the foundational model of anatomy (fma) ontology

Session 2: Introduction to OntologySession 2: Introduction to Ontology

The Foundational Model of Anatomy (FMA) Ontology:The Foundational Model of Anatomy (FMA) Ontology: Framework for Cellular and Subcellular Anatomy Framework for Cellular and Subcellular Anatomy

Onard Mejino Onard Mejino Structural Informatics GroupStructural Informatics Group

Department of Biological StructureDepartment of Biological StructureUniversity of WashingtonUniversity of Washington

NCBO Workshop on Ontologies of Cellular Networks NCBO Workshop on Ontologies of Cellular Networks (March 27-28, 2008)(March 27-28, 2008)

Continuants and OccurrentsContinuants and Occurrents

Post-synaptic densitiesPost-synaptic densities

Physicalmodel

Knowledgeresource

FMA

GO, etc.

structural_relation

Physicalentity

OBO-SR

has_property

Physicallaw

Physicalproperty

has_playerOPB*

*Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.*Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.

OPB* biophysical representational schemaOPB* biophysical representational schema

Physicalmodel

Knowledgeresource

FMA

GO, etc.

structural_relation

Physicalentity

OBO-SR

has_property

Physicallaw

Physicalproperty

has_playerOPB*

*Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.*Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.

part_of, contains,

continuous_with, attached_to…

atom, molecule,

cell, organ…

OPB* biophysical representational schemaOPB* biophysical representational schema

Physicalmodel

Knowledgeresource

FMA

GO, etc.

structural_relation

Physicalentity

law of mass action,Ohm’s law,

Newton’s law

e..g, chemical concentration,free energy,

molecular shape,pressure, tension

OBO-SR

has_property

Physicallaw

Physicalproperty

has_playerOPB*

*Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.*Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.

OPB* biophysical representational schemaOPB* biophysical representational schema

Physicalmodel

Knowledgeresource

FMA

GO, etc.

structural_relation

Physicalentity

OBO-SR

has_property

Physicallaw

Physicalproperty

has_playerOPB*

*Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.*Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.

OPB* biophysical representational schema: processOPB* biophysical representational schema: process

A physical process occurs when energy is transformed or exchanged within or between physical entities.

Process manifestation are the changes of entity property magnitudes or structural relations that are a consequence of a process

FMA FMA is a is a spatial-structural ontologyspatial-structural ontology of the of the entities and relations which together form entities and relations which together form the the phenotypic structurephenotypic structure of the human of the human organism at all biologically salient organism at all biologically salient levels of levels of granularitygranularity..

Theory of AnatomyTheory of Anatomy

Anatomical StructuresAnatomical Structures

Thorax

Lung

Heart

CellMacro-molecule

What is the Foundational Model of Anatomy (FM)?

The Digital Anatomist Foundational ModelThe Digital Anatomist Foundational Modelis a is a symbolic modelsymbolic model of the physical organization of the human body; of the physical organization of the human body;

declares the principlesdeclares the principles for including concepts and relationships for including concepts and relationships that are implicitly assumed that are implicitly assumed when knowledge of anatomywhen knowledge of anatomyis applied in different contexts;is applied in different contexts;

explicitly definesexplicitly definesconcepts and relationships concepts and relationships

necessary and sufficient for consistently necessary and sufficient for consistently modeling the structure of the modeling the structure of the human body.human body.

• Constraint principle• Definition principle• Constitutive principle• Organizational unit principle• Structural relationship principle

Foundational Principles of AnatomyFoundational Principles of Anatomy

Anatomical Entity

Physical Anatomical Entity

Material Anatomical Entity

-is a-

Immaterial Anatomical Entity

Non-physicalAnatomical Entity

AnatomicalStructure

Portion of Body Substance

Anatomical Entity

Physical Anatomical Entity

Material Anatomical Entity

-is a-

Immaterial Anatomical Entity

Non-physicalAnatomical Entity

AnatomicalStructure

Has_dimensionHas_dimension

Has_massHas_mass

Portion of Body Substance

Has_inherent_shapeHas_inherent_shape

Foundational Principles of AnatomyFoundational Principles of Anatomy

Definition Principle: Definition Principle:

Defining attributes of anatomical entities Defining attributes of anatomical entities should be specified in terms of should be specified in terms of

physical attributes and physical attributes and structural relationships ofstructural relationships of

the anatomical entitythe anatomical entity

Anatomical Entity

Physical Anatomical Entity

Material Anatomical Entity

-is a-

Immaterial Anatomical Entity

Non-physicalAnatomical Entity

AnatomicalStructure

Portion of Body Substance

Anatomical structure Anatomical structure is_a is_a material anatomical entitymaterial anatomical entity

which has (which has (by transitive inheritanceby transitive inheritance))massmass and and dimensiondimension..

• Constraint principle• Definition principle• Constitutive principle• Organizational unit principle• Structural relationship principle

Foundational Principles of AnatomyFoundational Principles of Anatomy

Anatomical Entity

Physical Anatomical Entity

Material Physical Anatomical Entity

-is a-

Immaterial Physical Anatomical Entity

Non-physicalAnatomical Entity

HumanBody

AnatomicalStructure

Portion ofBody Substance

BiologicalMacromolecule

AcellularAnatomicalStructure

Space Surface Line

OrganSystemOrganCell Cardinal

Organ PartPortion of

Tissue

Organ component Organ region

Cell Part

CardinalBodyPart

Foundational Principles of AnatomyFoundational Principles of Anatomy

Organizational Unit Principle: Organizational Unit Principle: [Principle of Granular partitions][Principle of Granular partitions]

OrganOrgan

CellCell

Biological macromoleculeBiological macromolecule

Other subclasses of Other subclasses of Anatomical structureAnatomical structureconstitute cells or organsconstitute cells or organsconstituted by cells or organsconstituted by cells or organs

Anatomical Entity

Physical Anatomical Entity

Material Physical Anatomical Entity

-is a-

Non-material Physical Anatomical Entity

Non-physicalAnatomical Entity

CardinalBodyPart

HumanBody

OrganSystemOrganCell Cardinal

Organ PartPortion of

Tissue

Organ component Organ region

AnatomicalStructure

BodySubstance

Cell Part

BiologicalMacromolecule

AcellularAnatomicalStructure

Space Surface Line

FMA TaxonomyFMA Taxonomy

• Constraint principle• Definition principle• Constitutive principle• Organizational unit principle• Structural relationship principle

Foundational Principles of AnatomyFoundational Principles of Anatomy

Apical Apical bronchopulmonary bronchopulmonary

segmentsegment

AnteriorAnterior bronchopulmonarybronchopulmonary

segmentsegment

has part

part of

Volume (3-D)Volume (3-D)

has part

Apical segmental bronchial treeApical segmental bronchial tree

Wall of Wall of anterior segmental bronchial treeanterior segmental bronchial tree

Parenchyma of anterior segmentParenchyma of anterior segment

Mucosa of bronchusMucosa of bronchus

Parenchyma of apical segmentParenchyma of apical segment

LobeLobe

Organ Organ componentcomponent

Organ PartOrgan Part

Anatomical StructureAnatomical Structure

-is a--is a-

Volume (3-D)Volume (3-D)

Anatomy TaxonomyAnatomy Taxonomy

-has volume--has volume-

Upper lobe ofright lung(3-D)

Anterior segmental bronchial treeAnterior segmental bronchial tree

Lumen of Lumen of anterior segmental bronchial treeanterior segmental bronchial treeCartilage of bronchusCartilage of bronchus

Pulmonary alveolusPulmonary alveolusPulmonary Pulmonary

capillary bedcapillary bed

Part_of NetworkPart_of Network

has part

has part

has part

ASA = (Dt, Bn, Pn, SAn) ASA = (Dt, Bn, Pn, SAn) (2)(2)

where:where:DtDt = Dimensional taxonomy= Dimensional taxonomyBnBn = Boundary network= Boundary networkPnPn = Part-of network= Part-of networkSAnSAn = Spatial Association network= Spatial Association network

FMA = (At, ASA, ATA, Mk) (1)

Anatomical Structural AbstractionAnatomical Structural Abstraction

Structural RelationshipsStructural Relationships

CardiacChamber

OrganComponent

Cardinal Organ Part

Anatomical StructureAnatomy Taxonomy

-is a-

Polyhedron

Volume (3-D)

Dimensional Taxonomy

Part-ofNetwork

HeartHeart

Part_of

Inflow partInflow part of RVof RV

Infundibulum

Wall of RVWall of RVCavity of RVCavity of RV

part

-has shape

has

Cavity ofCavity of infund.infund.

Cavity ofCavity ofinfl.partinfl.part

hashasadjacencyadjacency

anterioranterior inferiorinferiorto leftto left

LeftLeftventricleventriclePericardialPericardial

sacsac

hashasadjacencyadjacency

DiaphragmDiaphragm

inferiorinferior

Spatial Association NetworkSpatial Association Network

Sternocostal Surface

Diaphragmatic Surface

bounded by

boundary of

Anatomical Surface

Surface (2-D)

bounded by RightCoronary Sulcus

AnteriorInterventricular Sulcus

Line (1-D)

bounded by

Coronary Sulcus

Inferior margin of heart

Apex

Boundary NetworkBoundary Network

-is a-

Posterior IV Sulcus

Crux of heart

Anatomical Landmark

Point (1-D)

-is a-

Right Ventricle

wherewhereAtAt = Anatomy taxonomy= Anatomy taxonomyASAASA = Anatomical Structural Abstraction= Anatomical Structural AbstractionATAATA = Anatomical Transformation Abstraction= Anatomical Transformation AbstractionMkMk = Metaknowledge = Metaknowledge

(principles, rules, axioms)(principles, rules, axioms)

Foundational Model of Anatomy OntologyFoundational Model of Anatomy Ontology

FMA = (At, ASA, ATA, Mk)FMA = (At, ASA, ATA, Mk)

FMA in ProtegeFMA in Protege

FMA in ProtegeFMA in Protege

Anatomy TaxonomyAnatomy Taxonomy(AT)(AT)

Anatomical Anatomical Structural abstractionStructural abstraction

(ASA)(ASA)

AnatomicalStructure

BiologicalMacromolecule

AcellularAnatomical

StructureCell Cell Part

Generic cell Specialized cell

Skeletalmuscle fiber

Cell TaxonomyCell Taxonomy

Cell TaxonomyCell Taxonomy

• Presence of nucleus• Somatic, germ• Embryonic derivation• Tissue type• Free, fixed

Cell TaxonomyCell Taxonomy• Presence of nucleus• Somatic, germ• Embryonic derivation• Tissue type• Free, fixed

• Proliferative stage• Structural properties

Lobocyte or filocyte Vibriocyte or nonvibrio-cyte

• Secretory, non-secretory• Membrane markers/surface antigens• Gene expression

Parts of the CellParts of the Cell

Frame of CellFrame of Cell

Cell-Specific AttributesCell-Specific Attributes

Cell-Specific AttributesCell-Specific Attributes

AnatomicalStructure

BiologicalMacromolecule

AcellularAnatomical

StructureCell Cell Part

CellappendageOrganelleProtoplasmPlasma

membrane

Cytoskeleton

Test: What is a cytoskeleton?Test: What is a cytoskeleton?

Actin filament

Intermediate filament

Microtubule

What is a cytoskeleton?What is a cytoskeleton?

What is a cytoskeleton?What is a cytoskeleton?

• “ The term cytoskeleton is used to denote a system of filamentous intracellular proteins of different shapes and sizes which form a complex often interconnected network throughout the cytoplasm, sometimes invading the nucleus of the cell.’

Gray’s Anatomy, 38th Gray’s Anatomy, 38th edition, p. 36edition, p. 36

What is a cytoskeleton?What is a cytoskeleton?

Definition: The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.

What is a cytoskeleton?What is a cytoskeleton?

• Is it one integral, connected unit consisting of all 3 types of protein filaments?

• Is it a set of disjoint systems of filaments?

• What other parts are there besides filaments?

FMA Ontology in Protege

FMA Ontology in Protege

Reference OntologiesReference Ontologies

CharacteristicsCharacteristics• Deal with domains of basic sciencesDeal with domains of basic sciences• Developed top downDeveloped top down• Focus on overall semantic structureFocus on overall semantic structure• Do notDo not target specific target specific

applicationsapplicationsuser groupsuser groups

• Conform to sound ontological principles Conform to sound ontological principles • Correlate with high level, formal ontologiesCorrelate with high level, formal ontologies

http://sig.biostr.washington.edu/projects/fm/

FMA OntologyFMA Ontology

• Accommodate different viewpointsAccommodate different viewpoints• Reconcile different terminologiesReconcile different terminologies• Generalize to other domainsGeneralize to other domains• Must be scalableMust be scalable