Safe and Economic Re-Use of Ontologies: A Logic-Based Methodology and Tool Support
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1 Safe and Economic Re-Use of Ontologies: A Logic-Based Methodology and Tool Support Ernesto Jiménez-Ruiz 1 Bernardo Cuenca Grau 2 Ulrike Sattler 3 Thomas Schneider 3 Rafael Berlanga 1 1 Computer Languages and Systems, Universitat Jaume I, Spain 2 Computing Laboratory, University of Oxford, UK 3 Computer Science, University of Manchester, UK OWLED, 1 2 April 2008
2 Our approach in a nutshell Logic-based methodology for the re-use of ontologies Safe use of imported symbols 1 Don t change their meaning! E Economic import of the external ontologies 2 Import only the relevant parts... L 3... without loss of information! Tool support Protégé plugin Work in progress!
3 Our approach in a nutshell Logic-based methodology for the re-use of ontologies Safe use of imported symbols 1 Don t change their meaning! E Economic import of the external ontologies 2 Import only the relevant parts... L 3... without loss of information! 1 Tool support Protégé plugin Work in progress!
4 Our approach in a nutshell Logic-based methodology for the re-use of ontologies Safe use of imported symbols 1 Don t change their meaning! Economic import of the external ontologies 2 Import only the relevant parts... L 3... without loss of information! E Tool support Protégé plugin Work in progress!
5 Our approach in a nutshell Logic-based methodology for the re-use of ontologies Safe use of imported symbols 1 Don t change their meaning! Economic import of the external ontologies 2 Import only the relevant parts... L 3... without loss of information! E Tool support Protégé plugin Work in progress!
6 And now... 1 Why ontology re-use? 2 A safe and economic methodology 3 Tool support and experiments 4 Perspectives
7 A re-use scenario: the Health-e-Child project Arthropathy Arthritis Autoimmune Disease Rheumatologic Disorder Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis Juvenile Rheumatoid Arthritis
8 A re-use scenario: the Health-e-Child project Arthropathy Arthritis Autoimmune Disease Rheumatologic Disorder Atrophic Arthritis Polyarthritis Rheumatoid Arthritis NCI Juvenile Chronic Polyarthritis Juvenile Rheumatoid Arthritis Arthritis diseases affects Joints JRAO C 1...C 7 istreatedby Galen Drugs
9 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis A case for safe and economic re-use NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen Reasons for re-use Saves time for re-writing Provides access to well-established knowledge Doesn t require expertise in drugs, proteins, anatomy etc. Guarantees to provide [safe] Importing terms doesn t change their meaning. [eco] Import all relevant parts of external ontologies. [aux] The order of imports doesn t matter.
10 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis And now... NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen 1 Why ontology re-use? 2 A safe and economic methodology 3 Tool support and experiments 4 Perspectives
11 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis A working cycle: the offline phase NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen O F F L I N E Load local ontology L Repeat at user s discretion Choose set S i of external symbols plus associated ontology E i Make sure the S i are pairwise disjoint For each S i do Select refinement view or generalisation view ONLINE
12 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis A working cycle: the offline phase NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen O F F L I N E Load local ontology L Repeat at user s discretion Choose set S i of external symbols plus associated ontology E i Make sure the S i are pairwise disjoint For each S i do Select refinement view or generalisation view S 1 = {JRA} E 1 = NCI ONLINE
13 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis A working cycle: the offline phase NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen O F F L I N E Load local ontology L Repeat at user s discretion Choose set S i of external symbols plus associated ontology E i Make sure the S i are pairwise disjoint For each S i do Select refinement view or generalisation view S 1 = {JRA} E 1 = NCI S 2 = {KneeJoint, Fever} E 2 = Galen ONLINE
14 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis A working cycle: the offline phase NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen O F F L I N E Load local ontology L Repeat at user s discretion Choose set S i of external symbols plus associated ontology E i Make sure the S i are pairwise disjoint For each S i do Select refinement view or generalisation view S 1 = {JRA} E 1 = NCI S 2 = {KneeJoint, Fever} E 2 = Galen Refine S 1 Refine + reference S 2 ONLINE
15 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis A working cycle: the offline phase NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen O F F L I N E Load local ontology L Repeat at user s discretion Choose set S i of external symbols plus associated ontology E i Make sure the S i are pairwise disjoint For each S i do Select refinement view or generalisation view S 1 = {JRA} E 1 = NCI S 2 = {KneeJoint, Fever} E 2 = Galen Refine S 1 Refine + reference S 2 Safety ONLINE
16 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis Formalising the Safety Guarantee NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen Safety Importing terms doesn t change their meaning. Example JRAO NCI = JRA GeneticDisorder iff NCI = JRA GeneticDisorder. Definition (Safety) L guarantees safety if for every i = 1,..., n: For every E i with Sig(L) Sig(E i ) S i, L E i is a conservative extension of E i.
17 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis Formalising the Safety Guarantee NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen Safety Importing terms doesn t change their meaning. Example JRAO NCI = JRA GeneticDisorder iff NCI = JRA GeneticDisorder. Definition (Safety) L guarantees safety if for every i = 1,..., n: For every E i with Sig(L) Sig(E i ) S i, L E i is a conservative extension of E i.
18 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis Providing safety NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen Theorem [Cuenca Grau, Horrocks, Kazakov, Sattler 2007] If L is local w.r.t. each S i, then L guarantees safety. Locality... is a syntactic approximation of conservativity. can be decided efficiently; conservativity often can t. comes in two flavours for refinement/generalisation. is sufficient, but not necessary, for safety. If non-local axioms are found, the user may want to repair L. Example: C 7 JRA GeneticDisorder C 7 JRA GeneticDisorder
19 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis The online phase NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen OFFLINE O N L I N E Repeat at user s discretion Select an S i Load external ontology E i for S i Customise scope of module Extract module Ei M Import Ei M into L from E i
20 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis The online phase NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen OFFLINE KneeJoint } 1 level } O N L I N E Repeat at user s discretion Select an S i Load external ontology E i for S i Customise scope of module Extract module Ei M Import Ei M into L from E i 3 levels
21 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis The online phase NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen OFFLINE KneeJoint } 1 level } O N L I N E Repeat at user s discretion Select an S i Load external ontology E i for S i Customise scope of module Extract module Ei M Import Ei M into L from E i 3 levels Module Coverage
22 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis Formalising the Module Coverage Guarantee NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen Module coverage Import all relevant parts of external ontologies. Example JRAO NCI = JRA GeneticDisorder iff JRAO NCI-module = JRA GeneticDisorder. Definition (Module coverage) Let E M i E i with S i Sig(Ei M ). Ei M guarantees coverage of S i if: For every L with Sig(L ) Sig(E i ) S i, L E i is a conservative extension of L E M i.
23 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis Formalising the Module Coverage Guarantee NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen Module coverage Import all relevant parts of external ontologies. Example JRAO NCI = JRA GeneticDisorder iff JRAO NCI-module = JRA GeneticDisorder. Definition (Module coverage) Let E M i E i with S i Sig(Ei M ). Ei M guarantees coverage of S i if: For every L with Sig(L ) Sig(E i ) S i, L E i is a conservative extension of L E M i.
24 Arthropathy Arthritis Autoimmune Disease Atrophic Arthritis Polyarthritis Rheumatoid Arthritis Juvenile Chronic Polyarthritis C1 C7 Rheumatologic Disorder Juvenile Rheumatoid Arthritis Providing coverage NCI JRAO... Arthritis diseases affects istreatedby Joints Drugs Galen Coverage is again provided using locality. Locality-based modules = syntactic approximations of conservativity-based modules in general not minimal efficiently computable
25 And now... 1 Why ontology re-use? 2 A safe and economic methodology 3 Tool support and experiments 4 Perspectives
26 Safe Protégé Manager: a plugin
27 Synthetic experiments Setting Randomly generated signatures of size Computed Lower of Upper Module (LUM) for each such signature Results 99 % of Galen LUMs contain < 5 % of Galen s axioms similar findings for NCI
28 Statistics
29 Real-life experiments Setting LUMs for manually selected signatures from Galen and NCI (Health-e-Child context: JRA + Cardiomyopathies) Results Ext. Ont. # Sig. # axioms Galen (2.5 %) Galen (14.9 %) Galen (17.6 %) NCI (0.1 %) NCI (1.2 %) NCI (1.3 %)
30 Comparing experiments Setting SNOMED Initial signatures: (health care; restricted language; 350,000 axioms) terms from intensive care unit Compared UM, LUM to MEX (conservativity-based modules) and SRS (Seidenberg/Rector segments) Results # axioms in % # Sig. MEX SRS (L)UM 4, , , time 4 5 s 1 s 4 7 s MEX LUM R S C D C D SRS UM
31 And now... 1 Why ontology re-use? 2 A safe and economic methodology 3 Tool support and experiments 4 Perspectives
32 Perspectives Extend module scope customisation: shopping for symbols Browse external ontology and pick symbols At each stage, view resulting module Check out module Optimise module extraction Import by reference as opposed to by value Multi-user scenario Perform user study and improve interface We want you to test our plugin and give us feedback... r favourite ontologies and real-life signatures!
33 Perspectives Extend module scope customisation: shopping for symbols Browse external ontology and pick symbols At each stage, view resulting module Check out module Optimise module extraction Import by reference as opposed to by value Multi-user scenario Perform user study and improve interface We want you to test our plugin and give us feedback... r favourite ontologies and real-life signatures!
34 More about the plugin Fancy a demo? I m happy to give one during the next break. Want to try the plugin yourself? protege.stanford.edu krono.act.uji.es/people/ernesto/safety-ontology-reuse These slides will be online soon at owl.cs.manchester.ac.uk
35 More about the plugin Fancy a demo? I m happy to give one during the next break. Want to try the plugin yourself? protege.stanford.edu krono.act.uji.es/people/ernesto/safety-ontology-reuse These slides will be online soon at owl.cs.manchester.ac.uk
36 More about the plugin Fancy a demo? I m happy to give one during the next break. Want to try the plugin yourself? protege.stanford.edu krono.act.uji.es/people/ernesto/safety-ontology-reuse These slides will be online soon at owl.cs.manchester.ac.uk Thank you!
37 More links Health-e-Child NCI and Galen nciterms.nci.nih.gov/ncibrowser/dictionary.do ftp1.nci.nih.gov/pub/cacore/evs/ncithesaurus
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