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.IX Title "GMOD_BULK_LOAD_PUBMED 1p"
.TH GMOD_BULK_LOAD_PUBMED 1p "2018-09-27" "perl v5.26.2" "User Contributed Perl Documentation"
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.SH "NAME"
gmod_bulk_load_pubmed.pl \- stores pubmed entries in the database
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.Vb 1
\& Usage: perl gmod_bulk_load_pubmed.pl \-H [dbhost] \-D [dbname]  [\-vt] \-i file
.Ve
.PP
parameters
.IP "\-H" 6
.IX Item "-H"
hostname for database
.IP "\-D" 6
.IX Item "-D"
database name
.IP "\-i" 6
.IX Item "-i"
input file [required]
.IP "\-v" 6
.IX Item "-v"
verbose output
.IP "\-t" 6
.IX Item "-t"
trial mode. Do not perform any store operations at all.
.IP "\-g" 6
.IX Item "-g"
\&\s-1GMOD\s0 database profile name (can provide host and \s-1DB\s0 name) Default: 'default'
.SS "If not using a \s-1GMOD\s0 database profile (option \-g) then you must provide the following parameters"
.IX Subsection "If not using a GMOD database profile (option -g) then you must provide the following parameters"
.IP "\-u" 3
.IX Item "-u"
user name
.IP "\-d" 3
.IX Item "-d"
database driver name (i.e. 'Pg' for postgres)
.IP "\-p" 3
.IX Item "-p"
password for youe user to connect to the database
.PP
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= \s-1PMID,\s0
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)
.SS "This script works with Chado schema and accesse the following tables:"
.IX Subsection "This script works with Chado schema and accesse the following tables:"
.IP "pub" 5
.IX Item "pub"
.PD 0
.IP "pubauthor" 5
.IX Item "pubauthor"
.IP "pubprop" 5
.IX Item "pubprop"
.IP "dbxref" 5
.IX Item "dbxref"
.IP "pub_dbxref" 5
.IX Item "pub_dbxref"
.PD
.SH "AUTHOR"
.IX Header "AUTHOR"
Naama Menda <nm249@cornell.edu>
.SH "VERSION AND DATE"
.IX Header "VERSION AND DATE"
Version 1.1, April 2010.