gmod_bulk_load_pubmed.pl(1p)

Overview

 Usage: perl gmod_bulk_load_pubmed.pl -H [dbhost] -D [dbname]  [-vt] -i file

parameters

-H: hostname for database

-D: database name

-i: input file [required]

-v: verbose output

-t: trial mode. Do not perform any store operations at all.

-g: GMOD database profile name (can provide host and DB name) Default: 'default'

If not using a GMOD database profile (option -g) then you must provide the following parameters

-u: user name

-d: database driver name (i.e. 'Pg' for postgres)

-p: password for youe user to connect to the database

The script stores pubmed entries in the database. Existing ones are ignored. Input file should contain a list of pubmed ids. Then a new Publication object (Bio::Chado::Schema::Pub::Pub) with accession= PMID, the publication specs are fetched from Entrez (using eUtils) which sets the different fields in the Publication object. When the publication is stored, a new dbxref is stored first (see Chado General module)

This script works with Chado schema and accesse the following tables:

pub

pubauthor

pubprop

dbxref

pub_dbxref

Version and date

Version 1.1, April 2010.

Releases

6 releases since Debian 8 (Jessie); the text changed 3 times.