September 6, 2013 A HUBzero Extension for Automated Tagging Jim Mullen Advanced Biomedical IT Core Indiana University

My Work on Extension I implemented the automated tagging extension, but others came up with the idea and contributed to the design, including Bill Barnett, Michael Grobe and Anurag Shankar. September 6, 2013A HUBzero Extension for Automated Tagging

Automated Tagging Extension Goal. Support automated tagging of Indiana CTSI (Clinical and Translational Sciences Institute) Hub ( pages using the NCBO (National Center for Biomedical Ontology) Annotatorhttp://indianactsi.org Motivation. Tagging (assigning terms from a controlled vocabulary/ontology to pages) can be very helpful for site search and navigation, but manual tagging is expensive. September 6, 2013A HUBzero Extension for Automated Tagging

September 6, 2013A HUBzero Extension for Automated Tagging NCBO Annotator A web site that includes web services for annotating text using various controlled vocabularies and ontologies, such as SNOMED and MeSH (Medical Subject Headings).

NCBO Annotator Example Text: “Gene therapy vectors based on murine retroviruses have now been in clinical trials for over 20 years. During that time, a variety of novel vector pseudotypes were developed in an effort to improve gene transfer.” Ontology: MeSH Terms/Tags: Genes Gene Therapy Retroviridae therapy Time Transfer (Psychology) September 6, 2013A HUBzero Extension for Automated Tagging

Extension Overview The Indiana CTSI HUB was built using HUBzero ( which was built on top of the Joomla content management system. Extension works with Joomla (version 1.5) as well as HUBzero Extension consists of: o Plugin – conditionally tags pages when they are accessed, and displays the tags on pages o Component – provides user interface for search and navigation and administrative interface for configuration September 6, 2013A HUBzero Extension for Automated Tagging

Extension Overview (continued) User interface (front-end) o Information/help page o Multi-word auto-complete tag search o Tag cloud o Tag information page Admin interface (back-end) o Configuration of extension September 6, 2013A HUBzero Extension for Automated Tagging

Tags on Pages September 6, 2013A HUBzero Extension for Automated Tagging The extension adds tags to the bottom of pages (using a plugin).

Information/Help Page September 6, 2013A HUBzero Extension for Automated Tagging You can create an article that users will be directed to when they click on the “What’s this?” link.

Tag Search September 6, 2013A HUBzero Extension for Automated Tagging You can select the ontology to use for the search. Auto-completion is provided for search terms.

Tag Cloud September 6, 2013A HUBzero Extension for Automated Tagging The size of a term is proportional to the number of pages that are tagged with it

Tag Information Page September 6, 2013A HUBzero Extension for Automated Tagging The Tag Info page lists the pages that contain the specified tag.

Extension Installation September 6, 2013A HUBzero Extension for Automated Tagging Upload a zip file using the HUBZero / Joomla admin interface

Extension Configuration September 6, 2013A HUBzero Extension for Automated Tagging After the component is installed, the component’s admin interface is used to configuring the component

Component Configuration - Steps 1.Get and enter an NCBO API key 2.Download ontology information from NCBO 3.Select the ontologies to use and a primary/default ontology 4.Set tagging options 5.Turn tagging on September 6, 2013A HUBzero Extension for Automated Tagging

Component Configuration Tagging Display Options September 6, 2013A HUBzero Extension for Automated Tagging

Extension Configuration Tagging Update Options Turn on/off tag updates Limit IP addresses for tag updates Time limit before tag updates are made Pages to exclude from tagging Components to exclude from tagging September 6, 2013A HUBzero Extension for Automated Tagging

Conclusions Pros Automatically tags pages Will work on all pages (not component-dependent) Works with Joomla as well as HUBzero Cons Tagging dependent on NCBO annotator: o Does not seem to be very intelligent o Too slow to have real-time tagging o Extension will break if NCBO changes their web services o Limited to biomedical ontologies It’s possible to change the extension’s annotator, so this extension could be used as a basis for using or testing other annotators. September 6, 2013A HUBzero Extension for Automated Tagging

September 6, 2013A HUBzero Extension for Automated Tagging License Terms Please cite as: Mullen, J. A HUBzero Extension for Automated Tagging Presentation. Presented at HUBbub 2013 (Indianapolis, IN, 6 September 2013). Items indicated with a © are under copyright and used here with permission. Such items may not be reused without permission from the holder of copyright except where license terms noted on a slide permit reuse. Except where otherwise noted, contents of this presentation are copyright 2013 by the Trustees of Indiana University. This document is released under the Creative Commons Attribution 3.0 Unported license ( This license includes the following terms: You are free to share – to copy, distribute and transmit the work and to remix – to adapt the work under the following conditions: attribution – you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work.