Pathways to GO
Code for converting between biological pathways (e.g. Reactome, Wikipathways) expressed using the BioPAX standard and the Gene Ontology Causal Activity OWL Model (GO-CAM) structure.
- GO-wiki, http://wiki.geneontology.org/index.php/Biological_Pathways_as_GO-CAMs
- Slides describing rules for converting Reactome pathways (via BioPAX) to GO-CAMs.
Related Code Repositories
- Web editor for GO-CAMs: https://github.com/geneontology/noctua
- Web server for hosting, reasoning over GO-CAMs https://github.com/geneontology/minerva
- Rule-based OWL reasoner optimized for large t-box, small a-box https://github.com/balhoff/arachne
- Work in progress OWL reasoner https://github.com/balhoff/whelk
- Current home of generated GO-CAM models - https://github.com/geneontology/noctua-models/tree/dev
- Development browser/editor with pathways converted to GO-CAMs http://noctua-dev.berkeleybop.org
- Keynote at Rocky Bioinformatics https://www.slideshare.net/goodb/integrating-pathway-databases-with-gene-ontology-causal-activity-models
- "Arachne: an OWL RL reasoner applied to Gene Ontology Causal Activity Models (and beyond)" ISWC, http://ceur-ws.org/Vol-2180/paper-05.pdf
- Clone repo, Maven build (developing with Eclipse and Maven plugin)
- Not ready for prime time. (If you want to run it now, get in touch.)