Use Cases and top level: Afternoon Discussion (CBO 2009)

After the presentations finished, the discussion of what use cases to use started. What is the scope of the cell behaviour. Specifically,  it describes how cells behave seen as agents (deliberately neglecting subcellular and tissue/organ details). For example, cell adhesion, cell-cell adhesion and others.

I had a lot of fragmented notes during this discussion, but discovered that I was contributing so much that I didn’t have good notes. Luckily, Benjamin has been taking excellent notes which I think should shortly appear on the CBO wiki. I’ll link them from this post as soon as I have it.

There was a really interesting discussion within today’s session about whether or not cell shapes should be included in CBO. It wasn’t so much the cell shape example that was interesting to me (as it is my opinion that shapes are not behaviours – it is the changing from one shape to the next that is a behaviour), but it was the way that it exposed the differences in thinking in the members of the workshop had about what constituted a behaviour, and hence what the scope of the ontology should be.

This is my interpretation of the top level and a very rough binning of the other terms with respect to that top level

  • division
  • cell fragmentation
  • cell movement (linear rate, persistence)
    • movement of single cell
    • movement of clusters of cells
    • movement of sheets of cells
    • follow field (chemotaxis, haptotaxis)
    • polarize – movement within oneself?
    • cell traction
      • between other cells
      • ecm (rearrange ecm); basement membrane
  • shape change
    • cell contraction (apical, area change, in epithelia)
    • shape changes that result in a reduction in volume (defined class?)
    • shape changes that result in an increase in volume (defined class?)
    • shape changes that do not result in a volume change
    • assembly of ecm
    • cell protrusion (life timel orientation; duration; lamellipodia (directed; random); filopodia;retraction fibers)
    • length, width, anterior, posterior changes
    • cilia direction
    • flagella, microvilli
    • ruffle membrane
    • restructure cytoskeleton?
  • exert force / pull
  • delaminate
  • interact with other cells
    • the process of contacting with another cell
    • the process of contacting with something that isn’t a cell
    • cell-cell communication
  • secrete (export)
    • vesicle secretion
    • molecule secretion
  • excrete (export)
  • absorb (import)
    • digestion (e.g. osteoclast)
  • adsorb (import)
  • cell rearrangement – is this always with >1 cell?
    • change neighbours
    • directed rearrangement
    • random rearrangement
  • disappear
    • cell death
    • extinction
  • fusion
  • give off heat
  • change electrical field
  • interact with ecm
    • pull on ecm (also a child of force / pull)

    Alter subcellular distribution

  • alter extracellular distribution
  • alter mechanical properties
  • remodel EC environment

Personal Note: There needs to be a delination between the behavior of a single cell and the behaviors that are only relevant in the context of other cells. Many of the above should probably become defined classes to prevent multiple asserted hierarchy. This is just a representation of what was discussed this afternoon, and is not how it is meant to be in a final form. Particularly, some things that are presented as a top-level (e.g. the two types of interactions) are actually children of a not-yet-extant parent term.

Some terms that didn’t fit in these lists but which were suggested: live cell, cell activation, response to external stimuli, cell metabolism. They may not belong, or they may belong but haven’t been binned.

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