.\" Automatically generated by Pod::Man 4.11 (Pod::Simple 3.35)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "GMOD_BULK_LOAD_PUBMED 1p"
.TH GMOD_BULK_LOAD_PUBMED 1p "2019-12-05" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.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.
