12 APR 2011 RefGen Phone Conference (Archived)

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Present

Action items

  • Everyone needs to communicate to the software team to upload the MF-BP inferences on the FTP site (ADD LINK TO DOCUMENTATION).

(Rama, everyone)


Reference genome annotation targets

  • Transcription factors from the wnt pathway
  • Varsha: pick targets
  • Paul and his group: send list of protein members


'Response to' guidelines

  • Pascale

Change in definition - Response to terms

No one commented in the SF entry regarding the change of definition: http://sourceforge.net/tracker/?func=detail&aid=3234988&group_id=36855&atid=440764

So I am happy to go ahead and change the definitions from: A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.

to:

Any process that results in a change in state or activity of a cell or organism as the result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.


Annotation Guidelines for response to Terms

  1. High level ‘response to’ terms should not directly be used for annotation
  2. Encourage the use of granular terms for ‘responses’ (update documentation)
  3. Be careful to use IEP when the experiment is observing expression level:
    • see incorrect annotations: IDA rather than IEP - PMID 11606197 (A. thaliana BIP1) and PMID: 12746488 (Human IL1A)
    • see also UBR1 and UBR2 to 'GO:0071233 cellular response to leucine' from reading PMID:20298436
      • Suggestion from Becky: I would have annotated to 'leucine binding (IPI with CHEBI:25017 leucine)' and 'negative regulation of TOR signaling cascade' (IMP).

Apoptosis Annotation Project

(Emily): Discussion of the BCL family of proteins Apoptosis_Reference_Genome_Targets#BCL_family_Proteins

PAINT evidence codes

  • IBA: biological aspect of ancestor : A type of phylogenetic evidence whereby an aspect of a descendent is inferred through the characterization of an aspect of a ancestral gene
  • IBD: biological aspect of descendant: A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
  • IKR (synonym IMR): phylogenetic determination of loss of key residues => NOT
  • IRD: A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event => NO ANNOTATION