental Factor Ontology (EFO)

  Python

  •1515 forks•6464 stars•182182 issues•1212 pull requests•Updated Aug 14, 2026Aug 14, 2026

• oxo2

  Public
  A SSSOM compliant implementation of OxO that is backwards compatible with OxO version 1

  Java

  •

  Apache License 2.0

  •00 forks•11 star•11 issue•77 pull requests•Updated Aug 14, 2026Aug 14, 2026

• GWAS_Catalog-workshop

  Public archive
  Training material for the GWAS Catalog REST API workshop

  Jupyter Notebook

  •44 forks•1313 stars•00 issues•11 pull request•Updated Aug 13, 2026Aug 13, 2026

• horned-owl

  Public
  Rust

  •

  GNU Lesser General Public License v3.0

  •1919 forks•00 stars•00 issues•00 pull requests•Updated Aug 11, 2026Aug 11, 2026

• PEGASUS

  Public
  Predicted effector gene standard

  TypeScript

  •00 forks•33 stars•00 issues•1919 pull requests•Updated Aug 11, 2026Aug 11, 2026

• hermit-rs

  Public
  Rust

  •2727 forks•11 star•00 issues•00 pull requests•Updated Aug 6, 2026Aug 6, 2026

• whelk-rs

  Public
  Whelk is an OWL EL reasoner

  Rust

  •

  MIT License

  •99 forks•00 stars•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• GrEBI

  Public
  HPC aggregation pipeline and API/MCP server for LLM-mediated biomedical data integration

  data-miningbioinformaticsneo4j+ 5

  data-miningbioinformaticsneo4jmcpdata-integrationontologiesknowledge-graphsmcp-server

  Jupyter Notebook

  •

  Apache License 2.0

  •44 forks•44 stars•1717 issues•11 pull request•Updated Jul 17, 2026Jul 17, 2026

• cohort-ontology

  Public
  A lightweight ontology for consistent identification and description of human cohorts. It defines a unique cohort identifier with minimal metadata, enabling lin…

  Makefile

  •

  Creative Commons Zero v1.0 Universal

  •00 forks•55 stars•33 issues•00 pull requests•Updated Jul 16, 2026Jul 16, 2026

• environmental-exposure-ontology

  Public
  Modular environmental exposures ontology

  Makefile

  •

  Other

  •2121 forks•00 stars•00 issues•11 pull request•Updated Jul 16, 2026Jul 16, 2026

• pretty_rdf

  Public
  Rust

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jun 29, 2026Jun 29, 2026

• zooma2

  Public
  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•11 pull request•Updated May 29, 2026May 29, 2026

• gwas-solr-slim

  Public archive
  Python

  •00 forks•11 star•11 issue•33 pull requests•Updated May 22, 2026May 22, 2026

• otar_profiler

  Public
  Pipeline for creating Open Targets profile and slim files from EFO.

  Ruby

  •00 forks•44 stars•00 issues•00 pull requests•Updated May 20, 2026May 20, 2026

• efo-llm-assessment

  Public
  Github repo for testing the LLM capabilities to edit the Experimental Factor Ontology (EFO)

  Makefile

  •1515 forks•00 stars•00 issues•33 pull requests•Updated May 7, 2026May 7, 2026

• gwas-sumstats-harmoniser-documentation

  Public archive
  gwas-sumstats-harmoniser-documentation

  TypeScript

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• scatlas_ontology

  Public
  SCA_Ontology

  Makefile

  •22 forks•55 stars•1212 issues•33 pull requests•Updated Jan 19, 2026Jan 19, 2026

• hancestro

  Public
  obofoundry

  obofoundry

  Makefile

  •

  Creative Commons Attribution 4.0 International

  •22 forks•77 stars•99 issues•00 pull requests•Updated Oct 14, 2025Oct 14, 2025

• ontoSPOT-annotation

  Public
  A set of tools that annotate free text to ontologies using LLMs.

  Python

  •00 forks•22 stars•11 issue•00 pull requests•Updated Aug 18, 2025Aug 18, 2025

• monarch_pheval

  Public
  Jinja

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Mar 25, 2025Mar 25, 2025

• curategpt

  Public
  LLM-driven curation assist tool

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •2323 forks•00 stars•00 issues•00 pull requests•Updated Mar 12, 2025Mar 12, 2025

• gwas-sumstats-tools-documentation

  Public archive
  Documentation to gwas-sumstats-tools

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 14, 2025Jan 14, 2025

• gwas-curation-utils

  Public archive
  Scripts to help enhance GWAS curation tasks.

  Python

  •00 forks•00 stars•00 issues•11 pull request•Updated Oct 16, 2024Oct 16, 2024

• gwas-associationFilter

  Public archive
  Python

  •00 forks•00 stars•00 issues•11 pull request•Updated Oct 16, 2024Oct 16, 2024

• BioSolr

  Public
  A project aiming "to significantly advance the state of the art with regard to indexing and querying biomedical data with freely available open source software"

  Java

  •

  Apache License 2.0

  •2828 forks•1111 stars•00 issues•44 pull requests•Updated Jul 30, 2024Jul 30, 2024

• eshg-2024-workshop

  Public archive
  Workshop material for the European Human Genetics Conference 2024

  HTML

  •

  Creative Commons Attribution 4.0 International

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 22, 2024Jul 22, 2024

• ontotools-docker

  Public
  Configuration to deploy ontotools using docker compose

  Shell

  •

  Apache License 2.0

  •1212 forks•55 stars•55 issues•00 pull requests•Updated Jun 4, 2024Jun 4, 2024

• EFO-website

  Public
  Source code for the EFO website at http://www.ebi.ac.uk/efo

  HTML

  •

  Apache License 2.0

  •00 forks•11 star•11 issue•11 pull request•Updated May 22, 2024May 22, 2024

• oxo1-sssom2neo

  Public
  SSSOM to Neo4J loader compliant with OxO 1 Neo4j database. Initially cloned from https://github.com/mapping-commons/sssom2neo

  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 9, 2024Feb 9, 2024