The Body Region Connection CalculusAnalyzing anatomical ontologies

with the RCC-8 model

SongmaoSongmao Zhang ZhangOlivier BodenreiderOlivier Bodenreider

Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical Communications

Bethesda, Maryland - USABethesda, Maryland - USA

April 18, 2005Buffalo, NY

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OutlineOutline

ObjectivesObjectivesRCC8RCC8Anatomical relations in the FMAAnatomical relations in the FMAMapping anatomical relations to FMAMapping anatomical relations to FMAResultsResultsDiscussionDiscussionConclusionsConclusions

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ObjectivesObjectives

To investigate consistency in the FMATo investigate consistency in the FMAComplementary to ontological analyses such as:Complementary to ontological analyses such as:

Zhang S, Bodenreider O.Zhang S, Bodenreider O.Law and order: Assessing and enforcing complianceLaw and order: Assessing and enforcing compliancewith ontological modeling principleswith ontological modeling principles..Computers in Biology and Medicine 2005:(in press).Computers in Biology and Medicine 2005:(in press).

Focus on anatomical relationsFocus on anatomical relationsAssigned manuallyAssigned manuallyLittle enforcement possible in ProtégéLittle enforcement possible in Protégé

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General idea General idea OverviewOverview

Anatomical relations RCC-8 relations

****************EQEQ

****************NTPPiNTPPi

****************TPPiTPPi

****************NTPPNTPP

****************TPPTPP

****************POPO

****************ECEC

****************DCDC

EQEQNTNTTPiTPi

TPTPPiPi

NTNTPPPP

TPPTPPPOPOECECDCDC

RCC-8consistency?

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General idea General idea DetailsDetails

FMA FMA-RCCconversion rules

RCC

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Foundational Model of AnatomyFoundational Model of Anatomy

Dec. 2, 2004Dec. 2, 200471,202 classes71,202 classes220 slots220 slots

7 7 part_ofpart_of slots slots81 slots for associative relations (81 slots for associative relations (branch ofbranch of, , containscontains))

101,200 101,200 partitivepartitive relations relations33,685 associative relations33,685 associative relations

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Region Connection Calculus (RCC)Region Connection Calculus (RCC)

Axiomatic theory of spatial relationsAxiomatic theory of spatial relationsSpatial reasoningSpatial reasoning8 topological relations (JEPD)8 topological relations (JEPD)

DCDC DisconnectionDisconnectionECEC External ConnectionExternal ConnectionPOPO Partial OverlapPartial OverlapTPPTPP Tangential Proper Part (+ inverse)Tangential Proper Part (+ inverse)NTPPNTPP Non-Tangential Proper Part (+ inverse)Non-Tangential Proper Part (+ inverse)EQEQ EqualityEquality

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RCC RCC 8 topological relations8 topological relations

Disconnection

a b

ExternalConnection

a b

PartialOverlap

a b

Equality

a b

TangentialProper Part

a b

Non-TangentialProper Part

a b

TangentialProper Part (inv)

b a

Non-TangentialProper Part (inv)

b a

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Composition table for the 8 RCC relationsComposition table for the 8 RCC relations

[Bennett, 1997]

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Mapping FMA relations to RCC (1)Mapping FMA relations to RCC (1)

part ofgeneral part ofconstitutional part ofsystemic part ofclinical part ofregional part of2D part ofcustom partonomy of

TPP ∨ NTPP

partgeneral partconstitutional partsystemic partclinical partregional part2D partcustom partonomy

TPPi ∨ NTPPi

attributed partattributed constitutional partattributed regional part

TPPi ∨ NTPPi

TangentialProper Part

a b

Non-TangentialProper Part

a b

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Mapping FMA relations to RCC (2)Mapping FMA relations to RCC (2)

adjacent tocontinuous withcontinuous with proximallycontinuous with distallybranch ofbranchtributary oftributary

EC

muscle originmuscle insertionmuscle attachmentlocation+adjacent(true)attributed continuous with+adjacent(true)

http://www.rad.washington.edu/atlas/tricepsbrachii.html

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Mapping FMA relations to RCC (3)Mapping FMA relations to RCC (3)

drainsdrains tovenous drainage ofvenous drainagelymphatic drainage oflymphatic drainage

DC ∨ EC

EQbounded bybounds

EC ∨ EQsurrounded bysurrounds

EC Lung | venous drainage | Bronchial vein

DC Right paratracheal lymph node | drains to | Right bronchomediastinal lymphatic trunk

EQ Surface of thorax | bounds | Thorax

EQ Pleural sac | surrounds | Lung

EC Wall of right side of heart | surrounds | Cavity of right atrium

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Mapping FMA relations to RCC (4)Mapping FMA relations to RCC (4)arterial supply ofvenous supply ofnerve supply of

arterial supplyvenous supplynerve supply

DC ∨ PO ∨TPPi ∨ NTPPi

DC ∨ PO ∨TPP ∨ NTPP

DC Gastric branch of right vagus nerve | nerve supply of | Stomach

DC Spinal cord | arterial supply | Vertebral artery

TPP Right coronary artery | arterial supply of | Heart

location+adjacent(false)attributed continuous with+adjacent(false) DC

PO ∨ TPPi ∨ NTPPi ∨ EQ PO ∨ TPP ∨ NTPP ∨ EQcontains contained in

TPP Posterior compartment of arm|contains|Triceps brachii

DC / POvs. EC ??

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Example (direct)Example (direct)

Tricepsbrachii

Long headof TB

part of

regional part of

attributed part of

Tricepsbrachii

Long headof TB

TPPi ∨ NTPPi

TPPi ∨ NTPPi

TPPi ∨ NTPPi

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Example (indirect)Example (indirect)

Tricepsbrachii

Long headof TB

muscleattachment

Infraglenoidtubercle

muscleattachment

Tricepsbrachii

Long headof TB

EC

Infraglenoidtubercle

EC

Tricepsbrachii

Long headof TB

DC ∨ EC ∨ PO ∨TPPi ∨ EQ

Tricepsbrachii

Long headof TB

TPPi ∨ NTPPi

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Quantitative resultsQuantitative results

ConversionConversion84,284 pairs with RCC relations84,284 pairs with RCC relations

18,112 with only one relation18,112 with only one relation66,172 with multiple relations66,172 with multiple relations

–– 64,354 consistent64,354 consistent–– 1,818 inconsistent1,818 inconsistent

CompositionComposition707,284 pairs707,284 pairs

698,588698,588

8,6968,696

75,58875,588

compositioncomposition conversionconversion

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Quantitative resultsQuantitative results

CompositionComposition698,588 pairs specific to composition698,588 pairs specific to composition

28,042 with only one relation28,042 with only one relation670,546 with multiple relations670,546 with multiple relations

–– 669,026 consistent669,026 consistent–– 1,520 inconsistent1,520 inconsistent

InconsistentInconsistentConflicting relationsConflicting relationsInaccurate conversion rulesInaccurate conversion rules

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Example of inconsistencyExample of inconsistencySurface of brain | bounds | Brain EQ

Surface of brain | bounds | Forebrain EQForebrain | regional part of | Brain TPP � NTPP

EQ TPP � NTPP TPP � NTPP

(TPP � NTPP) ∧ EQ = ⊥

EQbounded bybounds ?

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AdvantagesAdvantages

Supports consistency analysis of spatial relationsSupports consistency analysis of spatial relationsAlmost fully automaticAlmost fully automatic

Except for establishing the mapping between FMA andExcept for establishing the mapping between FMA andRCC relationsRCC relationsAnalysis requires domain knowledgeAnalysis requires domain knowledge

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LimitationsLimitations

Loss in expressivenessLoss in expressivenessDifferent FMA relations are converted into the sameDifferent FMA relations are converted into the sameRCC relationRCC relation(e.g., (e.g., continuous withcontinuous with and and adjacent toadjacent to into EC) into EC)

InterpretationInterpretationInconsistent is not necessarily wrongInconsistent is not necessarily wrongConsistent is not necessarily validConsistent is not necessarily valid

Granularity issuesGranularity issuesIssue with shared partsIssue with shared parts

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Shared part issueShared part issueEsophagogastric junction | regional part of | Abdominal part of esophagus TPP � NTPPAbdominal part of esophagus | regional part of | Esophagus TPP � NTPP

Esophagogastric junction | part of | Stomach TPP � NTPPStomach | continuous with | Esophagus EC

TPP � NTPPTPP � NTPP

TPP � NTPPEC

TPP � NTPP

DC � EC

(TPP � NTPP) ∧ (DC � EC) = ⊥

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ConclusionsConclusions

RCC relationsRCC relationsLess expressive than FMA relationsLess expressive than FMA relationsEnable reasoningEnable reasoningUseful for detecting inconsistencyUseful for detecting inconsistency

Disjunctions can be reduced by comparing directDisjunctions can be reduced by comparing directrelations to composed relationsrelations to composed relationsUsage in FMAUsage in FMA

Detect potentially inconsistent representationDetect potentially inconsistent representationFocus the effort of expertsFocus the effort of experts

Refine conversion rulesRefine conversion rules

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ReferencesReferences

D A D A RandellRandell, Z Cui, and A G Cohn. , Z Cui, and A G Cohn. A spatialA spatiallogic based on regions and connectionlogic based on regions and connection. In Proc.. In Proc.3rd Int. Conf. on Knowledge Representation and3rd Int. Conf. on Knowledge Representation andReasoning, pages 165--176, San Mateo, 1992.Reasoning, pages 165--176, San Mateo, 1992.Morgan KaufmannMorgan KaufmannB. Bennett. B. Bennett. Spatial reasoning with propositionalSpatial reasoning with propositionallogicslogics. In J Doyle, E . In J Doyle, E SandewallSandewall, and P , and P TorassoTorasso,,editors, editors, Principles of Knowledge RepresentationPrinciples of Knowledge Representationand Reasoningand Reasoning: Proceedings of the 4th: Proceedings of the 4thInternational Conference (KR94), San Francisco,International Conference (KR94), San Francisco,CA., 1994. Morgan KaufmannCA., 1994. Morgan Kaufmann

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ReferencesReferences

Bennett, B. (1998). Bennett, B. (1998). Determining consistency ofDetermining consistency oftopological relationstopological relations. Constraints, 3, 213--225.. Constraints, 3, 213--225.Schulz S, Hahn U, Schulz S, Hahn U, RomackerRomacker M. M. ModelingModelinganatomical spatial relations with descriptionanatomical spatial relations with descriptionlogicslogics. Proc AMIA . Proc AMIA SympSymp. 2000;:779-83.. 2000;:779-83.

MedicalOntologyResearch

Olivier BodenreiderOlivier Bodenreider

Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical CommunicationsBethesda, Maryland - USABethesda, Maryland - USA

Contact:Contact:Web:Web:

olivier@nlm.nih.govolivier@nlm.nih.govmor.nlm.nih.govmor.nlm.nih.gov