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.

perl v5.30.0                                       2019-12-05                          GMOD_BULK_LOAD_PUBMED(1p)