NCBO Workshop on Ontologies of Cellular Networks (March 27-28, 2008) Session 2: Introduction to Ontology The Foundational Model of Anatomy (FMA) Ontology: Framework for.
Download ReportTranscript NCBO Workshop on Ontologies of Cellular Networks (March 27-28, 2008) Session 2: Introduction to Ontology The Foundational Model of Anatomy (FMA) Ontology: Framework for.
NCBO Workshop on Ontologies of Cellular Networks (March 27-28, 2008) Session 2: Introduction to Ontology The Foundational Model of Anatomy (FMA) Ontology: Framework for Cellular and Subcellular Anatomy Onard Mejino Structural Informatics Group Department of Biological Structure University of Washington Continuants and Occurrents Post-synaptic densities OPB* biophysical representational schema Knowledge resource Physical model OBO-SR structural_relation FMA GO, etc. Physical entity has_property Physical property OPB* has_player Physical law *Ontology of Physics for Biology (OPB), Daniel L. Cook, et al. OPB* biophysical representational schema Knowledge resource Physical model OBO-SR structural_relation FMA GO, etc. Physical entity part_of, contains, continuous_with, attached_to… atom, molecule, cell, organ… has_property Physical property OPB* has_player Physical law *Ontology of Physics for Biology (OPB), Daniel L. Cook, et al. OPB* biophysical representational schema Knowledge resource Physical model OBO-SR structural_relation FMA GO, etc. Physical entity has_property e..g, chemical concentration, free energy, molecular shape, pressure, tension Physical property OPB* has_player Physical law law of mass action, Ohm’s law, Newton’s law *Ontology of Physics for Biology (OPB), Daniel L. Cook, et al. OPB* biophysical representational schema: process Knowledge resource Physical model OBO-SR structural_relation FMA GO, etc. Physical entity has_property OPB* Physical property A physical process occurs when energy is transformed or exchanged within or between physical entities. has_player Process manifestation are the changes of entity property magnitudes or structural relations that are a consequence of a process Physical law *Ontology of Physics for Biology (OPB), Daniel L. Cook, et al. Theory of Anatomy FMA is a spatial-structural ontology of the entities and relations which together form the phenotypic structure of the human organism at all biologically salient levels of granularity. Anatomical Structures Lung Thorax Cell Heart Macromolecule What is the Foundational Model of Anatomy (FM)? The Digital Anatomist Foundational Model is a symbolic model of the physical organization of the human body; declares the principles for including concepts and relationships that are implicitly assumed when knowledge of anatomy is applied in different contexts; explicitly defines concepts and relationships necessary and sufficient for consistently modeling the structure of the human body. Foundational Principles of Anatomy • • • • • Constraint principle Definition principle Constitutive principle Organizational unit principle Structural relationship principle Anatomical Entity Physical Anatomical Entity Material Anatomical Entity Portion of Body Substance -is a- Non-physical Anatomical Entity Immaterial Anatomical Entity Anatomical Structure Anatomical Entity Physical Anatomical Entity -is aNon-physical Has_dimension Anatomical Entity Has_mass Material Anatomical Entity Immaterial Anatomical Entity Has_inherent_shape Portion of Body Substance Anatomical Structure Foundational Principles of Anatomy Definition Principle: Defining attributes of anatomical entities should be specified in terms of physical attributes and structural relationships of the anatomical entity Anatomical Entity Physical Anatomical Entity Material Anatomical Entity Portion of Body Substance -is a- Non-physical Anatomical Entity Immaterial Anatomical Entity Anatomical Structure Anatomical structure is_a material anatomical entity which has (by transitive inheritance) mass and dimension. Foundational Principles of Anatomy • • • • • Constraint principle Definition principle Constitutive principle Organizational unit principle Structural relationship principle Anatomical Entity Physical Anatomical Entity Non-physical Anatomical Entity -is a- Material Physical Anatomical Entity Portion of Body Substance Immaterial Physical Anatomical Entity Anatomical Structure Space Surface Human Biological Macromolecule Body Cardinal Acellular Anatomical Structure Cell Part Line BodyPart Cell Portion of Tissue Cardinal Organ Part Organ component Organ Organ region Organ System Foundational Principles of Anatomy Organizational Unit Principle: [Principle of Granular partitions] Organ Cell Biological macromolecule Other subclasses of Anatomical structure constitute cells or organs constituted by cells or organs Anatomical Entity Physical Anatomical Entity Non-physical Anatomical Entity -is a- Material Physical Anatomical Entity Body Substance Non-material Physical Anatomical Entity Anatomical Structure Space Surface Human Biological Macromolecule Body Cardinal Acellular Anatomical Structure Cell Part Line BodyPart Cell Portion of Tissue Cardinal Organ Part Organ component Organ Organ region Organ System FMA Taxonomy Foundational Principles of Anatomy • • • • • Constraint principle Definition principle Constitutive principle Organizational unit principle Structural relationship principle Part_of Network Anatomy Taxonomy Pulmonary alveolus Anatomical Structure Volume (3-D) Organ Part Volume (3-D) Pulmonary capillary bed -has volumeParenchyma of apical segment Organ component Upper lobe of Lobe right lung (3-D) has part Apical bronchopulmonary has part segment -is a- Apical segmental bronchial tree part of Parenchyma of anterior segment Anterior bronchopulmonary segment has part Anterior segmental bronchial tree Mucosa of bronchus Wall of anterior segmental bronchial tree has part Cartilage of bronchus has part Lumen of anterior segmental bronchial tree Structural Relationships Anatomical Structural Abstraction FMA = (At, ASA, ATA, Mk) ASA = (Dt, Bn, Pn, SAn) where: Dt Bn Pn SAn (1) (2) = Dimensional taxonomy = Boundary network = Part-of network = Spatial Association network Dimensional Taxonomy Anatomy Taxonomy Anatomical Structure Volume (3-D) -has shape Boundary Network Line (1-D) Surface (2-D) Cardinal Organ Part Anterior Interventricular Sulcus Anatomical Surface Organ Component Polyhedron -is a- Heart Cardiac Chamber Part-of Network -is a- Wall of RV bounded by Right Coronary Sulcus Part_of bounded by Infundibulum Inflow part of RV Sternocostal Surface has part Cavity of RV Cavity of Cavity of infund. infl.part Right Ventricle Inferior margin of heart boundary of Diaphragmatic Surface bounded by has adjacency has adjacency to left anterior Pericardial sac inferior Left ventricle Coronary Sulcus Posterior IV Sulcus Anatomical Landmark inferior Diaphragm Spatial Association Network -is aPoint (1-D) Apex Crux of heart Foundational Model of Anatomy Ontology FMA = (At, ASA, ATA, Mk) where At ASA ATA Mk = Anatomy taxonomy = Anatomical Structural Abstraction = Anatomical Transformation Abstraction = Metaknowledge (principles, rules, axioms) FMA in Protege FMA in Protege Anatomy Taxonomy (AT) Anatomical Structural abstraction (ASA) Anatomical Structure Cell Cell Part Biological Macromolecule Acellular Anatomical Structure Generic cell Specialized cell Skeletal muscle fiber Cell Taxonomy Cell Taxonomy • • • • • Presence of nucleus Somatic, germ Embryonic derivation Tissue type Free, fixed Cell 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 Cell Frame of Cell Cell-Specific Attributes Cell-Specific Attributes Anatomical Structure Cell Plasma membrane Cell Part Protoplasm Biological Macromolecule Organelle Acellular Anatomical Structure Cell appendage Test: What is a cytoskeleton? Cytoskeleton What is a cytoskeleton? Microtubule Intermediate filament Actin filament 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 edition, p. 36 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? • 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 Ontologies Characteristics • Deal with domains of basic sciences • Developed top down • Focus on overall semantic structure • Do not target specific applications user groups • Conform to sound ontological principles • Correlate with high level, formal ontologies FMA Ontology http://sig.biostr.washington.edu/projects/fm/ • Accommodate different viewpoints • Reconcile different terminologies • Generalize to other domains • Must be scalable