12 APR 2011 RefGen Phone Conference (Archived)
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
- High level ‘response to’ terms should not directly be used for annotation
- Encourage the use of granular terms for ‘responses’ (update documentation)
- 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)
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