Repositories list

• edamontology

  Public
  EDAM is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and data life cycle. Targetting usability by diverse users, EDAM's structure is relatively simple, divided into 4 sections: Topic, Operation, Data, and Format.

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

  Shell

  •

  Creative Commons Attribution Share Alike 4.0 International

  •58•120•196•31•Updated Nov 7, 2024Nov 7, 2024

• edamontology.org

  Public
  Static EDAM website

  HTML

  •

  Creative Commons Attribution Share Alike 4.0 International

  •4•0•8•3•Updated Oct 30, 2024Oct 30, 2024

• edam-bioimaging

  Public
  Ontology of bioimage informatics operations, topics, types of data, and data formats. EDAM-Bioimaging is an extension of the EDAM ontology (edamontology.org) dedicated to bioimaging data analysis, and developed in an open collaboration including partners from NEUBIAS (neubias.org), COMULIS (comulis.eu), and ELIXIR (elixir-europe.org)..

  Shell

  •

  Creative Commons Attribution Share Alike 4.0 International

  •8•10•18•2•Updated Oct 30, 2024Oct 30, 2024

• caseologue

  Public
  Validation tools for the EDAM ontology

  quality-controlcontinuous-integrationontology+ 1sparql-query

  CSS

  •

  MIT License

  •3•1•6•1•Updated Sep 13, 2024Sep 13, 2024

• edammap

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

  Java

  •

  GNU General Public License v3.0

  •5•9•1•0•Updated Sep 2, 2024Sep 2, 2024

• 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 Aug 29, 2024Aug 29, 2024

• edam-sandbox

  Public
  Miscellaneous files for test purposes

  Jupyter Notebook

  •2•1•37•6•Updated Jul 6, 2024Jul 6, 2024

• edam-browser

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

  ontologiesontology-searchedam+ 6edam-annotationsontology-servicesontology-engineeringedam-ontologyvisualization-javascript-widgetvisualization

  JavaScript

  •

  MIT License

  •23•14•27•5•Updated Jul 5, 2024Jul 5, 2024

• edam2json-js

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

  JavaScript

  •

  MIT License

  •2•3•1•0•Updated Jul 5, 2024Jul 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, emergency management, etc. Everyone welcome to view & comment at https://webprotege.stanford.edu/#projects/69591619-4eda-4f03-9e7f-65b213038fe1/edit/Classes (free registration needed).

  geospatialgisearth+ 7humanitariangeographic-dataecologybiodiversityclimate-scienceinterdisciplinaryscience

  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-ontology.py

  Public
  Python

  •

  Other

  •0•2•0•0•Updated Aug 3, 2021Aug 3, 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

  •10•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 references to the debtags volcabulary export file.

  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