Difference between revisions of "Attaching Genes to Papers"
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− | ==Gene | + | ==Gene Associations Based on Curated Data== |
Data types for which curation is stored in postgres: | Data types for which curation is stored in postgres: |
Revision as of 21:21, 9 November 2010
Gene Associations Based Upon Abstracts
When papers are added to postgres using the Enter New Papers function of the Paper Editor, the corresponding abstracts are scanned, via a script, for matches to loci, sequence names, and synonyms.
Postgres tables used for this are:
gin_locus
gin_seqname
gin_synonyms
To view the contents of these tables, perform the following type of query using the referenceform.cgi:
SELECT * FROM gin_locus;
Updating the script:
The script that associates genes based upon abstracts does miss some genes because of the way they're expressed in the abstract.
Some ideas on what to change:
1) With the exception of a dash (-), split text (words or letters) from punctuation and then look for matches to the approved gene list.
For example, fem-1(hc17ts) would become fem-1 ( hc17ts )
Papers where gene associations have been missed for checking and re-training the script:
WBPaper00035164 - missed BLI-4
WBPaper00035239 - missed CATP-5
WBPaper00035289 - missed SPP-5
WBPaper00035423 - missed PAR-1
WBPaper00035449 - missed gas-1, isp-1, daf-2, sod-2
WBPaper00035474 - missed fem-1, fem-3
WBPaper00035490 - missed daf-16
WBPaper00035559 - missed NMY-2, GPR-1/2, LIN-5
Gene Associations Based on Curated Data
Data types for which curation is stored in postgres:
Antibody
Concise Descriptions
Gene Interactions
Gene Ontology
Gene Regulation
Picture
Transgenes
Variation Phenotype
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