|
|
| (156 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''' <br \>
| |
| − | <Gene> encodes .....;
| |
| − |
| |
| − |
| |
| − | '''Orthology/Similarity''' <br \>
| |
| − | <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''' <br \>
| |
| − | <Gene> interacts genetically with (gene1, gene2) in <Process, Pathway>;
| |
| − |
| |
| − | '''Physical interaction''' <br \>
| |
| − | <Protein> physically interacts with (<protein>, DNA, RNA) .....;
| |
| − |
| |
| − | '''Molecular Function''' <br \>
| |
| − | <Protein> has ..... activity in (in vitro, in vivo) assays;
| |
| − |
| |
| − | '''Tissue Expression''' <br \>
| |
| − | <Gene/Protein> is expressed in ..... and expression in ..... is (positively, negatively) regulated by <Gene/Protein>.....;
| |
| − |
| |
| − | '''Sub-cellular localization''' <br \>
| |
| − | <Gene/Protein> is localized to <cellular component> and expression in <cellular component> is (positively, negatively) regulated by .....
| |
