Difference between revisions of "2010 GO camp Use of Regulation issues"

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m (Created page with ' =1. Background= * This includes process beginning/end (maybe in the context of the new signaling terms) * How to decide whether to annotate to 'regulates process x' or 'process …')
 
m (2. Review of current GO annotation practices)
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Questions: How do groups decide on when to annotate to 'regulates process x' or 'process x'?  
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Question 1: How do groups decide on when to annotate to 'regulates process x' or 'process x'?  
 
For instance does SLIT regulate axon guidance or involved in the process of axon guidance?
 
For instance does SLIT regulate axon guidance or involved in the process of axon guidance?
 
Val - this depends on the defined start/end of a process and somethings can be annotated to BOTH the regulates term and also directly to the process term.  
 
Val - this depends on the defined start/end of a process and somethings can be annotated to BOTH the regulates term and also directly to the process term.  
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When should annotations be inherited up the regulates relationship?
 
When should annotations be inherited up the regulates relationship?
  
Notes: Annotations could be checked more efficiently if GO term definitions could include the beginning and end of a process.
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Question 2: Annotations could be checked more efficiently if GO term definitions could include the beginning and end of a process.
 
 
(Comment from Ruth: Should we also consider how the 'activity' of a protein is defined when making these regulation/process decisions. The definition for transcription factor activity is: The function of binding to a specific DNA sequence in order to modulate transcription.... This suggests that a transcription factor is involved in the process of regulating transcription rather than involved in the process of transcription itself. However, some of us in the UK feel that many transcription factors are involved in the transcription process itself definition: The synthesis of either RNA on a template of DNA or DNA on a template of RNA. Does the definition for transcription factor activity need modification to enable this annotation, or are only the polymerases involved in the synthesis?)
 
  
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Question 3 (from Ruth):  Should we also consider how the 'activity' of a protein is defined when making these regulation/process decisions. The definition for transcription factor activity is: The function of binding to a specific DNA sequence in order to modulate transcription.... This suggests that a transcription factor is involved in the process of regulating transcription rather than involved in the process of transcription itself. However, some of us in the UK feel that many transcription factors are involved in the transcription process itself definition: The synthesis of either RNA on a template of DNA or DNA on a template of RNA. Does the definition for transcription factor activity need modification to enable this annotation, or are only the polymerases involved in the synthesis?)
  
 
=3. Proposed annotation policy=
 
=3. Proposed annotation policy=

Revision as of 06:40, 18 March 2010

1. Background

  • This includes process beginning/end (maybe in the context of the new signaling terms)
  • How to decide whether to annotate to 'regulates process x' or 'process x'?

2. Review of current GO annotation practices

Question 1: How do groups decide on when to annotate to 'regulates process x' or 'process x'? For instance does SLIT regulate axon guidance or involved in the process of axon guidance? Val - this depends on the defined start/end of a process and somethings can be annotated to BOTH the regulates term and also directly to the process term. Some groups decide that if removing the activity of a gene product produces an all/nothing event - then they define it as being part of the process. When should annotations be inherited up the regulates relationship?

Question 2: Annotations could be checked more efficiently if GO term definitions could include the beginning and end of a process.

Question 3 (from Ruth): Should we also consider how the 'activity' of a protein is defined when making these regulation/process decisions. The definition for transcription factor activity is: The function of binding to a specific DNA sequence in order to modulate transcription.... This suggests that a transcription factor is involved in the process of regulating transcription rather than involved in the process of transcription itself. However, some of us in the UK feel that many transcription factors are involved in the transcription process itself definition: The synthesis of either RNA on a template of DNA or DNA on a template of RNA. Does the definition for transcription factor activity need modification to enable this annotation, or are only the polymerases involved in the synthesis?)

3. Proposed annotation policy

4. Examples (papers) and discussion of GO annotation issues

5. Suggestions for Quality Control procedures


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