Abstraction and Visualization to Support Access to NPO’s Structure and Content Michael Halper,...

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

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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

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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

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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

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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