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 <[email protected]>
VERSION AND DATE
Version 1.1, April 2010.