===== Welcome to the CBO3 Conference Repository. ===== The third workshop for the development of the **Cell Biology Ontology** (CBO) was held in Edinburgh Scotland on October 15 & 16 at the [[http://www.ed.ac.uk/schools-departments/informatics/|Informatics Institute of The University of Edinburgh]]. Materials presented during, and otherwise related to, CBO3 are shared here. ====Attendees==== ^ Name ^ Affiliation ^ Email ^ |Victor Andreev|University of Miami,\\ USA |vandreev_a_t_med.miami.edu| |Patryk Burek|University of Leipzig,\\ Germany |burek_a_t_informatik.uni-leipzig.de| |Joseph Dada|University of Manchester,\\ UK |dada_a_t_ieee.org| |James Glazier|Indiana University,\\ USA |glazier_a_t_indiana.edu| |Michael Hucka|California Institute of Technology,\\ USA |mhucka_a_t_caltech.edu| |Hila Kroll|Weizmann Institute of Science,\\ Israel |krollhd_a_t_netvision.net.il| |Nick Monk|University of Nottingham,\\ UK |nick.monk_a_t_nottingham.ac.uk| |Tomas Nahlik|Institute of Physical Biology,\\ Czech Republic |nahlik_a_t_greentech.cz| |David Nickerson|University of Auckland,\\ New Zealand |d.nickerson_a_t_auckland.ac.nz| |James Osborne|Oxford University,\\ UK |james.osborne_a_t_comlab.ox.ac.uk| |Markus Owen|University of Nottingham,\\ UK |markus.owen_a_t_nottingham.ac.uk| |Nadine Peyriéras|Institut Alfred Fessard,\\ France |nadine.peyrieras_a_t_inaf.cnrs-gif.fr| |Jim Sluka|Indiana University,\\ USA |jsluka_a_t_indiana.edu| |Rod Smallwood|University of Sheffield,\\ UK |r.smallwood_a_t_shef.ac.uk| |Dalibor Stys|Institute of Physical Biology,\\ Czech Republic |stys_a_t_jcu.cz| |Thomas Suetterlin|University of Heidelberg,\\ Germany |thomas.suetterlin_a_t_bioquant.uni-heidelberg.de| |Maciej Swat|Indiana University,\\ USA |maciekswat_a_t_gmail.com| ==== Presentations ==== {{ :cellgenonto.pdf | Towards an Ontology of Time Lapse Experiments (Cellular Genealogies). Patryk Burek, et al. }} {{ :davidnickerson.pdf | CellML modularity and the Physiome Model Repository. David Nickerson, et al. }} {{:jamesosborne2010.ppt| Multi-scale, multi-cell modeling using CHASTE. James Osborne }} {{:maciejswat_cellbasedmodeling_compucell3d_edinburgh_2010.pdf | Multi-Cell Modeling of Complex Biological Systems: Past, Now (CompuCell3D) and Future. Maciej Swat }} {{:mikehuckasbml.pdf | SBML fly-by. Mike Hucka}} {{:rodpredictingchange.pdf | Predicting Change. Rod Smallwood }} {{:jpspresentation.pptx | The Cell Behavior Ontology: Current Status, Roadmap & Challenges. James Sluka (pptx)}} =====Use Cases for Multi-Cell Modeling===== The Use Cases are located [[cbo_use_cases|here]]. =====Cell Biology Ontology (CBO): Level 0.1===== The goal of the Level 0.1 CBO is to provide: - Minimal set of high level objects, processes and behaviors specifically for describing multi-cell based models. - Computational Modality Specific tags to link modality specific parameters? 0 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". - Entities - Processes - Properties - Material Types - Observable Changes - Relations (may just use the [[http://www.obofoundry.org/ro/|OBO Relationship Ontology]]) ====Entities==== *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. ====Processes==== * 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 ====Properties==== *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 ====Material Types==== *Fluid *Solute *Solid *Gel ====Observable Changes==== * 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 ====Relations==== (may just use the [[http://www.obofoundry.org/ro/|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 ====CBO version 0.1 alpha==== 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