Provided by: chado-utils_1.31-5_all bug

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.