Post on 24-May-2015
description
A Justification-based Semantic Framework for Representing, Evaluating
and Utilizing Terminology MappingsEHR4CR, Open PHACTS, SALUS and W3C collaboration
Sajjad Hussain1, Hong Sun2, Gokce Banu Laleci Erturkmen3, Mustafa Yuksel3,Charlie Mead4, Alasdair Gray5, Kerstin Forsberg6
19-Oct-2014EHR4CR: 1INSERM UMRS 1142, Paris, France; AstraZeneca, 6R&D Information, Mölndal Sweden
Open PHACTS: 5School of Mathematical and Computer Sciences, Heriot-Watt UniversitySALUS: 3Software Research, Development and Consultancy, Ankara, Turkey,
2Advanced Clinical Applications Research Group, Agfa HealthCare, Gent, BelgiumW3C: 4Health Care and Life Sciences IG,
1Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014 Version 1.0
Objective• Enable a more collaborative semantic landscape with
providers and consumers of terminology mappings.– A framework built upon existing terminology mappings
to: • Infer new mappings for different use cases.• Present provenance of the together with the
justification for the mappings.• Perform mapping validation in order to show that
inferred mappings can be erroneous.
• Discuss a Justification Vocabulary for Mapping Terminology Concepts/Terms
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Semantic landscape 1(3)
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Consumers and, somewhat reluctant, creators of mappings
Semantic landscape 2(3)
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Consumers and, somewhat reluctant, creators of mappings
Providers of terminology mappings,some examples
Semantic landscape 3(3)
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Providers of terminologies,some examples
Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014
Consumers and, somewhat reluctant, creators of mappings
Providers of terminology mappings,some examples
Example Scenario
• Challenging nature of mapping utilization, or “How hard can it be?” – Appear to the uninitiated as a simple exercise like “this
term in this terminology is the same as that term in that terminology”
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Example Scenario 1(3)
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Defined
Mappings
Example Scenario 2(3)
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matches
matches
matches
Defined
Mappings
Inferred
Mappings
Example Scenario 3(3)
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matches
matches
matches
Defined
Mappings
Inferred
Mappings
matches
Problematic
Mappings
• Availability of up-to-date information to assess the suitability of a given terminology for a particular use case.
• Difficulty of correctly using complex, rapidly evolving terminologies.
• Differences in granularity between the source and target terminologies.
• Lack of semantic mappings in order to completely and unambiguously define computationally equivalent semantics.
• Lack of provenance information, i.e. how, when and for what purposes the mappings were created.
• Time and effort required to complete and evaluate mappings.
“It’s complicated”. So, we often become, somewhat reluctant, creators of our own mappings
10Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014
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Value adding providers of terminologies
Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014
Informed consumers of terminology mappings
Value adding providers of terminology mappings
Objective: A more collaborative semantic landscape
Framework
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• Lexical Mappings (LOOM) generated by performing lexical comparison between preferred labels and alternative labels of terms. These mappings are represented via skos:closeMatch property.
• Xref OBO Mappings Xref and Dbxref are properties used by ontology developers to refer to an analogous term in another vocabulary. These mappings are represented via skos:relatedMatch property.
• CUI Mappings from UMLS are extracted by utilizing the same Concept Unique Identifier (CUI) annotation as join point of similar terms from different vocabularies. These mappings are represented via skos:closeMatch property.
• URI-based Mappings are generated identity mappings between term concepts in different ontologies that are represented by the same URI. These mappings are represented via skos:exactMatch property.
Mapping Strategies
13Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014
Terminology Mappings Validation Schemes
Collaborative semantic landscape
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Enabled by applications of RDF
Value adding providers of terminologies
Informed consumers of terminology mappings
Value adding providers of terminology mappings
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Application of RDF torepresent mappings
Enabled by applications of the RDF standard
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Application of RDF torepresent provenance
Enabled by applications of RDF
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Applications of RDF for packaging assertions (e.g. mappings) with provenance
Enabled by applications of RDF
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Applications of RDF for describing datasets and linksets with justifications
Enabled by applications of RDF
Example Scenario
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matches
matches
matches
Defined
Mappings
Inferred
Mappings
matches
Problematic
Mappings
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Example Scenario, zoom in
matches
Defined
Mappings
Inferred
Mappings
matches
Defined
Mappings
Inferred
Mappings
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SKOS/RDF to represent the mappings
ICD9CM:999.4 skos:exactMatch SNOMEDCT:21332003
SNOMEDCT:21332003 skos:exactMatch MedDRA:10067113
ICD9CM:999.4 skos:exactMatch MedDRA:10067113
matches
Defined
Mappings
Inferred
Mappings
Nanopublication/RDF for packaging mappings together with their provenance and justification
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ICD9CM:999.4 skos:exactMatch MedDRA:10067113Assertion
Justification trace generated from EYE reasoning engine
Justification Vocabulary forMapping Terminology Concepts/Terms
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??Workshop on Context, Interpretation and Meaning (CIM2014)
http://slideshare.net/kerfors/CIM2014
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Applications of RDF for describing datasets and linksets with justifications
Enabled by applications of the RDF standard
Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014
Linksets: Justification Vocabulary Terms 1(3)
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Linksets: Justification Vocabulary Terms 2(3)
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Linksets: Justification Vocabulary Terms 3(3)
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Acknowledgments• Session chair• CIM2014 organizers• SALUS team: Hong Sun, Ali Anil Sinaci, Gokce Banu Laleci Erturkmen
– Support from the European Community’s Seventh Framework Programme (FP7/2007–2013) under Grant Agreement No. ICT-287800, SALUS Project (Scalable, Standard based Interoperability Framework for Sustainable Proactive Post Market Safety Studies).
• EHR4CR team: WP4, WPG2, WP7 members– Support from the Innovative Medicines Initiative Joint Undertaking under grant
agreement n° [No 115189]. European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies
• Open PHACTS team: Alasdair Gray• W3C HCLS team: Eric Prud’Hommeaux, Charlie Mead
29Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014
Reference material
• Projects/organisations of the authors of this paper• Example
– Mapping Representation using SKOS– Mapping Provenance Representation
30Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014
EHR4CRElectronic Healthcare Record For Clinical Research
http://www.ehr4cr.eu/
• IMI (Innovative Medicine Initiative)– Public-Private Partnership between EU and EFPIA
• ICT platform: using EHR data for supporting clinical research
• Protocol feasibility• Patient recruitment• Clinical trial execution: Clinical Research Forms (eCRF)/
Individual Case Safety Reports (ICSR) prepopulation
• 33 European academic and industrial partners– 11 pilot sites from 5 countries – 4 millions patients
31Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014
Open PHACTSOpen Pharmacology Spacehttp://www.openphacts.org/
• IMI (Innovative Medicine Initiative)• 31 partners: 10 pharma – 21 academic / SME
• The Challenge - Open standards for drug discovery data – Develop robust standards for solid
integration between data sources via semantic technologies
– Implement the standards in a semantic integration hub (“Open Pharmacological Space”)
– Deliver services to support on-going drug discovery programs in pharma and public domain
32Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014
SALUSSustainable Proactive Post Market Safety Studies
http://www.salusproject.eu/
• European Commission (STREP)• ICT platform : using EHRs data to improve post-
market safety activities on a proactive basis• Semi-automatic notification of suspected adverse events • Reporting adverse events (Individual Case Safety Reports
(ICSR) prepopulation)• Post Marketing safety studies
• 8 European academic and industrial partners– 2 pilot sites
• Lombardia Region (Italy) and Eastern Saxony (Germany)
33Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014
W3CSemantic Web Health Care and Life Sciences Interest
Group (HCLS IG) http://www.w3.org/2001/sw/
• ..
34Workshop on Context, Interpretation and Meaning (CIM2014) http://slideshare.net/kerfors/CIM2014
Mapping Representation using SKOS
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<http://purl.bioontology.org/ontology/ICD9CM/999.4> <http://www.w3.org/2004/02/skos/core#broadMatch>
<http://purl.bioontology.org/ontology/MDR/10002198>, <http://purl.bioontology.org/ontology/MDR/10002199>, <http://purl.bioontology.org/ontology/MDR/10020751>, <http://purl.bioontology.org/ontology/MDR/10067484> . <http://purl.bioontology.org/ontology/MDR/10002198> a <http://www.w3.org/2004/02/skos/core#Concept>; <http://purl.bioontology.org/ontology/MDR/level> "PT"; <http://www.w3.org/2004/02/skos/core#broader> <http://purl.bioontology.org/ontology/MDR/10002220>, <http://purl.bioontology.org/ontology/MDR/10057181>; <http://www.w3.org/2004/02/skos/core#inScheme> <http://purl.bioontology.org/ontology/MDR>; <http://www.w3.org/2004/02/skos/core#notation> "10002198"; <http://www.w3.org/2004/02/skos/core#prefLabel> "Anaphylactic reaction" . <http://purl.bioontology.org/ontology/MDR/10002199> a <http://www.w3.org/2004/02/skos/core#Concept>; <http://purl.bioontology.org/ontology/MDR/level> "PT"; <http://www.w3.org/2004/02/skos/core#broader> <http://purl.bioontology.org/ontology/MDR/10002220>, <http://purl.bioontology.org/ontology/MDR/10009193>; <http://www.w3.org/2004/02/skos/core#inScheme> <http://purl.bioontology.org/ontology/MDR>; <http://www.w3.org/2004/02/skos/core#notation> "10002199"; <http://www.w3.org/2004/02/skos/core#prefLabel> "Anaphylactic shock" . <http://purl.bioontology.org/ontology/MDR/10020751> a <http://www.w3.org/2004/02/skos/core#Concept>; <http://purl.bioontology.org/ontology/MDR/level> "PT"; <http://www.w3.org/2004/02/skos/core#broader> <http://purl.bioontology.org/ontology/MDR/10027654>; <http://www.w3.org/2004/02/skos/core#inScheme> <http://purl.bioontology.org/ontology/MDR>; <http://www.w3.org/2004/02/skos/core#notation> "10020751"; <http://www.w3.org/2004/02/skos/core#prefLabel> "Hypersensitivity" . <http://purl.bioontology.org/ontology/MDR/10067484> a <http://www.w3.org/2004/02/skos/core#Concept>; <http://purl.bioontology.org/ontology/MDR/level> "PT"; <http://www.w3.org/2004/02/skos/core#broader> <http://purl.bioontology.org/ontology/MDR/10043409>; <http://www.w3.org/2004/02/skos/core#inScheme> <http://purl.bioontology.org/ontology/MDR>; <http://www.w3.org/2004/02/skos/core#notation> "10067484"; <http://www.w3.org/2004/02/skos/core#prefLabel> "Adverse reaction" .
Mapping Provenance Representation
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:NanoPub_1_Supporting_2 = {
[ a r:Proof, r:Conjunction; r:component <#lemma1>; r:component <#lemma2>; r:component <#lemma3>; r:component <#lemma4>; r:component <#lemma5>; r:component <#lemma6>; r:gives { <http://purl.bioontology.org/ontology/ICD9CM/999.4> skos:prefLabel "Anaphylactic shock due to serum, not elsewhere classified". <http://purl.bioontology.org/ontology/SNOMEDCT/213320003> skos:prefLabel "Anaphylactic shock due to serum". <http://purl.bioontology.org/ontology/MDR/10067113> skos:prefLabel "Anaphylactic transfusion reaction". <http://purl.bioontology.org/ontology/ICD9CM/999.4> skos:exactMatch <http://purl.bioontology.org/ontology/SNOMEDCT/213320003>. <http://purl.bioontology.org/ontology/SNOMEDCT/213320003> skos:exactMatch <http://purl.bioontology.org/ontology/MDR/10067113>. <http://purl.bioontology.org/ontology/ICD9CM/999.4> skos:exactMatch <http://purl.bioontology.org/ontology/MDR/10067113>. }].…….…….…….<#lemma13> a r:Inference; r:gives {<http://purl.bioontology.org/ontology/ICD9CM/999.4> skos:exactMatch <http://purl.bioontology.org/ontology/MDR/10067113>}; r:evidence ( <#lemma11> <#lemma12>); r:binding [ r:variable [ n3:uri "http://localhost/var#x0"]; r:boundTo [ n3:uri "http://purl.bioontology.org/ontology/ICD9CM/999.4"]]; r:binding [ r:variable [ n3:uri "http://localhost/var#x1"]; r:boundTo [ n3:uri "http://purl.bioontology.org/ontology/SNOMEDCT/213320003"]]; r:binding [ r:variable [ n3:uri "http://localhost/var#x2"]; r:boundTo [ n3:uri "http://purl.bioontology.org/ontology/MDR/10067113"]]; r:rule <#lemma14>.
<#lemma14> a r:Extraction; r:gives {@forAll var:x0, var:x1, var:x2. {var:x0 skos:exactMatch var:x1. var:x1 skos:exactMatch var:x2} => {var:x0 skos:exactMatch var:x2}}; r:because [ a r:Parsing; r:source <file:///Users/sajjad/workspace/terminology-reasoning-test-case/example-term-map.n3>].}.