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

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

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

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  1. NCBO Workshop on Ontologies of Cellular Networks (March 27-28, 2008) Session 2: Introduction to OntologyThe Foundational Model of Anatomy (FMA) Ontology: Framework for Cellular and Subcellular AnatomyOnard Mejino Structural Informatics GroupDepartment of Biological StructureUniversity of Washington

  2. Continuants and Occurrents Post-synaptic densities

  3. OPB* Physical law OPB* biophysical representational schema Knowledge resource Physical model OBO-SR structural_relation FMA Physical entity GO, etc. has_property Physical property has_player *Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.

  4. OPB* Physical law OPB* biophysical representational schema part_of, contains, continuous_with, attached_to… Knowledge resource Physical model OBO-SR structural_relation atom, molecule, cell, organ… FMA Physical entity GO, etc. has_property Physical property has_player *Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.

  5. OPB* Physical law OPB* biophysical representational schema Knowledge resource Physical model OBO-SR structural_relation e..g, chemical concentration, free energy, molecular shape, pressure, tension FMA Physical entity GO, etc. has_property Physical property law of mass action, Ohm’s law, Newton’s law has_player *Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.

  6. OPB* Physical law OPB* biophysical representational schema: process Knowledge resource Physical model OBO-SR structural_relation FMA Physical entity GO, etc. has_property A physical processoccurs when energy is transformed or exchanged within or between physical entities. Physical property has_player Process manifestationare the changes of entity property magnitudes or structural relations that are a consequence of a process *Ontology of Physics for Biology (OPB), Daniel L. Cook, et al.

  7. 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.

  8. Anatomical Structures Lung Thorax Heart Macro- molecule Cell

  9. 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.

  10. Foundational Principles of Anatomy • Constraint principle • Definition principle • Constitutive principle • Organizational unit principle • Structural relationship principle

  11. Anatomical Entity -is a- Physical Anatomical Entity Non-physical Anatomical Entity Material Anatomical Entity Immaterial Anatomical Entity Portion of Body Substance Anatomical Structure

  12. Anatomical Entity -is a- Physical Anatomical Entity Non-physical Anatomical Entity Has_dimension Has_mass Material Anatomical Entity Immaterial Anatomical Entity Has_inherent_shape Portion of Body Substance Anatomical Structure

  13. 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

  14. Anatomical Entity -is a- Physical Anatomical Entity Non-physical Anatomical Entity Material Anatomical Entity Immaterial Anatomical Entity Portion of Body Substance Anatomical Structure Anatomical structure is_a material anatomical entity which has (by transitive inheritance) mass and dimension.

  15. Foundational Principles of Anatomy • Constraint principle • Definition principle • Constitutive principle • Organizational unit principle • Structural relationship principle

  16. Anatomical Entity Physical Anatomical Entity -is a- Non-physical Anatomical Entity Material Physical Anatomical Entity Immaterial Physical Anatomical Entity Portion of Body Substance Space Surface Line Anatomical Structure Human Body Biological Macromolecule Cardinal BodyPart Acellular Anatomical Structure Cell Part Cell Portion of Tissue Cardinal Organ Part Organ Organ System Organ component Organ region

  17. 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

  18. Anatomical Entity Physical Anatomical Entity -is a- Non-physical Anatomical Entity Material Physical Anatomical Entity Non-material Physical Anatomical Entity Body Substance Space Surface Line Anatomical Structure Human Body Biological Macromolecule Cardinal BodyPart Acellular Anatomical Structure Cell Part Cell Portion of Tissue Cardinal Organ Part Organ Organ System Organ component Organ region

  19. FMA Taxonomy

  20. Foundational Principles of Anatomy • Constraint principle • Definition principle • Constitutive principle • Organizational unit principle • Structural relationship principle

  21. Part_of Network Anatomy Taxonomy Pulmonary alveolus Anatomical Structure Volume (3-D) Pulmonary capillary bed Volume (3-D) Organ Part -has volume- Parenchyma of apical segment Organ component Upper lobe of right lung (3-D) has part Apical bronchopulmonary segment Lobe -is a- has part Apical segmental bronchial tree part of Parenchyma of anterior segment Anterior bronchopulmonary segment has part Anterior segmental bronchial tree Wall of anterior segmental bronchial tree has part Mucosa of bronchus has part Lumen of anterior segmental bronchial tree Cartilage of bronchus

  22. Structural Relationships Anatomical Structural Abstraction FMA = (At, ASA, ATA, Mk) (1) ASA = (Dt, Bn, Pn, SAn) (2) where: Dt = Dimensional taxonomy Bn = Boundary network Pn = Part-of network SAn = Spatial Association network

  23. Dimensional Taxonomy Boundary Network Line (1-D) Surface (2-D) Volume (3-D) Anterior Interventricular Sulcus Anatomical Surface Polyhedron -is a- Right Coronary Sulcus Sternocostal Surface bounded by bounded by Inferior margin of heart boundary of Diaphragmatic Surface Coronary Sulcus has adjacency bounded by has adjacency Posterior IV Sulcus Anatomical Landmark to left anterior inferior inferior Left ventricle -is a- Pericardial sac Diaphragm Apex Crux of heart Point (1-D) Spatial Association Network Anatomy Taxonomy Anatomical Structure Cardinal Organ Part Organ Component -has shape Heart Cardiac Chamber Part-of Network -is a- Part_of Infundibulum Inflow part of RV has Right Ventricle part Wall of RV Cavity of RV Cavity of infund. Cavity of infl.part

  24. Foundational Model of Anatomy Ontology FMA = (At, ASA, ATA, Mk) where At = Anatomy taxonomy ASA = Anatomical Structural Abstraction ATA = Anatomical Transformation Abstraction Mk = Metaknowledge (principles, rules, axioms)

  25. FMA in Protege

  26. FMA in Protege Anatomical Structural abstraction (ASA) Anatomy Taxonomy (AT)

  27. Anatomical Structure Cell Cell Part Biological Macromolecule Acellular Anatomical Structure

  28. Generic cell Specialized cell Skeletal muscle fiber

  29. Cell Taxonomy

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

  31. 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

  32. Parts of the Cell

  33. Frame of Cell

  34. Cell-Specific Attributes

  35. Cell-Specific Attributes

  36. Anatomical Structure Cell Cell Part Biological Macromolecule Acellular Anatomical Structure Plasma membrane Protoplasm Organelle Cell appendage

  37. Test: What is a cytoskeleton? Cytoskeleton

  38. What is a cytoskeleton? Microtubule Intermediate filament Actin filament

  39. 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

  40. What is a cytoskeleton?

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

  42. 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?

  43. FMA Ontology in Protege

  44. FMA Ontology in Protege

  45. 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

  46. FMA Ontology http://sig.biostr.washington.edu/projects/fm/

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