Difference between revisions of "Textpresso-based automated extraction of concise descriptions"

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====Patterns of occurence====
 
====Patterns of occurence====
 +
('....' denotes some words).
 +
 +
 
'''Molecular identity''' <br \>
 
'''Molecular identity''' <br \>
<Gene> encodes .....;
+
<Gene> encodes ....
  
  
 
'''Orthology/Similarity''' <br \>
 
'''Orthology/Similarity''' <br \>
<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''' <br \>
 
'''Genetic interaction with respect to Process or Pathway''' <br \>
<Gene> interacts genetically with (gene1, gene2) in <Process, Pathway>;
+
<Gene> interacts genetically with (gene1, gene2) in <Process, Pathway>
  
 
'''Physical interaction''' <br \>
 
'''Physical interaction''' <br \>
<Protein> physically interacts with (<protein>, DNA, RNA) .....;
+
<Protein> physically interacts with (<protein>, DNA, RNA)
  
 
'''Molecular Function''' <br \>
 
'''Molecular Function''' <br \>
<Protein> has ..... activity in (in vitro, in vivo) assays;
+
<Protein> has .... activity in (in vitro, in vivo) assays
  
 
'''Tissue Expression''' <br \>
 
'''Tissue Expression''' <br \>
<Gene/Protein> is expressed in ..... and expression in ..... is (positively, negatively) regulated by <Gene/Protein>.....;
+
<Gene/Protein> is expressed in .... and expression in .... is (positively, negatively) regulated by <Gene/Protein>
  
 
'''Sub-cellular localization''' <br \>
 
'''Sub-cellular localization''' <br \>
<Gene/Protein> is localized to <cellular component> and expression in <cellular component> is (positively, negatively) regulated by .....
+
<Gene/Protein> is localized to <cellular component> and expression in <cellular component> is (positively, negatively) regulated by ....

Revision as of 21:48, 8 May 2014

Generating gene sets with and without concise descriptions

Set of genes with a concise description

Query for all genes with a concise description from Postgres: Relevant postgres table names:

  • con_wbgene: Stores the WBGene ID and gene names
  • con_desctype: Type of description (relevant for us: Concise_description)
  • con_desctext: Text of the concise description

Query for all WBGenes that have a concise description (in con_desctext AND con_desctype):

SELECT DISTINCT(con_wbgene) FROM con_wbgene WHERE joinkey IN (SELECT joinkey FROM con_desctext WHERE con_desctext IS NOT NULL) AND joinkey IN (SELECT joinkey FROM con_desctype WHERE con_desctype IS NOT NULL) ORDER BY con_wbgene;

  • Number of genes with a concise description (as of 05.07.2014)=6,624

Set of genes with no concise description

Set of genes with no concise description and at least one published paper

Semantic categories targeted for extraction from the literature

1. Molecular identity
2. Orthology/Similarity
Wild type Function
3. Processes
4. Pathways
5. Mutant Phenotypes
Interactions
6. Genetic Interaction
7. Physical Interaction
8. Molecular Function
Expression
9. Tissue expression (may include life-stage)
10. Sub-cellular localization (may include life-stage)

Patterns of occurence

('....' denotes some words).


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 <Gene/Protein>

Sub-cellular localization
<Gene/Protein> is localized to <cellular component> and expression in <cellular component> is (positively, negatively) regulated by ....