BioPAX Database Conversion Status

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This Page is an Archive and has not been updated - June 11th 2010

In addition to the tools supporting BioPAX listed on Biological software supporting BioPAX, the following biological pathway databases support BioPAX.

BioPAX Level 1 Datasources

*BioCyc - Status: Export complete by BioCyc group. Files in version 9.1 release passed user testing and available from BioCyc download page. (Last updated May.25.2005)
*WIT2/PUMA2 - Status: Under development by WIT group. (Last updated Mar.23.2005)
*KEGG Pathways - Status: Under development by aMAZE/Sander groups. (Last updated Mar.23.2005)
*Biowarehouse - Status: Completed by the SRI group using SPARQL and the Spring Framework (Last updated Mar.27.2005)

BioPAX Level 2 Datasources

*Reactome - Status: Final version available. Data is available via BioPAX links on Reactome web pages for any pathway and as a single file from the download page. (Last updated April.8.2006)
*INOH - Status: 57 signal transduction pathways with more than 1300 interactions are available from Pathway data page. (Last updated Sep.28.2006)
*PSI-MI - Status: In progress by Frank Gibbons + BioPAX Boston Group + Gary Bader. Issue: waiting for BioPAX Level 2 finalization. (Last updated Jun.30.2005)
  • A BioPAX version of the PSI-MI export of the BIND database is available at [1]. An XQuery file that can be used to convert PSI-MI XML files to BioPAX is also available there (has not been tested with the most recent version of the PSI-MI schema).
*aMAZE - Status: Planning, waiting for BioPAX Level 2 finalization. (Last updated May.4.2005)
*The Cancer Cell Map from Memorial Sloan-Kettering Cancer Center - Status: Final version available (Last updated April.8.2006)