10 MAY 2011 RefGen Phone Conference (Archived)

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Present

  • Pascale - dictyBase
  • Rama SGD
  • Donghui TAIR
  • Mike L. PPOD
  • Judy, Mary, Li Dmitry MGI
  • Emily, Yasmin, Becky, Paola, EBI
  • Flybase Susan
  • Varsha, Ruth UCL
  • Ranjana, Kimberly, wormbase

Reference genome annotation targets

  • Heart Development Transcription factors [1]
  • Varsha: pick targets
  • Paul and his group: send list of protein members

Triangulation

Pascale will go over the triangulation - description, how does it differ from other methods of annotation inference. File:Triangulation.pdf


Action items from previous call

Done ??

  1. Move PAINT evidence codes to official documentation (Done, Rama)
  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.

PAINT evidence codes

Done??

  • 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.

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.


'Response to' guidelines (Pascale)

Have those been implemented?

Change in definition - Response to terms

No one commented in the SF entry regarding the change of definition.

Becky was to 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.


NB: These edits were done in ontology release 1.1960 (Becky):

response to stimulus ; GO:0050896
Any process that results in 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. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
cellular response to stimulus 
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The  process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
All child terms have been modified to begin with 'Any process that results in a change.....'.

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).

Annotation Guidelines for Downstream Process Terms

Guidelines can be viewed here http://wiki.geneontology.org/index.php/Guidelines_from_Annotation_Camp#Downstream_Process_guidelines

The diagram for annotating downstream processes to gene products in a ligand-receptor signaling pathway has been updated in light of the changes to signaling.