ontology views an update
DESCRIPTION
Ontology Views An Update. A BISTI Collaborative RO1 with the National Center for Biomedical Ontology James F. Brinkley, PI Structural Informatics Group University of Washington. Personnel. Dan Suciu Linda Shapiro Marianne Shaw Gary Yngve Todd Detwiler Joshua Franklin Onard Mejino. - PowerPoint PPT PresentationTRANSCRIPT
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Ontology ViewsAn Update
A BISTI Collaborative RO1 with the National Center for Biomedical Ontology
James F. Brinkley, PI
Structural Informatics GroupUniversity of Washington
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Personnel
• Dan Suciu
• Linda Shapiro
• Marianne Shaw
• Gary Yngve
• Todd Detwiler
• Joshua Franklin
• Onard Mejino
• Dan Cook
• John Gennari
• Daniel Rubin
• Natasha Noy
• Mark Musen
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Motivation
• Large number of application ontologies• Need to link them together into the semantic
web• Reference ontologies as one way to do this• But reference ontologies are (or will be) too
large for practical use• How can reference ontologies be made practical
for applications, yet retain potential to link application ontologies?
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Approach
• Application ontologies as views over one or more reference ontologies
• A view is a query that defines a formal transformation from one or more source ontologies to a target application ontology
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Main advantage of views
• View query describes the specific operations used to create the application ontology– Therefore the connection to the source(s) are
not lost– If the query can be made bidirectional (a
mapping) then application ontologies can be related to each other via views
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Secondary advantages
• View query can be re-run at any time as the reference ontology changes
• The query is formal so can be manipulated by a GUI
• Application ontology need not be materialized, so the update problem is not an issue (but there may be other reasons to materialize views)
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FMA
anatomist
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FMA
Wrapper
anatomist
Q1: What are all the cavities of organ parts?
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Q1: What are all the cavities of organ parts?
R1:N=263
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FMA
Wrapper
Use case 1: Image annotation
anatomist
Q1: What are all the cavities of organ parts?
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FMA
Wrapper
V1
Use case 1: Image annotation
anatomist
Q1: What are all the cavities of organ parts?
Heart AnatomyA1
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FMA
Wrapper
V1
Use case 1: Image annotation
anatomist
Q1: What are all the cavities of organ parts?
A1: Heart AnatomyA1
V1 V1: What are the parts of the heart and their types?
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FMA
Wrapper
V1
Use case 1: Image annotation
anatomist
Q1: What are all the cavities of organ parts?
A1: Heart AnatomyA1
V1 V1: What are the parts of the heart and their types?
VGen
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V1
A1
VQP
FMA
Wrapper
Use case 1: Image annotation
anatomist
Q1: What are all the cavities of organ parts?
A1: Heart Anatomy
V1: What are the parts of the heart and their types?
VGen
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V1
A1
VQP
FMA
Wrapper
Use case 1: Image annotation
anatomist
Q1: What are all the cavities of organ parts?
A1: Heart Anatomy
V1: What are the parts of the heart and their types?
VGenQ2: What are the cavities of organ parts that
are parts of the heart?
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R2:
Q2: What are the cavities of organ parts that are parts of the heart?
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FMA
Wrapper
V1
A1
VQP
VGen
Use case 1: Image annotation
anatomist
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FMA
Wrapper
V1
A1
VQP
VGen
Use case 1: Image annotation
anatomist
Features
•View query is a basis for linking
•Application ontologies are always up-to-date
•Application ontologies are composable
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FMA
Wrapper
V1
A1
VQP
OPB
Wrapper
VGen
Use case 1: Image annotation
anatomist physiologist
A1: Heart Anatomy
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V1
A1
VQP
V2
A2
VQP
VGen VGen
Use case 1: Image annotation
anatomist physiologist
FMA
Wrapper
OPB
Wrapper
A2: Heart PhysiologyA1: Heart Anatomy
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V1
A1
VQP
V2
A2
VQP
VGen VGen
Use case 1: Image annotation
Use case 2: Model merging
anatomist physiologist
FMA
Wrapper
OPB
Wrapper
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VGen
R1
W1
V1
A1VQP
Basic Architecture
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Web Services
FMA OPBOntologies
Query &Visualization Services
Editors & Tools
VQP
Wrappers
VGen Presentation Layer
Service Layer
Data and Knowledge Layer
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Research Issues (aims)
1. How to define the view
2. How to implement the view query processor
3. How to graphically generate views
Driven by and evaluated in terms of use cases
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Current Results
• Ontology web services• Extensions to SparQL
– Regular path expressions– Subqueries and recursive queries
• Graphical view generation• FMA-RADLEX use case• Other use cases
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FMA in OWL via an Ontology Web Service
---------------------------| object |===========================| fma:Right_side_of_heart || fma:Left_side_of_heart |---------------------------
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All the parts of the heart
#Select all parts of the heart
SELECT ?object
WHERE
{
fma:Heart fma:part ?object .
}
----------
| object |
==========
----------
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Gleen: SparQL Regular Path LibraryTodd Detwiler
• Property Function library for ARQ/Jena2 (Java)• Supports processing of regular paths in SparQL
queries– + : one or more– * : zero or more– ? : zero or one– / : concatenation– | : alternation– [] : grouping and property delineation
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Regional or constitutional parts#Select either regional or constitutional parts of the heart
SELECT ?object
WHERE
{
fma:Heart gleen:OnPath ("[fma:regional_part|fma:constitutional_part]" ?object) .
}
ORDER BY ?object
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Results----------------------------------------
| object |
========================================
| fma:Aortic_valve |
| fma:Atrioventricular_septum |
| fma:Cardiac_vein |
| fma:Cavity_of_left_atrium |
| fma:Cavity_of_left_ventricle |
| fma:Cavity_of_right_atrium |
| fma:Cavity_of_right_ventricle |
| fma:Coronary_sinus |
| fma:Fibrous_skeleton_of_heart |
| fma:Interatrial_septum |
| fma:Interventricular_septum |
| fma:Left_coronary_artery |
| fma:Left_side_of_heart |
| fma:Lymphatic_capillary_bed_of_heart |
| fma:Mitral_valve |
| fma:Neural_network_of_heart |
| fma:Pulmonary_valve |
| fma:Right_coronary_artery |
| fma:Right_side_of_heart |
| fma:Systemic_capillary_bed_of_heart |
| fma:Tricuspid_valve |
| fma:Wall_of_heart |
----------------------------------------
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Transitive closure#Select either regional or constitutional parts of the heart
SELECT ?object
WHERE
{
fma:Heart gleen:OnPath ("[fma:regional_part|fma:constitutional_part]*" ?object) .
}
ORDER BY ?object
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#Construct heart parts as either the regional or constitutional parts of the heartCONSTRUCT{fma:Heart fma:part ?object}
WHERE{fma:Heart gleen:OnPath ("[fma:regional_part|fma:constitutional_part]*" ?object) .}ORDER BY ?object
Constructing a part view
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SELECT ?prop ?val WHERE{ nci:Gastric_Mucosa-Associated_Lymphoid_Tissue_Lymphoma gleen:OnPath ( "[[owl:equivalentClass]?/[owl:intersectionOf]/[rdf:rest]*/[rdf:first]]+" ?restriction ) . ?restriction owl:onProperty ?prop . ?restriction gleen:OnPath ( "[owl:someValuesFrom|owl:allValuesFrom]" ?val ). }ORDER BY ?prop
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CONSTRUCT{ nci:Gastric_Mucosa-Associated_Lymphoid_Tissue_Lymphoma ?prop ?val }WHERE{ nci:Gastric_Mucosa-Associated_Lymphoid_Tissue_Lymphoma gleen:OnPath ( "[[owl:equivalentClass]?/[owl:intersectionOf]/[rdf:rest]*/[rdf:first]]+" ?restriction ) . ?restriction owl:onProperty ?prop . ?restriction gleen:OnPath ( "[owl:someValuesFrom|owl:allValuesFrom]" ?val ). }
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DemoDemo
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SparQL Extensions: vSparQLMarianne Shaw and Dan Suciu
• Subqueries
• Recursive Queries
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vSparQL Subqueries
• Builds upon CONSTRUCT query
• Subqueries treated as data source• Named or unnamed data source
CONSTRUCT { ?subj ?prop ?obj }FROM < ... >WHERE { ?subj ?prop ?obj }
SELECT ...FROM NAMED <subquery_name> [ CONSTRUCT { ... } FROM < ... > WHERE { ... }]WHERE { GRAPH <subquery_name> { ... } }
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vSparQL Example Subquery
• Get all of the direct regional_parts of the liver
PREFIX dl: <http://.../fmaOwlDlComponent_2_0#>
SELECT ?objFROM NAMED <subquery> [ CONSTRUCT { dl:Liver dl:regional_part ?a } FROM <http://.../fmaOwlFullComponent_2_0> WHERE { dl:Liver dl:regional_part ?a }]WHERE { GRAPH <subquery> { ?subj ?prop ?obj } }
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Results
-----------------------------| obj |=============================| dl:Caudate_lobe_of_liver || dl:Right_lobe_of_liver || dl:Left_lobe_of_liver || dl:Quadrate_lobe_of_liver |-----------------------------
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vSparQL Recursive Subqueries
SELECT ...FROM NAMED <recursive_subq> [ CONSTRUCT { ... } # Base queries FROM < ... > WHERE { ... }
UNION # Set union CONSTRUCT { ... } # Recursive queries FROM NAMED <recursive_subq> FROM < ... > WHERE { GRAPH <recursive_subq> { ... } . ... }]WHERE { GRAPH <recursive_subq> { ... } }
• Union of CONSTRUCT queries
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vSparQL Recursive QueryRegional_parts of the liver, transitive closurePREFIX dl: <http://.../fmaOwlDlComponent_2_0#>
SELECT ?objFROM NAMED <liver> [
# Base case: get the direct regional_parts of the liverCONSTRUCT {dl:Liver dl:regional_part ?z}FROM <http://.../fmaOwlFullComponent_2_0>WHERE {dl:Liver dl:regional_part ?z .}
UNION# Get all of the regional_parts of the liver recursivelyCONSTRUCT {?c dl:regional_part ?d}FROM NAMED <liver>FROM NAMED <http://.../fmaOwlFullComponent_2_0>WHERE { GRAPH <liver> { ?a ?b ?c . } . GRAPH <http://.../fmaOwlFullComponent_2_0> { ?c dl:regional_part ?d . } .
}]WHERE { GRAPH <liver> {?subj ?prop ?obj .} }
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Results• Get all of the regional_parts of the liver
--------------------------------------------------------------------------| obj |==========================================================================| dl:Lateral_inferior_area_of_lateral_segment_of_left_lobe_of_liver || dl:Lateral_superior_area_of_lateral_segment_of_left_lobe_of_liver || dl:Quadrate_lobe_of_liver || dl:Caudate_lobe_of_liver || dl:Left_lobe_proper_of_liver || dl:Lateral_segment_of_left_lobe_of_liver || dl:Medial_segment_of_left_lobe_of_liver || dl:Quadrate_lobe_of_liver || dl:Left_lobe_of_liver || dl:Right_lobe_of_liver || dl:Caudate_lobe_of_liver || dl:Medial_superior_area_of_medial_segment_of_left_lobe_of_liver || dl:Medial_inferior_area_of_medial_segment_of_left_lobe_of_liver || dl:Posterior_segment_of_right_lobe_of_liver || dl:Anterior_segment_of_right_lobe_of_liver || dl:Posterior_superior_area_of_posterior_segment_of_right_lobe_of_liver || dl:Posterior_inferior_area_of_posterior_segment_of_right_lobe_of_liver || dl:Papillary_process_of_caudate_lobe_of_liver || dl:Caudate_process_of_caudate_lobe_of_liver || dl:Left_segment_of_caudate_lobe_of_liver || dl:Right_segment_of_caudate_lobe_of_liver || dl:Anterior_superior_area_of_anterior_segment_of_right_lobe_of_liver || dl:Anterior_inferior_area_of_anterior_segment_of_right_lobe_of_liver |--------------------------------------------------------------------------
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Current Work
• Investigating different DBMS formats– Especially important for recursive queries
• Pushing recursive queries to DBMS• Combining Gleen with vSparQL
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Research Issues (aims)
1. How to define the view
2. How to implement the view query processor
3. How to graphically generate views
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Graphical View GenerationGary Yngve and Linda Shapiro
PREFIX dl: <http://.../fmaOwlDlComponent_2_0#>
SELECT ?objFROM NAMED <liver> [
# Base case: get the direct regional_parts of the liverCONSTRUCT {dl:Liver dl:regional_part ?z}FROM <http://.../fmaOwlFullComponent_2_0>WHERE {dl:Liver dl:regional_part ?z .}
UNION# Get all of the regional_parts of the liver recursivelyCONSTRUCT {?c dl:regional_part ?d}FROM NAMED <liver>FROM NAMED <http://.../fmaOwlFullComponent_2_0>WHERE { GRAPH <liver> { ?a ?b ?c . } . GRAPH <http://.../fmaOwlFullComponent_2_0>
{ ?c dl:regional_part ?d . } . }]WHERE { GRAPH <liver> {?subj ?prop ?obj .} }
DemoDemo
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The FMA-RadLex Use CaseOnard Mejino and Daniel Rubin
• RadLex
• Need to reorganize
• Use FMA as an organizing framework for the anatomy component
• Don’t need or want all of FMA
• Need a view
• Serves as initial validation for various approaches
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Approaches
• Manual generation of the view
• Creating the view using the graphical ontology browser
• Creating the view using vSparQL and GLEEN
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FMA ontology
FMA-RadLex
FMA ontology
FMA-RadLex
Manual Approach
Onard Mejino
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Graphical Approach
Onard Mejino
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Application view required
1. Add class/node ‘Abdominal organ’ to class/node ‘Organ’2. Reassign existing and appropriate organ to ‘Abdominal organ’3. Reassign all other organs as direct subclasses of ‘Organ’4. Remove intervening or intermediate classes/nodes
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Create new class ‘Abdominal organ’
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Organs reassigned to new class ‘Abdominal organ’
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Rest of organs are reassigned directly under superclass ‘Organ’
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Deleted ‘Solid Organ’
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Deleted ‘Cavitated Organ’
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Hide deleted classes
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Using vSparQL Marianne Shaw
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Combining vSparQL and GLEENTodd Detwiler and Marianne Shaw DemoDemo
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Initial conclusions from RadLeX Use Case
• Graphical view generation– Promising but too “granular”– Incomplete and somewhat buggy– Does not generate queries
• Queries– vSparQL plus GLEEN seems promising– Need to look at other use cases
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Image Annotation Use CaseDemoDemo
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Other Use Cases
• Spatial/Symbolic Query Processor
• Dynamic Scene Generation
• Distributed XQuery-Based Data Integration
• Model annotation and merging
• Clinical trials data integration (possible)
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Planned work
• Graphical view generation– Develop less granular operations– Generate view queries– Compare with other approaches
• Query generation– Extend expressiveness– Optimize– Explore view composition
• Explore how to integrate with BioPortal
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Conclusions
• A query-based approach to deriving application ontologies from reference ontologies– Facilitates interoperability and version control– Promotes a service-oriented view
• Significant research issues
• Solutions could help to achieve at least part of the vision of the semantic web