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gmod_bulk_load_pubmed.plp - Online in the Cloud

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PROGRAM:

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

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