|
|
| (150 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 \>
| |
| − | 3. Processes <br \>
| |
| − | 4. Pathways <br \>
| |
| − | 5. Mutant Phenotypes <br \>
| |
| − | 6. Genetic Interaction<br \>
| |
| − | 7. Physical Interaction <br \>
| |
| − | 8. Molecular Function <br \>
| |
| − | 9. Tissue expression (may include life-stage) <br \>
| |
| − | 10. Sub-cellular localization (may include life-stage) <br \>
| |
| − |
| |
| − | ====Publications related to Text-mining methods====
| |
| − | *Automatically generating gene summaries from biomedical literature.
| |
| − |
| |
| − | Ling X, Jiang J, He X, Mei Q, Zhai C, Schatz B.
| |
| − |
| |
| − | Pac Symp Biocomput. 2006:40-51.
| |
| − |
| |
| − | PMID:17094226
| |
| − |
| |
| − | *Generating gene summaries from biomedical literature: A study of semi-structured summarization
| |
| − |
| |
| − | Xu Ling *, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, Bruce Schatz
| |
| − |
| |
| − | Information Processing and Management 43 (2007) 1777–1791
| |
| − |
| |
| − |
| |
| − | Back To [[Concise Descriptions]]
| |
