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Class Summary
| Class |
Description |
| GSEAConverter |
Converts a BioPAX model to the GMT format (used by GSEA software).
|
Package org.biopax.paxtools.io.gsea Description
This package contains a simple GSEA converter.
Converts a BioPAX model to GSEA (GMT format).
Creates GSEA entries from the protein references's xrefs contained in the BioPAX model.
One entry (id-list) per pathway per organism. If there are no pathways,
then simply - per organism (i.e., all available protein types are considered).
- One identifier per protein reference (not guaranteed to be the primary one).
All identifiers can only be of the same type, e.g., UniProt,
and the converter does not do any id-mapping; so a protein without
the required identifier type will not be listed.
Note, to effectively enforce cross-species violation, bio-sources must
be annotated (have a unification xref) with "taxonomy" database name
and id, and pathways's, protein references's "organism" property - not empty.
Note, this code assumes that the model has successfully been validated
and normalized (e.g., using the BioPAX Validator for Level3 data).
L1 and L2 models are first converted to L3 (this however does not
fix BioPAX errors, if any present, but possibly adds new)