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
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