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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, 2013

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.


September 6, 2013

A HUBzero Extension for Automated Tagging

September 6, 2013

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).

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, 2013

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:

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, 2013

A 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, 2013

A HUBzero Extension for Automated Tagging

Tags on Pages

September 6, 2013

A HUBzero Extension for Automated Tagging



The
extension
adds tags
to the
bottom of
pages
(using a
plugin).

Information/Help Page

September 6, 2013

A 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, 2013

A 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, 2013

A 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, 2013

A HUBzero Extension for Automated Tagging

The Tag Info
page lists
the pages
that contain
the specified
tag.

Extension Installation

September 6, 2013

A HUBzero Extension for Automated Tagging

Upload a
zip file
using the
HUBZero

/
Joomla

admin
interface

Extension Configuration

September 6, 2013

A 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, 2013

A HUBzero Extension for Automated Tagging

Component Configuration

Tagging Display Options

September 6, 2013

A 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, 2013

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:

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, 2013

A HUBzero Extension for Automated Tagging