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)