paxtools is a component for the BioPAX language. BioPAX - A Data Exchange Format for Biological Pathway Information. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently.

Available operations:
1. merge : file1 file2 output merges file2 into file1 and writes it into output
2. toSif : file1 output converts model to the simple interaction format
3. toSifnx : file1 outEdges outNodes writePublications prop1,prop2,.. converts model to the extendent simple interaction format
4. validate : path out [xml|html|biopax] [auto-fix] [normalize] [only-errors] [maxerrors=n] validates the BioPAX file (or all the files in the directory); writes the html report, xml report (including fixed xml-escaped biopax), or the biopax (fixed/normalized) only; see also: www.biopax.org/biopax-validator/ws.html
5. integrate : file1 file2 output integrates file2 into file1 and writes it into output (experimental)
6. toLevel3 : file1 output converts level 1 or 2 to the level 3 file
7. fromPsimi : level file1 output converts PSI-MI Level 2.5 to biopax level 2 or 3 file
8. toGSEA : file1 output database crossSpeciesCheck converts level 1 or 2 or 3 to GSEA output. Searches database for participant id or uses biopax rdf id if database is "NONE". Cross species check ensures participant protein is from same species as pathway (set to true or false).
9. fetch : file1 id1,id2,.. output extracts a sub-model from file1 and writes BioPAX to output
10. getNeighbors : file1 id1,id2,.. output nearest neighborhood graph query (id1,id2 - of Entity sub-class only)
11. help : prints helps and exits

Requirements:
* Java

The license of this software is Free, you can free download and free use this application software.