10 AUG 2010 RefGen Phone Conference (Archived)

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  • PPOD: Kara Dolinski, Mike Livstone
  • dictyBase: Pascale
  • MGI: Mary
  • UCL: Ruth
  • wormbase: Kimberly
  • GOA: Becky, Yasmin
  • SGD: Rama
  • RGD: Stan

Action items

  • What should be the cellular component of a ligand? ie, should the wnt be annotated to plasma membrane? or just extracellular space? It seems this is a case where there may be differences in how annotators interpret the information. Mike to provide examples
  • Pascale Next targets: send an email to request suggestions

wnt project

WNTs have cytokine activity [Ruth/Alex]

  • see PMID:18986540
  • Wnts identified as affecting the formation of synapses is controlling an effector function of cells.
  • Note due to lack of information provided in this paper only Wnt5a (R&D Systems only sells mouse Wnt5a) and Wnt7a (R&D Systems only sells human Wnt7a) can be annotated.

Update on annotations from all groups

  • Many groups seem to be up to date. Are there any comments/problems?
  • We have asked the ontology development to process ref genome SF items with higher priority. Please use the SF priority settings and set to a higher priority when you submit a ref genome request.

Tree annotation [Mike]

I began PAINTing PTHR12027, the Wnt family, Monday August 2, two weeks after the literature curation, to allow time for the annotations to percolate into PAINT. Since the literature curation went for 2 weeks, I am allowing myself a little extra time beyond the standard 1 week to PAINT this family. Here is a preliminary list of questions that have arisen so far.

These questions have been moved to http://gocwiki.geneontology.org/index.php/PTHR12027 -Mike

Subfamilies annotation report from Mary Dolan

I have put together a report (subfamilies.xlsx posted ftp://ftp.informatics.jax.org/pub/curatorwork/Pascale/) that summarizes the GO annotation status (as of August 1,2010) of all Panther subfamilies according to the type of annotation for each refG organism. These few slides give an overview of the report. File:Whats-in panther-subfamilies GOreport.pdf

There are separate sheets for function, process, and component. For each subfamily that contains a refG organism member, I display the type (color-coded) of annotation: experimental (green), ISS-type (yellow), other (red), no annotation (plain text), or no gene (empty slot). I include the ICs as experimental annotations; ND annotations are not counted. I have added a few mappings from panther ids to ga file ids for completeness.

I see this as providing information that is complementary to the careful group by group literature curation followed by PAINT review, which, of course, provides the best comprehensive annotation. This, on the other hand, provides a view of the maximum possible gain of shared information we could get for 'free' for other refG MODs or other genome annotation groups for their organism's Panther subfamily genes. For example, of the 69,566 panther subfamilies: 32,991 have one or more model organism members. Of these: 24,265 (74%) have some GO function annotation to one or more organisms; 15,276 (46%) have either experimental or ISS annotation; and 11,653 (35%) have experimental annotation. The numbers are similar for process and component.

Hoping this will be useful, I look forward to your comments. Thanks. Mary

Annotation Status report

http://amigo.berkeleybop.org/cgi-bin/amigo/phylotree Sven, Seth, Chris

Action items from last call

Action items for the Sept GOC meeting

  • Action: All annotation groups to review PAINT annotation sets with a view to integrating them into their association files [all groups]. Manager: Pascale
    • Are all groups okay with integrating annotations in terms of the review process?
  • Action: Reference Genome group needs to explore ways of improving the target list selection method to ensure a greater participation by all curation groups [Pascale and Kara].
    • Now doing wnt pathway. Do we have suggestions for future projects? Please add here:


  • Action: Figure out a mechanism by which taxonomic restrictions derived from PAINT could be fed back into the ontology taxon restrictions file [Paul and Jane]. Manager: Jane.
    • Pascale emailed Jane and Paul to check the status of that one.


Following last month's call: Suzi will write a script to run on a regular basis (daily? weekly?) either from Berkeley or at Stanford. This script will generate 13 GAF files and place them in the go/gene-associations directory where the other gaf files are kept. These files will be named thusly:

gene_association.paint_XXX.gz (where XXX will be substituted by the name of one of the ref. genome organisms) gene_association.paint_other.gz (for the platypus, opossums, and all the other non-ref. genome organisms)

If a MOD curator decides they would like to look at a particular annotation they would still have the option of retrieving all the files needed to load that particular family into PAINT from the file directory located here: go/gene-associations/submission/paint/PTHRnnnnn (where nnnnn is the number of that family). The script will be using these as the source to build the files listed above.

Other discussion topics