An Intuitive Graphical Query Interface for Protégé Knowledge Bases

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An Intuitive Graphical

Query Interface for

Protégé Knowledge Bases

Landon Todd Detwiler,

Cornelius Rosse, Linda Shapiro

Structural Informatics Group University of Washington

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Emily

Query interface for Protégé

Query interface for Protégé KBsKBs

Graphical, pointGraphical, point--andand--clickclick

StandStand--alone Java application alone Java application

Built on the Protégé API libraryBuilt on the Protégé API library

ClassClass--toto--class relationshipsclass relationships

Foundational Model of Anatomy (FMA) Foundational Model of Anatomy (FMA) Goal: Usable by novice users with little Goal: Usable by novice users with little

instruction instruction

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FMA

Foundational Model of Anatomy Foundational Model of Anatomy Symbolic model of the physical Symbolic model of the physical organization of the human body organization of the human body

Goals Goals

Foundation for interoperability between Foundation for interoperability between

biological domains

Basis for the construction of intelligent Basis for the construction of intelligent

biomedical applications

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FMA Complications

Space complexity Space complexity > 70,000 classes> 70,000 classes > 185,000 frames> 185,000 frames

> 170 slots in use> 170 slots in use

> 1.5 million slot values > 1.5 million slot values

Classes without the instances (individuals) Classes without the instances (individuals)

Existing tools and the FMA Existing tools and the FMA

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Example Questions

What is the heart? What is the heart?

What are the parts of the heart? What are the parts of the heart?

Is the epicardium a part of the heart? Is the epicardium a part of the heart?

Which part of the heart is continuous with Which part of the heart is continuous with

the superior pulmonary vein? the superior pulmonary vein?

What is the relationship between the What is the relationship between the

right atrium and blood? right atrium and blood?

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Example Questions

What is the heart?

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Composing a Simple Query

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Composing a Simple Query

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What is the heart?

Subject

Subject RelationshipRelationship ObjectObject Heart

Heart has superclass has superclass (directly)

(directly)

Unknown

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Subject Tree

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Relationship Tree

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Object Tree

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What is the heart?

Subject

Heart has superclass has superclass (directly) (directly) Unknown Unknown Results Results

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Example Questions

What are the parts of the heart?

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What are the parts of the heart?

Subject

Heart has part has part

(directly)

Unknown

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What are the parts of the heart?

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Example Questions

Is the epicardium a part of the heart?

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Is the epicardium a part of

the heart?

Why was Epicardium not in the previous Why was Epicardium not in the previous

result set? result set?

Epicardium not a direct part of heartEpicardium not a direct part of heart

HeartHeart has part has part Wall of heartWall of heart which has part which has part

Epicardium

But aren’t the parts of any direct part of the But aren’t the parts of any direct part of the

Heart still a part of the Heart? Heart still a part of the Heart?

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Relationship Tree

Directly related Transitively related

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Is the epicardium a part of

the heart?

Subject

Heart has parthas part EpicardiumEpicardium

Results

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Example Questions

Which part of the heart is continuous with

the superior pulmonary vein?

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Which part of the heart is continuous

with the superior pulmonary vein?

What is the Subject?

What is the Relationship? What is the Relationship?

What is the Object? What is the Object?

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Compound queries

Two methods for creating compound Two methods for creating compound

queries queries

Query chainingQuery chaining

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Subject:

Subject: part of the heartpart of the heart Relationship:

Relationship: is continuous withis continuous with Object:

Object: Superior pulmonary veinSuperior pulmonary vein

Which part of the heart is continuous

with the superior pulmonary vein?

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Subject:

Subject: part of the heartpart of the heart

Subject: Subject: HeartHeart

Relationship: Relationship: has parthas part

Object: Object: UnknownUnknown

Relationship:

Which part of the heart is continuous

with the superior pulmonary vein?

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Subject:

Subject: U1U1 Relationship:

Which part of the heart is continuous

with the superior pulmonary vein?

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Which part of the heart is continuous

with the superior pulmonary vein?

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Which part of the heart is continuous

with the superior pulmonary vein?

Subject

Heart has parthas part Unknown (U1)Unknown (U1) U1

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Result Sets

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Query History Panel

U1 U2

What part of the heart is

continuous with the superior

pulmonary vein?

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Compound queries

Two methods for creating compound Two methods for creating compound

queries queries

Query chainingQuery chaining

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Set Operations

Results of some queries are sets Results of some queries are sets

Available operations Available operations ANDAND OROR NOTNOT

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Which part of the heart is continuous

with the superior pulmonary vein?

Subject

Heart has parthas part Unknown (U1)Unknown (U1) Unknown (U2)

Unknown (U2) is continuous withis continuous with Superior Superior

pulmonary vein

U1

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Set Operations

What part of the heart is

continuous with the superior

pulmonary vein?

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Example Questions

What is the relationship between the

right atrium and blood?

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Unknown Relationship

What if the user chooses the ‘Unknown’ What if the user chooses the ‘Unknown’

node for the query relationship? node for the query relationship?

FMA is highly connectedFMA is highly connected

Many paths between classes

Not practical (nor useful) to find all paths

First pathFirst path

Assumption: The simplest path is likely to be the

most desirable

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Unknown Relationship

Algorithm Algorithm

Direct connectionsDirect connections

Transitive closure connectionsTransitive closure connections

Predetermined connection typesPredetermined connection types

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What is the relationship between

the right atrium and blood

Subject

Subject RelationshipRelationship ObjectObject Right atrium

Right atrium UnknownUnknown BloodBlood

Results

Right atrium part Cavity of right atrium contains

Blood in right atrium :DIRECT-SUPERCLASSES

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Issues

Translating into S

Translating into S--RR--O tripleO triple Translating into FMA terms Translating into FMA terms

Attributed relationships (e.g. right lateral Attributed relationships (e.g. right lateral

adjacency) adjacency)

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Conclusion

Simple, point

Simple, point--andand--click query constructionclick query construction Query types Query types SimpleSimple CompoundCompound

“Real world” limits “Real world” limits

Triple formulationTriple formulation

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Future Work

Web accessibility Web accessibility

Improved transitive closure performance Improved transitive closure performance

Attributed relationship handling Attributed relationship handling Hierarchical transitive closures Hierarchical transitive closures

Relationship synonyms Relationship synonyms

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Simple Queries

Subject

Subject –– Relationship Relationship –– Object tripletsObject triplets

Basic English sentence structureBasic English sentence structure

Choose an icon from each fieldChoose an icon from each field

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Query chaining

Heart has part Unknown

(U1)

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Query chaining

U1 is continuous with U1 is continuous with Unknown (U2) Unknown (U2) U1 U2

What part of the heart is What part of the heart is continuous with the superior continuous with the superior pulmonary vein?

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Subject:

Subject: U1U1 Relationship:

Object: UnknownUnknown