Owner

wikipathways

10 indexed repositories · View on GitHub

wikipathways-database
WikiPathways Database

Shell · 19 stars
wikipathways.github.io
GitHub pages for GPML-Repo

HTML · 12 stars
GPML2RDF
GPML2RDF converter

Java · 4 stars
SARS-CoV-2-WikiPathways
Temporary repository of RDF of selected pathways from WikiPathways, supporting the Wikidata bot.

Java · 2 stars
sandbox-wp-db
Playground for new GPML processing and curation

Shell · 1 star
WikiPathwaysCurator
Unit tests that validate the WikiPathways content and support the curation of the knowledge base.

Java · 1 star
wikipathways-data-release
Monthly data release

HTML · 1 star
wikipathways-iri-resolver

Python · 0 stars
fdp
Repository with the content of the WikiPathways FAIR Data Point.

HTML · 0 stars
wikipathways-collection

Java · 0 stars

Beginner friendly Everything

Open All

"on pull request" not robust enough Open

bug

wikipathways/wikipathways-database#117 · 2 assignees · Opened Sep 7, 2026
Update documentation to run tests on a batch of GPMLs Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

wikipathways/WikiPathwaysCurator#35 · Opened Sep 3, 2026
add EFSA funding to AOP Portal Open

wikipathways/wikipathways-database#103 · 1 assignee · Opened Aug 23, 2026
Author order in pathway model Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

wikipathways/wikipathways.github.io#158 · Opened Jul 6, 2026
Add link to database location for each pathway Open

enhancement question

wikipathways/wikipathways.github.io#154 · 4 comments · 1 reaction · 1 assignee · Opened Apr 30, 2026
Load FOAF ontology Open

wikipathways/GPML2RDF#123 · 2 comments · 2 assignees · Opened Feb 10, 2026
IRIs are http:// and not http:// Open

wikipathways/wikipathways-iri-resolver#10 · 1 assignee · Opened Feb 6, 2026
Add RDF portal information to landing page Open

wikipathways/wikipathways-iri-resolver#9 · 1 assignee · Opened Feb 6, 2026
Semantic Interactions (wp) IRI resolution Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

wikipathways/wikipathways-iri-resolver#8 · Opened Feb 6, 2026
Complex IRI resolution Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

wikipathways/wikipathways-iri-resolver#7 · Opened Feb 6, 2026
PublicationXref IRI resolution Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

wikipathways/wikipathways-iri-resolver#6 · Opened Feb 6, 2026
Group IRI resolution Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

wikipathways/wikipathways-iri-resolver#5 · Opened Feb 6, 2026
Interaction (gpml) IRI resolution Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

wikipathways/wikipathways-iri-resolver#4 · Opened Feb 6, 2026
DataNode IRI resolution Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

wikipathways/wikipathways-iri-resolver#3 · Opened Feb 6, 2026
User IRI resolution Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

wikipathways/wikipathways-iri-resolver#2 · Opened Feb 6, 2026
Pathway IRI resolution Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

wikipathways/wikipathways-iri-resolver#1 · Opened Feb 6, 2026
interaction not recognized Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

wikipathways/GPML2RDF#122 · Opened Jan 25, 2026
Disease ontology term not converted correctly from gpml to md Open

bug

wikipathways/wikipathways-database#70 · 1 comment · 1 assignee · Opened Dec 13, 2025
Guidance needed for communities in account profiles Open

documentation

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

wikipathways/wikipathways.github.io#146 · 1 comment · Opened Sep 9, 2025
add a "download GPML" for the PR version Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

wikipathways/sandbox-wp-db#38 · Opened Aug 14, 2025
Include biodirectional interactions in WP RDF Open

enhancement

wikipathways/GPML2RDF#121 · 1 assignee · Opened Jul 24, 2025
Handling of deleted duplicate pathways Open

enhancement

wikipathways/wikipathways.github.io#142 · 1 assignee · Opened Jun 6, 2025
Test for errors in `rdf:type` annotations Open

wikipathways/GPML2RDF#120 · 1 comment · 1 assignee · Opened Apr 16, 2025
Add monthly data release stats/info on front page Open

enhancement

wikipathways/wikipathways.github.io#126 · 2 comments · 1 assignee · Opened Jan 24, 2025
Report for "at least one reference" reports pathways with non-PMC references Open

wikipathways/wikipathways-collection#5 · 1 comment · 1 assignee · Opened Jan 7, 2025
Not all interaction are created, e.g. not for things annotated with disease (or so it seems) Open

bug enhancement

wikipathways/GPML2RDF#119 · 1 assignee · Opened Dec 27, 2024
Feature request: Show citations in the svg image on WikiPathways website Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

wikipathways/wikipathways.github.io#123 · Opened Oct 31, 2024
Suggested updates to Reviewer Checklist for "new pathway submission" PRs Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

wikipathways/sandbox-wp-db#27 · 1 reaction · Opened Oct 21, 2024
Proposed change: Add URL as acceptable reference for "atLeastOneReference" test Open

question

Difficulty 3/5 1-2 days Newbie friendliness 35/100

wikipathways/WikiPathwaysCurator#33 · Opened Sep 23, 2024
delete action Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

wikipathways/sandbox-wp-db#26 · Opened Sep 19, 2024
Parsing newlines in GPML description causes error Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

wikipathways/sandbox-wp-db#24 · Opened Sep 19, 2024
License info is missing Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

wikipathways/wikipathways-database#62 · Opened Aug 11, 2024
SARS-CoV-2 protein identifiers not loaded and mappings not available in the assets Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

wikipathways/wikipathways-database#59 · Opened May 23, 2024
WP2804 contains SBGN notation which breaks the build process Open

help wanted

wikipathways/wikipathways-database#58 · 1 assignee · Opened Mar 17, 2024
Use the GitHub discussion actions to automatically post daily GPML sync reports as discussion comments Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

wikipathways/wikipathways-database#56 · 1 comment · Opened Mar 15, 2024
add statistics #swat4hcls Open

wikipathways/fdp#6 · 1 assignee · Opened Feb 27, 2024
Add step to search action log for "Exception" and "Error" Open

wikipathways/sandbox-wp-db#21 · 1 assignee · Opened Jan 23, 2024
Compare old and new .md files Open

wikipathways/sandbox-wp-db#20 · 1 assignee · Opened Jan 23, 2024
Another way to check for community pathways not yet approved Open

documentation

wikipathways/wikipathways-database#53 · 1 comment · 1 assignee · Opened Jan 23, 2024
Todo items for migration Open

wikipathways/sandbox-wp-db#14 · 1 comment · 2 assignees · Opened Nov 30, 2023
Prioritize exact matches in search results Open

wikipathways/wikipathways.github.io#109 · 1 comment · 1 assignee · Opened Nov 9, 2023
generate-references fails to log error with incorrect PubMed ID Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

wikipathways/wikipathways-database#50 · 1 comment · Opened Nov 8, 2023
Tests to run Open

wikipathways/sandbox-wp-db#6 · 1 comment · 2 assignees · Opened Nov 1, 2023
Add content describing the process to become part of Reviewer of the Week Open

documentation planned

wikipathways/wikipathways.github.io#103 · 1 comment · 1 assignee · Opened Oct 6, 2023
Update WikiPathways videos on Youtube for new website Open

documentation planned

wikipathways/wikipathways.github.io#101 · 2 comments · 1 assignee · Opened Sep 30, 2023
ChatGPT-powered JSON API queries Open

wikipathways/wikipathways.github.io#99 · 1 assignee · Opened Sep 20, 2023
report in the FDP about the WikiPathways Communities/Portals Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

wikipathways/fdp#5 · Opened Sep 10, 2023
report on the rare diseases found in WikiPathways Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

wikipathways/fdp#4 · Opened Sep 10, 2023
Add participant tsv download to first download button Open

wikipathways/wikipathways.github.io#97 · 1 assignee · Opened Sep 4, 2023
update needed for fetching the right BridgeDb Derby files Open

wikipathways/wikipathways-database#47 · 1 assignee · Opened Aug 8, 2023

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