Repositories list

• edamontology

  Public
  EDAM is an ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, …

  sciencedatatopic+ 11topicsformatontologydata-analysisweb-ontology-languageidentifieroperation+ 4

  Shell

  •

  Creative Commons Attribution Share Alike 4.0 International

  •58•134•191•37•Updated Feb 3, 2026Feb 3, 2026

• edam-ontology.py

  Public
  Python

  •

  Other

  •1•3•0•0•Updated Feb 2, 2026Feb 2, 2026

• pubfetcher

  Public
  A Java command-line tool and library to download and store publications with metadata by combining content from various online resources

  scrapingdoipubmed+ 3publicationsjournalseurope-pmc

  Java

  •

  GNU General Public License v3.0

  •1•8•0•0•Updated Jan 22, 2026Jan 22, 2026

• edammap

  Public
  A tool for mapping various text input to EDAM ontology concepts

  Java

  •

  GNU General Public License v3.0

  •5•10•1•0•Updated Jan 22, 2026Jan 22, 2026

• edamontology.org

  Public
  Static EDAM website

  HTML

  •

  Creative Commons Attribution Share Alike 4.0 International

  •4•0•9•3•Updated Nov 19, 2025Nov 19, 2025

• caseologue

  Public
  Validation tools for the EDAM ontology

  quality-controlcontinuous-integrationontology+ 1sparql-query

  CSS

  •

  MIT License

  •3•2•6•1•Updated Nov 12, 2025Nov 12, 2025

• edammcp

  Public
  Python

  •

  MIT License

  •11•10•22•3•Updated Nov 6, 2025Nov 6, 2025

• edam-bioimaging

  Public
  An ontology of imaging and related techniques and technologies, image processing and analysis, image data and formats, within bio- and other sciences.

  ontologyartificial-intelligenceimaging+ 1image-analysis-and-processing

  Shell

  •

  Creative Commons Attribution Share Alike 4.0 International

  •8•11•19•2•Updated Oct 26, 2025Oct 26, 2025

• edam2json-js

  Public
  Javascript library to convert EDAM to JSON/JSON-LD

  JavaScript

  •

  MIT License

  •2•3•1•1•Updated Jun 18, 2025Jun 18, 2025

• edam-browser

  Public
  Stand-alone, lightweight, and fast JavaScript browser for EDAM and other ontologies

  visualizationontologiesontology-search+ 6edamedam-annotationsontology-servicesontology-engineeringedam-ontologyvisualization-javascript-widget

  JavaScript

  •

  MIT License

  •25•15•29•4•Updated May 9, 2025May 9, 2025

• .github

  Public
  Repo for organisation-level README

  0•0•0•0•Updated Mar 19, 2025Mar 19, 2025

• scripts

  Public
  A repo for various kinds of scripts that do something around EDAM

  Python

  •0•0•0•0•Updated Feb 18, 2025Feb 18, 2025

• edam-sandbox

  Public
  Miscellaneous files for test purposes

  Jupyter Notebook

  •2•1•37•6•Updated Dec 5, 2024Dec 5, 2024

• edam-fu

  Public
  EDAM ontology formatting utility

  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 4, 2024Jul 4, 2024

• edamontology.github.io

  Public
  obsolete repo for the EDAM ontology website (redirects to edamontology.org)

  HTML

  •1•0•0•0•Updated Jul 4, 2024Jul 4, 2024

• edamxpathvalidator

  Public archive
  Verification script for the EDAM ontology

  Python

  •

  GNU General Public License v3.0

  •0•0•15•1•Updated Jul 4, 2024Jul 4, 2024

• edam-geo

  Public
  Extension of EDAM towards geo- and other sciences, including Earth and planetary sciences, climate science, ecology, public health, environmental monitoring, em…

  sciencegeospatialgis+ 7earthhumanitariangeographic-dataecologybiodiversityclimate-scienceinterdisciplinary

  Shell

  •

  Creative Commons Attribution Share Alike 4.0 International

  •0•0•0•0•Updated May 31, 2024May 31, 2024

• edam2json

  Public
  utility to export EDAM to various sorts of JSON formats (JSON-LD, bio.tools JSON)

  Python

  •

  MIT License

  •2•2•0•0•Updated Feb 1, 2024Feb 1, 2024

• edamontologyDocs

  Public
  Documentation for EDAM.

  Makefile

  •

  Creative Commons Attribution Share Alike 4.0 International

  •3•1•18•0•Updated Apr 20, 2023Apr 20, 2023

• edam-geo-wp-dump

  Public
  EDAM ("Geo"), raw download from WebProtégé

  0•0•0•0•Updated Mar 19, 2023Mar 19, 2023

• edam-popovers

  Public
  A Firefox & Chrome extension that displays detailed information about EDAM concepts

  firefox-addonpopoverontologies+ 4chrome-extensionsedamontology-servicesedam-ontology

  JavaScript

  •

  MIT License

  •3•4•11•0•Updated Nov 15, 2022Nov 15, 2022

• logoi

  Public
  Various suggestions of logoi for EDAM and related tools

  Creative Commons Attribution Share Alike 4.0 International

  •5•0•0•3•Updated Dec 29, 2021Dec 29, 2021

• jupyterlab-test

  Public
  Testing OWL tools in JupyterLab (in usegalaxy.eu)

  Jupyter Notebook

  •0•0•0•0•Updated Aug 18, 2021Aug 18, 2021

• edam-geo-test.bak

  Public
  Extension of the EDAM ontology for geo-related concepts, including areas of Earth and planetary sciences, climate research, ecology, public health, etc.

  Shell

  •

  Creative Commons Attribution Share Alike 4.0 International

  •0•0•0•1•Updated Aug 16, 2021Aug 16, 2021

• edam-stub-experiment

  Public
  Creative Commons Attribution Share Alike 4.0 International

  •1•0•1•2•Updated May 17, 2021May 17, 2021

• benten

  Public
  A language server for Common Workflow Language

  Python

  •

  Apache License 2.0

  •9•0•0•0•Updated May 11, 2021May 11, 2021

• debtag2edam2debtags

  Public
  The EDAM ontology for bioinformatics tools and services should be come compatible with the Debtags and vice versa. This project starts out with adding EDAM refe…

  2•0•0•0•Updated Mar 27, 2021Mar 27, 2021

• edam-playground

  Public
  Slides, swings, and sandbox ontology

  sandboxslidesedam+ 1swings

  Shell

  •

  Creative Commons Attribution Share Alike 4.0 International

  •0•0•0•0•Updated Mar 7, 2021Mar 7, 2021