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==
Curators as a general rule make sure that the following key facts are captured in a concise description, when this information is available in the published literature. Please do not use information from meeting abstracts, Worm Breeder Gazette articles, personal observations, etc.:
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Gene descriptions are concise descriptions about gene function, they appear at the top of gene pages in WormBase in the 'Overview' widget.
 +
 
 +
The following key facts are captured in a concise description, when this information is available in the published literature. Please do not use information from meeting abstracts, Worm Breeder Gazette articles and personal observations/communications.
  
 
*Molecular identity
 
*Molecular identity
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*Sub cellular localization
 
*Sub cellular localization
  
So, the template for a concise description will look like:
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So, the template for a concise description would look like:
 
  '''Molecular identity'''
 
  '''Molecular identity'''
 
  <Gene> encodes .....;
 
  <Gene> encodes .....;
 +
 
  '''Orthology/Similarity'''
 
  '''Orthology/Similarity'''
 
  <Gene> is <orthologous, similar) to .....;
 
  <Gene> is <orthologous, similar) to .....;
 +
 
  '''Process/Pathway'''
 
  '''Process/Pathway'''
 
  <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'''
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  <Gene> interacts genetically with <gene1, gene2>..... in <Process, Pathway>;
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  '''Genetic interaction'''
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  <Gene> interacts genetically with <gene1, gene2> ..... in <Process, Pathway>;
 +
 
  '''Physical interaction'''
 
  '''Physical interaction'''
  <Protein> physically interacts with <protein, DNA, RNA).......;
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  <Protein> physically interacts with <protein, DNA, RNA) .....;
 +
 
  '''Molecular Function'''
 
  '''Molecular Function'''
  <Protein> has ……… 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)  
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  <Gene/Protein> is expressed in ..... and expression in ..... is (positively, negatively)  
  regulated by   .......;
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  regulated by .....;
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  '''Sub-cellular localization'''  
 
  '''Sub-cellular localization'''  
  <Protein> is localized to <sub-cellular component> or .......and expression in <sub-cellular component> is
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  <Protein> is localized to <cellular component> and expression in <cellular component>  
  <positively, negatively> regulated by ........
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  is <positively, negatively> regulated by .....
  
 
Note that the above template is to be used as a guide, and not all descriptions may follow the exact order or choice of words.   
 
Note that the above template is to be used as a guide, and not all descriptions may follow the exact order or choice of words.   
 +
 
Examples of concise descriptions written by WormBase:
 
Examples of concise descriptions written by WormBase:
  
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  lin-10 encodes a PDZ and PTB domain-containing protein that is homologous to mammalian Munc interacting proteins  
 
  lin-10 encodes a PDZ and PTB domain-containing protein that is homologous to mammalian Munc interacting proteins  
 
  (Mint1) and is required for polarized protein localization; LIN-10 is required for proper localization of the  
 
  (Mint1) and is required for polarized protein localization; LIN-10 is required for proper localization of the  
  LET-23 EGF receptor to the basolateral membrane of the vulval precursor cells and for proper postsynaptic localization  
+
  LET-23 EGF receptor to the basolateral membrane of the vulval precursor cells and for proper postsynaptic localization  
 
  of GLR-1, an AMPA-type glutamate receptor in interneurons; LIN-10 is detected in the cytoplasm, membrane, and  
 
  of GLR-1, an AMPA-type glutamate receptor in interneurons; LIN-10 is detected in the cytoplasm, membrane, and  
 
  at particularly high levels in the Golgi.
 
  at particularly high levels in the Golgi.
  
Example: lon-2
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Example: lon-1
 
  The lon-1 gene encodes a protein belonging to the PR-protein superfamily that is a target of DBL-1 (TGF-beta)  
 
  The lon-1 gene encodes a protein belonging to the PR-protein superfamily that is a target of DBL-1 (TGF-beta)  
 
  signaling, and that regulates polyploidization and body length.
 
  signaling, and that regulates polyploidization and body length.

Latest revision as of 03:38, 3 June 2015

Writing a concise description for a C. elegans gene

Gene descriptions are concise descriptions about gene function, they appear at the top of gene pages in WormBase in the 'Overview' widget.

The following key facts are captured in a concise description, when this information is available in the published literature. Please do not use information from meeting abstracts, Worm Breeder Gazette articles and personal observations/communications.

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

So, the template for a concise description would look 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
<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 <cellular component> and expression in <cellular component> 
is <positively, negatively> regulated by .....

Note that the above template is to be used as a guide, and not all descriptions may follow the exact order or choice of words.

Examples of concise descriptions written by WormBase:

Example: lin-10

lin-10 encodes a PDZ and PTB domain-containing protein that is homologous to mammalian Munc interacting proteins 
(Mint1) and is required for polarized protein localization; LIN-10 is required for proper localization of the 
LET-23 EGF receptor to the basolateral membrane of the vulval precursor cells and for proper postsynaptic  localization 
of GLR-1, an AMPA-type glutamate receptor in interneurons; LIN-10 is detected in the cytoplasm, membrane, and 
at particularly high levels in the Golgi.

Example: lon-1

The lon-1 gene encodes a protein belonging to the PR-protein superfamily that is a target of DBL-1 (TGF-beta) 
signaling, and that regulates polyploidization and body length.