---
name: "gmod_bulk_load_pubmed.pl"
section: "1p"
platform: "linux"
package: "chado-utils"
version: "1.31-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmod_bulk_load_pubmed.pl"
---

# gmod\_bulk\_load\_pubmed.pl(1p)

stores pubmed entries in the database

## 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.