The third workshop for the development of the Cell Biology Ontology (CBO) was held in Edinburgh Scotland on October 15 & 16 at the Informatics Institute of The University of Edinburgh.

Materials presented during, and otherwise related to, CBO3 are shared here.

Towards an Ontology of Time Lapse Experiments (Cellular Genealogies). Patryk Burek, et al.

CellML modularity and the Physiome Model Repository. David Nickerson, et al.

Multi-scale, multi-cell modeling using CHASTE. James Osborne

Multi-Cell Modeling of Complex Biological Systems: Past, Now (CompuCell3D) and Future. Maciej Swat

SBML fly-by. Mike Hucka

Predicting Change. Rod Smallwood

The Cell Behavior Ontology:Current Status, Roadmap & Challenges. James Sluka (pptx)

The Use Cases are located here.

The goal of the Level 0.1 CBO is to provide:

1. Minimal set of high level objects, processes and behaviors specifically for describing multi-cell based models.
2. Computational Modality Specific tags to link modality specific parameters?

<cell type=epithelial metaData="FMA:Preferred Name:Epithelial cell" metaData="FMA:Synonym:Epitheliocyte" metaData="FMA:FMAID:66768">
  <motility>0
    <solverSpecific=CompuCell3D API="motility" variable="temperature" value=10/>
  </motility>

Below is a rough outline of the basic entities in a first pass on the CBO. There are six major classifications, all of which are subclasses of the top level class “CBO”.

1. Entities
2. Processes
3. Properties
4. Material Types
5. Observable Changes
6. Relations (may just use the OBO Relationship Ontology)

• Derived Entities
• Discrete Entities (Discrete/continuous equivalent to cell/non-cell)
  • Cell
  • Subcellular Entities
    • Nucleus
      • Nuclear membrane (Required for a simple compartmental model of cell)
    • Membrane (Compound entities e.g. 'membrane' AND 'basal part' to give 'basal part of membrane')
      • Surface bound molecules
        • Receptors
        • Bonds
      • Transport system
        • Gap junctions
        • Pumps
        • Ion channels
      • Local structures
        • Filopodia
        • Brush border
    • Structure (Needed for physical properties)
      • Cytoskeleton components
• Continuous Entities (Discrete/continuous equivalent to cell/non-cell)
  • Extracellular matrix
  • Basement laminar
  • Field
• Temporal Entities
  • OPB (Link directly to OPB?)
• Geometrical Entities
  • Boundary
  • Cellular regions
    • Basal part
    • Apical part
    • Lateral Part
    • Medial Part

May want to remove the top level distinction of “Discrete Entities” and “Continuous Entities” and use them as descriptors instead of classes. That would allow cells, molecules etc. to be treated (specified) as either continuous or discrete.

• Cellular Processes
  • Existential Cellular Processes
    • Cell Division
      • Symmetric
      • Asymmetric
    • Cell Death
    • Cell Fusion
    • Differentiation
  • Cell - Environment Processes
    • Cell-related Transport
      • Transentity Transport
        • Import
        • Export
    • Intraentity Transport
      • Advection
    • Cell-Cell Contact
    • Cell-Noncell Contact
  • Cellular Structural Processes
  • Cellular Property Processes
    • Cellular Mechanical Processes
    • Cellular Kinetic Processes
    • Geometrical Cellular Processes
      • Cell Movement
        • Displacement
        • Motility
      • Cell Volume Change
      • Cell Shape Change
      • Cell Orientation Change
      • Cell Adhesion
        • Cell-Cell
        • Cell-ECM
    • Cellular Electrical Processes
    • Cellular Chemical Processes
  • Cell-Cell Processes
  • Geometrical Cellular Processes
    • Cell Displacement
    • Cell Volume Change
    • Cell Shape Change
    • Cell Orientation Change
• Transport
  • Interentity Transport (Can also apply to transport across fiat boundaries
    • Import
      • Molecular targeting
    • Export
  • Intraentity Transport
    • Advection
    • Molecular targeting
  • Diffusion

• Geometrical Properties
  • Volume
  • Shape
    • Body
      • Anisotropy
        • Directed
          • Polarity
        • Undirected
          • Elongation
      • Isotropy
    • Protrusions
  • Position
  • Orientation
  • Surface Area
  • Extent
    • Continuous
    • Discrete
  • Dimensionality
    • 1D
    • 2D
    • Fractal
    • 3D
  • Texture
    • Uniformity
    • Pattern
    • Gradient
• Kinetic Properties
  • Mass
• Mechanical Properties
  • Yielding threshold
  • Young's Modulus
  • Pressure
  • Adhesive properties
  • Tension
  • Stiffness
  • Poisson ratio
• Chemical Properties
  • Localization
  • Affinity
  • Pattern
    • Gradient
  • Density
• Electrical Properties
  • Charge
  • Voltage
  • Current
  • Capacity (capacitance)
  • Resistance/Conductivity
• Gravity
• “Movement field”
• Statistical Properties
  • Random

• Fluid
• Solute
• Solid
  • Gel

• Kinetic properties (should this go to processes?)
  • Persistence length (This word has multiple meanings, spatial and temporal)
  • Inertia (biological)
  • Potential to move
    • Diffusion coefficient
    • Undirected cell Motility (as a property cf. parameter T in CPM)
• Existential Changes

(may just use the OBO Relationship Ontology)

• Structural Relations
  • Interior
  • Exterior
  • Contains (Contains differs from has part because it implies a location within the boundary of the container.)
  • Has region
  • Has part
• Numerical
  • Larger
  • Smaller
• Is a
• Participates in
• Using
• Has property
  • Has physical property
• Has participant
• Has observable changes
• Temporal Relations
  • Has interval
  • Has instant
• Geometrical Relations
  • Interior
  • Exterior

January 31, 2012 The above set of objects has been instantiated underneath a Basic Formal Ontology (BFO) top layer in Protege 4.

• RO is used as the relation list.
• There are very few annotations.
• There are very few non isA links.
• BFO terms have the annotation “creator:BFO”
• CBO terms have the annotation “creator:CBO”

… need an svn or some other repository with versioning