mgi-go-cams

Model Generation Process

Fetch current MGI data

wget http://www.informatics.jax.org/downloads/custom/go_cam_mgi.gpad -P source/
wget http://www.informatics.jax.org/downloads/custom/mgi.gpi -P source/

Fetch current GO and RO JSON

wget http://current.geneontology.org/ontology/go.json
wget http://purl.obolibrary.org/obo/ro.owl
robot convert -i ro.owl -o ro.json

Produce validated GPAD

ontobio-parse-assocs.py --file source/go_cam_mgi.gpad --format GPAD --gpi source/mgi.gpi -o products/go_cam_mgi_valid.gpad --report-md products/go_cam_mgi.report.md -r go.json -l "all" convert --to GPAD --format-version 2.0

Generate GO-CAM TTL files

validate.py -v gpad2gocams --gpad_path products/go_cam_mgi_valid.gpad --gpi_path source/mgi.gpi --target models/ --ontology go.json --ontology ro.json --ttl -s production

Dependencies

• ontobio>=2.2.0
• ROBOT