Presentations and Publications/ISMB2008BOF

Pathway information sharing birds of a feather at ISMB, Toronto
 * Monday, July 21, 2008

About 45 attendees

Presentation by Gary Bader, Chris Sander, Emek Demir: attachment:pathwayBOF.ppt

Issues raised by attendees
 * Tool availability needs to be much better
 * Format validation is important
 * Pathway editing would be useful
 * Basic layout information in BioPAX would be useful
 * Automatic pathway layout would be useful. Perhaps a web service, like PATIKA, that inputs a BioPAX file and returns layout information.
 * BioPAX RDF – proper URIs stored in BioPAX. Suggestion from the bio2rdf project – add a URI property to xref which would store URIs in the form of biopax.org:database:identifier. Also, maintain a list of approved database names in a controlled vocabulary to encourage use of only a single spelling of the database name everywhere.
 * Author entry systems would encourage community annotation - freebase is a free generic database that you could add facts to. Wikipathways was also represented and suggested as a way to add pathway facts to a database.
 * A flat file format for BioPAX would be useful – just a standard set of columns in a tab delimited or excel file that could be converted to BioPAX would make it much easier for non XML experts to create data in BioPAX format. This would be similar to tools available to convert PSI-MI TAB format to PSI-MI XML format.