Get Involved!

BioPAX is a community effort based on the idea that if we can coordinate work we need to do anyway, we can avoid duplication of effort and make our projects more efficient. We need help defining and critiquing the format, translating existing pathway information into it, and defining and managing the process of working together.

If you think there is something that needs to be done, please add it to this page or communicate it to the mailing lists. In addition, there are a number of interesting tasks that the community has identified as important, but not all of them have champions.

If you want to lead one of these projects because you need it for your own work (or you would just like to contribute), put your name and contact information next to the task and/or start working on it.

>> Frank Gibbons (fgibbons at hms DOT harvardDOTedu): ''I have an almost-complete stylesheet to (unidirectionally) convert PSI-MI to BioPAX. I will post to biopax-discuss within a few days, once I've had a chance to test it.''
 * Data conversion
 * PSI-MI to BioPAX conversion. This will allow conversion of BIND, DIP, MINT, IntAct and HPRD databases to BioPAX format.  PSI-MI Level 1 and Level 2 can be converted to BioPAX Level 2.  The reverse conversion from a subset of BioPAX data to PSI Level 2 would be useful as well.

*BioPAX Format Validation. Implement a Java library to check if a given BioPAX document is valid and follows best practices. *Pathway visualizers that support BioPAX can be built.
 * Biowarehouse to BioPAX interconversion.
 * Represent BioPAX as an XML Schema and build a converter to and from this format. This will allow BioPAX users to use mature XML Schema tools to build software that makes use of BioPAX information.
 * Validation
 * BioPAX normalizer. Implement a Java library to take a valid, best practice BioPAX document and convert it to common representational styles (e.g. signal transduction style to metabolic style, or signal transduction style to binary interactions)
 * OWL Diff tool. This would allow one to find the differences between two OWL ontologies. This would help during BioPAX ontology development.
 * Shared Curation
 * Shared curation portal. Pathway curation is more complex than DNA sequence curation, since for DNA sequence curation, there are N possible genes, whereas pathways contain at last N squared possible relationships between genes, all of which are highly dynamic and contextual. The only manageable way to collect this information is a computer readable format is to efficiently share the task. A web portal where participating databases can advertise their progress on curating specific pathways to encourage collaboration and coordination on pathway curation tasks could be built to help manage this.
 * Pathway editor. An open-source pathway editor for building pathways that can be saved in BioPAX format would allow many people to share the pathway curation task.
 * Visualization and Analysis

Feel free to add new tasks.