9 NOV 2010 RefGen Phone Conference (Archived)

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  • dictyBase: Pascale
  • PPOD: Mike, Kara
  • Panther: Paul
  • MGI: Judy, Li, Dmitry, Mary
  • UCL: Ruth, Varsha
  • wormbase: Kimberly, Ranjana
  • GOA: Yasmin, Becky
  • SGD: Rama
  • RGD:
  • Berkeley: Chris, Suzi
  • TAIR: Tanya

Action items:

  • Kara and Mike will get a list of conserved genes for primary annotations over the new few weeks
  • Paul: start SOP documentation - update the existing documentation


(Paul): Website that allows to browse all annotations, loaded from cvs/PAINT

  • Pantree.org
  • all curated families are here: http://pantree.org/tree/treeList.jsp
  • On family pages there is a link to the tree and a link to the notes; there are also annotations to sequences IDs from all sequences from the tree; and annotations to the different nodes

Plan for tree curation

Rama, Li, Dmitry, and maybe others will start doing tree annotations. In December we should make a big push to annotate families that were curated over the past 4 years, or those that have lots of EXP data, or those that have very little.

Issues with annotated trees

  • Paul: issues were related to either (1) problems with visualization of the inferences, (and in this case the annotations were mostly correct, and (2) real issues with propagation to species for which the annotation was not relevant, in which case the taxon triggers would have caught those problems. implementing the taxon triggers is on the high priority list for PAINT development.

MSH2 issues

p53 issues

Status of the wnt project


  • Batch 1 has been annotated by most MODs
  • PAINT curation status (Mike)
  • We intended to send a second batch of wnt targets, but those have not yet been selected. Also, since curators from MGI will be doing tree curation over the next few weeks, it would be too much work for them to also do curation of the big wnt families. So it was decided to use the list from Mary Dolan of conserved proteins, which often do not have a lot of primary literature.