Attaching Genes to Papers

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.

An idea on what to change:

1) With the exception of a dash (-), split text from punctuation and then look for matches to the approved gene list.

For example, fem-1(hc17ts) would become fem-1 ( hc17ts )

DAF-18/PTEN would become DAF-18 / PTEN

Papers where gene associations have been missed for testing 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

WBPaper00037741 - missed DAF-18, PHA-4, HSF-1, SIR-2.1, AAK-2

WBPaper00037686 - missed bus-2, bus-4, bus-12, srf-3, bus-8, bus-17

WBPaper00037794 - missed MIG-14

This will update the script we run on incoming papers, but we will need to decide what to do about previous papers. About a year ago, Juancarlos wrote a script to retroactively associate proteins with papers; perhaps we could similarly modify that script to run on previous papers?

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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