2010 GO-camp Response to terms issues: Difference between revisions
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=Background= | =1. Background= | ||
(from old source forge item: [http://sourceforge.net/tracker/index.php?func=detail&aid=1601609&group_id=36855&atid=440764]) | (from old source forge item: [http://sourceforge.net/tracker/index.php?func=detail&aid=1601609&group_id=36855&atid=440764]) | ||
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= Review of current GO annotation policy for bindings and interactions= | = 2. Review of current GO annotation policy for bindings and interactions= | ||
(Review of the annotation guidelines, questions/discussions) | (Review of the annotation guidelines, questions/discussions) | ||
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=3. Proposed updates to annotation procedures= | |||
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=4. Examples (papers) and discussion of GO annotation issues = | |||
** Transcription factors: O35780 (BHE40_RAT) is annotated to "entrainment of circadian clock" from PMID 12397359. The experiments show it is a transcription factor for genes involved in the circadian clock. Two questions: (i) is the term correct? or should it be annotated to the parent (regulation of circadian rhythm); or to both? (ii) is the IDA evidence code correct? | ** Transcription factors: O35780 (BHE40_RAT) is annotated to "entrainment of circadian clock" from PMID 12397359. The experiments show it is a transcription factor for genes involved in the circadian clock. Two questions: (i) is the term correct? or should it be annotated to the parent (regulation of circadian rhythm); or to both? (ii) is the IDA evidence code correct? | ||
*** The F/P transcription regulator activity IDA annotations are missing. Is there any way we could have checks that would catch that? | *** The F/P transcription regulator activity IDA annotations are missing. Is there any way we could have checks that would catch that? | ||
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** (B) Similar to (A) example: "Two highly divergent human MHC class I genes, MICA (Q29983) and MICB (Q29980), are regulated by promoter heat shock elements", protein: PMID: 8901601. '''Should this protein (Q00649) be annotated to "response to heat" by IDA or IEP? ''' | ** (B) Similar to (A) example: "Two highly divergent human MHC class I genes, MICA (Q29983) and MICB (Q29980), are regulated by promoter heat shock elements", protein: PMID: 8901601. '''Should this protein (Q00649) be annotated to "response to heat" by IDA or IEP? ''' | ||
** (C) Q16576 Sc RBBP7 (aka RBAP46) is annotated to "cellular heat acclimation" by IDA from PMID:7503932. Is this annotation correct? | ** (C) Q16576 Sc RBBP7 (aka RBAP46) is annotated to "cellular heat acclimation" by IDA from PMID:7503932. Is this annotation correct? | ||
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=5. Suggestions for Quality Control procedures= | |||
Revision as of 12:55, 17 March 2010
1. Background
(from old source forge item: [1])
The GO definition for response to stimulus (and similarly for many response to XXX terms) is, “ 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 specified stimulus.”
This definition seems to imply that a wide array of proteins, including receptors, intracellular proteins directly bound to the receptor, subsequent downstream signaling molecules, transcription factors and the genes that they regulate may all be considered as part of a response to a stimulus.
We desire clarification on this point, whether all these classes of proteins may be considered for curation of terms within the response to stimulus hierarchy, or should curation within this hierarchy be limited to only certain classes of proteins?
2. Review of current GO annotation policy for bindings and interactions
(Review of the annotation guidelines, questions/discussions)
Previous discussions:
3. Proposed updates to annotation procedures
4. Examples (papers) and discussion of GO annotation issues
- Transcription factors: O35780 (BHE40_RAT) is annotated to "entrainment of circadian clock" from PMID 12397359. The experiments show it is a transcription factor for genes involved in the circadian clock. Two questions: (i) is the term correct? or should it be annotated to the parent (regulation of circadian rhythm); or to both? (ii) is the IDA evidence code correct?
- The F/P transcription regulator activity IDA annotations are missing. Is there any way we could have checks that would catch that?
- Transcription factors: O35780 (BHE40_RAT) is annotated to "entrainment of circadian clock" from PMID 12397359. The experiments show it is a transcription factor for genes involved in the circadian clock. Two questions: (i) is the term correct? or should it be annotated to the parent (regulation of circadian rhythm); or to both? (ii) is the IDA evidence code correct?
- What evidence code should be used to 'response to' annotations?
- (A) For example in PMID: 2071672, the authors say "Exposure of the latter cells to 45 degrees C resulted in over 15-fold increase in the apparent level of the 25-kD IAP protein, confirming that its expression is regulated by heat shock". Should this protein (Q00649) be annotated to "response to heat" by IDA or IEP?
- (B) Similar to (A) example: "Two highly divergent human MHC class I genes, MICA (Q29983) and MICB (Q29980), are regulated by promoter heat shock elements", protein: PMID: 8901601. Should this protein (Q00649) be annotated to "response to heat" by IDA or IEP?
- (C) Q16576 Sc RBBP7 (aka RBAP46) is annotated to "cellular heat acclimation" by IDA from PMID:7503932. Is this annotation correct?
5. Suggestions for Quality Control procedures
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