scale and context: issues in ontologies to link health- and bio-informatics
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Scale and Context: Issues in Ontologies to link Health- and Bio-Informatics. Alan Rector, Jeremy Rogers, Angus Roberts, Chris Wroe Bio and Health Informatics Forum/ Medical Informatics Group Department of Computer Science, University of Manchester - PowerPoint PPT PresentationTRANSCRIPT
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Scale and Context: Issues in Scale and Context: Issues in Ontologies to link Health- and Bio-Ontologies to link Health- and Bio-
InformaticsInformatics Alan Rector, Jeremy Rogers, Alan Rector, Jeremy Rogers,
Angus Roberts, Chris WroeAngus Roberts, Chris Wroe
Bio and Health Informatics Forum/Bio and Health Informatics Forum/Medical Informatics GroupMedical Informatics Group
Department of Computer Science, University of Department of Computer Science, University of ManchesterManchester
[email protected]@cs.man.ac.ukwww.cs.man.ac.uk/mig img.man.ac.ukwww.cs.man.ac.uk/mig img.man.ac.uk
www.clinical-escience.orgwww.clinical-escience.orgwww.opengalen.orgwww.opengalen.org
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Organisation of TalkOrganisation of Talk
• Informal presentation, motivation & examples
• Intro to logic based ontologies
• How to use logic based ontologies to represent scales and context– Making context modular – normalisation– Recurrent distinctions
• and tests for those distinctions
• Summary
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Example Problems of ContextExample Problems of Context• Classification by multiple axes
– e.g. Molecular action, physiologic, and pathological effects
• Chloride transport & Cystic fibrosis
• Biological Scope
– eg. Normal/Abnormal, Human/Mouse
• Conceptual view– e.g. the Digital Anatomist Foundational Model of
organs vs Clinical convention – Is the pericardium a part of the heart?
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Basic ApproachBasic Approach
• Separate information into independent modules– Normalise the ontology
• Represent knowledge cleanly
• Add explicit contextual information– Don’t distort the clean structure
• Add context to it explicitly
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Why use Logic-based Ontologies?Why use Logic-based Ontologies?
because
Knowledge is Fractal!&
Changeable!
&Contextual!
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Logic-based Ontologies: Logic-based Ontologies: Conceptual LegoConceptual Lego
hand
extremity
body
acute
chronic
abnormal
normalischaemic
deletion
bacterial
polymorphism
cell
protein
gene
infection
inflammation
Lung
expression
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Logic-based Ontologies: Logic-based Ontologies: Conceptual LegoConceptual Lego
“SNPolymorphism of CFTRGene causing Defect in MembraneTransport of ChlorideIon causing Increase in Viscosity of Mucus in CysticFibrosis…”
“Hand which isanatomicallynormal”
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Logic based ontologiesLogic based ontologies
• A formalisation of semantic nets, frame systems, and object hierarchies via KL-ONE and KRL
• “is-kind-of” = “implies” (“logical subsumption”)– “Dog is a kind of wolf”
means“All dogs are wolves”
• Modern examples: DAML+OIL /“OWL”?)• Older variants LOOM, CLASSIC, BACK, GRAIL, K-REP, …
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Encrustation
+ involves: MitralValve
Thing
+ feature: pathological
Structure
+ feature: pathological
+ involves: Heart
Logic Based Ontologies: The basicsLogic Based Ontologies: The basics
Thing
Structure
Heart MitralValve EncrustationMitralValve* ALWAYS partOf: Heart
Encrustation* ALWAYS feature: pathological
Feature
pathological red
+ (feature: pathological)
red
+ partOf: Heart
red
+ partOf: Heart
Primitives Descriptions Definitions Reasoning Validating
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Bridging Bio and Health Bridging Bio and Health InformaticsInformatics
• Define concepts with ‘pieces’ from different scales and disciplines and then combine them– “Polymorphism which causes defect which causes
disease”
• Use concepts which make context explicit– “ ‘Hand which is anatomically normal’ has five
fingers”
• Use different subproperties for different contexts – “Abnormalities of clinical parts of the heart”
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Bridging Scales Bridging Scales with Ontologieswith Ontologies
GenesSpecies
Protein
Function
Disease
Protein coded by(CFTRgene & in humans)
Membrane transport mediated by (Protein coded by (CFTRgene in humans))
Disease caused by (abnormality in (Membrane transport mediated by (Protein coded by (CTFR gene & in humans))))
CFTRGene in humans
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Use composition to express Use composition to express contextcontext
• Normal and abnormalHand isSubdivisionOf some UpperExtremityHand & AnatomicallyNormal hasSubdivision exactly-
5 fingers
• Homologies and OrthologiesThumb of Hand of Human hasFeature Opposable
Thumb of Hand of NonHumanPrimate ¬hasFeature Opposable
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Represent context and views by Represent context and views by variant propertiesvariant properties
Organ
HeartPericardium
OrganPart
CardiacValve
Disease of part_of Heart
Disease of Pericardium
is_part_of
is_structurally_part_ofis_clinically_part_of
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Context can give combinatorial Context can give combinatorial explosionsexplosions
• Avoid the “Exploding Bicycle” From “phrase book” to “dictionary + grammar” – 1980 - ICD-9 (E826) 8 – 1990 - READ-2 (T30..) 81– 1995 - READ-3 87– 1996 - ICD-10 (V10-19 Australian) 587
• V31.22 Occupant of three-wheeled motor vehicle injured in collision with pedal cycle, person on outside of vehicle, nontraffic accident, while working for income
– and meanwhile elsewhere in ICD-10• W65.40 Drowning and submersion while in bath-tub, street
and highway, while engaged in sports activity
• X35.44 Victim of volcanic eruption, street and highway, while resting, sleeping, eating or engaging in other vital activities
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The Cost 1: Normalising (untangling) The Cost 1: Normalising (untangling) OntologiesOntologies
StructureFunction
Part-wholeStructure Function
Part-w
hole
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The Cost 1: Normalising (untangling) The Cost 1: Normalising (untangling) OntologiesOntologies
Making each meaning explicit and separateMaking each meaning explicit and separatePhysSubstance Protein ProteinHormone Insulin Enzyme Steroid SteroidHormone Hormone ProteinHormone^ Insulin^ SteroidHormone^ Catalyst Enzyme^
Hormone = Substance & playsRole-HormoneRoleProteinHormone = Protein & playsRole-HormoneRoleSteroidHormone = Steroid & playsRole-HormoneRoleCatalyst = Substance & playsRole CatalystRoleInsulin playsRole HormoneRole
...and helping keep argument rational and meetings short!
Enzyme ?=? Protein & playsRole-CatalystRole
PhysSubstance Protein ‘ ProteinHormone’ Insulin ‘Enzyme’ Steroid ‘SteroidHormone’ ‘Hormone’ ‘ProteinHormone’ Insulin^ ‘SteroidHormone’ ‘Catalyst’ ‘Enzyme’
… ActionRole PhysiologicRole HormoneRole CatalystRole …
… Substance BodySubstance Protein Insulin Steroid …
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The Cost: 2 – Clean Distinctions & The Cost: 2 – Clean Distinctions & TestsTests
• Repeating patterns within levels– Structures vs Substances– Flavours of part-whole– Part-whole vs containment, connection, branching– Process/Event vs Thing (“Endurant” vs
“Perdurant”)– …
• Repeating patterns across levels– Multiples at one level act as substances at the
next– Substances span levels; structures are specific to
a level
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Repeating Patterns within each Repeating Patterns within each level level
• Structures vs Substances (Discrete vs Mass)– Structures are made of substances
• Organs are made of tissue
– Parts & portions• Structures have parts & subdivisions,…• Substances have portions
– Portions can have proportions & concentrations
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TestsTests
• Structures (Discrete) – Can you count it? Is one part different
from another? Is it made of something(s)?
• Books, organs, ideas, individual cells, organisations, …
• Substance (Mass)– Are all bits the same? Can something be
made of it? Can you talk about “A piece of it”? “A lump of it”? “A stream of it”? …
• Water, sodium, tissue, blood, …
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Repeating Patterns within each Repeating Patterns within each levellevel
• Part-whole vs containment– Parthood is organisational
• The wall is part of the cell; • cornea is part of the eye
– Containment is physical• The inclusion is contained in the cell• The marrow is contained in the bone
– Often occur together• Nucleus is a part of and contained in the cell• The retina is part of and contained in the eye
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TestsTests
• Parts– If I take the part away, is the whole
incomplete?– If the part is damaged is the whole
damaged?– If I do something to the part do I do
something to the whole?
• Containment– Is the contained thing inside the container?– Is the relationship spatial/physical?
(or temporal?)
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Repeating Patterns bridging Repeating Patterns bridging levelslevels
• Multiples of structures at one level behave as substances at the next
– “Blood is made of in part a multiple of red cells”“Tissue is made of in part a multiple of cells”“A rash is a multiple of spots”“Polyposis is a multiple of polyps”“A flock is a multiple of birds”
• Multiples are not Sets– Note defined by members
• Membership can change (intensional rather than extensional)– Action on the singleton is not action on the multiple;
Action on the whole is (usually) action on the singletons• If I treat a spot, I do not treat the rash• If I treat the rash, I treat the spots
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TestsTests
• Multiples– Name for the singleton – “grain”,
“cell”, “bird”?– Singletons are countable?– Multiple is measurable rather than
countable?– Odd to say part-of “This cell is part of
the Arm”?
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SummarySummaryLet the logic engine do the workLet the logic engine do the work
• Logic based ontologies can bridge granularities & represent context explicitly– And manage the potential combinatorial
explosions
• To do so– Structure must
• Make all relevant information explicit• Be modular
– Conception must• Make ontological distinctions cleanly
– Parts, wholes, containment, structures, substances, …• Developers need systematic tests for each distinction
Be normalised