Ontology Views An Update

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Ontology ViewsAn Update

• A BISTI Collaborative RO1 with the National
  Center for Biomedical Ontology
• James F. Brinkley, PI
• Structural Informatics Group
• University 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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Q1 What are all the cavities of organ parts?
anatomist
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Q1 What are all the cavities of organ parts?
N263
R1
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Use case 1 Image annotation
Q1 What are all the cavities of organ parts?
anatomist
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Use case 1 Image annotation
Q1 What are all the cavities of organ parts?
Heart Anatomy
A1
V1
anatomist
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Use case 1 Image annotation
Q1 What are all the cavities of organ parts?
A1 Heart Anatomy
A1
V1
V1
V1 What are the parts of the heart and their
types?
anatomist
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Use case 1 Image annotation
Q1 What are all the cavities of organ parts?
A1 Heart Anatomy
A1
V1
V1
V1 What are the parts of the heart and their
types?
VGen
anatomist
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Use case 1 Image annotation
Q1 What are all the cavities of organ parts?
A1 Heart Anatomy
V1 What are the parts of the heart and their
types?
VGen
anatomist
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Use case 1 Image annotation
Q1 What are all the cavities of organ parts?
A1 Heart Anatomy
V1 What are the parts of the heart and their
types?
VGen
Q2 What are the cavities of organ parts that are
parts of the heart?
anatomist
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Q2 What are the cavities of organ parts that are
parts of the heart?
R2
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Use case 1 Image annotation
VGen
anatomist
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Use case 1 Image annotation

• Features
• View query is a basis for linking
• Application ontologies are always up-to-date
• Application ontologies are composable

VGen
anatomist
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Use case 1 Image annotation
A1 Heart Anatomy
VGen
physiologist
anatomist
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Use case 1 Image annotation
A2 Heart Physiology
A1 Heart Anatomy
VGen
VGen
physiologist
anatomist
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Use case 1 Image annotation
Use case 2 Model merging
VGen
VGen
physiologist
anatomist
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Basic Architecture
VGen
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Data and Knowledge Layer
Ontologies
FMA
OPB
Wrappers
Query Visualization Services
VQP
Service Layer
Web Services
Editors Tools
VGen
Presentation Layer
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Research Issues (aims)

• How to define the view
• How to implement the view query processor
• 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

fmaRight_side_of_heart fmaLeft_side_of_heart
---------------------------
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All the parts of the heart

• Select all parts of the heart
• SELECT ?object
• WHERE
• fmaHeart fmapart ?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
• fmaHeart gleenOnPath ("fmaregional_partfmaco
  nstitutional_part" ?object) .
• ORDER BY ?object

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Results

• ----------------------------------------
• object
• fmaAortic_valve
• fmaAtrioventricular_septum
• fmaCardiac_vein
• fmaCavity_of_left_atrium
• fmaCavity_of_left_ventricle
• fmaCavity_of_right_atrium
• fmaCavity_of_right_ventricle
• fmaCoronary_sinus
• fmaFibrous_skeleton_of_heart
• fmaInteratrial_septum
• fmaInterventricular_septum
• fmaLeft_coronary_artery
• fmaLeft_side_of_heart
• fmaLymphatic_capillary_bed_of_heart
• fmaMitral_valve
• fmaNeural_network_of_heart

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Transitive closure

• Select either regional or constitutional parts
  of the heart
• SELECT ?object
• WHERE
• fmaHeart gleenOnPath ("fmaregional_partfmaco
  nstitutional_part" ?object) .
• ORDER BY ?object

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Constructing a part view
Construct heart parts as either the regional or
constitutional parts of the heart CONSTRUCT fmaH
eart fmapart ?object WHERE fmaHeart
gleenOnPath ("fmaregional_partfmaconstitution
al_part" ?object) . ORDER BY ?object
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SELECT ?prop ?val WHERE nciGastric_Mucosa-As
sociated_Lymphoid_Tissue_Lymphoma gleenOnPath (
"owlequivalentClass?/owlintersectionOf/rd
frest/rdffirst" ?restriction ) .
?restriction owlonProperty ?prop .
?restriction gleenOnPath ( "owlsomeValuesFromo
wlallValuesFrom" ?val ). ORDER BY ?prop
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CONSTRUCT nciGastric_Mucosa-Associated_Lymphoid_
Tissue_Lymphoma ?prop ?val WHERE
nciGastric_Mucosa-Associated_Lymphoid_Tissue_Lymp
homa gleenOnPath ( "owlequivalentClass?/o
wlintersectionOf/rdfrest/rdffirst"
?restriction ) . ?restriction owlonProperty
?prop . ?restriction gleenOnPath (
"owlsomeValuesFromowlallValuesFrom" ?val ).

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Demo
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SparQL Extensions vSparQLMarianne Shaw and Dan
Suciu

• Subqueries
• Recursive Queries

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vSparQL Subqueries

• Builds upon CONSTRUCT query

CONSTRUCT ?subj ?prop ?obj FROM lt ... gt WHERE
?subj ?prop ?obj

• Subqueries treated as data source
• Named or unnamed data source

SELECT ... FROM NAMED ltsubquery_namegt
CONSTRUCT ... FROM lt ... gt WHERE
... WHERE GRAPH ltsubquery_namegt ...
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vSparQL Example Subquery

• Get all of the direct regional_parts of the liver

PREFIX dl lthttp//.../fmaOwlDlComponent_2_0gt
SELECT ?obj FROM NAMED ltsubquerygt
CONSTRUCT dlLiver dlregional_part ?a
FROM lthttp//.../fmaOwlFullComponent_2_0gt
WHERE dlLiver dlregional_part ?a WHERE
GRAPH ltsubquerygt ?subj ?prop ?obj
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Results
----------------------------- obj

dlCaudate_lobe_of_liver dlRight_lobe_of_liv
er dlLeft_lobe_of_liver
dlQuadrate_lobe_of_liver ----------------------
-------
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vSparQL Recursive Subqueries

• Union of CONSTRUCT queries

SELECT ... FROM NAMED ltrecursive_subqgt
CONSTRUCT ... Base queries
FROM lt ... gt WHERE ... UNION
Set union CONSTRUCT ...
Recursive queries FROM NAMED
ltrecursive_subqgt FROM lt ... gt WHERE
GRAPH ltrecursive_subqgt ... . ...
WHERE GRAPH ltrecursive_subqgt ...
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vSparQL Recursive Query

• Regional_parts of the liver, transitive closure

PREFIX dl lthttp//.../fmaOwlDlComponent_2_0gt
SELECT ?obj FROM NAMED ltlivergt Base case
get the direct regional_parts of the
liver CONSTRUCT dlLiver dlregional_part
?z FROM lthttp//.../fmaOwlFullComponent_2_0gt W
HERE dlLiver dlregional_part ?z . UNION
Get all of the regional_parts of the liver
recursively CONSTRUCT ?c dlregional_part
?d FROM NAMED ltlivergt FROM NAMED
lthttp//.../fmaOwlFullComponent_2_0gt WHERE
GRAPH ltlivergt ?a ?b ?c . . GRAPH
lthttp//.../fmaOwlFullComponent_2_0gt ?c
dlregional_part ?d . . WHERE
GRAPH ltlivergt ?subj ?prop ?obj .
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Results

• Get all of the regional_parts of the liver

--------------------------------------------------
------------------------ obj


dlLateral_inferior_a
rea_of_lateral_segment_of_left_lobe_of_liver
dlLateral_superior_area_of_lateral_segment_of
_left_lobe_of_liver dlQuadrate_lobe_of_l
iver
dlCaudate_lobe_of_liver
dlLeft_lobe_proper_o
f_liver
dlLateral_segment_of_left_lobe_of_liver
dlMedial_segment_of_
left_lobe_of_liver
dlQuadrate_lobe_of_liver
dlLeft_lobe_of_liver

dlRight_lobe_of_liver
dlCaudate_lobe_of_li
ver
dlMedial_superior_area_of_medial_segment_of_l
eft_lobe_of_liver dlMedial_inferior_ar
ea_of_medial_segment_of_left_lobe_of_liver
dlPosterior_segment_of_right_lobe_of_liver
dlAnterior_segment_o
f_right_lobe_of_liver
dlPosterior_superior_area_of_posterior_segmen
t_of_right_lobe_of_liver dlPosterior_inferior
_area_of_posterior_segment_of_right_lobe_of_liver
dlPapillary_process_of_caudate_lobe_of_liver
dlCaudate_process_of
_caudate_lobe_of_liver
dlLeft_segment_of_caudate_lobe_of_liver
dlRight_segment_of_c
audate_lobe_of_liver
dlAnterior_superior_area_of_anterior_segment_
of_right_lobe_of_liver dlAnterior_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)

• How to define the view
• How to implement the view query processor
• How to graphically generate views

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Graphical View GenerationGary Yngve and Linda
Shapiro
Demo
PREFIX dl lthttp//.../fmaOwlDlComponent_2_0gt
SELECT ?obj FROM NAMED ltlivergt Base case
get the direct regional_parts of the
liver CONSTRUCT dlLiver dlregional_part
?z FROM lthttp//.../fmaOwlFullComponent_2_0gt W
HERE dlLiver dlregional_part ?z . UNION
Get all of the regional_parts of the liver
recursively CONSTRUCT ?c dlregional_part
?d FROM NAMED ltlivergt FROM NAMED
lthttp//.../fmaOwlFullComponent_2_0gt WHERE
GRAPH ltlivergt ?a ?b ?c . . GRAPH
lthttp//.../fmaOwlFullComponent_2_0gt ?c
dlregional_part ?d . . WHERE
GRAPH ltlivergt ?subj ?prop ?obj .
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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
• Dont 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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Manual Approach
Onard Mejino
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Graphical Approach
Onard Mejino
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• Application view required
• Add class/node Abdominal organ to class/node
  Organ
• Reassign existing and appropriate organ to
  Abdominal organ
• Reassign all other organs as direct subclasses of
  Organ
• 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
Demo
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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 Case
Demo
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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