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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

-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

AUTHOR

Naama Menda <nm249@cornell.edu>

VERSION AND DATE

Version 1.1, April 2010.
2019-12-05 perl v5.30.0