Visualizing Ontologies and Ontology Mappings

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Oct 29, 2013 (3 years and 11 months ago)

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Visualizing
Ontologies

and

Ontology Mappings

May 17
th
, 2012

(NIH/NCI
Nano

Working Group)

Margaret
-
Anne Storey
, Bo Fu, Lars Grammel,

The CHISEL Group, University of Victoria



1


National Center for Biomedical Ontology



Goal:

develop innovative technology and methods that
allow scientists to record, manage, and disseminate
biomedical information and knowledge in both
human
readable

and
machine
-
processable

form.


the CHISEL group, University of Victoria




2

Our goal: Provide
cognitive support

for ontology
developers and users through visual and intelligent
user interfaces


Visualizing
ontologies
:


Diamond: Degree of interest browsing


Jambalaya:
visualizing
ontologies


FlexViz

(currently in
BioPortal
)


BioMixer

(coming soon)

Visualizing mappings and alignment:


CogZ
: Cognitive support for ontology alignment


Visualizing mappings (coming soon)


What
is cognitive support
?

A form of “
mental assistance
” during thinking and

problem solving



We often provide support through automation
but real complexity is left to the user


Distributed cognition



DIaMOND

Degree of Interest Modeling for Ontology
Navigation and Development


http://
www.thechiselgroup.org
/diamond


Motivation



Navigating
ontologies

can be tedious…


Long scrolling lists, expanding/collapsing nodes


Large number of irrelevant elements occlude
relevant information



Users often don’t know where to start when
navigating an unfamiliar ontology


Might appreciate “worn paths”


DIaMOND

--

Approach



Applies principles of attention
-
reactive
interfaces


Mechanism to calculate user’s degree of interest
(DOI)


Dynamic display of information using the DOI



Goals


Draw user’s attention to interesting elements


Reduce navigation overhead


DIaMOND

(Protégé plug
-
in)


Three levels of interest


Interesting


Has been interacted with such that the DOI value
exceeds a threshold value


Uninteresting


DOI value falls below the threshold value


Landmark:

Hub concept


Manually specified by user


DOI value exceeds a
threshold

value


Lightweight
, easily reversible focus techniques


Consistent

with existing, familiar Protégé views


Highlighting and Filtering in the Class
Browser:

standard, highlighting, highlighting and filtering.

Diamond’s Future
Work?



Sharing

DOI among users (many requests)


Role and Task
-
based

DOI calculations


Use of instance
data

and annotated data to
supplement DOI calculations



Integrate and evaluate Diamond approach in
BioPortal


Develop
heatmaps

showing which concepts
are navigated to and used


Jambalaya

Visualization of
ontologies

to support navigation

Visualization and Jambalaya


Why are visualizations important?


Ontologies

can be extremely large and complex, difficult to navigate
using just trees and lists


Visualizations help users understand
ontologies

by showing overviews
and hub concepts




Other visualization approaches:


OntoViz
,
OWLViz
,
TGViz
,
ezOWL
,
Ontorama
,
Ontobroker



IsaViz
: visual RDF editor


Many graph
-
like visualization tools
!


Indented lists, trees, landscapes, matrix, hyperbolic, 3D,
treemap
,
zoomable
, radar views etc.


Main Features in Jambalaya


Classes and instances/individuals are
represented by nodes in the graph


Slots or properties are represented by
arcs between nodes


the CHISEL group, University of Victoria

the CHISEL group, University of Victoria

the CHISEL group, University of Victoria

the CHISEL group, University of Victoria

Inconsistencies “pop
-
out” in some
views

Composite Arcs



High level edges (lifted)

Different Views



Nested View (Default)


Flat views


Class Tree


Class & Instance Tree


Domain & Range (OWL)



TreeMap

View



Query View



Filmstrip



Customized views


FlexViz


Some ideas from Jambalaya ported to a flash
implementation and integrated with
BioPortal


Goals:


Reach a larger audience (web)


Promote socialization around the visualizations


Reduce task complexity (no install)


Track user
behaviour

(could inform Diamond
-
like
features)


Exploratory interaction (as opposed to overviews)


21

FlexViz

Some
FlexViz

features


Ontology
tree

synchronization with
graph

view


Export

graph as an image or an xml file, can
be emailed as an attachment


Example
layouts

-

ForceDirectedLayout
,
SpringLayout
, and
IndentedTreeLayout


FlexViz

widget

(embed
within

other websites)





But!



Flexviz

visualizations

were
cumbersome to
customize


Integration

with other sites requires
programming


Used
Flash



Flexviz

Towards Visualization
as a
Service


Enable the
flexible visual exploration and
analysis

of biomedical
ontologies

and data


Support collaboration
in visual exploration and
analysis of biomedical
ontologies

and data


Enable
presentation

of analysis artifacts on the
web

Visual analytics over the web…

For example, IBM
ManyEyes


NCBO Presentation March 2, 2011

BioMixer

An online platform for the visual exploration of
multiple biomedical
ontologies

27

BioMixer

vs.
FlexViz
: Motivation

28

BioMixer

Architecture/Vision

29

Web
-
based Collaborative Workspaces

30

Multiple Coordinated Visualizations

31

Visualization Embeds


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src
="http://bio
-
mixer.appspot.com/?viewId=188001"
width="480" height="400">Sorry, your
browser doesn't support
iFrames
</
iframe
>

32

BioPortal


precanned
” Embeds:

33

Visualizing
BioPortal

usage data

Comparing some ontology
usage across countries

Summary: Bio
-
Mixer Contributions


Exploration of
multiple ontologies and their
mappings

in a single graph visualization


Multiple
coordinated

ontology visualizations


Web
-
based
and

team enabled

visual ontology
exploration workspaces


Authoring of
visualization embeds
for inclusion
in
BioPortal

and external web content

36

Visualizing Mappings between

Terms and between
Ontologies

37

CogZ

Cognitive Support and Visualization for Human
-
Guided Mapping Systems

Ontology alignment


Mapping terms from one ontology to another,
preserving structural relationships


Research emphasis mostly on the algorithm

Select

ontologies

Alignment

algorithm

Potential

mappings

Verified

mappings

Mapping

complete

Ontology alignment continued


Cognitively challenging


The user must:


Make decisions about mapping candidates


Supply custom mappings that were missed


Understand the domains and structure of both
ontologies


Remember decisions that were made


Can be made easier through
cognitive support

Visualization plug
-
in for Prompt


Prompt:

framework to support ontology
alignment


Added
a
plug
-
in mechanism

and
perspectives

to
Prompt to support other algorithms and
visualizations


CogZ
: Integrating various
visualizations
and
filters
to support the user’s decision making
process

the CHISEL group, University of Victoria


CogZ

on the web (prototype only)

Multiple Ontologies and Mappings

44

Mappings between Terms
-

Matrix

45


Mappings between
Ontologies


46


Next steps


Integrating the matrix and graph based
mapping views in
BioMixer


Appreciate feedback on these views!

47

Nanoparticle

ontology


University of Victoria

48

University of Victoria

49

Mappings between NPO and other
ontologies

Visualization requirements for
Nanoparticle

ontology?


Exploration, navigation, search? Support
error

checking?


Changes across
ontology versions
? Publication and
syndication of changes?


Distinguish between original and

imported
classes/
ontologies

(upper versus domain
ontologies
)?


Distinguish
actual from inferred
relations?


Mappings
? Support for alignment?


Scalability? Is NPO stable in terms of size?


Non graph views? e.g.
charts
?


Collaboration

features?


Need for
embeds
?

51