Repositories list

• wikipathways-collection

  Public
  Java

  •1•0•1•0•Updated Jan 12, 2025Jan 12, 2025

• wikipathways-database

  Public
  WikiPathways Database

  bioinformaticsbiologypathway-analysis+ 2wikipathwayspathway-enrichment-analysis

  Shell

  •15•5•16•1•Updated Jan 12, 2025Jan 12, 2025

• wikipathways-homology

  Public
  Pathway database for homology-mapped content

  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated Jan 12, 2025Jan 12, 2025

• wikipathways.github.io

  Public
  GitHub pages for GPML-Repo

  HTML

  •18•7•13•0•Updated Jan 10, 2025Jan 10, 2025

• wikipathways-data-release

  Public
  Monthly data release

  HTML

  •

  Creative Commons Zero v1.0 Universal

  •1•1•2•0•Updated Jan 10, 2025Jan 10, 2025

• wikipathways-assets

  Public
  Accessory files generated downstream of approved GPMLs

  Creative Commons Zero v1.0 Universal

  •1•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• wikipathways-pmcfigurebot

  Public
  Query figures indexed by PubMed Central and collect metadata

  R

  •

  Creative Commons Zero v1.0 Universal

  •4•0•1•0•Updated Jan 6, 2025Jan 6, 2025

• SARS-CoV-2-WikiPathways

  Public
  Temporary repository of RDF of selected pathways from WikiPathways, supporting the Wikidata bot.

  wikipathwayscovid-19sars-cov-2

  Java

  •

  Creative Commons Zero v1.0 Universal

  •3•2•1•0•Updated Dec 30, 2024Dec 30, 2024

• sr24-curation

  Public
  Java

  •0•0•0•0•Updated Dec 28, 2024Dec 28, 2024

• WikiPathwaysCurator

  Public
  Unit tests that validate the WikiPathways content and support the curation of the knowledge base.

  Java

  •

  MIT License

  •2•1•11•0•Updated Dec 28, 2024Dec 28, 2024

• wikipathways-api-client-java

  Public
  Java library for WikiPathways webservice

  Java

  •

  Apache License 2.0

  •4•1•3•1•Updated Dec 28, 2024Dec 28, 2024

• GPML2RDF

  Public
  GPML2RDF converter

  semantic-webwikipathwayswikipathways-gpml-files+ 1java

  Java

  •

  Apache License 2.0

  •2•4•38•0•Updated Dec 28, 2024Dec 28, 2024

• academy

  Public
  Organized training examples for new WikiPathways authors

  JavaScript

  •

  Creative Commons Zero v1.0 Universal

  •4•2•7•0•Updated Dec 23, 2024Dec 23, 2024

• pfocr-database

  Public
  Jekyll setup and database for the Pathway Figure OCR project

  HTML

  •

  Creative Commons Zero v1.0 Universal

  •3•0•5•0•Updated Dec 16, 2024Dec 16, 2024

• Jiffy

  Public template
  A template Jekyll site with wiki functionality

  HTML

  •

  MIT License

  •0•0•1•0•Updated Dec 11, 2024Dec 11, 2024

• SPARQLQueries

  Public
  Queries for the WikiPathways SPARQL endpoint.

  wikipathwayssparqlrdf

  Python

  •

  GNU General Public License v3.0

  •2•2•4•0•Updated Nov 13, 2024Nov 13, 2024

• pfocr-curation

  Public
  A curation tool for fixing and annotating the data associated with Pathway Figure OCR results.

  R

  •

  Apache License 2.0

  •0•1•0•0•Updated Nov 6, 2024Nov 6, 2024

• rWikiPathways

  Public
  R package for WikiPathways API

  bioinformaticspathwaysdata-access+ 1rpackage

  HTML

  •

  MIT License

  •6•15•4•0•Updated Oct 30, 2024Oct 30, 2024

• pfocr-pmcfigurebot

  Public
  Query figures indexed by PubMed Central and collect metadata

  R

  •

  Creative Commons Zero v1.0 Universal

  •4•1•0•0•Updated Oct 24, 2024Oct 24, 2024

• pywikipathways

  Public
  Python Client Package for WikiPathways

  pythonbiologywikipathways+ 1pathway-enrichment-analysis

  Python

  •

  MIT License

  •4•16•1•0•Updated Oct 19, 2024Oct 19, 2024

• fdp

  Public
  Repository with the content of the WikiPathways FAIR Data Point.

  fdpfair-data-pointwikipathway

  HTML

  •0•0•4•0•Updated Oct 18, 2024Oct 18, 2024

• sr24-subdomain

  Public
  HTML

  •

  Creative Commons Zero v1.0 Universal

  •0•1•2•0•Updated Oct 13, 2024Oct 13, 2024

• sandbox-wp-db

  Public
  Playground for new GPML processing and curation

  Shell

  •4•0•9•3•Updated Oct 9, 2024Oct 9, 2024

• gpml-to-cx2

  Public
  GPML to CX2 Converter

  convertergpmlcx2

  JavaScript

  •1•2•5•1•Updated Oct 5, 2024Oct 5, 2024

• wikipathways-java-client

  Public
  Java library for WikiPathways webservice

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

• wikipathways-help

  Public
  1•1•3•0•Updated Sep 23, 2024Sep 23, 2024

• daphnia-subdomain

  Public
  HTML

  •1•0•0•0•Updated Sep 21, 2024Sep 21, 2024

• sandbox-wp-assets

  Public
  Playground for actions dealing with wikipathways-assets repo

  0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

• cytoscape-wikipathways-app

  Public
  WikiPathways app for Cytoscape to open and access pathways from WikiPathways

  Java

  •

  Apache License 2.0

  •7•5•21•1•Updated Aug 22, 2024Aug 22, 2024

• EuropePMCLinks

  Public
  Repository for code to create the Europe PMC external links

  alphawikipathwayseuropepmc

  Groovy

  •

  MIT License

  •0•0•1•0•Updated Aug 7, 2024Aug 7, 2024