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Generating Application Ontologies from Reference Ontologies

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Generating Application Ontologies from Reference Ontologies. Marianne Shaw. Todd Detwiler ... Open Biomedical Ontologies (OBO), 50 ontologies ... – PowerPoint PPT presentation

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Title: Generating Application Ontologies from Reference Ontologies


1
Generating Application Ontologies from Reference
Ontologies
  • Marianne Shaw
  • Todd Detwiler
  • Jim Brinkley
  • Dan Suciu
  • University of Washington

2
Motivation
  • Growing of specialized ontologies
  • Open Biomedical Ontologies (OBO), gt50 ontologies
  • Unified Medical Language System (UMLS), gt90
    ontologies
  • Link ontologies via reference ontologies
  • Reference ontologies are
  • Large
  • e.g. Foundational Model of Anatomy (FMA)
  • 75,000 classes 120,000 terms 168 relationship
    types
  • gt2.1 million relationship instances
  • Complex
  • Comprehensive

3
Problem Statement
  • How can we enable large ontologies to be used to
    create application ontologies?

4
Problem Statement
  • How can we enable large ontologies to be used to
    create application ontologies?
  • Approach Add Views to SPARQL

5
Outline
  • Motivation / Problem Statement
  • SPARQL
  • Our Solution vSPARQL
  • Subqueries
  • Recursive Queries
  • Skolem Functions
  • Radiology Example
  • Related Work
  • Conclusions

6
The Basics SPARQL
  • SPARQL W3Cs standard for querying RDF
  • RDF (subject, predicate, object) triples
  • Simple SPARQL query over FMA
  • Creates a new RDF graph
  • Get direct properties of liver

PREFIX fma lthttp//.../fma_1_4_0gt CONSTRUCT
fmaLiver ?y ?z FROM lthttp//.../fma_1_4_0gtWHER
E fmaLiver ?y ?z
7
Outline
  • Motivation / Problem Statement
  • SPARQL
  • Our Solution vSPARQL
  • Subqueries
  • Recursive Queries
  • Skolem Functions
  • Radiology Example
  • Related Work
  • Conclusions

8
vSPARQL
  • Extend SPARQL to support views
  • Extensions enable three types of functionality
  • Querying over existing queries
  • Gathering subgraphs of an ontology
  • Creating new data by combining data from multiple
    ontologies

9
Subqueries Querying over an existing query
  • Alices ontology contains info queried from FMA
  • Get organs their direct properties

Query1
Alices Organ Ontology
CONSTRUCT ?sub ?prop ?val FROM
lthttp//.../fma_1_4_0gtWHERE ?sub
rdfssubClassOf fmaOrgan . ?sub ?prop ?val
FMA
10
Subqueries Querying over an existing query
  • Alices ontology contains info queried from FMA
  • Bob only interested in Alices info about liver
  • Subqueries allow us to query existing queries

Query2
Bobs Liver Ontology
Query1
Alices Organ Ontology
FROM NAMED ltsubquerygt CONSTRUCT
WHERE
FMA
11
Subqueries Querying over an existing query
  • Bob only interested in Alices info about liver

Query2
Bobs Liver Ontology
CONSTRUCT fmaLiver ?lprop ?lval FROM
ltalice_ontologygt CONSTRUCT ?sub ?prop
?val FROM lthttp//.../fma_1_4_0gt WHERE
?sub rdfssubClassOf fmaOrgan .
?sub ?prop ?val . WHERE fmaLiver
?lprop ?lval .
Query1
Alices Organ Ontology
FMA
12
Recursive queries Gathering subgraphs
  • What if we only want a portion of an ontology?





13
Recursive queries Gathering subgraphs
  • What if we only want a portion of an ontology?
  • Only want parts of the liver


Liver





14
Recursive queries Gathering subgraphs
  • What if we only want a portion of an ontology?
  • Only want parts of the liver
  • Recursive queries allow us to query for
    arbitrary subgraphs


Liver


FROM NAMED ltrecursive_livergt CONSTRUCT
WHERE UNION CONSTRUCT
FROM ltrecursive_livergt WHERE GRAPH
ltrecursive_livergt
Base case


Recursive case

15
Recursive example All parts of the liver
CONSTRUCT ?sub ?prop ?obj . FROM NAMED
ltrecursive_livergt CONSTRUCT fmaLiver
fmapart ?obj . FROM lthttp//.../fma_1_4_0gt
WHERE fmaLiver fmapart ?obj .
UNION CONSTRUCT ?c fmapart ?d FROM
lthttp//.../fma_1_4_0gt FROM NAMED
ltrecursive_livergt WHERE GRAPH
ltrecursive_livergt ?a ?b ?c . . ?c
fmapart ?d . WHERE GRAPH
ltrecursive_livergt ?sub ?prop ?obj
// Base Direct parts of liver

// Recursive Transitively, parts of liver
Liver





16
Skolem Functions Combining data from two
ontologies
  • Ontology of Physics for Biology (OPB)
  • FMA

17
Skolem Functions Combining data from two
ontologies
  • OPB
  • FMA
  • Combine OPBFluidPressure, FMAAorticBlood

Pressure
FluidPressure
OPB
AorticBlood Pressure
Aortic Blood
FMA
18
Skolem Functions Combining data from two
ontologies
  • OPB
  • FMA
  • Combine OPBFluidPressure, FMAAorticBlood
  • Skolem Functions generate new nodes from queried
    info

Pressure
FluidPressure
OPB
AorticBlood Pressure
Aortic Blood
ltskolem_function_urlgt(arg1, ...)
FMA
19
Skolem Functions Combining data from two
ontologies
PREFIX fma lthttp//.../fma_1_4_0gt PREFIX opb
lthttp//.../opbgt PREFIX new lthttp//.../new_ont
ologygtCONSTRUCT newfma_phys(fmaAorti
c_Blood,opbFluidPressure) ?p_prop ?p_obj
.FROM NAMED lthttp//.../fma_1_4_0gtFROM NAMED
lthttp//.../opbgtWHERE GRAPH
lthttp//.../fma_1_4_0gt
fmaAortic_Blood ?ab_prop ?ab_obj . GRAPH
lthttp//.../opbgt opbFluidPressure
?p_prop ?p_obj .
Pressure
FluidPressure
Aortic Blood Pressure
OPB
Aortic Blood
FMA
20
Outline
  • Motivation / Problem Statement
  • SPARQL
  • Our Solution vSPARQL
  • Subqueries
  • Recursive Queries
  • Skolem Functions
  • Radiology Example
  • Related Work
  • Conclusions

21
Example Radiology Ontology from FMA
  • All of the visible parts of the liver?

22
Radiology Ontology Results
lthttp//.../fma_1_4_0Right_portal_veingt
lthttp//.../fma_1_4_0partgt
lthttp//.../fma_1_4_0Anterior_branch_of_right_por
tal_veingt lthttp//.../fma_1_4_0partgt
lthttp//.../fma_1_4_0Caudate_lobe
_branch_of_right_portal_veingt
lthttp//.../fma_1_4_0partgt
lthttp//.../fma_1_4_0Trunk_of_right_portal_veingt
lthttp//.../fma_1_4_0partgt
lthttp//.../fma_1_4_0Posterior_branch_of_ri
ght_portal_veingt .lthttp//.../fma_1_4_0Segment_
of_livergt lthttp//.../fma_1_4_0partgt
lthttp//.../fma_1_4_0Subsegment_of_
livergt .lthttp//.../fma_1_4_0Parenchymatous_org
angt lthttp//www.w3.org/2000/01/rdf-schemasu
bClassOfgt lthttp//.../fma_1_4_
0Organgt .lthttp//.../fma_1_4_0Caudate_lobe_of_
livergt lthttp//.../fma_1_4_0partgt
lthttp//.../fma_1_4_0Papillary_process
_of_caudate_lobe_of_livergt
lthttp//.../fma_1_4_0partgt
lthttp//.../fma_1_4_0Left_segment_of_caudate_lobe
_of_livergt lthttp//.../fma_1_4_0partgt
lthttp//.../fma_1_4_0Caudate_pro
cess_of_caudate_lobe_of_livergt
23
Radiology Ontology Results
  • FMA ontology size
  • 1.7 million RDF triples
  • 178MB text file
  • Radiology Ontology size
  • 164 RDF triples
  • 38KB text file

24
Related Work
  • Subqueries
  • Schenk S. A SPARQL Semantics Based on Datalog. KI
    2007 Advances in Artificial Intelligence.
  • Regular Expressions
  • Detwiler LT, Suciu D, Brinkley J. Regular paths
    in SPARQL Querying the NCI Thesaurus. AMIA08.
  • Kochut K, Janik M. SPARQLer Extended SPARQL for
    Semantic Association Discovery. ESWC 2007.
  • Alkhateeb F, Baget JF, Euzenat J. RDF with
    Regular Expressions. http//hal.inria.fr/inria-001
    44922/en.
  • Views
  • Noy NF, Musen MA. Specifying Ontology Views by
    Traversal. ISWC 2004.
  • Magkanaraki A, et al. Viewing the Semantic Web
    through RVL lenses. ISWC 2003.
  • Miklos Z, et al. Querying Semantic Web Resources
    using TRIPLE Views. ISWC 2003.

25
WrapUp
  • Reference ontologies can be used to link together
    specialized ontologies
  • Views can make large reference ontology datasets
    manageable
  • vSPARQL extends SPARQL
  • Subqueries
  • Recursive queries
  • Skolem Functions
  • vSPARQL can be used to generate application
    ontologies using views over reference ontologies

26
Questions?
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