No description, website, or topics provided.
Switch branches/tags
Nothing to show
Clone or download
Pull request Compare This branch is 130 commits ahead of andrawaag:master.
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
diseases
genes
pathways
proteins
variants
README.md
manifest.json

README.md

genewiki Shape Expressions.

Shapes

Shape name source Jenkins Jupyter shex.js Shaclex
human genes - + + -
human proteins - + + -
mouse proteins - + + -
diseases - + + -
pathways (wikipathways) - + + -
pathway (reactome) - + + -
variants - - - -

This repository collects Shape Expression to model and validate Wikidata items added by bots developed and maintained in the Gene wiki project.

Installation

Running Shape expressions requires shex.js. Installation instructions can be found here

Usage

With shex.js running the following commands downloads the shapes collected here and run them against a select set of on topic items.

Human gene

./bin/validate -x https://raw.githubusercontent.com/shexSpec/schemas/master/Wikidata/genewiki/wikidata_human-genes.shex -d https://www.wikidata.org/wiki/Special:EntityData/Q17853226.ttl

Disease

./bin/validate -x https://raw.githubusercontent.com/shexSpec/schemas/master/Wikidata/genewiki/wikidata_disease.shex -d https://www.wikidata.org/wiki/Special:EntityData/Q35869.ttl -s wikidata-disease -n http://www.wikidata.org/entity/Q35869

CIViC variant

.//Users/andra/bin/validate -x https://raw.githubusercontent.com/shexSpec/schemas/master/Wikidata/genewiki/wikidata-civic.shex -d https://www.wikidata.org/wiki/Special:EntityData/Q21851559.ttl -s wikidata-civic_variant_record -n http://www.wikidata.org/entity/Q21851559

Contributing

  1. Fork it!
  2. Create your feature branch: git checkout -b my-new-feature
  3. Commit your changes: git commit -am 'Add some feature'
  4. Push to the branch: git push origin my-new-feature
  5. Submit a pull request :D