H H Adh
type: Class
subclass of: CellCellAdhesion
comment: Adhesion process between a pair of Hypoxic Tumor Cells.
creator: JPS

H T Adh
type: Class
subclass of: CellCellAdhesion
comment: Adhesion process between a "Hypoxic Tumor Cell" and a "Tumor Cell".
creator: jps

HypoxicTumorCell
type: Class
equivalent class: Restriction
  on property: hasVTKtypeID
  has value: 2
subclass of: Cell
subclass of: CorpuscularEntity
disjoint with: TumorCell
creator: JPS
comment: A hypoxic (insufficient oxygen) tumor cell.

Axiom
annotated target: MP:0005039
comment: MP (Mammalian Phenotype) Hypoxia MP:0005039 definition reduced concentration of O2 in the blood, alveoli or other tissues resulting in the decreased pressure of this component of body gases preferred name hypoxia exact synonym decreased partial O2 level xref_definition ISBN:0-683-40008-8
annotated source: HypoxicTumorCell
annotated property: isDefinedBy

M H Adh
type: Class
subclass of: CellCellAdhesion
comment: Adhesions between a portion of media and a Hypoxic cell.
creator: JPS

M M Adh
type: Class
subclass of: CellCellAdhesion
comment: Adhesion between portions of media.
creator: JPS

M T Adh
type: Class
subclass of: CellCellAdhesion
comment: Adhesion between a portion of media and a Tumor cell.
creator: JPS

Media
type: Class
subclass of: ExtraCellularFluid
subclass of: Fill
subclass of: Restriction
  on property: hasVTKtypeID
  has value: 0
comment: The fluid (and everything) else that is distinct from the cells.

T T Adh
type: Class
subclass of: CellCellAdhesion
comment: Adhesion process between a pair of "Tumor Cells".
creator: JPS

TumorCell
type: Class
equivalent class: Restriction
  on property: hasVTKtypeID
  has value: 1
subclass of: Cell
subclass of: CorpuscularEntity
creator: JPS
comment: These cells are named "normal" in the publication.

HypTumCell death
type: NamedIndividual
type: Necrosis
comment: Death of a HypoxicTumorCell.

TumorGrowthWithAgniogenesis VTK FileTimeStep
type: NamedIndividual
type: VTK FileTimeStep
has unit: minute
has float value: 1

TumorGrowthWithAngiogenesis
type: NamedIndividual
type: System
creator: JPS
comment: Tumor Growth with Angiogenesis. Note that only some of the objects and processes in the reference are described in this use case.
is defined by: Shirinifard A, et al. (2009) "3D Multi-Cell Simulation of Tumor Growth and Angiogenesis" PLoS ONE 4(10): e7190.
has quality: TumorGrowthWithAgniogenesis VTK FileTimeStep
has quality: TumorGrowthWithAngiogenesis VTK InitialFile
has quality: systemPix2DistSc
has quality: tumorGrowthWithAngiogenesis VTK FileRoot
has quality: use case 1 extent

TumorGrowthWithAngiogenesis VTK InitialFile
type: NamedIndividual
type: VTK InitialCondition
has string value: use_case_1_0000000000.vtk

Tumor 2 hypoxic switch
type: NamedIndividual
type: PhenotypicChange
comment: Conversion of a Tumor cell instance to an instance of a Hypoxic tumor cell, or vice versa.

systemPix2DistSc
type: NamedIndividual
type: SystemPixelDistanceScale
has float value: 4.44
has unit: UO:micrometer

tumorGrowthWithAngiogenesis VTK FileRoot
type: NamedIndividual
type: VTK FileRoot
has string value: use_case_1

use case 1 extent
type: NamedIndividual
type: DiscreteExtent
has extent value set3 d: 180,180,180
comment: These are the X, Y and Z extents of the box defining the model's universe.
has unit: UO:micrometer