wikipathways/bulk-gpml2biopax-js

Name: bulk-gpml2biopax-js

Owner: WikiPathways

Description: null

Created: 2015-09-25 05:06:03.0

Updated: 2016-02-01 20:11:33.0

Pushed: 2016-02-01 20:11:32.0

Homepage: null

Size: 20

Language: JavaScript

GitHub Committers

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README

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:

 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:

 lib/run-biopax-validator.js

Reports currently available on pointer. Synced with

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

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