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GMOD_BULK_LOAD_PUBMED(1p) User Contributed Perl Documentation GMOD_BULK_LOAD_PUBMED(1p)

NAME

gmod_bulk_load_pubmed.pl - stores pubmed entries in the database

DESCRIPTION

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

parameters

hostname for database
database name
input file [required]
verbose output
trial mode. Do not perform any store operations at all.
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

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

AUTHOR

Naama Menda <nm249@cornell.edu>

VERSION AND DATE

Version 1.1, April 2010.

2019-12-05 perl v5.30.0