RefGenome9Sept08 Phone Conference (Archived)

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Present

Review old/ongoing action items

  1. (Debby) Put in a SourceForge request that definitions of terms for oligomerization, dimerization, protein complex assembly etc. should be clarified as to their use and annotations using these terms be checked and, if necessary, changed.
  1. Emily will make a SourceForge request to get the mappings for GO:0006556 S-adenosylmethionine biosynthetic process changed.
  1. (Susan) Request new term for Regulation of GTP Cyclohydrolase I activity.
  1. (Victoria) Make a SourceForge request to clarify the definitions of unfolded/misfolded protein binding and add chaperone activity as a synonym to both of the terms. Also add ‘de novo’ synonym to ‘unfolded protein binding’.
  1. “Process IC or IDA?”
  1. Discuss microarray data further, possibly GOC meeting item.
  1. (Stacia) Send around SGDs SOP for HTP annotation; SOPs are here SGD_GO_HTP_guidelines
  1. Make HTP annotation
  1. (Becky) Move discussion to email on whether we need more terms under protein binding to describe protein binding as a target for a process
  1. (Pascale) Discuss IEP: Some people had annotated 'response to heat' by IDA for the heat shock protein; while what was measured was the level of transcript/protein. There are 38 genes annotated to 'response to heat shock' with IDA in the GO database. Those should be checked? (we'll discuss, see below)
  • Another question arising from this is how to you have an IDA to 'response to xx'?(we'll discuss, see below)
  1. Discuss xx binding in the context of gene product. In this case I (Pascale) think the 'coenzyme' rather refers to the gene product. Most/many people seem to use 'coenzyme binding' only to annotate proteins that bind a coenzyme for activity. However the definition does not specify that. (we'll discuss, see below)
  1. All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table [1] see also Annotation_QC for some general documentation and previous issues
  2. All (ongoing): Annotation Quality control: Have a look at the SF items and see if the ortholog from your organism is correctly annotated ("comprehensive"). Let lead curator for that set know that you're done.


Curation Targets

September 2008: Val's lists of 'unknowns'

PPOD update

PANTHR update

Annotation tracker update

Source Forge QC discussion

Next conference call

Tuesday October 14, 2008, 10 AM CDT, 8 AM PDT, 4 PM BST



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