Harmony 2013 Update

[Emek Demir]

Hello All

We are currently wrapping up the Harmony meeting and I wanted to summarize BioPAX related items that we discussed for those who could not participate. I think Level 3 is now widely adopted and it is time to start discussing Level 4.  

1) We have discussed what kind of new data can be captured and exchanged in BioPAX. Some of those were more detailed kinetic data ( as captured by Sabio-rk, PharmGKB or Brenda), genomic alterations and diseases (as captured by Reactome).In the upcoming weeks  we will start contacting potential data sources and try to develop requirements documents for those. Please chime in if you feel you have additional information that is currently not captured in BioPAX.

2) We have discussed how to develop and support extensions in BioPAX. All the present participants felt that this would be useful for prototyping and testing proposals for the upcoming level 4. A key complaint was to lack of support for extensions in Paxtools. After reviewing several options in detail, we agreed on a relatively simple implementation. I will be implementing this in the upcoming weeks and will announce in this list.

3) We made good progress in implementing polymerization in BioPAX at least on a logical level. We will be circulating a proposal soon.

4) We “hacked” a little to use BioPAX w/ Groovy. Martijn van Iersel demonstrated how one can “extend” BioPAX w/ groovy and Jena. And I biefly discussed how to use Groovy Console+Paxtools as a Read-Evaluate-Print loop for development and prototyping purposes. Martijn will publish the former on his blog and I will add a section on Paxtools user's guide for the latter.

5) We had a chance to discuss one-on-one several data export issues. Perhaps most importantly we were able to debug the BioPAX export problems in the recently published Recon2 metabolic map and hopefully we will have a valid BioPAX export of it soon.

Stay tuned.

Best,
ED