Textpresso-based automated extraction of concise descriptions

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

Semantic categories targeted for extraction from the literature

1. Molecular identity 2. Orthology/Similarity Wild type Function <\br> 3. Processes 4. Pathways 5. Mutant Phenotypes Interactions <\br> 6. Genetic 7. Physical 8. Molecular Function Expression <\br> 9. Tissue expression 10. Sub-cellular localization