12 APR 2011 RefGen Phone Conference (Archived): Difference between revisions
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#Move PAINT evidence codes to official documentation | #Move PAINT evidence codes to official documentation | ||
#Reported for the next meeting: | |||
==Loading PAINT inferences== | ==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. | 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. |
Revision as of 11:15, 12 April 2011
Present
- Pascale
- Emily, Becky, Paola, Yasmin GOA
- Susan Flybase
- Donghui TAIR
- Sven, Mike PPOD
- Stan RGD
- Rama SGD
- Li MGI
- Laksmi Agbase
ACTION ITEMS:
- Move PAINT evidence codes to official documentation
- 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
- Prototype is at http://amigo-sven.princeton.edu/cgi-bin/amigo/phylotree?mode=pager
- Sven will do a 'demo'
'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)
- Donghui: I changed the evidence code for BIP1 annotation from IDA to IEP (PMID 8888624, http://www.arabidopsis.org/servlets/TairObject?accession=locus:2182783). Will do a check to see if there are other similar cases.
- 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).
- see incorrect annotations: IDA rather than IEP - PMID 11606197 (A. thaliana BIP1) and PMID: 12746488 (Human IL1A)
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