Difference between revisions of "Attaching Genes to Papers"
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Some ideas on what to change: | Some ideas on what to change: | ||
| − | 1) With the exception of a dash (-), split text (words or letters) from punctuation. | + | 1) With the exception of a dash (-), split text (words or letters) from punctuation and then look for matches to the approved gene list. |
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| + | For example, fem-1(hc17ts) would become fem-1 ( hc17ts ) | ||
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WBPaper00035449 - missed gas-1, isp-1, daf-2, sod-2 | WBPaper00035449 - missed gas-1, isp-1, daf-2, sod-2 | ||
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| + | WBPaper00035474 - missed fem-1, fem-3 | ||
Revision as of 20:49, 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 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
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