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Cell Ontology Workshop 2010
(Bar Harbor, May 18-19, 2010)
The Foundational Model of Anatomy (FMA) Ontology:
Framework for Cell Classification
Onard Mejino
Structural Informatics Group
Department of Biological Structure
University of Washington
Anatomical Structures
Lung
Thorax
Cell
Heart
Macromolecule
Background
1838: Theory of Cell by Schleiden and Schwan
1. All living things are made up of cells.
2. Cells are the smallest units of living things
3. Cells only rise from existing cells by division.
Modern tenets added:
4. Cells contains hereditary information which is passed from
cell to cell during cell division
5. All cells are basically the same in chemical composition.
6. All energy flow (metabolism & biochemistry) of life occurs
within cells
Background
1838: Theory of Cell by Schleiden and Schwan
Cell classification
- informatics
organize and integrate data
- based on traditional contemporary hard copy sources
inadequate and inconsistent
- requires ontology
human readable
machine-processible
Problem
What is a cell?
Definition
Problem
What is a cell?
Definition
The cell is the functional basic unit of life.
Problem
What is a cell?
Definition
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.
Problem
What is a cell?
Definition
-based on structure
Generalia
Differentia
Problem
What is a cell?
Definition
Generalia
wall
compartment (Latin cella)
Differentia
Generic cell
Specialized cell
Muscle fiber
Neuron
Problem
How are cells classified?
From available sources, we can identify at least ten different ways to classify
cells:
•Cell shape (squamous, cuboidal, columnar)
•Tissue type (muscle, nervous tissue, epithelium)
•Nucleated, non-nucleated
•Somatic, germ
•Colligocyte (fixed), Solocyte (free)
•Differentiated, precursor
•Lobocyte/filocyte,
•Vibriocyte/non-vibriocyte
•Embryonic lineage (endoderm, mesoderm, ectoderm)
•Secretory, non-secretory
•Proliferating, non-proliferating
Cell Taxonomy
Cell Taxonomy
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Presence of nucleus
Somatic, germ
Tissue type
Embryonic derivation
Free, fixed
Cell Taxonomy
• Presence of nucleus
• Somatic, germ
• Tissue type
• Embryonic derivation
• Free, fixed
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Proliferative stage
Structural properties
Lobocyte or filocyte
Vibriocyte or nonvibrio-cyte
Secretory, non-secretory
Membrane markers/surface antigens
Cell-Specific Attributes
Cell-Specific Attributes
Cell-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)