LEGO May 4 2015

Agenda

Continued Discussion of March Consistency Exercise Paper

• http://www.ncbi.nlm.nih.gov/pubmed/12048186

Specific Questions/Issues

• Here are the links to the models built by David, Kimberly and Rama

David- http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_559292-5525a0fc0000001
Kimberly- http://go-genkisugi.rhcloud.com/seed/model/gomodel:5525a0fc0000032
Rama- http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_559292-5525a0fc0000061#

• Use of in_absence_of and in_presence_of annotation extensions.
• How to adequately capture the effects of protein binding on subsequent complex formation and resulting molecular functions.

Begin Discussion of April Consistency Exercise Paper

• http://www.ncbi.nlm.nih.gov/pubmed/24349431

Specific Questions/Issues

• Use of occurs_in relation for molecular function annotations
  • What constitutes sufficient evidence for adding this extension, as CC annotations may be from a different experiment than the MF annotation?
  • For example, protein binding based on Y2H or whole cell lysates (IPI) with separate experiments describing localization (IDA).
• Links to models built by David, Kimberly and Rama
  • http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_559292-5525a0fc0000003
  • http://go-genkisugi.rhcloud.com/seed/model/gomodel:5525a0fc0000051
  • http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_10090-5525a0fc0000066?barista_token=dtbkqlv0g2qj0oodfx68#

Discussion

March paper

• We all looked at the model Paul built.
• We want the ability to capture functions of complexes. Noctua should load complex IDs from IntAct. Make a github ticket for this request.