UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for...
Transcript of UMLS-SKOS - BioPortal · SKOS provides a simple to understand, easy to extend framework for...
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
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
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
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
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
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
UMLS - SKOSSK
OS/
SKO
S-X
L
ConceptScheme
Concept
UMLS - Semantic Net
Entity Event
Label
rdfs:subClassOf
7Thursday, December 3, 2009
UMLS - SKOSSK
OS/
SKO
S-X
L
ConceptScheme
Concept
UMLS - Semantic Net
Entity Event
Label
rdfs:subClassOf
7Thursday, December 3, 2009
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
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
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
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
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
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
UMLS-SKOS
SKOS SKOS-XL
Semantic Net
Metathesaurus
SNOMEDCT MeSH MedDRA NCI ...
8Thursday, December 3, 2009
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
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
The Semantic Network
11Thursday, December 3, 2009
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
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
UMLS-Metatesaurus and Source Vocabularies
13Thursday, December 3, 2009
UMLS-Metathesaurus and Labels and Notations
14Thursday, December 3, 2009
UMLS-Metathesaurus Relations (Hierarchies)
15Thursday, December 3, 2009
UMLS-Metathesaurus Relations (associations)
16Thursday, December 3, 2009
UMLS-Metathesaurus - Relations (mappings)
17Thursday, December 3, 2009
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
UMLS-Metathesaurus Concepts
19Thursday, December 3, 2009
“Achondroplasia” in Turtle!
20Thursday, December 3, 2009
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
Abdominal Pain (C0000737)
22Thursday, December 3, 2009
Abdominal Pain (C0000737)
23Thursday, December 3, 2009
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
UMLS-SKOS
SKOS SKOS-XL
Semantic Net
Metathesaurus
SNOMEDCT MeSH MedDRA RCD NCI
25Thursday, December 3, 2009
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
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
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
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
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
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
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
Live Demo
450+ MTH Concepts,
300 Common in MeSH and SNOMEDCT
32Thursday, December 3, 2009
Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method
BLUE - Text
!"#$%&'()*)#
+&,-./01/#
!"#$%&'()*##
+(,-.%/0%#
!"#$%&'()##
*)%+,-./-#
!"#$%$&'
!"#$%"()'
!"#$%$*+$'
33Thursday, December 3, 2009
Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method
BLUE - Text
!"#$%&'()*)#
+&,-./01/#
!"#$%&'()*##
+(,-.%/0%#
!"#$%&'()##
*)%+,-./-#
!"#$%$&'
!"#$%"()'
!"#$%$*+$'
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
Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method
BLUE - Text
!"#$%&'()*)#
+&,-./01/#
!"#$%&'()*##
+(,-.%/0%#
!"#$%&'()##
*)%+,-./-#
!"#$%$&'
!"#$%"()'
!"#$%$*+$'
34Thursday, December 3, 2009
Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method
BLUE - Text
!"#$%&'()*)#
+&,-./01/#
!"#$%&'()*##
+(,-.%/0%#
!"#$%&'()##
*)%+,-./-#
!"#$%$&'
!"#$%"()'
!"#$%$*+$'
34Thursday, December 3, 2009
Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method
BLUE - Text
!"#$%&'()*)#
+&,-./01/#
!"#$%&'()*##
+(,-.%/0%#
!"#$%&'()##
*)%+,-./-#
!"#$%$&'
!"#$%"()'
!"#$%$*+$'
34Thursday, December 3, 2009
Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method
BLUE - Text
!"#$%&'()*)#
+&,-./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
Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method
BLUE - Text
!"#$%&'()*)#
+&,-./01/#
!"#$%&'()*##
+(,-.%/0%#
!"#$%&'()##
*)%+,-./-#
!"#$%$&'
!"#$%"()'
!"#$%$*+$'
34Thursday, December 3, 2009
Biomedical Language Understanding and Extraction A Minimal Syntactic, Semantic Method
BLUE - Text
!"#$%&'()*)#
+&,-./01/#
!"#$%&'()*##
+(,-.%/0%#
!"#$%&'()##
*)%+,-./-#
!"#$%$&'
!"#$%"()'
!"#$%$*+$'
34Thursday, December 3, 2009
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.
35Thursday, December 3, 2009
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
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
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
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
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
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
Dry_Skin Gastrointestinal_Syndrome
patient1
Dehydration
BLUE-Text: Dehydration? (1)
Results - Output representation
39Thursday, December 3, 2009
Dry_Skin Gastrointestinal_Syndrome
patient1
Dehydration
BLUE-Text: Dehydration? (1)
Results - Output representation
39Thursday, December 3, 2009
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
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
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
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
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
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
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
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
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
Designer Services
Admin Projects
Manage Question
SODS Services at a Glance
47Thursday, December 3, 2009
Designer Services
Admin Projects
Manage Question
SODS Services at a Glance
47Thursday, December 3, 2009
Designer Services
Admin Projects
Manage Question
SODS Services at a Glance
47Thursday, December 3, 2009
Designer Services
Admin Projects
Manage Question
Ontology Services
UMLS-SKOS
Local Vocab.
SODS Services at a Glance
47Thursday, December 3, 2009
Designer Services
Admin Projects
Manage Question
Ontology Services
UMLS-SKOS
Local Vocab.
SODS Services at a Glance
47Thursday, December 3, 2009
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Thank You
53Thursday, December 3, 2009