untitled-ontology-286
type: Ontology
version info: 1.0.0
created by: J. Sluka
creation date: 2013-3-7
description: This is a CBO-OWL description of a tumor growth with angiogenesis multi-cell model using Compucell3D.
imports: CBO 1 0
imports: uo.owl

OBO REL derives from
date: 2013-2-27
description: Endothelial-derived short diffusing VEGF isoform.
creator: jps

Glucose
type: Class
subclass of: DiffuseEntity
subclass of: MolecularField
subclass of: Molecule
subclass of: Restriction
  on property: OBO REL derives from
  some values from: Glucose creation
subclass of: Restriction
  on property: OBO REL derives from
  some values from: Glucose deletion
date: 2013-2-27
description: Glucose (as a representitive limiting nutrient)
creator: jps

Glucose creation
type: Class
subclass of: MoleculeCreation
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Class
    union of: NeoVascular
    union of: Vascular
creator: jps
date: 2013-2-27
description: Process that describes the creation of the Glucose field.

Glucose deletion
type: Class
subclass of: MoleculeDeletion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Class
    union of: Medium
    union of: Proliferating
description: Process that describes the deletion (consumption, degradation, clearance) of the Gucose field.
date: 2013-2-27
creator: jps

Axiom
comment: GO:vascular endothelial growth factor production
annotated target: http://purl.obolibrary.org/obo/GO_0010573
annotated source: Glucose deletion
annotated property: isDefinedBy

M M Adh
type: Class
subclass of: CellInterstitialMatrixAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Medium
description: Process for the adhesion of 'Medium' cells to 'Medium' cells.
date: 2013-2-27
creator: jps

Medium
type: Class
equivalent class: Restriction
  on property: hasVTKtypeID
  has value: 0
subclass of: Cell
subclass of: ContinuousEntity
subclass of: Fill
date: 2/13/2013
description: A portion of extracellular matrix.
creator: jps

NV M Adh
type: Class
subclass of: CellInterstitialMatrixAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: NeoVascular
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Medium
creator: jps
date: 2013-2-27
description: Process for the adhesion of 'NeoVascular' cells to 'Medium' cells.

NV NV Adh
type: Class
subclass of: CellCellAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: NeoVascular
creator: jps
date: 2013-2-27
description: Process for the adhesion of 'NeoVascular' cells to 'NeoVascular' cells.

NV N Adh
type: Class
subclass of: CellCellAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: NeoVascular
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Necrotic
description: Process for the adhesion of 'NeoVascular' cells to 'Necrotic' cells.
date: 2013-2-27
creator: jps

NV P Adh
type: Class
subclass of: CellCellAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: NeoVascular
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Proliferating
creator: jps
description: Process for the adhesion of 'NeoVascular' cells to 'Proliferating' cells.
date: 2013-2-27

NV V Adh
type: Class
subclass of: CellCellAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: NeoVascular
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Vascular
description: Process for the adhesion of 'NeoVascular' cells to 'Vascular' cells.
date: 2013-2-27
creator: jps

N M Adh
type: Class
subclass of: CellInterstitialMatrixAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Medium
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Necrotic
description: Process for the adhesion of 'Necrotic' cells to 'Medium' cells.
date: 2013-2-27
creator: jps

N N Adh
type: Class
subclass of: CellCellAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Necrotic
date: 2013-2-27
creator: jps
description: Process for the adhesion of 'Necrotic' cells to 'Necrotic' cells.

N P Adh
type: Class
subclass of: CellCellAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Proliferating
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Necrotic
creator: jps
date: 2013-2-27
description: Process for the adhesion of 'Necrotic' cells to 'Proliferating' cells.

Necrotic
type: Class
equivalent class: Restriction
  on property: hasVTKtypeID
  has value: 2
subclass of: Cell
subclass of: CorpuscularEntity
subclass of: IsNecrotic
creator: jps
description: A necrotic tumor cell.
date: 2/13/2013

Necrotic Growth
type: Class
subclass of: CellGrowth
subclass of: Restriction
  on property: OBO REL has participant
  on class: Necrotic
  qualified cardinality: 1
date: 2013-3-4
creator: jps
description: Cell volumetric growth process for cells of type 'necrotic' in which the cell's volume decreases over time.

Axiom
comment: SNOMEDCT:Shrinkage
annotated target: http://purl.bioontology.org/ontology/SNOMEDCT/73238002
annotated source: Necrotic Growth
annotated property: isDefinedBy

NeoVascular
type: Class
equivalent class: Restriction
  on property: hasVTKtypeID
  has value: 4
subclass of: Cell
subclass of: CorpuscularEntity
subclass of: IsGrowing
description: A proliferating vascular portion. Note that this "cell" type represents a portion of a capilary including both the endothelium and the lumen.
creator: jps
date: 2/13/2013

NeoVascular Growth
type: Class
subclass of: CellGrowth
subclass of: Restriction
  on property: OBO REL has participant
  on class: Proliferating
  qualified cardinality: 1
date: 2013-3-4
description: Cell volumetric growth process for cells of type 'NewVascular'.
creator: jps

NeoVascular Mitosis
type: Class
subclass of: SymmetricCellDivisionRandomCleavagePlane
subclass of: Class
  intersection of: Restriction
    on property: OBO REL derived into
    some values from: NeoVascular
  intersection of: Restriction
    on property: OBO REL has participant
    some values from: NeoVascular
description: Mitosis process for the division of a NewVascular cell creating a pair of NewVascular cells.
creator: jps
date: 2013-3-04

P M Adh
type: Class
subclass of: CellInterstitialMatrixAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Proliferating
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Medium
description: Process for the adhesion of 'Proliferating' cells to 'Medium' cells.
date: 2013-2-27
creator: jps

P P Adh
type: Class
subclass of: CellCellAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Proliferating
date: 2013-2-27
description: Process for the adhesion of 'Proliferating' cells to 'Proliferating' cells.
creator: jps

Proliferating
type: Class
equivalent class: Restriction
  on property: hasVTKtypeID
  has value: 1
subclass of: Cell
subclass of: CorpuscularEntity
subclass of: IsGrowing
creator: jps
date: 2/13/2013
description: A proliferating tumor cell

Proliferating 2 Necrotic
type: Class
subclass of: PhenotypicChange
subclass of: Class
  intersection of: Restriction
    on property: OBO REL derived into
    some values from: Necrotic
  intersection of: Restriction
    on property: OBO REL has participant
    some values from: Proliferating
date: 2013-3-4
creator: jps
description: Conversion of a Proliferating cell into Necrotic cell when the cell's glucose level follows below a threshold.

Proliferating Growth
type: Class
subclass of: CellGrowth
subclass of: Restriction
  on property: OBO REL has participant
  on class: Proliferating
  qualified cardinality: 1
description: Cell volumetric growth process for cells of type 'Proliferating'.
date: 2013-3-4
creator: jps

Proliferating Mitosis
type: Class
subclass of: SymmetricCellDivisionRandomCleavagePlane
subclass of: Class
  intersection of: Restriction
    on property: OBO REL derived into
    some values from: Proliferating
  intersection of: Restriction
    on property: OBO REL has participant
    some values from: Proliferating
creator: jps
date: 2013-3-04
description: Mitosis process for the division of a Proliferating cell creating a pair of Proliferating cells.

VEGF1
type: Class
subclass of: DiffuseEntity
subclass of: MolecularField
subclass of: Molecule
subclass of: Restriction
  on property: OBO REL derives from
  some values from: VEGF1 deletion
subclass of: Restriction
  on property: OBO REL derives from
  some values from: VEGF1 creation
comment: Need suitable annotations to indicate this is the short diffusing (rapidly degraded in the interstitial space) isoform.
date: 2013-2-27
creator: jps
description: Endothelial-derived short diffusing VEGF isoform.

Axiom
comment: MeSH:Vascular Endothelial Growth Factor A (Medical Subject Headings)
annotated target: http://purl.bioontology.org/ontology/MSH/D042461
annotated source: VEGF1
annotated property: isDefinedBy

Axiom
comment: PR:vascular endothelial growth factor A (protein ontology)
annotated target: http://purl.obolibrary.org/obo/PR_000017284
annotated source: VEGF1
annotated property: isDefinedBy

VEGF1 chemotaxis
type: Class
subclass of: Chemotaxis
subclass of: Restriction
  on property: OBO REL has participant
  all values from: Class
    intersection of: VEGF1
    intersection of: Class
      union of: NeoVascular
      union of: Vascular
creator: jps
date: 2013-3-7
description: Chemotaxis process for cells that chemotax to the VEGF1 field.

VEGF1 creation
type: Class
subclass of: MoleculeCreation
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Class
    union of: NeoVascular
    union of: Vascular
date: 2013-2-27
creator: jps
description: Process that describes the creation of the VEGF1 field.

Axiom
comment: GO:vascular endothelial growth factor production
annotated target: http://purl.obolibrary.org/obo/GO_0010573
annotated source: VEGF1 creation
annotated property: isDefinedBy

VEGF1 deletion
type: Class
subclass of: MoleculeDeletion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Class
    intersection of: Class
      complement of: NeoVascular
    intersection of: Class
      complement of: Vascular
date: 2013-2-27
description: Process that describes the deletion (consumption, degradation, clearance) of the VEGF1 field.
creator: jps

Axiom
comment: GO:vascular endothelial growth factor production
annotated target: http://purl.obolibrary.org/obo/GO_0010573
annotated source: VEGF1 deletion
annotated property: isDefinedBy

VEGF2
type: Class
subclass of: DiffuseEntity
subclass of: MolecularField
subclass of: Molecule
subclass of: Restriction
  on property: OBO REL derives from
  some values from: VEGF2 deletion
subclass of: Restriction
  on property: OBO REL derives from
  some values from: VEGF2 creation
creator: jps
description: tumor-derived long diffusing VEGF isoform
date: 2013-2-27

Axiom
comment: PR:vascular endothelial growth factor A (protein ontology)
annotated target: http://purl.obolibrary.org/obo/PR_000017284
annotated source: VEGF2
annotated property: isDefinedBy

Axiom
annotated target: http://purl.bioontology.org/ontology/MSH/D042461
comment: MeSH:Vascular Endothelial Growth Factor A (Medical Subject Headings)
annotated source: VEGF2
annotated property: isDefinedBy

VEGF2 chemotaxis
type: Class
subclass of: Chemotaxis
subclass of: Restriction
  on property: OBO REL has participant
  some values from: NeoVascular
subclass of: Restriction
  on property: OBO REL has participant
  some values from: VEGF1
date: 2013-3-7
description: Chemotaxis process for cells that chemotax to the VEGF2 field.
creator: jps

VEGF2 creation
type: Class
subclass of: MoleculeCreation
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Proliferating
description: Process that describes the creation of the VEGF2 field.
date: 2013-2-27
creator: jps

Axiom
comment: GO:vascular endothelial growth factor production
annotated target: http://purl.obolibrary.org/obo/GO_0010573
annotated source: VEGF2 creation
annotated property: isDefinedBy

VEGF2 deletion
type: Class
subclass of: MoleculeDeletion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Class
    union of: NeoVascular
    union of: Vascular
date: 2013-2-27
creator: jps
description: Process that describes the deletion (consumption, degradation, clearance) of the VEGF2 field.

Axiom
comment: GO:vascular endothelial growth factor production
annotated target: http://purl.obolibrary.org/obo/GO_0010573
annotated source: VEGF2 deletion
annotated property: isDefinedBy

V M Adh
type: Class
subclass of: CellInterstitialMatrixAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Medium
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Vascular
creator: jps
description: Process for the adhesion of 'Vascular' cells to 'Medium' cells.
date: 2013-2-27

V N Adh
type: Class
subclass of: CellCellAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Necrotic
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Proliferating
date: 2013-2-27
creator: jps
description: Process for the adhesion of 'Vascular' cells to 'Necrotic' cells.

V P Adh
type: Class
subclass of: CellCellAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Vascular
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Proliferating
creator: jps
date: 2013-2-27
description: Process for the adhesion of 'Vascular' cells to 'Proliferating' cells.

V V Adh
type: Class
subclass of: CellCellAdhesion
subclass of: Restriction
  on property: OBO REL has participant
  some values from: Vascular
date: 2013-2-27
creator: jps
description: Process for the adhesion of 'Vascular' cells to 'Vascular' cells.

Vascular
type: Class
equivalent class: Restriction
  on property: hasVTKtypeID
  has value: 3
subclass of: Cell
subclass of: CorpuscularEntity
description: A vascular portion. Note that this "cell" type represents a portion of a capilary including both the endothelium and the lumen.
creator: jps
date: 2/13/2013

TumorWithAngiogenesis
type: NamedIndividual
type: System
comment: The top class for our angiogenesis ontology based on CBO.
has quality: TumorWithAngiogenesis VTKtimestep
has quality: TumorWithAngiogenesis Xbound
has quality: TumorWithAngiogenesis Ybound
has quality: TumorWithAngiogenesis Zbound
has quality: TumorWithAngiogenesis extents
has quality: TumorWithAngiogenesis pixel2dist
has quality: TumorWithAngiogenesis platform

TumorWithAngiogenesis VTKtimestep
type: NamedIndividual
type: VTK FileTimeStep
type: UO_0000031
has float value: 1.0

TumorWithAngiogenesis extents
type: NamedIndividual
type: DiscreteExtent
has extent value set3 d: 50,50,80
comment: These are the X, Y and Z extents of the box defining the model's universe.

TumorWithAngiogenesis pixel2dist
type: NamedIndividual
type: SystemPixelDistanceScale
type: UO_0000017
has float value: 4.0

Thing
created by: Jim Sluka
description: OWL:CBO description of a Compucell3D model of tumor growth with angiogenesis (blood vessel growth).
creation date: 7 Feb. 2013