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UMLS-SKOS A Semantic Web Framework for Representing Biomedical Knowledge 1 Parsa Mirhaji MD, PhD December 2009 The School of Health Information Sciences The University of Texas at Houston 1 Thursday, December 3, 2009

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Page 1: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS-SKOSA Semantic Web Framework for Representing Biomedical Knowledge

1

Parsa Mirhaji MD, PhD

December 2009

The School of Health Information Sciences

The University of Texas at Houston

1Thursday, December 3, 2009

Page 2: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

What to expect

Background

What is SKOS

UMLS - SKOS

Method

Discussion

SKOS vs Domain Ontology

Integrity and Gap Analysis

Use Cases

Remaining Work

2Thursday, December 3, 2009

Page 3: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Simple Knowledge Organization SystemSKOS

A framework for use of thesauri, classification schemes, subject heading systems, controlled vocabularies, and taxonomies within the framework of the Semantic Web

Supports representing terminological knowledge and its linkage with domain knowledge in unambiguous, reusable, encapsulated and traceable fashion

Exploits Semantic Web for information sharing and reuse on distributed environment (web)

Enables construction of mashup meta-thesauri unambiguously using multiple sources of knowledge (e.g PHIN-VADS, HL7)

Enables extension or adoption of standards based terminology systems in novel ways to meet local demands (e.g PHIN-VADS, HL7)

3Thursday, December 3, 2009

Page 4: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Abdominal Pain In SKOS

C0000737

C0232487

C0238551

C0151767

skos:broader

skos:narrower

skos:re

lated

“Abdominal Pain”

“abdominal pain”“Abdominal Pain, NOS”“Bellyache”

“Pain, Abdominal”

“Adbominal pain”

“Adominal pain”

“Adominal pain”

skos:prefLabel

“Abdominal Cramp”

skos:altLabel

skos:hiddenLabel

“A clinical syndrome with acute abdominal pain that is severe, localized, and rapid onset. Acute abdomen may be caused by a variety of disorders, injuries, or diseases.”

skos

:defin

ition

Acute abdomen (disorder)

Abdominal discomfort

MTH

skos

:inSc

hem

e“C0000737”

skos:n

otation

4Thursday, December 3, 2009

Page 5: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Abdominal Pain In SKOS

C0000737

“Abdominal Pain”@Enskos:prefLabel

MTH skos:inScheme “Dolore addominale”@It

“Douleur abdominale”@Fr

“Dolor abdominal”@Spskos:prefLabel

skos:prefLabel

skos:prefLabel

21522001

“Abdominal Pain”

SNOMEDCT

skos:inScheme

207230000

“Abdominal Pain NOS”

139313005

“Abdominal Pain (finding)”skos:inSchemesko

s:inSc

heme

skos

:exac

tMatc

h

skos:broadMatch

skos:narrowMatch

5Thursday, December 3, 2009

Page 6: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Acute Abdomen in SNOMED-CT

6

A2988568

Acute abdomen (disorder)

9209005

A15111904

“Surgical Abdomen”

A4752082

Acute abdominal pain syndrome

A4966409

Acute abdomen

(skos-xl:labelRelation) synonym

(skos-xl:prefLabel) PT

(skos-xl:altLabel) FN

118948005 140460009 113345001

789.00

Disease of abdomen Abdomen - acute Abdomen NOSABDMNAL PAIN UNSPCF SITE

SNOMEDCT

ICD-9-CM

skos:inScheme

skos:inScheme

(skos:exactMatch) mapsTo(skos:related) has_finding_site

(skos:r

elated

) mayb

e_a

(skos:broader) is

a

(skos-x

l:altLa

bel) S

Y

(skos-xl:altL

abel) SY

6Thursday, December 3, 2009

Page 7: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS - SKOSSK

OS/

SKO

S-X

L

ConceptScheme

Concept

UMLS - Semantic Net

Entity Event

Label

rdfs:subClassOf

7Thursday, December 3, 2009

Page 8: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS - SKOSSK

OS/

SKO

S-X

L

ConceptScheme

Concept

UMLS - Semantic Net

Entity Event

Label

rdfs:subClassOf

7Thursday, December 3, 2009

Page 9: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS - SKOSSK

OS/

SKO

S-X

L

ConceptScheme

Concept

UMLS - Semantic Net

Entity Event

Label

AUI

SUI

rdfs:subClassOfrdf:type

UMLS - MTH

STR

7Thursday, December 3, 2009

Page 10: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS - SKOSSK

OS/

SKO

S-X

L

ConceptScheme

Concept

UMLS - Semantic Net

Entity Event

Label

SAB

AUI

SUI

MeSH

SNOMEDCT

MedDRA

rdfs:subClassOfrdf:type

UMLS - MTH

MTH

STR

7Thursday, December 3, 2009

Page 11: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS - SKOSSK

OS/

SKO

S-X

L

ConceptScheme

Concept

UMLS - Semantic Net

Entity Event

Label

SAB

AUI

SUI

MeSH

SNOMEDCT

MedDRA

rdfs:subClassOfrdf:type

UMLS - MTH

MTH

STR

7Thursday, December 3, 2009

Page 12: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS - SKOSSK

OS/

SKO

S-X

L

ConceptScheme

Concept

UMLS - Semantic Net

Entity Event

Label

SAB

AUI

SUI

MeSH

SNOMEDCT

MedDRA

C000737

rdfs:subClassOfrdf:type

C0172359 C0232487

C0238551

“Abdominal Pain”

“C0000737”

skos:semanticRelation skos:narrower

skos:broader

UMLS - MTH

skos-xl:prefLabel

skos:prefLabel

skos:notation

S035799

skos-xl:label

MTH

STR

skos:inScheme

7Thursday, December 3, 2009

Page 13: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS - SKOSSK

OS/

SKO

S-X

L

ConceptScheme

Concept

UMLS - Semantic Net

Entity Event

Label

SAB

AUI

SUI

MeSH

SNOMEDCT

MedDRA

C000737

rdfs:subClassOfrdf:type

C0172359 C0232487

C0238551

“Abdominal Pain”

“C0000737”

skos:semanticRelation skos:narrower

skos:broader

UMLS - MTH

9209005

113345001 140460009

skos:semanticRelation

skos:narrower

118948005

skos:broader

“Abdominal Pain”

“9209005”

SNOMEDCT

skos:exactMatch

skos-xl:prefLabel

skos:prefLabel

skos:notation

S035799

skos:prefLabel

skos:notationA05

4930

2

skos-xl:label

skos-xl:prefLabel

MTH

STR

skos:inScheme

7Thursday, December 3, 2009

Page 14: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

MSH

UMLS - SKOSSK

OS/

SKO

S-X

L

ConceptScheme

Concept

UMLS - Semantic Net

Entity Event

Label

SAB

AUI

SUI

MeSH

SNOMEDCT

MedDRA

C000737

rdfs:subClassOfrdf:type

C0172359 C0232487

C0238551

“Abdominal Pain”

“C0000737”

skos:semanticRelation skos:narrower

skos:broader

UMLS - MTH

9209005

113345001 140460009

skos:semanticRelation

skos:narrower

118948005

skos:broader

“Abdominal Pain”

“9209005”

SNOMEDCT

M0024135

M0008124 M0004742

skos:semanticRelation

skos:narrower

M0015742

skos:broader“Abdominal Pain”

“M00

2413

5”

skos:exactMatch

skos-xl:prefLabel

skos:prefLabel

skos:notation

S035799

skos:prefLabel

skos:notationA05

4930

2

A0978543

skos-xl:label

skos-xl:prefLabel

skos-xl:prefLabel

MTH

STR

skos:inScheme

7Thursday, December 3, 2009

Page 15: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS-SKOS

SKOS SKOS-XL

Semantic Net

Metathesaurus

SNOMEDCT MeSH MedDRA NCI ...

8Thursday, December 3, 2009

Page 16: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Method

Namespaces

UMLS-Semantic Network

Semantic Types and Semantic Relations

Assumptions

UMLS-MTH

CUIs, SUI and Labels

Hierarchies

Semantic Relations and Mappings

Source Vocabularies

Terms, AUI and Labels

Semantic Relations

Label Relations

9Thursday, December 3, 2009

Page 17: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Namespaces

SKOS: http://www.w3.org/2004/02/skos/core#

SKOS-XL: http://www.w3.org/2008/05/skos-xl#

Semantic Network: http://semanticnetwork.nlm.nih.gov/

Metathesaurus: http://umls.nlm.nih.gov/

SourceVocabularies: http://umls.nlm.nih.gov/%sab%/

SNOMEDCT: http://umls.nlm.nih.gov/SNOMEDCT/

MeSH: http://umls.nlm.nih.gov/MeSH/

10Thursday, December 3, 2009

Page 18: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

The Semantic Network

11Thursday, December 3, 2009

Page 19: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

The Semantic Network Assumptions

All Semantic Types are modeled as owl:Class and rdfs:subClassOf skos:Concept

The ‘isa’ relations between the Semantic Types and Relations are modeled as ‘rdfs:subClassOf’ and rdfs:subPropertyOf

All other semantic relations are modeled as sub-properties of skos:related

A relation is defined as symmetric if its ‘owl:inverseOf’ was self reflexive

Inverse of a property is sub-property of the inverse of its super-property: “If B is inverse Of A, and A is subProperty of C, and D is inverse of C, then B is subProperty of D”.

12Thursday, December 3, 2009

Page 20: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

The Semantic Network Assumptions

All Semantic Types are modeled as owl:Class and rdfs:subClassOf skos:Concept

The ‘isa’ relations between the Semantic Types and Relations are modeled as ‘rdfs:subClassOf’ and rdfs:subPropertyOf

All other semantic relations are modeled as sub-properties of skos:related

A relation is defined as symmetric if its ‘owl:inverseOf’ was self reflexive

Inverse of a property is sub-property of the inverse of its super-property: “If B is inverse Of A, and A is subProperty of C, and D is inverse of C, then B is subProperty of D”.

12Thursday, December 3, 2009

Page 21: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS-Metatesaurus and Source Vocabularies

13Thursday, December 3, 2009

Page 22: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS-Metathesaurus and Labels and Notations

14Thursday, December 3, 2009

Page 23: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS-Metathesaurus Relations (Hierarchies)

15Thursday, December 3, 2009

Page 24: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS-Metathesaurus Relations (associations)

16Thursday, December 3, 2009

Page 25: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS-Metathesaurus - Relations (mappings)

17Thursday, December 3, 2009

Page 26: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS-MTH and Concepts

C0000737

C0232487

C0238551

C0151767

umls:rn

umls:rb

umls:ro

“Abdominal Pain”

“abdominal pain”

“Abdominal Pain, NOS”

“Bellyache”

skos:prefLabel

“Abdominal Cramp”

skos:altLabel

“A clinical syndrome with acute abdominal pain that is severe, localized, and rapid onset. Acute abdomen may be caused by a variety of disorders, injuries, or diseases.”

umls

:defi

nitio

n

Acute abdomen (disorder)

Abdominal discomfort

MTH skos:inScheme

“C0000737”

umls:

cui

S0983771

“Abdominal Pain”

skos-xl:prefLabel

S0983771

S0983771

S0983771

“abdominal pain”

“Abdominal Pain, NOS”

“Bellyache”

skos-xl:altLabel

Synonymous

18Thursday, December 3, 2009

Page 27: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS-Metathesaurus Concepts

19Thursday, December 3, 2009

Page 28: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

“Achondroplasia” in Turtle!

20Thursday, December 3, 2009

Page 29: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Source Vocabularies by Example: SNOMED-CT

A2988568

Acute abdomen (disorder)

9209005

A15111904

“Surgical Abdomen”

A4752082

Acute abdominal pain syndrome

A4966409

Acute abdomen

(skos-xl:labelRelation) synonymous

(skos-xl:prefLabel) PT

(skos-xl:altLabel) FN

118948005 140460009 113345001

789.00

Disease of abdomen Abdomen - acute Abdomen NOSABDMNAL PAIN UNSPCF SITE

SNOMEDCT

ICD-9-CM

skos:inScheme

skos:inScheme

(skos:exactMatch) mapsTo(skos:related) has_finding_site

(sko

s:rel

ated

) may

be_a

(skos:b

roader)

isa

(skos-x

l:altLa

bel) S

Y

(skos-xl:altL

abel) SY

C0000737MTH correspondsTo

21Thursday, December 3, 2009

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Abdominal Pain (C0000737)

22Thursday, December 3, 2009

Page 31: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Abdominal Pain (C0000737)

23Thursday, December 3, 2009

Page 32: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

MSH

UMLS - SKOSSK

OS/

SKO

S-X

L

ConceptScheme

Concept

UMLS - Semantic Net

Entity Event

Label

SAB

AUI

SUI

MeSH

SNOMEDCT

MedDRA

C000737

rdfs:subClassOfrdf:type

C0172359 C0232487

C0238551

“Abdominal Pain”

“C0000737”

skos:semanticRelation

skos:narrower

skos:broader

UMLS - MTH

9209005

113345001 140460009

skos:semanticRelation

skos:narrower

118948005

skos:broader

“Abdominal Pain”

“9209005”

SNOMEDCT

M0024135

M0008124 M0004742

skos:semanticRelation

skos:narrower

M0015742

skos:broader“Abdominal Pain”

“M00

2413

5”

skos:exactMatch

skos-xl:prefLabel

skos:prefLabel

skos:notation

S035799

skos:prefLabel

skos:notationA05

4930

2

A0978543

skos-xl:label

skos-xl:prefLabel

skos-xl:prefLabel

MTH

STR

skos:inScheme

24Thursday, December 3, 2009

Page 33: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

UMLS-SKOS

SKOS SKOS-XL

Semantic Net

Metathesaurus

SNOMEDCT MeSH MedDRA RCD NCI

25Thursday, December 3, 2009

Page 34: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Integrity of UMLS SKOS Representation -1

Disjointness of skos:ConceptScheme and skos:Concept

Source vocabularies are Metathesaurus Concepts and have CUI

Exact Cardinality of 1 for skos:prefLabel per language (UMLS does not provide any axioms for labels)

SKOS supports different languages through language tags. No new notation or IRIs are provided for the same concept in different languages

26Thursday, December 3, 2009

Page 35: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

skos:topConcept is not explicitly supported by UMLS-MTH or its sources of vocabularies (should be manually added)

skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. However umls:rn, umls:rb and umls:ro are not.

skos:mappingRelation and skos-xl:labelRelations are not explicitly modeled in UMLS and

Integrity of UMLS SKOS Representation - II

UMLS uses the same kinds of relations for mapping between labels (lexical forms) or concepts, and to establish hierarchies between concepts and terms

Rigorous and automated analysis and enforcement of UMLS-SKOS integrity requires OWL-2 constructs such as disjoint properties and HasKey

27Thursday, December 3, 2009

Page 36: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

skos:topConcept is not explicitly supported by UMLS-MTH or its sources of vocabularies (should be manually added)

skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. However umls:rn, umls:rb and umls:ro are not.

skos:mappingRelation and skos-xl:labelRelations are not explicitly modeled in UMLS and

Integrity of UMLS SKOS Representation - II

UMLS uses the same kinds of relations for mapping between labels (lexical forms) or concepts, and to establish hierarchies between concepts and terms

Rigorous and automated analysis and enforcement of UMLS-SKOS integrity requires OWL-2 constructs such as disjoint properties and HasKey

27Thursday, December 3, 2009

Page 37: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Gap Analysis

LUIs are not modeled

Provenance of relations and definitions are modeled as reified statements that incorporates

English language terms only (yet). No language tags are currently used to specify language

All attributes (from mrSAT table) are modeled as annotations

Semantic relations are modeled between source specific skos:Concepts and not in the MTH level (between CUIs) to ensure integrity and modularity

Between source relationships (mappings) are not modeled (yet)

SPECIALIST component not modeled (yet)

28Thursday, December 3, 2009

Page 38: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Conclusions

Formal representation of the terminological knowledge (using SW technologies) enables unambiguous sharing and reuse of the information in distributed environment and promotes better integration and interoperability

SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge

SKOS representation of biomedical knowledge available through UMLS-KS may facilitate access, retrieval and interpretation of information represented within the UMLS-KS by automated processes

Easier to understand and learn

Easier to access and retrieve information

Easier to extend and map to local vocabularies

Easier to manage, maintain and curate

Easier to share, distribute and reuse

Easier to build automated applications with

29Thursday, December 3, 2009

Page 39: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Conclusions (continued)

Separation of the terminological and domain knowledge (information model) in a consistent and maintainable way, where multiple sources of information can be combined to support semantic processing of data without

Resource intensive and extensive computational processing for realization of large ontologies

Logical inconsistencies that may arise by combining multiple incompatible conceptualizations

Rapid adoption and reuse of new sources of information with minimal effort (adoption of new versions of the same model, new extensions to a model etc)

30Thursday, December 3, 2009

Page 40: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

What do we have now?

An algorithm to consume UMLS-KS databases and automatically convert to an SKOS representation that conforms to the latest W3C recommendation (as of August 18 2009)

A Triple-store containing the following RDF graphs:

UMLS-Semantic Net in SKOS

UMLS-Metathesaurus in SKOS

SNOMED in SKOS

MeSH in SKOS

MedDRA in progress

Several proof of concept or running applications based on the UMLS-SKOS

31Thursday, December 3, 2009

Page 41: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Live Demo

450+ MTH Concepts,

300 Common in MeSH and SNOMEDCT

32Thursday, December 3, 2009

Page 42: UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for representation of terminological knowledge SKOS representation of biomedical knowledge

Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method

BLUE - Text

!"#$%&'()*)#

+&,-./01/#

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+(,-.%/0%#

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*)%+,-./-#

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33Thursday, December 3, 2009

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Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method

BLUE - Text

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Defs:No

Diarrhea

Vomiting

Nausea

Face

Rash Scar

Headache

precedes

Large Blister

Large Blister

contains

Abdomen

Toe Evidence Space 1 Evidence Space 2

Evidence Space 3

Defs:No

Diarrhea

Vomiting

Nausea

Face

Rash Scar

Headache

precedes

Large Blister

Large Blister

contains

Abdomen

Toe Evidence Space 1 Evidence Space 2

Evidence Space 3

34Thursday, December 3, 2009

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Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method

BLUE - Text

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34Thursday, December 3, 2009

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Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method

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34Thursday, December 3, 2009

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Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method

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34Thursday, December 3, 2009

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Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method

BLUE - Text

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+&,-./01/#

!"#$%&'()*##

+(,-.%/0%#

!"#$%&'()##

*)%+,-./-#

!"#$%$&'

!"#$%"()'

!"#$%$*+$'

Left Arm

modifies hasLocus SpatialModifier Locus

Spatial Concept Body Loc.Or

Region

C0205091 C0446516

Pain

SignorSyndrome

Sign Or

Syndrome

C0030193

InfM:

UMLS-SKOS:

Tokens:

correspondsToCUI

rdfs:subClassOf

rdf:type

rdf:type

Left Arm

modifies hasLocus SpatialModifier Locus

Spatial Concept Body Loc.Or

Region

C0205091 C0446516

Pain

SignorSyndrome

Sign Or

Syndrome

C0030193

InfM:

UMLS-SKOS:

Tokens:

correspondsToCUI

rdfs:subClassOf

rdf:type

rdf:type

34Thursday, December 3, 2009

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Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method

BLUE - Text

!"#$%&'()*)#

+&,-./01/#

!"#$%&'()*##

+(,-.%/0%#

!"#$%&'()##

*)%+,-./-#

!"#$%$&'

!"#$%"()'

!"#$%$*+$'

34Thursday, December 3, 2009

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Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method

BLUE - Text

!"#$%&'()*)#

+&,-./01/#

!"#$%&'()*##

+(,-.%/0%#

!"#$%&'()##

*)%+,-./-#

!"#$%$&'

!"#$%"()'

!"#$%$*+$'

34Thursday, December 3, 2009

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Obs1

umls: Co234211

Tingling

Pins and Needles

umls: Sign or Symptom

umls: Finding

Obs2

umls: C0091023

Fever

pyrexia

umls: Sign or Symptom

umls: Finding

ont: Constitutional_Syndrome

ont: Neurological_Syndrome

locus1

umls: C0134945

Finger

umls: Body_Part

umls: C038232 Hand

patient1

Def:No No

not

n’t

Def:Negation_Lex. Def:Objective_Negation

modifier

NegationModifier

modifiedBy

hasLocus

partOf

BLUE-Text: Encoding and Standards Based Extraction

Results - Output representation

a 13 years old teenager with nausea and vomitting after drinking bad milk. has taken Reglan that made her drowsy and confused. no fever and headache. Feels tingling on finger tips and around her mouth. dry skin in observation.

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Obs1

umls: Co234211

Tingling

Pins and Needles

umls: Sign or Symptom

umls: Finding

Obs2

umls: C0091023

Fever

pyrexia

umls: Sign or Symptom

umls: Finding

ont: Constitutional_Syndrome

ont: Neurological_Syndrome

locus1

umls: C0134945

Finger

umls: Body_Part

umls: C038232 Hand

patient1

Def:No No

not

n’t

Def:Negation_Lex. Def:Objective_Negation

modifier

NegationModifier

modifiedBy

hasLocus

partOf

BLUE-Text: Encoding and Standards Based Extraction

Results - Output representation

35Thursday, December 3, 2009

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hasObse

rvattio

n

umls: C0134945

TinglingPins and Needles

umls: C0091023

Feverpyrexia

umls: C0134945

Finger

patient1

Def:No No

Def:Objective_Negation

mod

ified

By

hasLocus

Fingers Entire

Finger

Fingers

Including thumb

Results - Output representation

BLUE-Text: Encoding and Standards Based Extraction

36Thursday, December 3, 2009

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hasObse

rvattio

n

umls: C0134945

TinglingPins and Needles

umls: C0091023

Feverpyrexia

umls: C0134945

Finger

patient1

Def:No No

Def:Objective_Negation

mod

ified

By

hasLocus

Fingers Entire

Finger

Fingers

Including thumb

Results - Output representation

BLUE-Text: Encoding and Standards Based Extraction

36Thursday, December 3, 2009

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hasObse

rvattio

n

umls: C0134945

TinglingPins and Needles

umls: C0091023

Feverpyrexia

umls: C0134945

Finger

patient1

Def:No No

Def:Objective_Negation

mod

ified

By

hasLocus

Fingers Entire

Finger

Fingers

Including thumb

Results - Output representation

BLUE-Text: Encoding and Standards Based Extraction

36Thursday, December 3, 2009

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umls: C0134945

Pins and Needles

umls: C0091023

Fever

umls: C0134945

Finger

patient1

Def:No

No

Def:Objective_Negation

modifiedByhasLocusSNOMED: M1090245

SNOMED: L8729384

SNOMED: M8342981

BLUE-Text: Encoding and Standards Based Extraction

hasO

bser

vatti

on

37Thursday, December 3, 2009

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Obs2

umls: C0027497

Nausea

umls: Sign or Symptom

Obs3

umls: C1278993

umls:Body_System

Dry_Skin

Gastrointestinal_Syndrome

Obs4

umls: C0042963

Vomiting

patient1

Dehydration

Gastrointestinal_Syndrome

∩ Manifestation

∩ (umls:indicates some Dry_Skin)

BLUE-Text: Dehydration due to Gastrointestinal Problems (1)

umls:indicate

locus

Skin

umls:C0205222

umls:Qualitative_Modifier

Dry

Results - Output representation

38Thursday, December 3, 2009

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Dry_Skin Gastrointestinal_Syndrome

patient1

Dehydration

BLUE-Text: Dehydration? (1)

Results - Output representation

39Thursday, December 3, 2009

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Dry_Skin Gastrointestinal_Syndrome

patient1

Dehydration

BLUE-Text: Dehydration? (1)

Results - Output representation

39Thursday, December 3, 2009

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Obs2

umls: C0027497

Nausea

Gastrointestinal_Syndrome

Obs4

umls: C0042963

Vomiting

patient1

BLUE-Text: Food Poisoning? Why?

context1

Food_Context

umls:C0026131

umls:Food

Milk

umls:C0260159

Qualitative_Modifier

Bad

modified

By

hasContext

context2umls:

C0231390

Temporal_Context

umls:Temporal_Concept

After

Status_Post

Food_Poisoning

Gastrointestinal_Syndrome

∩ (hasContext some (umls:Food_Context

∩ (hasContext some StatusPost)))

hasC

onte

xt

Results - Output representation

40Thursday, December 3, 2009

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umls: C0027497

Nausea Gastrointestinal_Syndrome

umls: C0042963

Vomiting

patient1

BLUE-Text: Food Poisoning? Why?

umls:C0026131

umls:Food

MilkBad

hasContext

umls:C0231390

After

Status_Post

Food_Poisoningumls:

C0260159

Qualitative_Modifier

Results - Output representation

41Thursday, December 3, 2009

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umls: C0027497

Nausea Gastrointestinal_Syndrome

umls: C0042963

Vomiting

patient1

BLUE-Text: Food Poisoning? Why?

umls:C0026131

umls:Food

MilkBad

hasContext

umls:C0231390

After

Status_Post

Food_Poisoningumls:

C0260159

Qualitative_Modifier

Results - Output representation

41Thursday, December 3, 2009

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umls: C0013144

Drowsiness Neurological_Syndrome

umls: C0009686

Confusion

patient1

BLUE-Text: Drug Adverse Reaction? Why?

umls:C0026131

umls:Pharmacological_subs.

Reglan

hasContext

AdverseReaction

Results - Output representation

42Thursday, December 3, 2009

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BLUE - Text and Decision Support

• Find candidate cases for a clinical research

• Patients with an adverse reaction to any “Dopamine Receptor Antagonist” and have indications of a “Neurological Syndrome” as a result

• All evidence pertaining to the conclusions made

Results - Output representation

43Thursday, December 3, 2009

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Neurological-Syndrome andAdverse_Reaction_to_Dopamine_Receptor_Antagonist

Neurological_Syndrome and (hasMedicationContext some Dopamine_Receptor_Antagonist))

(umls:Disease_or_Disorder or umls:Trauma_or_Injury) and

(erm:hasManifestation some (umls:indicates some erm:NeurologicalSignorSymptom))

Neurological Syndrome

Adverse Reaction to Dopamine_Receptor_Antagonist

BLUE-Text and Decision Support

Eligible Case for My Research

Results - Conclusions

44Thursday, December 3, 2009

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Neurological-Syndrome andAdverse_Reaction_to_Dopamine_Receptor_Antagonist

Neurological_Syndrome and (hasMedicationContext some Dopamine_Receptor_Antagonist))

(umls:Disease_or_Disorder or umls:Trauma_or_Injury) and

(erm:hasManifestation some (umls:indicates some erm:NeurologicalSignorSymptom))

Neurological Syndrome

Adverse Reaction to Dopamine_Receptor_Antagonist

BLUE-Text and Decision Support

Eligible Case for My Research

Results - Conclusions

44Thursday, December 3, 2009

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A Structured Data Entry (SDE) platform for health data collection

‣Automates design, implementation and deployment of a distributed and collaborative data collection instruments

‣ Eliminates Programming/Database Design phase

‣ Supports change throughout life-cycle of a project without loss of data

‣ Establishes and maintains a consistent and robust shared data dictionary

‣Automates integration of survey data within and between projects

‣ Supports repurposing and reuse of existing multi-source data

45Thursday, December 3, 2009

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Device3 Device2

imageNumeric

TextBoxDatetime

checkbox

SODS Ontologies at a Glance

Qx

Blood Transfusion ?

8

Enum

checklist

combo

radio

style1

Arial Blue

12

Blood Transfusion

Boolean Value Set

No

Yes

C0005841

Therapeutic or Preventive Procedure

LNC:LP32812-7

MSH:M0002721

SNOMEDCT:233557002

Qx.1 Qx.2 Qx.3 Qx.4

Blood Product Amount

Start timeEnd time

UMLS - SKOS Domain Ontologies (context) SODS Form Templates SODS GUI

FormTemplate1

Survey1Project1

Site1

Group3user1user1user1user1user1

Group2Group1 Device1

Web-Client Win. Vista

SODS ADMIN

1 Infusion

0 No Infusion

46Thursday, December 3, 2009

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Designer Services

Admin Projects

Manage Question

SODS Services at a Glance

47Thursday, December 3, 2009

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Designer Services

Admin Projects

Manage Question

SODS Services at a Glance

47Thursday, December 3, 2009

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Designer Services

Admin Projects

Manage Question

SODS Services at a Glance

47Thursday, December 3, 2009

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Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

SODS Services at a Glance

47Thursday, December 3, 2009

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Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

SODS Services at a Glance

47Thursday, December 3, 2009

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Client Services

Authenticate

Project Profile

Submissions

Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

SODS Services at a Glance

47Thursday, December 3, 2009

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Client Services

Authenticate

Project Profile

Submissions

Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

SODS Services at a Glance

47Thursday, December 3, 2009

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Client Services

Authenticate

Project Profile

Submissions

Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

SODS Services at a Glance

47Thursday, December 3, 2009

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Client Services

Authenticate

Project Profile

Submissions

Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

SODS Services at a Glance

47Thursday, December 3, 2009

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Client Services

Authenticate

Project Profile

Submissions

Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

SODS Services at a Glance

47Thursday, December 3, 2009

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Client Services

Authenticate

Project Profile

Submissions

Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

SODS Services at a Glance

47Thursday, December 3, 2009

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Client Services

Authenticate

Project Profile

Submissions

Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

Data Services

RDF Transformer

Relational Map

OPAL

SODS Services at a Glance

47Thursday, December 3, 2009

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Client Services

Authenticate

Project Profile

Submissions

Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

Data Services

RDF Transformer

Relational Map

OPAL

SODS Services at a Glance

47Thursday, December 3, 2009

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Client Services

Authenticate

Project Profile

Submissions

Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

Data Services

RDF Transformer

Relational Map

OPAL

SODS Services at a Glance

47Thursday, December 3, 2009

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Client Services

Authenticate

Project Profile

Submissions

Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

Data Services

RDF Transformer

Relational Map

OPAL

SODS Services at a Glance

47Thursday, December 3, 2009

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Client Services

Authenticate

Project Profile

Submissions

Designer Services

Admin Projects

Manage Question

Ontology Services

UMLS-SKOS

Local Vocab.

Data Services

RDF Transformer

Relational Map

OPAL

SODS Services at a Glance

47Thursday, December 3, 2009

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Semantic (Federated) I2B2

I2B2 is an NIH-National Centers for Biomedical Computing platform for integration of biomedical observations

Limited detail representation to achieve better integration and faster retrieval

Does not interoperate in a network of distributed collaborators seamlessly

Data is meaningful only if inside the system but looses context immediately after it leaves the system, and needs to be contextualized again to be used by secondary applications...

48Thursday, December 3, 2009

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Steps

Semantic Representation of Vocabulary Services to enable reuse and sharing of common concepts and unambiguous and precise extensions to support local needs

Semantic model representing the minimalistic approach I2B2 has taken to represent biomedical observation but:

Enable local extensions to support local needs without breaking the interoperability

Consistent mapping to semantic vocabulary services to enable consistent extraction of information in distributed environment

Building a semantic query formulation and execution API based on the SKOS and S-I2B2 backend

Semantic Wrapper API to facilitate porting data into S-I2B2 by novice and programmers not familiar with RDF/OWL

49Thursday, December 3, 2009

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Semantic Federated I2B2

50

Local-SKOS Vocabulary Extensions

S-I2B2 OntologyLocal Extensions

Instance Store(A-Box)

S-I2B2 APIFe

dera

ted

Que

ry S

ervi

ces

UMLS-SKOS Vocabulary

S-I2B2 Integration Ontology(T-Box)

Federated QueryServices

Houston

50Thursday, December 3, 2009

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Semantic Federated I2B2

50

Local-SKOS Vocabulary Extensions

S-I2B2 OntologyLocal Extensions

Instance Store(A-Box)

S-I2B2 APIFe

dera

ted

Que

ry S

ervi

ces

UMLS-SKOS Vocabulary

S-I2B2 Integration Ontology(T-Box)

Federated QueryServices

Houston

Local-SKOS Vocabulary Extensions

S-I2B2 OntologyLocal Extensions

Instance Store(A-Box)

S-I2B2 API

Fede

rate

d Q

uery

Ser

vice

s

UCSF

Fede

rate

d Q

uery

Ser

vice

s

Local-SKOS Vocabulary Extensions

S-I2B2 OntologyLocal Extensions

Instance Store(A-Box)

S-I2B2 API

Tufts

Fede

rate

d Q

uery

Ser

vice

s

Local-SKOS Vocabulary Extensions

S-I2B2 OntologyLocal Extensions

Instance Store(A-Box)

S-I2B2 API

Harvard

50Thursday, December 3, 2009

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Future Work

A more robust namespace and IRI assignment

A more robust (re)modeling of the MTH relations to make it conform to the SKOS (maps, label relations, concept relations)

A more elaborate reification to better support RUIs and their provenance

A secondary method: CUI based model where all relations and descriptions are attached to the CUI object

User interfaces to navigate and explore UMLS-SKOS

SOAP and REST based web services for remote invocation of UMLS-SKOS vocabulary services

Modeling toolkit for the extension and reuse of the UMLS-SKOS

51Thursday, December 3, 2009

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Acknowledgement

This work is funded in its entirety by theTelemedicine and Advanced Technology Research Center (TATRC)

through “the Texas Technology and Training for Terrorism and Trauma (T5)” and “the Texas Science, Humanitarian Intervention, Education and Leadership in

Disasters (TexSHIELD)” programs.

52Thursday, December 3, 2009

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Thank You

53Thursday, December 3, 2009