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

From WormBaseWiki
Jump to navigationJump to search
Line 19: Line 19:
 
==Semantic categories targeted for extraction from the literature==
 
==Semantic categories targeted for extraction from the literature==
  
1. Molecular identity
+
1. Molecular identity <br \>
2. Orthology/Similarity
+
2. Orthology/Similarity <br \>
Wild type Function <\br>
+
Wild type Function <br \>
3. Processes
+
3. Processes <br \>
4. Pathways
+
4. Pathways <br \>
5. Mutant Phenotypes
+
5. Mutant Phenotypes <br \>
Interactions <\br>
+
Interactions <br \>
6. Genetic
+
6. Genetic <br \>
7. Physical
+
7. Physical <br \>
8. Molecular Function
+
8. Molecular Function <br \>
Expression <\br>
+
Expression <br \>
9. Tissue expression
+
9. Tissue expression <br \>
10. Sub-cellular localization
+
10. Sub-cellular localization <br \>

Revision as of 17:43, 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;

  1. 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
7. Physical
8. Molecular Function
Expression
9. Tissue expression
10. Sub-cellular localization