Tripal Publication Quick Links

Module Description:

The Tripal Publication Module provides the functionality for adding, editing, deleting viewing and bulk importing of publications. This module additionally provides a search tool for finding publications that have been added to Chado database.

Setup Instructions:

1. Set Permissions: The publication module supports the Drupal user permissions interface for controlling access to publication content and functions. These permissions include viewing, creating, editing or administering of publications. The default is that only the original site administrator has these permissions. You can add roles for classifying users, assign users to roles and assign permissions for the publication content to those roles. For a simple setup, allow anonymous users access to view publication content and allow the site administrator all other permissions.

2. Sync Publications: If you already have publications in your Chado database, or you loaded them through a means other than Tripal, and you want those publications to appear on your site then you will need to "sync" them with Drupal. Use the page to sync all publications.

3. Configure the Search Behavior: Before allowing site visitors to search for publications visit the to disable or enable fields for searching. Tripal uses its own ontology for storing publication information in Chado, and all child terms of the "Publication Details" are made available for searching. However, some of these may not be desired for searching and can be disabled.

4. AGL Importer: Initially, the Tripal publication module supports creating publication importers using PubMed and the USDA National Agricultural Library (AGL). The AGL database uses a Z39.50 protocol for querying and therefore Tripal requires the 'YAZ' library to connect. Before you can query AGL you must install the YAZ library and the PHP YAZ library. The following steps can be used on an Ubuntu 12.04 server to intall the necessary pre-requisites:

   1. Install the YAZ libraries: sudo apt-get install yaz libyaz4-dev
   2. Install the PHP YAZ extension: sudo pecl install yaz
   3. Add the text 'extesion=yaz.so' to the appropriate php.ini file (e.g. /etc/php5/apache2filter/php.ini)
   4. Restart the webserver

Features of this Module:

• Add/Edit/Delete Publications: Publications can be maually added . Once added, publications can be modified or deleted by clicking the Edit tab at the top of a publication page.

• Publication Search Tool: A is provided for finding publications. Unlike most default search tools for Tripal, this tool does not rely on Drupal Views

• Bulk Import of Publications: Site administrators can which provides a set of search terms for querying a remote publication database (e.g. PubMed). Publications that matche the search terms can be imported when the publication import cron command is executed. The cron command can be executed using the Drush command: drush tpubs-import. This drush command can be added as a system-wide cron (in the same way the Tripal jobs cron is implemented) to be executed on a periodic basis. This will allow the site to import publications which have been newly added to remote databases and which are relative to the site. Site administrators can and edit, disable or delete the importers.