RefGenProgress 2009-02 (Archived)

PAINT tool for annotation of nodes of phylogenetic trees

• the tool is now fetching annotations from the GO database and displaying those
• for each 'node' (common ancestor sequence), a list of the annotations made to all sequences present in that group is available with the option to select (using check boxes) any GO term and apply those annotations to the ancestor sequence.

Reference Genome manuscript

• Paper was reviewed; we'll send back addressing the reviewers comments.

Conference call Feb 10, 2009

• Agreed that annotations done with the PAINT software will have the ISS evidence code.
• Discussed use of 'colocalizes with' and 'contributes to'; there are two meanings for each and that is confusing. This is important because in both cases, one of the meanings is 'weaker' and can probably not be used for propagation. Pascale will send to every group the annotations they have using those qualifiers.
• talked about obsoleting Fraction terms since those do not represent components but experimental procedures. However people disagree so we have not yet made a decision.

Electronic jamboree Feb 24, 2009

• Ontology modifications:
  • New terms requested:
    • carbomyl phosphate biosynthetic process GO:0070409
    • oxidized protein catabolic process GO:0070407 (BHF-UCL)
    • mitochondrial light strand promoter anti-sense binding GO:0070361 (GOA)
    • mitochondrial light strand promoter sense binding GO:0070363 (GOA)
    • mitochondrial heavy strand promoter anti-sense binding GO:0070362 (GOA)
    • mitochondrial heavy strand promoter sense binding GO:0070364 (GOA)

• • Asked to obsolete 'ATP dependent proteolysis'

• • AI: Ruth: add 'modification-initiated protein catabolic process' as a synonym and also add a synonym that includes the word proteolysis (this should be done for all children of proteolysis).

• Debated whether we need a term describing 'allosteric regulation'; however not sure, because that seems rather a mechanism of regulation rather than a separate process

• Karen to send email to GO : Should we make organelle specific terms for processes [and functions?] that aren't mechanistically different but use different gene sets?

• Discussing annotations to binding terms again: what experimental evidence supports an annotation to a binding term?

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