table of contents
| GMOD_BULK_LOAD_PUBMED(1p) | User Contributed Perl Documentation | GMOD_BULK_LOAD_PUBMED(1p) |
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:¶
AUTHOR¶
Naama Menda <nm249@cornell.edu>
VERSION AND DATE¶
Version 1.1, April 2010.
| 2019-12-05 | perl v5.30.0 |