12 APR 2011 RefGen Phone Conference (Archived)

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Present

  • Pascale
  • Emily, Becky, Paola, Yasmin GOA
  • Susan Flybase
  • Donghui TAIR
  • Sven, Mike PPOD
  • Stan RGD
  • Rama SGD
  • Li, Mary MGI
  • Lakshmi AgBase

Action items

  1. Move PAINT evidence codes to official documentation
  2. Reported from the previous meeting: Everyone needs to communicate to the software team to upload the MF-BP inferences on the FTP site (ADD LINK TO DOCUMENTATION). (Rama, everyone) On hold. Chris wants people to make the annotations manually on a common curation interface (to be presented at the next GOC meeting)
  3. Response to definition: Becky: go ahead and change the definition.

Reported for the next meeting

Loading PAINT inferences

POSTPONING We would to resolve the issue of what reference could be used for loading PAINT files. Donghui (TAIR) and Doug (Zfin) sent emails around and I suggested using GO_REF:000033. SGD also is planning to use GO_REF:0000033 for the same issues that Donghui mentioned. We would like to make progress in loading these annotations until a meaningful solution is reached.

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): A type of phylogenetic evidence characterized by the absence of key sequence residues. => NOT
  • IRD: A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event => NOT
  • When a curator is not convinced that a protein belongs to a tree, s/he can remove the offending branch using an operation called 'pruning' which stops propagation below that branch.

Curation report

Sven


'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).

Reference genome annotation targets

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