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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.
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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. A HUBzero Extension for Automated Tagging
Automated Tagging Extension Goal. Support automated tagging of Indiana CTSI (Clinical and Translational Sciences Institute) Hub (http://indianactsi.org) pages using the NCBO (National Center for Biomedical Ontology) Annotator 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. A 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). A HUBzero Extension for Automated Tagging
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) A HUBzero Extension for Automated Tagging
Extension Overview • The Indiana CTSI HUB was built using HUBzero (http://hubzero.org), 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: • Plugin – conditionally tags pages when they are accessed, and displays the tags on pages • Component – provides user interface for search and navigation and administrative interface for configuration A HUBzero Extension for Automated Tagging
Extension Overview (continued) • User interface (front-end) • Information/help page • Multi-word auto-complete tag search • Tag cloud • Tag information page • Admin interface (back-end) • Configuration of extension A HUBzero Extension for Automated Tagging
Tags on Pages The extension adds tags to the bottom of pages (using a plugin). A HUBzero Extension for Automated Tagging
Information/Help Page You can create an article that users will be directed to when they click on the “What’s this?” link. A HUBzero Extension for Automated Tagging
Tag Search You can select the ontology to use for the search. Auto-completion is provided for search terms. A HUBzero Extension for Automated Tagging
Tag Cloud The size of a term is proportional to the number of pages that are tagged with it A HUBzero Extension for Automated Tagging
Tag Information Page The Tag Info page lists the pages that contain the specified tag. A HUBzero Extension for Automated Tagging
Extension Installation Upload a zip file using the HUBZero / Joomla admin interface A HUBzero Extension for Automated Tagging
Extension Configuration After the component is installed, the component’s admin interface is used to configuring the component A HUBzero Extension for Automated Tagging
Component Configuration - Steps • Get and enter an NCBO API key • Download ontology information from NCBO • Select the ontologies to use and a primary/default ontology • Set tagging options • Turn tagging on A HUBzero Extension for Automated Tagging
Component ConfigurationTagging Display Options A HUBzero Extension for Automated Tagging
Extension ConfigurationTagging 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 A 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: • Does not seem to be very intelligent • Too slow to have real-time tagging • Extension will break if NCBO changes their web services • 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. A HUBzero Extension for Automated Tagging