Session 2: Introduction to Ontology The Foundational Model of Anatomy (FMA) Ontology: Framework for Cellular and Subcellular Anatomy Onard Mejino Structural.

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*


part_of, contains,

continuous_with, attached_to…

atom, molecule,

cell, organ…


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*



Physicalmodel

Knowledgeresource

FMA

GO, etc.

structural_relation

Physicalentity

OBO-SR

has_property

Physicallaw

Physicalproperty

has_playerOPB*


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 AnatomyFoundational Principles of AnatomyFoundational Principles of Anatomy

Anatomical EntityAnatomical Entity

Physical Anatomical Entity


Material Anatomical EntityMaterial Anatomical Entity

-is a--is a-

Immaterial Anatomical EntityImmaterial Anatomical Entity

Non-physicalAnatomical Entity


AnatomicalStructure

AnatomicalStructure

Portion of Body Substance






-is a--is a-




AnatomicalStructure

AnatomicalStructure

Has_dimensionHas_dimension

Has_massHas_mass



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





-is a--is a-




AnatomicalStructure

AnatomicalStructure



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..







Material Physical Anatomical Entity


-is a--is a-

Immaterial Physical Anatomical Entity

Immaterial Physical Anatomical Entity



HumanBody

HumanBody

AnatomicalStructure

AnatomicalStructure

Portion ofBody Substance

Portion ofBody Substance

BiologicalMacromolecule


AcellularAnatomicalStructure


SpaceSpace SurfaceSurface LineLine

OrganSystem

OrganSystemOrganOrganCellCell Cardinal

Organ Part

CardinalOrgan Part

Portion ofTissue

Portion ofTissue

Organ componentOrgan component Organ regionOrgan region

Cell PartCell Part

CardinalBodyPart

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






-is a--is a-

Non-material Physical Anatomical Entity

Non-material Physical Anatomical Entity



CardinalBodyPart

CardinalBodyPart

HumanBody

HumanBody

OrganSystem

OrganSystemOrganOrganCellCell Cardinal

Organ Part

CardinalOrgan Part

Portion ofTissue

Portion ofTissue

Organ componentOrgan component Organ regionOrgan region

AnatomicalStructure

AnatomicalStructure

BodySubstance

BodySubstance

Cell PartCell Part





SpaceSpace SurfaceSurface LineLine

FMA TaxonomyFMA TaxonomyFMA TaxonomyFMA Taxonomy




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-


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 tree

Cartilage 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)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

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

Anatomical Structural AbstractionAnatomical Structural AbstractionAnatomical Structural AbstractionAnatomical Structural Abstraction

Structural RelationshipsStructural Relationships

CardiacChamber CardiacChamber

OrganComponent OrganComponent

Cardinal Organ PartCardinal Organ Part

Anatomical StructureAnatomical StructureAnatomy TaxonomyAnatomy Taxonomy

-is a--is a-

PolyhedronPolyhedron


Dimensional TaxonomyDimensional Taxonomy

Part-ofNetworkPart-of

Network

HeartHeartHeartHeart

Part_ofPart_of

Inflow partInflow part of RVof RVInflow partInflow part of RVof RV

InfundibulumInfundibulum

Wall of RVWall of RVWall of RVWall of RVCavity of RVCavity of RVCavity of RVCavity of RV

part part

-has shape-has shape

hashas

Cavity ofCavity of infund.infund.Cavity ofCavity of infund.infund.

Cavity ofCavity ofinfl.partinfl.partCavity ofCavity ofinfl.partinfl.part

hashasadjacencyadjacency hashasadjacencyadjacency

anterioranterioranterioranterior inferiorinferiorinferiorinferiorto leftto leftto leftto left

LeftLeftventricleventricle LeftLeftventricleventriclePericardialPericardial

sacsacPericardialPericardial sacsac

hashasadjacencyadjacency hashasadjacencyadjacency

DiaphragmDiaphragmDiaphragmDiaphragm

inferiorinferiorinferiorinferior

Spatial Association NetworkSpatial Association NetworkSpatial Association NetworkSpatial Association Network

Sternocostal SurfaceSternocostal Surface

Diaphragmatic SurfaceDiaphragmatic Surface

bounded bybounded by

boundary ofboundary of

Anatomical SurfaceAnatomical Surface

Surface (2-D)Surface (2-D)

bounded bybounded by RightCoronary Sulcus

RightCoronary Sulcus

AnteriorInterventricular Sulcus

AnteriorInterventricular Sulcus

Line (1-D)Line (1-D)

bounded bybounded by

Coronary SulcusCoronary Sulcus

Inferior margin of heartInferior margin of heart

ApexApex

Boundary NetworkBoundary NetworkBoundary NetworkBoundary Network

-is a--is a-

Posterior IV SulcusPosterior IV Sulcus

Crux of heartCrux of heart

Anatomical LandmarkAnatomical Landmark

Point (1-D)Point (1-D)

-is a--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)

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)Anatomy TaxonomyAnatomy Taxonomy

(AT)(AT)

Anatomical Anatomical Structural abstractionStructural abstraction

(ASA)(ASA)

Anatomical Anatomical Structural abstractionStructural abstraction

(ASA)(ASA)

AnatomicalStructure

AnatomicalStructure



AcellularAnatomical

Structure

AcellularAnatomical

StructureCellCell Cell PartCell Part

Generic cell Specialized cell

Skeletalmuscle fiber

Cell TaxonomyCell TaxonomyCell TaxonomyCell Taxonomy


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

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


• Presence of nucleus

• Somatic, germ• Embryonic derivation• Tissue type• Free, fixed

• 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

• 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

AnatomicalStructure



AcellularAnatomical

Structure

AcellularAnatomical

StructureCellCell Cell PartCell Part

Cellappendage

CellappendageOrganelleOrganelleProtoplasmProtoplasmPlasma

membrane

Plasmamembrane

Cytoskeleton

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

Actin filament

Intermediate filament

Microtubule

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

• “ 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


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


• 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?

• 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

Session 2: Introduction to Ontology The Foundational Model of Anatomy (FMA) Ontology: Framework for Cellular and Subcellular Anatomy Onard Mejino Structural.

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