2010 GO-camp Response to terms issues

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  • How will these relate to signaling terms and to final cellular effect?

Definition of "response to stimulus" 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 stimulus."

  • Are we looking to describe the regulators of the response or the targets of the response?
  • For example many heat shock proteins are annotated to 'response to heat' because they are themselves upregulated in response to heat. Is this what we are looking for? For other branches of the ontology, the 'target' of a process is not annotated, for example, a kinase is annotated to 'phosphorylation', and not its target.
  • We also have a term called 'regulation of response'. What does that include? Would transcription factors and hormones be regulators of the response?

Examples

    • 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?


  • 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?




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