Abstraction and Visualization to Support Access to NPO’s Structure

and Content

Michael Halper, Vladimir Ventura, Yehoshua PerlSABOC

New Jersey Institute of TechnologyNewark, NJ 07102

2

Overview

• Abstraction Networks (“AbNs”) for Ontologies• Two example AbNs:– Area taxonomy– Partial-area taxonomy

• BLUOWL: taxonomy-based software tool• Application to the NPO• Conclusions

3

Ontology Excerpt

IS-A

wave speed

Parameter

length unit

unit of measurement

wave parameter

wavelengthwave amplitude

speed of sound wave

has_

unit_

of_m

easu

re

unit of velocity

wavelength of sound

frequency of sound

wave

frequency unit

wave frequency

amplitude of sound

wave

4

Abstraction Networks (“AbNs”)• An abstraction network (“AbN”) is derived from an

ontology’s content and structure and provides a compact (summarization) view

• AbNs group “similar” concepts together and represent them using a single node

• Nodes are organized into a hierarchy

5

Area and Partial-Area Taxonomies

• Area taxonomy summarizes structurally similar concepts

• Partial-area taxonomy refines the area taxonomy into hierarchically related groups of concepts

• Will review derivation using examples from NPO

6

Area Taxonomy Derivation

An area is a set of concepts that share the same relationship structure (structurally similar)

Areas

Participates_in6 concepts

Inheres_in, participates_in

37 concepts

6 Concepts

∅

Denoted_by, inheres_in,

participates_in 2 concepts

Has_DOI, hasPubMedID, has_abstract, has_author,

has_journal_name, has_publication_year,

inheres_in, participates_in1 concept

Inheres_in, participates_in,

unit_of121 concepts

+120 descendants

Thing

entity Premerged Concepts

Preretired Concepts

Retired Concepts

Current Year

Retired Concepts

continuant

Spatial region

One dimensional

region

Three dimensional

region

Two dimensional

region

Zero dimensional

region

Dependent_ continuant

Generically_ dependent_ continuant

Specifically_ dependent_ continuant

Journal article

Alphanumeric number

number Unit of measurement

Nanoparticle property

Surface property

Numeric number

+4 child concepts

+27 descendants

∅

Participates_ in

Inheres_in, participates_in

Has_DOI, hasPubMedID, has_abstract, has_author,

has_journal_name, has_publication_year

, inheres_in, participates_in

Inheres_in, participates_in,

unit_of

Denoted_by, inheres_in, participates_in

7

+120 descendants

Thing

entity Premerged Concepts

Preretired Concepts

Retired Concepts

Current Year

Retired Concepts

continuant

Spatial region

One dimensional

region

Three dimensional

region

Two dimensional

region

Zero dimensional

region

Dependent_ continuant

Generically_ dependent_ continuant

Specifically_ dependent_ continuant

Journal article

Alphanumeric number

number Unit of measurement

Nanoparticle property

Surface property

Numeric number

+4 child concepts

+27 descendants

∅

Participates_ in

Inheres_in, participates_in

Has_DOI, hasPubMedID, has_abstract, has_author,

has_journal_name, has_publication_year

, inheres_in, participates_in

Inheres_in, participates_in,

unit_of

Denoted_by, inheres_in, participates_in

Inheres_in, participates_in, unit_of

Participates_in

Inheres_in, participates_in

Denoted_by, inheres_in, participates_in

Has_DOI, hasPubMedID, has_abstract, has_author,

has_journal_name, has_publication_year, inheres_in,

participates_in

Ø

Dependent_ continuant

37 Concepts

Alphanumeric number

1 Concept

Numeric Number

1 Concept

Unit of Measurement121 Concepts

Journal1 Concept

Thing6 Concepts

continuant6 Concepts

Partial-Area Taxonomy Derivation

• Root: A concept with no parents in its area• Partial-area: A root + all its descendants in the area

(structurally similar and clustered similarly)

Root

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Overlapping Concepts• Partial-areas are not necessarily disjoint• A concept residing in two or more partial-areas

is called an overlapping concept

Dendrimer Repeat Unit

Fiat Dendrimer part Repeat Unit

overlapping

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Overlapping Metrics

Level Area Name # overlapping

3 has_function, part_of, participates_in 1

3 has_function, has_quality, participates_in 18

4 has_function, has_part, has_quality, participates_in 6

6 has_component_part, has_function, has_part, has_quality, has_role, participates_in 3

6has_output_participant, has_participant, negatively_regulates, positively_regulates, realizes, regulates 1

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Applications of Taxonomies

• QA (inconsistency detection and improved modeling)

• Summarization• Navigation• Proposed:– Support of ontology development – Support of various biomedical applications

where similar concepts need to be identified

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Taxonomy-Based Software Tool

• BLUOWL• Automatic generation of a variety of

taxonomy views• Concept-level browsing based on those

views• Aids for QA guidelines

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NPO Taxonomies

• Based on the inferred view of the NPO

• Relationships (object properties) defined in terms of domains

• And/or relationships defined as restrictions on concepts

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Conclusions

• Taxonomies are useful tools for getting a high-level view of NPO while ignoring minutiae

• BLUOWL automatically generates the taxonomies and permits customized browsing

• BLUOWL was demonstrated on the NPO

• Plan to work next on ChEBI