Difference between revisions of "How WormBase writes a concise description"

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==Writing a concise description for a C. elegans gene==
 
==Writing a concise description for a C. elegans gene==
Key facts captured in a concise description:
+
Curators as a general rule make sure that the following key facts are captured in a concise description, when this information is available in published literature, please do not use information from meeting abstracts, Worm Breeder Gazette articles, personal observations, etc.:
  
 
*Molecular identity
 
*Molecular identity
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*Sub cellular localization
 
*Sub cellular localization
  
 
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So, the template for a concise description will look something like:
 
  '''Molecular identity'''
 
  '''Molecular identity'''
 
  <Gene> encodes .....;
 
  <Gene> encodes .....;
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  <Gene> is <required, functions, regulates, is involved in, is part of> .....;
 
  <Gene> is <required, functions, regulates, is involved in, is part of> .....;
 
  '''Genetic interaction with respect to Process or Pathway'''
 
  '''Genetic interaction with respect to Process or Pathway'''
  <Gene> interacts genetically with ..... in <Process, Pathway>;
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  <Gene> interacts genetically with <gene1, gene2>..... in <Process, Pathway>;
 
  '''Physical interaction'''
 
  '''Physical interaction'''
  <Protein> physically interacts <invitro, invivo> with .......;
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  <Protein> physically interacts with <protein, DNA, RNA).......;
 
  '''Molecular Function'''
 
  '''Molecular Function'''
  <Protein> has or ……… activity in <in vitro, in vivo> assays;
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  <Protein> has ……… activity in <in vitro, in vivo> assays;
 
  '''Tissue Expression'''
 
  '''Tissue Expression'''
 
  <Gene/Protein> is expressed in …………and expression in ......is (positively, negatively)  
 
  <Gene/Protein> is expressed in …………and expression in ......is (positively, negatively)  
 
  regulated by  .......;
 
  regulated by  .......;
  '''Cellular Component/sub-cellular localization'''  
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  '''Sub-cellular localization'''  
  <Protein> is localized to <sub-cellular component> or .......and expression in  
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  <Protein> is localized to <sub-cellular component> or .......and expression in <sub-cellular component> is  
<sub-cellular component> is <positively, negatively> regulated by ........
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<positively, negatively> regulated by ........

Revision as of 18:57, 2 April 2013

Writing a concise description for a C. elegans gene

Curators as a general rule make sure that the following key facts are captured in a concise description, when this information is available in published literature, please do not use information from meeting abstracts, Worm Breeder Gazette articles, personal observations, etc.:

  • Molecular identity
  • Orthology
  • Process/Pathway
  • Genetic interactions
  • Physical interactions
  • Function/Molecular Activity
  • Tissue Expression
  • Sub cellular localization

So, the template for a concise description will look something like:

Molecular identity
<Gene> encodes .....;
Orthology/Similarity
<Gene> is <orthologous, similar) to .....;
Process/Pathway
<Gene> is <required, functions, regulates, is involved in, is part of> .....;
Genetic interaction with respect to Process or Pathway
<Gene> interacts genetically with <gene1, gene2>..... in <Process, Pathway>;
Physical interaction
<Protein> physically interacts with <protein, DNA, RNA).......;
Molecular Function
<Protein> has ……… activity in <in vitro, in vivo> assays;
Tissue Expression
<Gene/Protein> is expressed in …………and expression in ......is (positively, negatively) 
regulated by   .......;
Sub-cellular localization 
<Protein> is localized to <sub-cellular component> or .......and expression in <sub-cellular component> is 
<positively, negatively> regulated by ........