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bulk-gpml2biopax-js's Introduction

bulk-gpml2biopax-js

Convert GPML to BioPAX in RDF/XML format, in bulk.

Convert

To convert all curated pathways for a given organism, open main.js and set the organism. Also, ensure testing mode is false. Then run the following:

node index.js

The BioPAX RDF/XML output should be in test/biopax/source-all/...

Validate

To validate the generated BioPAX and optionally generate auto-fixed BioPAX, comment out/uncomment the desired sections from run-biopax-validator.js and then run it:

node lib/run-biopax-validator.js

Reports currently available on pointer. Synced with

 rsync -azvh --delete ./test/biopax/ <YOUR_USERNAME>@pointer.ucsf.edu:/var/www/d3/r/gpml2biopax

Latest bulk upload of BioPAX (Homo sapiens only for now).

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