The Foundational Model of Anatomy (FMA) Ontology: Framework for Cell Classification
Onard MejinoOnard MejinoStructural Informatics GroupStructural Informatics Group
Department of Biological StructureDepartment of Biological StructureUniversity of WashingtonUniversity of Washington
Cell Ontology Workshop 2010Cell Ontology Workshop 2010(Bar Harbor, May 18-19, 2010)(Bar Harbor, May 18-19, 2010)
Anatomical StructuresAnatomical Structures
Thorax
Lung
Heart
CellMacro-molecule
BackgroundBackground
1838: 1838: Theory of Cell Theory of Cell by Schleiden and Schwanby Schleiden and Schwan
1. All living things are made up of cells.1. All living things are made up of cells.2. Cells are the smallest units of living things2. Cells are the smallest units of living things3. Cells only rise from existing cells by division.3. Cells only rise from existing cells by division.
Modern tenets added:Modern tenets added:4. Cells contains 4. Cells contains hereditaryhereditary information which is passed from information which is passed from
cell to cell during cell divisioncell to cell during cell division5. All cells are basically the same in chemical composition. 5. All cells are basically the same in chemical composition. 6. All energy flow (metabolism & biochemistry) of life 6. All energy flow (metabolism & biochemistry) of life
occurs within cellsoccurs within cells
BackgroundBackground
1838: 1838: Theory of Cell Theory of Cell by Schleiden and Schwanby Schleiden and Schwan
Cell classificationCell classification- informatics- informatics
organize and integrate dataorganize and integrate data- based on traditional contemporary hard copy sources- based on traditional contemporary hard copy sources
inadequate and inconsistentinadequate and inconsistent- requires ontology - requires ontology
human readablehuman readablemachine-processiblemachine-processible
ProblemProblem
What is a cell? What is a cell?
DefinitionDefinition
ProblemProblem
What is a cell? What is a cell?
DefinitionDefinition
The cell is the functional basic unit of life.
ProblemProblem
What is a cell? What is a cell?
DefinitionDefinition
The cell is the functional basic unit of life.
the smallest living unit capable of independent function, consisting of cytoplasm containing various subcellular compartments (organelles and cytosol and separated from the external environment by the plasma membrane.
ProblemProblem
What is a cell? What is a cell?
Generalia
Differentia
DefinitionDefinition--based on structurebased on structure
ProblemProblem
What is a cell? What is a cell?
DefinitionDefinition
Generaliawallwallcompartment (compartment (LatinLatin cella) cella)
Differentia
Generic cell Specialized cell
Muscle fiber
Neuron
ProblemProblem
How are cells classified?How are cells classified?From available sources, we can identify at least ten different ways to classify From available sources, we can identify at least ten different ways to classify cells:cells:
•Cell shape (squamous, cuboidal, columnar)Cell shape (squamous, cuboidal, columnar)•Tissue type (muscle, nervous tissue, epithelium)Tissue type (muscle, nervous tissue, epithelium)•Nucleated, non-nucleatedNucleated, non-nucleated•Somatic, germSomatic, germ•Colligocyte (fixed), Solocyte (free)Colligocyte (fixed), Solocyte (free)•Differentiated, precursorDifferentiated, precursor•Lobocyte/filocyte,Lobocyte/filocyte,•Vibriocyte/non-vibriocyteVibriocyte/non-vibriocyte•Embryonic lineage (endoderm, mesoderm, ectoderm)Embryonic lineage (endoderm, mesoderm, ectoderm)•Secretory, non-secretorySecretory, non-secretory•Proliferating, non-proliferating
Cell TaxonomyCell Taxonomy
Cell TaxonomyCell Taxonomy
• Presence of nucleus• Somatic, germ• Tissue type• Embryonic derivation• Free, fixed
Cell TaxonomyCell Taxonomy• Presence of nucleus• Somatic, germ• Tissue type• Embryonic derivation• Free, fixed
• Proliferative stage• Structural properties
Lobocyte or filocyte Vibriocyte or nonvibrio-cyte
• Secretory, non-secretory• Membrane markers/surface antigens
Cell-Specific AttributesCell-Specific Attributes
Cell-Specific AttributesCell-Specific Attributes
Cell-Specific AttributesCell-Specific Attributes
Cell types
~ 750 human cell types (August Agoncillo)- 300 from UMLS and Cell Ontology
Pre-coordination
Post-coordination
myoepithelial cell (CL) of intralobular lactiferous duct (FMA)