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