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wikipathways-database

WikiPathways Database

https://github.com/wikipathways/wikipathways-database

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary

Keywords

bioinformatics biology pathway-analysis pathway-enrichment-analysis wikipathways
Last synced: 6 months ago · JSON representation

Repository

WikiPathways Database

Basic Info
Statistics
  • Stars: 11
  • Watchers: 11
  • Forks: 16
  • Open Issues: 15
  • Releases: 0
Topics
bioinformatics biology pathway-analysis pathway-enrichment-analysis wikipathways
Created about 4 years ago · Last pushed 6 months ago
Metadata Files
Readme Citation

README.md

Welcome to the WikiPathways Database

This repository is the primary database for pathway content for the WikiPathways project, including the source for content at www.wikipathways.org.

General Usage

Users may be directed here by edit links on the website (e.g., pencil icons). Changes made to the files here will be reflected on the website after a few minutes.

Technically, edits made using the pathway editor, PathVisio, also update the files here. However, most users do not need to worry about this.

If you want to make edits to a pathway at WikiPathways, DO NOT create pull requests directly for this repo. Instead, use the PathVisio tool with the WikiPathways plugin to edit existing pathways and contribute new pathways.

Development

Please use caution when commit directly to this repository. Various GitHub Action are triggered by new commits. Please review the workflows in the .github/workflows directory and ask other developers on Slack if uncertain before making changes.

Update Protocol

The GitHub actions specifiy versions for various tools and resources. Developers are responsible for keeping these up-to-date. GitHub Actions will report pending deprecations on each run. Please take note of these and update the version numbers accordingly. These might include: * Node.js * Ubuntu (consider using ubuntu-latest) * Syntax for things like environment variables and secrets

Marketplace actions also need to be updated. These might include: * actions/checkout * actions/setup-java * actions/setup-node * actions/setup-python * actions/cache * r-lib/actions/setup-r

Finally, our own tools and resources will require updates. These might include: * meta-data-action jar * SyncAction jar * Caches of bridgedb files

Owner

  • Name: WikiPathways
  • Login: wikipathways
  • Kind: organization

Open source software development related to the WikiPathways project

GitHub Events

Total
  • Issues event: 2
  • Watch event: 4
  • Issue comment event: 10
  • Push event: 1,148
  • Pull request event: 10
  • Fork event: 3
Last Year
  • Issues event: 2
  • Watch event: 4
  • Issue comment event: 10
  • Push event: 1,148
  • Pull request event: 10
  • Fork event: 3

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 3
  • Average time to close issues: 8 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 4.5
  • Average comments per pull request: 0.33
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 month
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.33
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • egonw (6)
  • AlexanderPico (1)
  • fehrhart (1)
  • jmillanacosta (1)
Pull Request Authors
  • fehrhart (4)
  • larsgw (1)
  • luiz-ladeira (1)
  • youphendriks (1)
  • hasanbalci (1)
  • pklemmer (1)
Top Labels
Issue Labels
enhancement (1) documentation (1) question (1) help wanted (1)
Pull Request Labels

Dependencies

.github/workflows/manual_jekyll_sync.yml actions
  • actions/checkout v2 composite
  • webfactory/ssh-agent v0.5.4 composite
.github/workflows/on_author_list_change.yml actions
  • jesalg/commit-hawk-action v1.1 composite
.github/workflows/on_citedin_change.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/on_communities_change.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • webfactory/ssh-agent v0.4.1 composite
.github/workflows/on_gpml_change.yml actions
  • actions/cache v2 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/checkout v2 composite
  • actions/setup-java v2 composite
  • actions/setup-node v3 composite
  • actions/setup-node v2.1.2 composite
  • actions/setup-python v2 composite
  • webfactory/ssh-agent v0.5.4 composite
.github/workflows/on_ndex_change.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/scheduled_bridge_cache.yml actions
  • actions/cache v2 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/setup-java v2 composite
.github/workflows/scheduled_citedin_update.yml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • stefanzweifel/git-auto-commit-action v4 composite
.github/workflows/scheduled_gpml_sync.yml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/setup-java v2 composite
  • ad-m/github-push-action master composite