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

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Line 12: Line 12:
  
  
  Molecular identity
+
  '''Molecular identity'''
 
  <Gene> encodes .....;
 
  <Gene> encodes .....;
  Orthology/Similarity
+
  '''Orthology/Similarity'''
  <Gene> is (drop down with values:orthologous,similar) to .....;
+
  <Gene> is to .....;
  Process/Pathway
+
  '''Process/Pathway'''
  <Gene> is (drop-down with values:
+
  <Gene> is <required,functions,regulates,is involved in,is part of> .....;
required,functions,regulates,is involved in,is part of) .....;
+
  '''Genetic interaction with respect to Process or Pathway'''
  (Sentence needs to be cloned if required)
+
  <Gene> interacts genetically with respect to ........;
Genetic interaction with respect to Process or Pathway
+
  '''Physical interaction'''
  <Gene> interacts genetically with (drop-down with ontology:WBGenes) with
+
  <Protein> physically interacts <invitro, invivo> with .......;
respect to ........;
+
  '''Molecular Function'''
  Physical interaction
+
  <Protein> has or ………  activity;
  <Protein> physically interacts (drop-down with values: invitro, invivo) with  
+
  '''Tissue Expression'''
(drop-down with proteins);
+
  <Gene/Protein> is expressed in …………and expression in ......is (positively, negatively)  
  Molecular Function
+
regulated by   .......;
  <Protein> has (drop down with ontology:GO molecular function) or ………  activity;
+
  '''Cellular Component/sub-cellular localization'''
  Tissue Expression
+
  <Protein> is localized to <sub-cellular component> or .......and expression in  
  <Gene/Protein> is expressed in …………and expression in ......is (drop-down
+
<sub-cellular component> is <positively, negatively> regulated by ........
with values: positively, negatively) regulated by .......;
 
  Cellular Component/sub-cellular localization  
 
  <Protein> is localized to (drop-down with ontology:GO cellular component)
 
or .......and expression in .....is (drop-down with values:
 
  positively, negatively) regulated by (drop-down with proteins)
 

Revision as of 22:52, 1 April 2013

Writing a concise description for a C. elegans gene

Key facts captured in a concise description:

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


Molecular identity
<Gene> encodes .....;
Orthology/Similarity
<Gene> is 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 respect to ........;
Physical interaction
<Protein> physically interacts <invitro, invivo> with .......;
Molecular Function
<Protein> has or ………  activity;
Tissue Expression
<Gene/Protein> is expressed in …………and expression in ......is (positively, negatively) 
regulated by   .......;
Cellular Component/sub-cellular localization 
<Protein> is localized to <sub-cellular component> or .......and expression in 
<sub-cellular  component> is <positively, negatively> regulated by ........