aligning representations of anatomical knowledge

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Aligning Representations of Anatomical Knowledge Songmao Zhang, Ph.D. Songmao Zhang, Ph.D. Mentor: Olivier Mentor: Olivier Bodenreider Bodenreider , M.D., Ph.D. , M.D., Ph.D. Lister Hill National Center Lister Hill National Center for Biomedical Communications for Biomedical Communications Bethesda, Maryland Bethesda, Maryland - - USA USA Medical Informatics Training Program Final Presentation March 30, 2005

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Page 1: Aligning Representations of Anatomical Knowledge

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

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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

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An overviewAn overviewof our alignment projectof our alignment project

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Generating direct

alignment

Concepts

1 : 1Structural similarity

Lexical similarity

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5Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

1:11:1 concept matchconcept match

Lexical alignmentLexical alignmentFMA:FMA: FibularisFibularis tertiustertius (synonym: (synonym: PeroneousPeroneous tertiustertius))GALEN:GALEN: PeroneusPeroneus TertiusTertius

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6Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

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

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Generating direct

alignment

Concepts

1 : 1

n : m

Structural similarity

Lexical similarity

Structural similarity

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8Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

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

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Generating direct

alignment

Concepts

Relationships

1 : 1

n : m

Structural similarity

Lexical similarity

Structural similarity

Structural similarity

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10Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

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

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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

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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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13Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

Approaches to aligning multiple Approaches to aligning multiple ontologiesontologies

Pairwisealignment

Alignment througha reference

Pairwisealignment

Alignment througha reference

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14Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

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

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MaterialsMaterials

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17Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

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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19Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

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

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MethodsMethods

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22Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

Direct alignment MA-FMA

Direct alignment NCI-FMA

MA NCIDirect alignment

MA-NCI

Alignment through the FMA

Three phasesThree phases

FMA

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Generating direct

alignment

Concepts

1 : 1Structural similarity

Lexical similarity

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24Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

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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31Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

Phase 3Phase 3 Comparison of two alignmentsComparison of two alignments

Directalignment

Indirectalignment

Sharedmatches

Specificmatches

Specificmatches

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ResultsResults

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33Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

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

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DiscussionDiscussion

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39Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

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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44Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

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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45Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

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)

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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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