Annotation consistency: 'Response to' terms
Group Members
(anyone can add themselves)
- Tanya Berardini, Emily Dimmer, Pascale Gaudet, Ruth Lovering
1. Issue
The 'response' terms have been in GO since the very beginning. Examples:
GO:0006950 OS stress response GO:0006951 OS heat shock response
The definitions of the 'response to x' terms are quite broad.
"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 ..."
The broadness of the definition leads to questions like these:
- When do we annotate to these terms?
- When a gene product is up-regulated following a stimulation should it be annotated to 'response to this stimulus'?
For example, should cell cycle genes up-regulated by insulin be included in 'response to insulin stimulus'?
Possibly the definition is so broad that all up-regulated genes could be included. But is this the intention of GO?
- How far down a series of events do we annotate a protein to the process?
For example GO:0032868 response to insulin stimulus Definition: 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 an insulin stimulus.
If we look at wikipedia's comments on the effects of insulin: http://en.wikipedia.org/wiki/Insulin then we would expect that insulin stimulation will cause changes to a wide variety of metabolic pathways and transport systems and increases in cell division associated pathways (replication, protein synthesis, cell cycle etc) etc.
I would have thought that the proteins associated with the 'response to insulin stimulus' would be: receptors detecting the stimulus, transducers ensuring that the response to insulin is initiated by the cell and that proteins involved in the change of the cell itself would not be included, ie not including proteins involved in the storage of glucose in liver (and muscle) cells in the form of glycogen.
Should insulin be associated with GO:0032868 response to insulin stimulus?
- Is there inconsistency in the annotation of proteins to these terms? If there is, is this related to whether the annotation is to multicellular organism or singled cell organism?
- Are there certain evidence codes that should/should not be used when annotating to these terms?
- Review of existing evidence codes used
From GO database:
+-----------------+ | code | count(*) | +------+----------+ | IEA | 82721 | | IEP | 2849 | | IMP | 2246 | | ISS | 2492 | | IDA | 1233 | | NAS | 207 | | RCA | 443 | | TAS | 469 | | IGI | 394 | | IC | 126 | | IPI | 21 | | ISO | 13 | | NR | 8 | +------+----------+
TAIR case: mostly IEP (majority are from Northern or RT-PCR experiments, fewer microarray), then about equal amounts of IMP (treat the mutant with a substance, don't get a response where you get one in the wild type or the reverse), ISS (TIGR inherited), IEA (INTERPRO2GO), fewer annotations with IGI, TAS, IDA, NAS
2. Proposed solution(s)
Review the intention of the 'response to' GO terms. Consider identifying start and finish of the 'response to' process. More broadly, refine the scope of these terms to be more clear.
Come up with guidelines of what experimental assays would provide supporting evidence for annotations using these terms.
Should this go to the annotation group? Should this go on the Montreal agenda?
3. Comments/counter arguments
SourceForge issue opened: 'response to stimulus' http://sourceforge.net/tracker/index.php?func=detail&aid=2094943&group_id=36855&atid=440764
Other related SF items:
'response to stimulus' http://sourceforge.net/tracker/index.php?func=detail&aid=1601609&group_id=36855&atid=440764
'protein stimulus' http://sourceforge.net/tracker/index.php?func=detail&aid=1601557&group_id=36855&atid=440764