RefGenProgress 2009-02 (Archived)

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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.
Mouse annotations for Lonp
Collected mammalian annotations for Lonp

February 2009 Annotation Targets

  • Selected because the CRYZ gene has different functions in different organisms (crystallin and quinone reductase), and we wanted to have an example of that type to discuss issues with annotation propagation.

Reference Genome manuscript

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

Conference call Feb 10, 2009

Minutes are here:

  • 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

Agenda, annotations and minutes are here:

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?

Annotation issues

  • Binding

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

  • IEP

There was concern about the aging annotation based on IEP in rat. General consensus is that this annotation is not valid. IEP-evidence should be used for expression of a gene being annotated and not the expression of targets.

  • Annotation to process: what evidence code to use? It's hard to find paper that show whole pathways (CPS1). We had the same problem with PFK at the last jamboree. This needs discussion and improving the documentation.

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