BioPAX
Validator (v2.0.0)
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Check BioPAX
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Choose up to 25 BioPAX files:
Check a BioPAX OWL at the location:
Options:
Auto-Fix! (
experimental:
some rules can do, e.g., fix xref db/id, controlled vocabularies, set 'displayName', remove duplicates, etc.)
Normalize! (
experimental:
where it is possible, - replaces identifiers of entity references, CVs, BioSource with Miriam's standard URNs; for xrefs, - generates new IDs like
urn:biopax:*Xref:<db>_<id>_<ver>
this makes BioPAX data integration and linking easier. if required, data are auto-converted to BioPAX Level3 first. It may remove some or add new BioPAX errors, especially if there were errors in the file.)
fix displayName (from names)
infer property: organism
infer property: dataSource
generate pathway relationship xrefs
generate interaction relationship xrefs
generate organism relationship xrefs
Set the level (do the job, do not report everything)
Show Warnings and Errors
Show Errors Only
Do not Show Me Problems :)
Set the limit (of type:ERROR, not fixed cases)
0
1
10
Report as:
HTML
XML (
unmarshalable
)
Modified BioPAX (only)
Actions:
Check (and optionally fix/normalize)
Links
Validator's Wiki Page
Rules's Wiki Page
Docs (auto-generated site)
Pathway Commons
MIRIAM
OBO