An Intuitive Graphical Query Interface for Protégé Knowledge Bases Landon Todd Detwiler, Cornelius Rosse, Linda Shapiro Structural Informatics Group University of Washington
Emily Emily Query interface for Proté ég gé é KBs KBs Query interface for Prot � Graphical, point Graphical, point- -and and- -click click � � Stand Stand- -alone Java application alone Java application � � Built on the Prot Built on the Proté ég gé é API library API library � � Class Class- -to to- -class relationships class 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
FMA 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 biological domains � Basis for the construction of intelligent Basis for the construction of intelligent � biomedical applications biomedical applications
FMA Complications 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
Example Questions 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?
Example Questions 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?
Composing a Simple Query Composing a Simple Query
Composing a Simple Query Composing a Simple Query Subject Relationship Object
What is the heart? What is the heart? Subject Relationship Object Subject Relationship Object Heart has superclass Unknown Heart has superclass Unknown (directly) (directly)
Subject Tree Subject Tree
Relationship Tree Relationship Tree
Object Tree Object Tree
What is the heart? What is the heart? Subject Relationship Object Subject Relationship Object Heart has superclass Unknown Heart has superclass Unknown (directly) (directly) Results Results Organ with cavitated organ parts
Example Questions 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?
What are the parts of the heart? What are the parts of the heart? Subject Relationship Object Subject Relationship Object Heart has part Unknown Heart has part Unknown (directly) (directly)
What are the parts of the heart? What are the parts of the heart?
Example Questions 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?
Is the epicardium a part of Is the epicardium a part of the heart? 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 heart Epicardium not a direct part of heart � � Heart Heart has part has part Wall of heart Wall of heart which has part which has part � Epicardium Epicardium But aren’ ’t the parts of any direct part of the t the parts of any direct part of the But aren Heart still a part of the Heart? Heart still a part of the Heart? � Yes, because part is transitive Yes, because part is transitive �
Relationship Tree Relationship Tree Directly related Transitively related
Is the epicardium a part of Is the epicardium a part of the heart? the heart? Subject Relationship Object Subject Relationship Object Heart has part Epicardium Heart has part Epicardium Results Results Yes
Example Questions 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?
Which part of the heart is continuous Which part of the heart is continuous with the superior pulmonary vein? with the superior pulmonary vein? What is the Subject? What is the Subject? What is the Relationship? What is the Relationship? What is the Object? What is the Object?
Compound queries Compound queries Two methods for creating compound Two methods for creating compound queries queries � Query chaining Query chaining � � Set operations Set operations �
Which part of the heart is continuous Which part of the heart is continuous with the superior pulmonary vein? with the superior pulmonary vein? Subject: part of the heart part of the heart Subject: Relationship: is continuous with is continuous with Relationship: Object: Superior pulmonary vein Superior pulmonary vein Object:
Which part of the heart is continuous Which part of the heart is continuous with the superior pulmonary vein? with the superior pulmonary vein? Subject: part of the heart part of the heart Subject: � Subject: Subject: Heart Heart � � Relationship: Relationship: has part has part U1 � � Object: Object: Unknown Unknown � Relationship: is continuous with is continuous with Relationship: Object: Superior pulmonary vein Superior pulmonary vein Object:
Which part of the heart is continuous Which part of the heart is continuous with the superior pulmonary vein? with the superior pulmonary vein? Subject: U1 U1 Subject: Relationship: is continuous with is continuous with Relationship: Object: Superior pulmonary vein Superior pulmonary vein Object:
Which part of the heart is continuous Which part of the heart is continuous with the superior pulmonary vein? with the superior pulmonary vein?
Which part of the heart is continuous Which part of the heart is continuous with the superior pulmonary vein? with the superior pulmonary vein? Subject Relationship Object Subject Relationship Object Heart has part Unknown (U1) Heart has part Unknown (U1) U1 is continuous with Unknown (U2) U1 is continuous with Unknown (U2)
Result Sets Result Sets
Query History Panel Query History Panel U1
U2 Query History Panel Query History Panel
Query History Panel Query History Panel What part of the heart is What part of the heart is continuous with the superior continuous with the superior pulmonary vein? pulmonary vein?
Compound queries Compound queries Two methods for creating compound Two methods for creating compound queries queries � Query chaining Query chaining � � Set operations Set operations �
Set Operations Set Operations Results of some queries are sets Results of some queries are sets Available operations Available operations � AND AND � � OR OR � � NOT NOT �
Which part of the heart is continuous Which part of the heart is continuous with the superior pulmonary vein? with the superior pulmonary vein? Subject Relationship Object Subject Relationship Object Heart has part Unknown (U1) Heart has part Unknown (U1) Unknown (U2) is continuous with Superior Unknown (U2) is continuous with Superior pulmonary vein pulmonary vein U1 AND U2 U1 AND U2
Set Operations Set Operations What part of the heart is What part of the heart is continuous with the superior continuous with the superior pulmonary vein? pulmonary vein?
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