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Aligning Representationsof Anatomical Knowledge
Songmao Zhang, Ph.D.Songmao Zhang, Ph.D.
Mentor: Olivier Mentor: Olivier BodenreiderBodenreider, M.D., Ph.D., M.D., Ph.D.Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical Communications
Bethesda, Maryland Bethesda, Maryland -- USAUSA
Medical Informatics Training ProgramFinal Presentation
March 30, 2005
2Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
General frameworkGeneral framework
Comparison and evaluation of structures and Comparison and evaluation of structures and reasoning potentials in different medical reasoning potentials in different medical knowledge representation systemsknowledge representation systems
Case study:Case study:Foundational Model of Anatomy (FMA)Foundational Model of Anatomy (FMA)
FrameFrame--based structurebased structure
GALEN common reference model (GALEN)GALEN common reference model (GALEN)Description logicDescription logic
An overviewAn overviewof our alignment projectof our alignment project
Generating direct
alignment
Concepts
1 : 1Structural similarity
Lexical similarity
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1:11:1 concept matchconcept match
Lexical alignmentLexical alignmentFMA:FMA: FibularisFibularis tertiustertius (synonym: (synonym: PeroneousPeroneous tertiustertius))GALEN:GALEN: PeroneusPeroneus TertiusTertius
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1:11:1 concept matchconcept matchStructural alignment: shared hierarchical relationships Structural alignment: shared hierarchical relationships among conceptamong concept
Muscle of leg
LegMuscle cell
is-a
part-ofhas-part
Muscle of Leg
LegMyocyte
is-a
part-ofhas-part
Fibularis tertius
Peroneous Tertius
FMA GALEN
Generating direct
alignment
Concepts
1 : 1
n : m
Structural similarity
Lexical similarity
Structural similarity
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n:mn:m concept matchconcept matchGALENFMA
Left thigh
Rightthigh
Right arm
Left arm
Arm Thigh
Proximal free limb segment
Arm Thigh Forearm
ExtremityLong Part
Leg
Left leg
Right leg
Right forearm
Left forearm
Forearm Leg
Middlefree limb segment
Generating direct
alignment
Concepts
Relationships
1 : 1
n : m
Structural similarity
Lexical similarity
Structural similarity
Structural similarity
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Associative relationship mapping patternsAssociative relationship mapping patterns
0.05%0.05%22boundsSpaceboundsSpace –– inverseinverse--isaisacontained incontained in
0.25%0.25%1010isNonPartitivelyContainedInisNonPartitivelyContainedInpartpart--of of –– contained incontained in
0.4%0.4%1616partpart--of of –– isServedByisServedBynerve supplynerve supply
1%1%4242isis--aamember ofmember of
8%8%310310isBranchOfisBranchOfbranch ofbranch of
FrequencyFrequency(N = 4,070)(N = 4,070)GALENGALENFMAFMA
Generating direct
alignment
Concepts
Relationships
1 : 1
n : m
Structural similarity
Lexical similarity
Structural similarity
Structural similarity
FMA and GALEN
MA and NCI
P Mork, etc., Schema matching algorithm for comparing FMA and GALEN
Manual review
Deriving indirect
alignment
MA and NCI through FMA as reference
Aligning multiple Aligning multiple ontologiesontologies of anatomyof anatomy
Deriving indirect mappings from Deriving indirect mappings from direct mappings to a referencedirect mappings to a reference
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Approaches to aligning multiple Approaches to aligning multiple ontologiesontologies
Pairwisealignment
Alignment througha reference
Pairwisealignment
Alignment througha reference
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O2O1
IntroductionIntroduction
Objective: to investigate the indirect alignment of Objective: to investigate the indirect alignment of two anatomical two anatomical ontologiesontologies through a reference through a reference ontologyontology
Direct alignment O1 – R
Direct alignment O2 – R
Direct alignment O1 – O2
Alignment through R
R
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IntroductionIntroduction
Three Three ontologiesontologies of anatomy:of anatomy:Adult Mouse Anatomical Dictionary (Adult Mouse Anatomical Dictionary (MAMA))Anatomy subset of NCI Thesaurus (Anatomy subset of NCI Thesaurus (NCINCI))Foundational Model of Anatomy (Foundational Model of Anatomy (FMAFMA))
First attempt to automatically derive mappings First attempt to automatically derive mappings among among ontologiesontologies from their alignments to a from their alignments to a reference ontologyreference ontology
MaterialsMaterials
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Adult Mouse Anatomical DictionaryAdult Mouse Anatomical Dictionary
Structured controlled vocabularyStructured controlled vocabulary2,404 concepts each identified by one name2,404 concepts each identified by one name
Head/neckHead/neck, , Adrenal arteryAdrenal artery259 synonyms259 synonyms
LimbLimb has a synonym has a synonym ExtremityExtremityDirected acyclic graphDirected acyclic graphTwo relationships: Two relationships: isis--aa and and partpart--ofof38% concepts have no 38% concepts have no isis--aa relationshiprelationship
KneeKnee partpart--of of HindlimbHindlimb4% concepts have more than one 4% concepts have more than one isis--aa relationshiprelationship
Hand phalanxHand phalanx isis--a a PhalanxPhalanxisis--a a Hand digit boneHand digit bone
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NCI ThesaurusNCI Thesaurus
Standard vocabularies for cancer researchStandard vocabularies for cancer researchAnatomy classAnatomy classAvailable in Ontology Web Language (OWL)Available in Ontology Web Language (OWL)4,410 concepts each identified by preferred name4,410 concepts each identified by preferred name
Abdominal esophagusAbdominal esophagus2,371 synonyms2,371 synonyms
OrbitOrbit has a synonym has a synonym Eye socketEye socketEvery concept has at least one Every concept has at least one isis--aa relationshiprelationship4% concepts have more than one 4% concepts have more than one isis--aa relationshiprelationship
Radius boneRadius bone isis--a a Long boneLong boneisis--a a Bone of the upper extremityBone of the upper extremity
Concepts are connected by a Concepts are connected by a partpart--ofof relationshiprelationshipAnatomic structure is physical part ofAnatomic structure is physical part of
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Foundational Model of AnatomyFoundational Model of Anatomy
Conceptualize the physical objects and spaces that Conceptualize the physical objects and spaces that constitute the human bodyconstitute the human bodyFrameFrame--based structure in Protbased structure in Protééggéé71,202 concepts each identified by preferred name71,202 concepts each identified by preferred name
Uterine tubeUterine tube
52,713 synonyms52,713 synonymsUterine tubeUterine tube has a synonym has a synonym OviductOviduct
Every concept has one and only one Every concept has one and only one isis--aa relationshiprelationshipSeven Seven partpart--ofof relationships and their inversesrelationships and their inverses
constitutional part of constitutional part of andand constitutional partconstitutional partregional part of regional part of andand regional partregional part
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is-a, part-of (7)is-a, part-ofis-a, part-ofHierarchical relationships
52,7132,371259Synonyms
-
2,404
Mouse anatomy
Directed acyclic graph
MAMA
-
4,410
Human anatomy related to cancers
Available in OWL
NCINCI
Human anatomyDomain coverage
71,202Concepts
inverse-isa, has-part (7)Inverses
Frame-based structure in Protégé
Underlying data model
FMAFMA
MA, NCI and FMAMA, NCI and FMA
MethodsMethods
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Direct alignment MA-FMA
Direct alignment NCI-FMA
MA NCIDirect alignment
MA-NCI
Alignment through the FMA
Three phasesThree phases
FMA
Generating direct
alignment
Concepts
1 : 1Structural similarity
Lexical similarity
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Phase 1Phase 1 Direct alignmentDirect alignment
Acquiring termsAcquiring termsIdentifying matches (i.e., shared concepts) lexicallyIdentifying matches (i.e., shared concepts) lexically
Acquiring (explicit and implicit) semantic relationsAcquiring (explicit and implicit) semantic relationsIdentifying matches structurallyIdentifying matches structurally
Lexical alignment
Structural alignment
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Direct alignmentDirect alignment Lexical alignmentLexical alignment
Comparing two Comparing two ontologiesontologies at the term levelat the term levelExact matchExact matchMatch after normalizationMatch after normalization
Preferred names and synonyms are usedPreferred names and synonyms are usedMA: MA: ForelimbForelimbNCI: NCI: Upper extremityUpper extremity (synonym: (synonym: ForelimbForelimb))
UMLS synonymy is used to identify additional UMLS synonymy is used to identify additional matchesmatches
MA: MA: ProfundaProfunda femorisfemoris arteryarteryNCI: NCI: Deep femoral arteryDeep femoral artery
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Direct alignmentDirect alignment Structural alignmentStructural alignment
Acquiring interAcquiring inter--concept hierarchical relationshipsconcept hierarchical relationshipsisis--aa, , partpart--of,of, and their inverses and their inverses inverseinverse--isaisa and and hashas--partpart
Complementing missing inverse relations Complementing missing inverse relations Generating new interGenerating new inter--concept relationships by concept relationships by applying inference rulesapplying inference rules
Thyroid gland lobeis-a part-of
part-ofPyramidal lobe Neck
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<X,<X, isis--a,a, Part of YPart of Y >>
<X,<X, partpart--of,of, Y >Y >
Direct alignmentDirect alignment Structural alignmentStructural alignment
Reification of Reification of partpart--ofof relationships in the relationships in the FMAFMA
Making explicit reified Making explicit reified partpart--ofof relations in the relations in the FMAFMAReified: Reified: <<HeelHeel, is, is--a, a, Subdivision of footSubdivision of foot>>Augmented: Augmented: <<HeelHeel, part, part--of, of, FootFoot>>
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Direct alignmentDirect alignment Structural alignmentStructural alignment
Positive evidence: structural similarityPositive evidence: structural similarity
ForelimbForelimb
ArmArm
LimbLimbMA:
Upper Upper extremityextremity
ArmArm
LimbLimbNCI: is-a
has-part
HandHand
HandHand
is-a
has-part
has-part
has-part
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Direct alignmentDirect alignment Structural alignmentStructural alignment
Negative evidence: structural conflictNegative evidence: structural conflict
Pericardial Pericardial cavitycavity PericardiumPericardiumMA:
Pericardial Pericardial cavitycavity PericardiumPericardiumPericardial Pericardial
sacsacFMA:
part-of
part-of part-of
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Phase 2Phase 2 Indirect alignmentIndirect alignment
• Upper limb• Forelimb• Upper extremity
• Upperextremity
• Forelimb
• Forelimb
MA NCI
FMA
directdirect
(direct)
indirect
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Phase 3Phase 3 Comparison of two alignmentsComparison of two alignments
Directalignment
Indirectalignment
Sharedmatches
Specificmatches
Specificmatches
ResultsResults
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Semantic relations acquiredSemantic relations acquired
59,802
45,302
-
7,250
7,250
NCINCI
5,553,48815,044Inferred
4,9772,926Complemented158,282-Augmented
6,117,79220,896Total
401,0452,926Explicitly represented
FMAFMAMAMATypes of hierarchical Types of hierarchical relationsrelations
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Three direct alignmentsThree direct alignments
4 (0.3%)
1,283 (94.8%)
66 (4.9%)
MAMA -- FMAFMA1,3531,353
matchesmatches
1,958 (90.1%)653 (91.3%)Positive evidence
10 (0.5%)0Negative evidence
205 (9.4%)62 (8.7%)No evidence
NCINCI -- FMAFMA2,1732,173
matchesmatches
MAMA -- NCINCI715715
matchesmatches
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Indirect alignmentIndirect alignment
MA NCI
1,353 matches in direct alignment
MA-FMA
2,173 matches in direct alignment
NCI-FMA
703 matches in alignment through
the FMA
715 matches in direct alignment
MA-NCI
FMA
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Comparison of two alignmentsComparison of two alignments
Directalignment
Indirectalignment
654
61 49
715 703
Directalignment
Indirectalignment
654
61 49
715 703
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Comparison of two alignmentsComparison of two alignments
654 shared matches 654 shared matches 583 (89%) supported by structural evidence in three 583 (89%) supported by structural evidence in three direct alignmentsdirect alignments
{{MAMA: : ForelimbForelimb, , NCINCI: : Upper extremityUpper extremity}}65 (10%) received no evidence in at least one of the 65 (10%) received no evidence in at least one of the three direct alignmentsthree direct alignments
ChondrocraniumChondrocranium in in MAMA, , NCINCI and and FMAFMA6 (1%) received negative evidence in one of the three 6 (1%) received negative evidence in one of the three direct alignmentsdirect alignments
Pericardial cavity Pericardial cavity received negative evidence in received negative evidence in MAMA--FMAFMAPericardial cavity Pericardial cavity received no evidence in received no evidence in MAMA--NCINCIPericardial cavity Pericardial cavity received positive evidence in received positive evidence in NCINCI--FMAFMA
DiscussionDiscussion
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Benefits of the indirect alignmentBenefits of the indirect alignment
49 matches are specific to the indirect alignment 49 matches are specific to the indirect alignment between MA and NCI through the FMAbetween MA and NCI through the FMA
7% of matches in the indirect alignment7% of matches in the indirect alignment45 received positive evidence in both direct alignments 45 received positive evidence in both direct alignments MAMA--FMAFMA and and NCINCI--FMAFMA2 received no evidence in one of the direct alignments 2 received no evidence in one of the direct alignments MAMA--FMAFMA and and NCINCI--FMAFMA2 received negative evidence in one of the direct 2 received negative evidence in one of the direct alignments alignments MAMA--FMAFMA and and NCINCI--FMAFMA
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Benefits of the indirect alignmentBenefits of the indirect alignment
Why are the 49 matches not identified in the Why are the 49 matches not identified in the direct alignment?direct alignment?
Additional synonyms by the FMAAdditional synonyms by the FMA
FMAMA: IntegumentalIntegumental systemsystem
NCI: IntegumentaryIntegumentary systemsystem
Additional relations by the FMAAdditional relations by the FMA
FMA: Hip BoneMA: Hip boneHip bone
NCI: Pelvic bonePelvic bone
NCI: IschiumIschium ((synsyn:: HipHip)) FMA: Hip
part-ofisa
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Benefits of the direct alignmentBenefits of the direct alignment
61 matches are specific to the direct alignment 61 matches are specific to the direct alignment MAMA--NCINCI
Account for 9% of matches in the direct alignmentAccount for 9% of matches in the direct alignment53 received positive evidence 53 received positive evidence 8 received no evidence8 received no evidence
44 matches identified both directly and indirectly, 44 matches identified both directly and indirectly, but received no structural evidence in the indirect but received no structural evidence in the indirect alignmentalignment
14 received positive evidence in the direct alignment14 received positive evidence in the direct alignment
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Benefits of the direct alignmentBenefits of the direct alignment
Why are the 61 matches not identified in the Why are the 61 matches not identified in the indirect alignment through the FMA?indirect alignment through the FMA?
Different coverageDifferent coverage
Common Common iliac arteryiliac artery
Internal Internal iliac arteryiliac artery
External External iliac arteryiliac artery
Iliac Iliac arteryarteryMA:
Common Common iliac arteryiliac artery
Internal Internal iliac arteryiliac artery
External External iliac arteryiliac artery
Iliac Iliac arteryartery
FMA:
Common Common iliac arteryiliac artery
Internal Internal iliac arteryiliac artery
External External iliac arteryiliac arteryNCI:
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Benefits of the direct alignmentBenefits of the direct alignment
Why are the 14 matches supported in the direct Why are the 14 matches supported in the direct alignment while having no evidence in the indirect alignment while having no evidence in the indirect alignment through the FMA?alignment through the FMA?
Different representationDifferent representation
Blood vesselBlood vesselArteryArtery
VeinVeinMA:
Blood vesselBlood vessel General anatomical termGeneral anatomical termFMA:
Blood vesselBlood vesselArteryArtery
VeinVeinNCI:
is-a
is-a
is-a
ArteryArtery
VeinVein
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Alignment through a reference vs. Alignment through a reference vs. pairwisepairwise alignmentalignment
Efficiency of alignment through a referenceEfficiency of alignment through a referencen(nn(n--1)/21)/2 pairwisepairwise mappingsmappings(n(n--1)1) mappings to a referencemappings to a reference
Feasibility of alignment through a referenceFeasibility of alignment through a referenceIdentified 91% of matches in the direct alignmentIdentified 91% of matches in the direct alignmentIdentified additional matches not discovered by the Identified additional matches not discovered by the direct alignmentdirect alignment
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Alignment through a reference vs. Alignment through a reference vs. pairwisepairwise alignmentalignment
Requirements for a reference ontologyRequirements for a reference ontologyBroad coverageBroad coverageStandard representation principlesStandard representation principles
The FMA serves as a reference ontologyThe FMA serves as a reference ontologyLarge number of conceptsLarge number of conceptsLarge number of synonymsLarge number of synonymsComprehensive relationships among conceptsComprehensive relationships among conceptsModeled by a set of declared foundational principlesModeled by a set of declared foundational principlesIndependent of biomedical applicationsIndependent of biomedical applications
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Current limitations and future workCurrent limitations and future work
764 matches identified together by direct and 764 matches identified together by direct and indirect alignments between MA and NCIindirect alignments between MA and NCI
32% of MA concepts32% of MA concepts17% of NCI anatomical concepts17% of NCI anatomical concepts
Relies heavily on lexical similarityRelies heavily on lexical similarityOnly identifies oneOnly identifies one--toto--one concept matchesone concept matchesFully automatic techniques without validation of Fully automatic techniques without validation of the alignmentsthe alignments
No manual validationNo manual validationBut crossBut cross--validationvalidation
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PublicationsPublications
SongmaoSongmao Zhang, Olivier Zhang, Olivier BodenreiderBodenreider, , Knowledge augmentation for Knowledge augmentation for aligning aligning ontologiesontologies: An evaluation in the biomedical domain.: An evaluation in the biomedical domain.Proceedings of the Semantic Integration Workshop at the Second Proceedings of the Semantic Integration Workshop at the Second International Semantic Web Conference (ISWC 2003)International Semantic Web Conference (ISWC 2003) 20032003:109:109--114114
SongmaoSongmao Zhang, Olivier Zhang, Olivier BodenreiderBodenreider, , Aligning representations of Aligning representations of anatomy using lexical and structural methods.anatomy using lexical and structural methods. Proceedings of AMIA Proceedings of AMIA Annual SymposiumAnnual Symposium 20032003:753:753--757757
SongmaoSongmao Zhang, Olivier Zhang, Olivier BodenreiderBodenreider, , Investigating implicit Investigating implicit knowledge in knowledge in ontologiesontologies with application to the anatomical domain.with application to the anatomical domain. In: In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Pacific Symposium on BiocomputingBiocomputing 20042004: World Scientific; : World Scientific; 20042004:250:250--261261
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PublicationsPublications
SongmaoSongmao Zhang, Peter Zhang, Peter MorkMork, Olivier , Olivier BodenreiderBodenreider, , Lessons learned Lessons learned from aligning two representations of anatomy.from aligning two representations of anatomy. In: Hahn U, Schulz S, In: Hahn U, Schulz S, Cornet R, editors. Cornet R, editors. ProceedingsProceedings ofof thethe FirstFirst International Workshop on International Workshop on FormalFormal BiomedicalBiomedical KnowledgeKnowledge RepresentationRepresentation ((KRKR--MEDMED 2004)2004); ; 20042004:102:102--108108
SongmaoSongmao Zhang, Olivier Zhang, Olivier BodenreiderBodenreider, , Comparing associative Comparing associative relationships among equivalent concepts across relationships among equivalent concepts across ontologiesontologies.. MedinfoMedinfo20042004:459:459--463463
SongmaoSongmao Zhang, Olivier Zhang, Olivier BodenreiderBodenreider, , Law and Order: Assessing and Law and Order: Assessing and enforcing compliance with ontological modeling principles.enforcing compliance with ontological modeling principles. Computers Computers in Biology and Medicinein Biology and Medicine; ; 20052005:(accepted):(accepted)
49Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
PublicationsPublicationsSongmaoSongmao Zhang, Peter Zhang, Peter MorkMork, Olivier , Olivier BodenreiderBodenreider, Philip A. , Philip A. Bernstein, Bernstein, Comparing two approaches for aligning representations of Comparing two approaches for aligning representations of anatomy.anatomy. Artificial Intelligence in MedicineArtificial Intelligence in Medicine; ; 20052005:(submitted):(submitted)
SongmaoSongmao Zhang, Olivier Zhang, Olivier BodenreiderBodenreider, , Alignment of multiple Alignment of multiple ontologiesontologies of anatomy: Deriving indirect mappings from direct of anatomy: Deriving indirect mappings from direct mappings to a reference.mappings to a reference. AMIAAMIA; ; 20052005:(submitted):(submitted)
Olivier Olivier BodenreiderBodenreider, Terry , Terry HayamizuHayamizu, Martin , Martin RingwaldRingwald, Sherri De , Sherri De Coronado, Coronado, SongmaoSongmao Zhang, Zhang, Of mice and men: aligning mouse and Of mice and men: aligning mouse and human anatomies.human anatomies. AMIAAMIA;; 20052005:(submitted):(submitted)
SongmaoSongmao Zhang, Olivier Zhang, Olivier BodenreiderBodenreider, , FrameFrame--based structures vs. based structures vs. description logics in representation and reasoning of the Foundadescription logics in representation and reasoning of the Foundational tional Model of Anatomy. Model of Anatomy. 20052005:(in preparation):(in preparation)
SongmaoSongmao Zhang, Olivier Zhang, Olivier BodenreiderBodenreider, , Structural alignment of Structural alignment of anatomical anatomical ontologiesontologies.. 20052005:(in preparation):(in preparation)
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