https://github.com/cthoyt/wikipathways-map

https://github.com/cthoyt/wikipathways-map

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• Host: GitHub
• URL: https://github.com/cthoyt/wikipathways-map
• Owner: cthoyt
• Created: 2021-01-06T14:18:17.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2021-01-06T18:58:25.000Z (almost 4 years ago)
• Last Synced: 2024-06-13T20:30:34.964Z (5 months ago)
• Language: Python
• Size: 700 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# wikipathways-map

This repository contains several python scripts to build a network of relations between WikiPathways pathways and

external vocabularies.

Presentation given to WikiPathways Developer Conference Call on January 6th, 2021: http://bit.ly/3neYZ5O

## Data

| File | Description |

| ---- | ----------- |

| [biomappings_subset.tsv](https://github.com/cthoyt/wikipathways-map/blob/main/resources/biomappings_subset.tsv) | Manually curated relationships from Biomappings relvant for WikiPathways |

| [compath_subset.tsv](https://github.com/cthoyt/wikipathways-map/blob/main/resources/compath_subset.tsv) | Manually curated relationships from ComPath relvant for WikiPathways |

| [diseases.tsv](https://github.com/cthoyt/wikipathways-map/blob/main/resources/diseases.tsv) | WikiPathway toDOID relationships extracted from WikiPathways SPARQL endpoint |

| [pw.tsv](https://github.com/cthoyt/wikipathways-map/blob/main/resources/pw.tsv) | WikiPathway to Pathway Ontology relationships extracted from WikiPathways SPARQL endpoint |

| [orthologs.tsv](https://github.com/cthoyt/wikipathways-map/blob/main/resources/orthologs.tsv) | Orthologous pathways inside WikiPathways generated by lexical matching with [Gilda](https://github.com/indralab/gilda) |

## Licensing

- Data from Biomappings are licensed under the CC-0 license.

- Data from ComPath are licensed under the MIT License.

- Data from WikiPathways are licensed under the CC-0 license.

- Original data in this repo are licensed under the CC-0 license.

- Code in this repo is licensed under the MIT License.

## Visualization

The network can be viewed on [NDEx](https://public.ndexbio.org/viewer/networks/2b3ed6af-5031-11eb-9e72-0ac135e8bacf).

## Sources

- [WikiPathways](https://www.wikidata.org/)

- [BioMappings](https://github.com/biomappings/biomappings)

- [ComPath](https://github.com/compath/compath-resources)

## Build

The code can be run with `tox` based on the `tox.ini` file to automatically acquire, build, and upload the resources to

NDEx.