|
|
(157 intermediate revisions by the same user not shown) |
Line 1: |
Line 1: |
− | ==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 <br \>
| |
− | 2. Orthology/Similarity <br \>
| |
− | Wild type Function <br \>
| |
− | 3. Processes <br \>
| |
− | 4. Pathways <br \>
| |
− | 5. Mutant Phenotypes <br \>
| |
− | Interactions <br \>
| |
− | 6. Genetic Interaction<br \>
| |
− | 7. Physical Interaction <br \>
| |
− | 8. Molecular Function <br \>
| |
− | Expression <br \>
| |
− | 9. Tissue expression (may include life-stage) <br \>
| |
− | 10. Sub-cellular localization (may include life-stage) <br \>
| |
− |
| |
− | ====Patterns of occurence====
| |
− | '''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 .....
| |