TEMP
type: Ontology
date: 14:01:2019 13:00
default-namespace: WC
has_obo_format_version: 1.4
saved-by: Jonathan Karr <karr@mssm.edu>
comment: distributed under the MIT License (https://github.com/KarrLab/wc_lang/blob/master/LICENSE)

definition
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

Clusters of orthologous groups
type: Class
subclass of: gene
definition: Clusters of Orthologous Groups
has_obo_namespace: WC
id: WC:COG

CTCF Binding Site
type: Class
subclass of: regulatory element Type
definition: CTCF Binding Site
has_obo_namespace: WC
id: WC:CTCFBindingSite

DNA
type: Class
subclass of: species_type
definition: DNA
database_cross_reference: SBO:0000251
has_obo_namespace: WC
id: WC:DNA

DNAABox
type: Class
subclass of: chromosomeFeature
definition: DNAABox
has_obo_namespace: WC
id: WC:DNAABox

DNA binding Type
type: Class
subclass of: model element
definition: DNA binding Type
has_obo_namespace: WC
id: WC:DNABinding

DNA Binding Site
type: Class
subclass of: chromosomeFeature
definition: DNA Binding Site
has_obo_namespace: WC
id: WC:DNABindingSite

DNA BindingSite Lon
type: Class
subclass of: chromosomeFeature
definition: DNA BindingSite Lon
has_obo_namespace: WC
id: WC:DNABindingSiteLon

DNA Cleavage
type: Class
subclass of: DNA repair reaction
definition: DNA Cleavage
has_obo_namespace: WC
id: WC:DNACleavage

DNA damage reaction
type: Class
subclass of: reaction
definition: DNA damage reaction
has_obo_namespace: WC
id: WC:DNADamage

DNA Ligation
type: Class
subclass of: DNA repair reaction
definition: DNA Ligation
has_obo_namespace: WC
id: WC:DNALigation

DNA Methylation
type: Class
subclass of: chromosomeFeature
definition: DNA Methylation
has_obo_namespace: WC
id: WC:DNAMethylation

DNA Methylation site
type: Class
subclass of: chromosomeFeature
definition: DNA Methylation site
has_obo_namespace: WC
id: WC:DNAMethylationSite

DNA Polymerization
type: Class
subclass of: DNA repair reaction
definition: DNA Polymerization
has_obo_namespace: WC
id: WC:DNAPolymerization

DNA repair reaction
type: Class
subclass of: reaction
definition: DNA repair reaction
has_obo_namespace: WC
id: WC:DNARepairreaction

DNA Restriction Modification
type: Class
subclass of: DNA repair reaction
definition: DNA Restriction Modification
has_obo_namespace: WC
id: WC:DNARestrictionModification

Ion
type: Class
subclass of: metabolite
definition: Ion
has_obo_namespace: WC
id: WC:Ion

RNA
type: Class
subclass of: species_type
definition: RNA
database_cross_reference: SBO:0000250
has_obo_namespace: WC
id: WC:RNA

RNA processing
type: Class
subclass of: Clusters of orthologous groups
definition: RNA processing
has_obo_namespace: WC
id: WC:RNAprocessing

TF Binding Site
type: Class
subclass of: regulatory element Type
definition: TF Binding Site
has_obo_namespace: WC
id: WC:TFBindingSite

tRNA aminoacylation reaction
type: Class
subclass of: reaction
definition: TRNAAminoacylation reaction
has_obo_namespace: WC
id: WC:TRNAAminoacylationReaction

TRNASynthClassI
type: Class
subclass of: protein
definition: TRNASynthClassI
has_obo_namespace: WC
id: WC:TRNASynthClassI

TRNASynthClassIB
type: Class
subclass of: protein
definition: TRNASynthClassIB
has_obo_namespace: WC
id: WC:TRNASynthClassIB

TRNASynthClassII
type: Class
subclass of: protein
definition: TRNASynthClassII
has_obo_namespace: WC
id: WC:TRNASynthClassII

TRNASynthClassII
type: Class
subclass of: complexes
definition: TRNASynthClassII
has_obo_namespace: WC
id: WC:TRNASynthClassIIComplex

tRRNA transfer reaction
type: Class
subclass of: reaction
definition: TRNA Transfer reaction
has_obo_namespace: WC
id: WC:TRNATransferReaction

Active
type: Class
subclass of: activity level
definition: Active
has_obo_namespace: WC
id: WC:active

activity level
type: Class
subclass of: model element
definition: activity level
has_obo_namespace: WC
id: WC:activityLevel

protein Modification Adduction
type: Class
subclass of: protein modification reaction
definition: Protein Modification Adduction
has_obo_namespace: WC
id: WC:adduction

Amino Acid
type: Class
subclass of: metabolite
definition: Amino Acid
has_obo_namespace: WC
id: WC:aminoAcid

Amino Acid Metabolism and Transport
type: Class
subclass of: Clusters of orthologous groups
definition: Amino Acid Metabolism and Transport
has_obo_namespace: WC
id: WC:aminoAcidMetabolismTransport

approximation
type: Class
subclass of: conclusion
definition: Approximation
has_obo_namespace: WC
id: WC:approximation

article
type: Class
subclass of: reference
definition: Article
database_cross_reference: BRO:JouRNAl_Article
database_cross_reference: IAO:0000013
has_obo_namespace: WC
id: WC:article

anti-sense RNA
type: Class
subclass of: RNA
definition: anti-sense RNA
has_obo_namespace: WC
id: WC:asRNA

assumption
type: Class
subclass of: conclusion
definition: Assumption
has_obo_namespace: WC
id: WC:assumption

author
type: Class
subclass of: provenance
definition: Author
database_cross_reference: foaf:Person
has_obo_namespace: WC
id: WC:author

DNA Damage Base Alkylation
type: Class
subclass of: DNA damage reaction
definition: DNA Damage Base Alkylation
has_obo_namespace: WC
id: WC:baseAlkylation

DNA Damage Base Amination
type: Class
subclass of: DNA damage reaction
definition: DNA Damage Base Amination
has_obo_namespace: WC
id: WC:baseAmination

DNA Damage Base Ethylation
type: Class
subclass of: DNA damage reaction
definition: DNA Damage Base Ethylation
has_obo_namespace: WC
id: WC:baseEthylation

Base Excision Repair
type: Class
subclass of: DNA repair reaction
definition: Base Excision Repair
has_obo_namespace: WC
id: WC:baseExcisionRepair

DNA Damage Base Glucosyl Transfer
type: Class
subclass of: DNA damage reaction
definition: DNA Damage Base Glucosyl Transfer
has_obo_namespace: WC
id: WC:baseGlucosylTransfer

DNA Damage Base Methylation
type: Class
subclass of: DNA damage reaction
definition: DNA Damage Base Methylation
has_obo_namespace: WC
id: WC:baseMethylation

DNA Damage Base Reduction
type: Class
subclass of: DNA damage reaction
definition: DNA Damage Base Reduction
has_obo_namespace: WC
id: WC:baseReduction

book
type: Class
subclass of: reference
definition: Book
database_cross_reference: BRO:Book
has_obo_namespace: WC
id: WC:book

boolean
type: Class
subclass of: value type
definition: boolean
has_obo_namespace: WC
id: WC:boolean

Carbohydrate Metabolism and Transport
type: Class
subclass of: Clusters of orthologous groups
definition: Carbohydrate Metabolism and Transport
has_obo_namespace: WC
id: WC:carbohydrateMetabolismTransport

Carbohydrate Sugar
type: Class
subclass of: metabolite
definition: Carbohydrate Sugar
has_obo_namespace: WC
id: WC:carbohydrateSugar

Carbohydrate Sugar Phosphate
type: Class
subclass of: metabolite
definition: Carbohydrate Sugar Phosphate
has_obo_namespace: WC
id: WC:carbohydrateSugarPhosphate

Carboxy Acid
type: Class
subclass of: metabolite
definition: Carboxy Acid
has_obo_namespace: WC
id: WC:carboxyAcid

Cell Cycle Control and Mitosis
type: Class
subclass of: Clusters of orthologous groups
definition: Cell Cycle Control and Mitosis
has_obo_namespace: WC
id: WC:cellCycleControlMitosis

Cell Motility
type: Class
subclass of: Clusters of orthologous groups
definition: Cell Motility
has_obo_namespace: WC
id: WC:cellMotility

Cell Wall Membrane Envelope Biogenesis
type: Class
subclass of: Clusters of orthologous groups
definition: Cell Wall Membrane Envelope Biogenesis
has_obo_namespace: WC
id: WC:cellWallMembraneEnvelopBiogenesis

change
type: Class
subclass of: provenance
definition: Change
definition: change
database_cross_reference: COMODI:Change
has_obo_namespace: WC
id: WC:change

Chemical reaction
type: Class
subclass of: reaction
definition: Chemical reaction
has_obo_namespace: WC
id: WC:chemicalReaction

Chromatin Structure Dynamics
type: Class
subclass of: Clusters of orthologous groups
definition: Chromatin Structure Dynamics
has_obo_namespace: WC
id: WC:chromatinStructureDynamics

Chromosome Condensation
type: Class
subclass of: complexFormation
definition: Chromosome Condensation
has_obo_namespace: WC
id: WC:chromosomeCondensation

chromosomeFeature
type: Class
subclass of: model element
definition: chromosomeFeature Type
has_obo_namespace: WC
id: WC:chromosomeFeature

Coenzyme Metabolites
type: Class
subclass of: Clusters of orthologous groups
definition: Coenzyme Metabolites
has_obo_namespace: WC
id: WC:coenzymeMetabolites

compartment
type: Class
subclass of: model element
definition: compartment
database_cross_reference: SBO:0000289
has_obo_namespace: WC
id: WC:compartment

complexes
type: Class
subclass of: species_type
definition: complexes
has_obo_namespace: WC
id: WC:complex

complexFormation
type: Class
subclass of: model element
definition: Complex Formation Type
has_obo_namespace: WC
id: WC:complexFormation

computation
type: Class
subclass of: conclusion
definition: Computation
has_obo_namespace: WC
id: WC:computation

conclusion
type: Class
subclass of: provenance
definition: Conclusion
database_cross_reference: SEPIO:0000000
database_cross_reference: SEPIO:0000001
has_obo_namespace: WC
id: WC:conclusion

copy
type: Class
subclass of: change
definition: Copy
has_obo_namespace: WC
id: WC:copy

Cytoskeleton
type: Class
subclass of: Clusters of orthologous groups
definition: Cytoskeleton
has_obo_namespace: WC
id: WC:cytoskeleton

dFBA terms
type: Class
subclass of: model element
definition: dFBA objective
has_obo_namespace: WC
id: WC:dFBA

decision
type: Class
subclass of: conclusion
definition: Decision
has_obo_namespace: WC
id: WC:decision

dephosphorylation Activating Protein Modification
type: Class
subclass of: protein modification reaction
definition: Dephosphorylation Activating Protein Modification
has_obo_namespace: WC
id: WC:dephosphorylationActivating

Dipeptide
type: Class
subclass of: metabolite
definition: Dipeptide
has_obo_namespace: WC
id: WC:dipeptide

Distal
type: Class
subclass of: regulationType
definition: Distal
has_obo_namespace: WC
id: WC:distal

double Strand DNA Binding Type
type: Class
subclass of: DNA binding Type
definition: double Strand DNA Binding Type
has_obo_namespace: WC
id: WC:dsDNA

Energy Production and Conversion
type: Class
subclass of: Clusters of orthologous groups
definition: Energy Production and Conversion
has_obo_namespace: WC
id: WC:energyProductionConversion

Enhancer
type: Class
subclass of: regulatory element Type
definition: Enhancer
has_obo_namespace: WC
id: WC:enhancer

environment
type: Class
subclass of: model element
definition: environment
has_obo_namespace: WC
id: WC:environment

evidence
type: Class
subclass of: provenance
definition: Evidence
database_cross_reference: SEPIO:0000002
has_obo_namespace: WC
id: WC:evidence

FattyAcylAcp
type: Class
subclass of: complexes
definition: FattyAcylAcp
has_obo_namespace: WC
id: WC:fattyAcylAcpComplex

float
type: Class
subclass of: value type
definition: float
has_obo_namespace: WC
id: WC:float

FtsZ Polymerization
type: Class
subclass of: complexFormation
definition: FtsZ Polymerization
has_obo_namespace: WC
id: WC:ftsZPolymerization

function
type: Class
subclass of: model element
definition: Function
database_cross_reference: SBO:0000064
has_obo_namespace: WC
id: WC:function

FunctionalDNAABox
type: Class
subclass of: chromosomeFeature
definition: FunctionalDNAABox
has_obo_namespace: WC
id: WC:functionalDNAABox

gene
type: Class
subclass of: loci
definition: gene
has_obo_namespace: WC
id: WC:gene

geneWiz Prediction
type: Class
subclass of: chromosomeFeature
definition: geneWiz Prediction
has_obo_namespace: WC
id: WC:geneWizPrediction

glycation Inactivating Protein Modification
type: Class
subclass of: protein modification reaction
definition: Glycation Inactivating Protein Modification
has_obo_namespace: WC
id: WC:glycationInactivating

Homologous Recombinationon
type: Class
subclass of: DNA repair reaction
definition: Homologous Recombination
has_obo_namespace: WC
id: WC:homologousRecombination

phosphorylation Inactivating Protein Modification
type: Class
subclass of: protein modification reaction
definition: Phosphorylation Inactivating Protein Modification
has_obo_namespace: WC
id: WC:inactivating

Inactive
type: Class
subclass of: activity level
definition: Inactive
has_obo_namespace: WC
id: WC:inactive

Inorganic Ion Transport
type: Class
subclass of: Clusters of orthologous groups
definition: Inorganic Ion Transport
has_obo_namespace: WC
id: WC:inorganicIonTransport

insertion
type: Class
subclass of: change
definition: Insertion
database_cross_reference: COMODI:Insertion
has_obo_namespace: WC
id: WC:insertion

integer
type: Class
subclass of: value type
definition: integer
has_obo_namespace: WC
id: WC:integer

intergenic RNA
type: Class
subclass of: RNA
definition: intergenic RNA
has_obo_namespace: WC
id: WC:intergenic

Intracellular Trafficing Secretion
type: Class
subclass of: Clusters of orthologous groups
definition: Intracellular Trafficing Secretion
has_obo_namespace: WC
id: WC:intracellularTrafficingSecretion

Ion transport reaction
type: Class
subclass of: reaction
definition: Ion transport reaction
has_obo_namespace: WC
id: WC:ionTransportReaction

protein Modification Ligation
type: Class
subclass of: protein modification reaction
definition: Protein Modification Ligation
has_obo_namespace: WC
id: WC:ligation

Lipid Metabolism
type: Class
subclass of: Clusters of orthologous groups
definition: Lipid Metabolism
has_obo_namespace: WC
id: WC:lipidMetabolism

lipo Protein Signal Sequence
type: Class
subclass of: signal Sequence Type
definition: lipo Protein Signal Sequence Type
has_obo_namespace: WC
id: WC:lipoProtein

loci
type: Class
subclass of: model element
definition: loci
has_obo_namespace: WC
id: WC:loci

Long Structural Region
type: Class
subclass of: chromosomeFeature
definition: Long Structural Region
has_obo_namespace: WC
id: WC:longStructuralRegion

messenger RNA
type: Class
subclass of: RNA
definition: messenger RNA
has_obo_namespace: WC
id: WC:mRNA

Macromolecular Complexation
type: Class
subclass of: complexFormation
definition: Macromolecular Complexation
has_obo_namespace: WC
id: WC:macromolecularComplexation

merge
type: Class
subclass of: change
definition: Merge
has_obo_namespace: WC
id: WC:merge

Metabolism
type: Class
subclass of: complexFormation
definition: Metabolism
has_obo_namespace: WC
id: WC:metabolism

metabolite
type: Class
subclass of: species_type
definition: Metabolite
database_cross_reference: SBO:0000299
has_obo_namespace: WC
id: WC:metabolite

mixed RNA
type: Class
subclass of: RNA
definition: mixed RNA
has_obo_namespace: WC
id: WC:mixed

model
type: Class
subclass of: model element
definition: model
has_obo_namespace: WC
id: WC:model

Modified base transport reaction
type: Class
subclass of: reaction
definition: Modified base transport reaction
has_obo_namespace: WC
id: WC:modifiedBaseTransportReaction

Modified Nucleobase
type: Class
subclass of: metabolite
definition: Modified Nucleobase
has_obo_namespace: WC
id: WC:modifiedNucleobase

move
type: Class
subclass of: change
definition: Move
database_cross_reference: COMODI:Move
has_obo_namespace: WC
id: WC:move

non-coding RNA
type: Class
subclass of: RNA
definition: non-coding RNA
has_obo_namespace: WC
id: WC:ncRNA

Nuclear Structure
type: Class
subclass of: Clusters of orthologous groups
definition: Nuclear Structure
has_obo_namespace: WC
id: WC:nuclearStructure

Nucleobase
type: Class
subclass of: metabolite
definition: Nucleobase
has_obo_namespace: WC
id: WC:nucleobase

Nucleotide Excision Repair
type: Class
subclass of: DNA repair reaction
definition: Nucleotide Excision Repair
has_obo_namespace: WC
id: WC:nucleotideExcisionRepair

Nucleotide Metabolism and Transport
type: Class
subclass of: Clusters of orthologous groups
definition: Nucleotide Metabolism and Transport
has_obo_namespace: WC
id: WC:nucleotideMetabolismTransport

observable
type: Class
subclass of: model element
definition: observable
has_obo_namespace: WC
id: WC:observable

observation
type: Class
subclass of: provenance
definition: observation
database_cross_reference: IAO:0000111
database_cross_reference: SEPIO:0000149
has_obo_namespace: WC
id: WC:observation

Open Chromatin Region
type: Class
subclass of: regulatory element Type
definition: Open Chromatin Region
has_obo_namespace: WC
id: WC:openChromatinRegion

oxidation Inactivating Protein Modification
type: Class
subclass of: protein modification reaction
definition: oxidation Inactivating Protein Modification
has_obo_namespace: WC
id: WC:oxidationInactivating

parameters
type: Class
subclass of: model element
definition: parameters
database_cross_reference: SBO:0000002
has_obo_namespace: WC
id: WC:parameter

DNA Damage Photooxidation
type: Class
subclass of: DNA damage reaction
definition: DNA Damage Photooxidation
has_obo_namespace: WC
id: WC:photoOxidation

Poised
type: Class
subclass of: activity level
definition: Poised
has_obo_namespace: WC
id: WC:poised

Post Translational Modification
type: Class
subclass of: Clusters of orthologous groups
definition: Post Translational Modification
has_obo_namespace: WC
id: WC:postTranslationalModification

preprint
type: Class
subclass of: reference
definition: preprint
has_obo_namespace: WC
id: WC:preprint

proceedings
type: Class
subclass of: reference
definition: Proceedings
database_cross_reference: BRO:Conference_Proceeding
has_obo_namespace: WC
id: WC:proceedings

process
type: Class
subclass of: model element
definition: process
database_cross_reference: BFO:0000015
has_obo_namespace: WC
id: WC:process

Promoter
type: Class
subclass of: loci
subclass of: regulatory element Type
definition: Promoter
has_obo_namespace: WC
id: WC:promoter

Promoter Flanking Region
type: Class
subclass of: regulatory element Type
definition: Promoter Flanking Region
has_obo_namespace: WC
id: WC:promoterFlankingRegion

protein
type: Class
subclass of: species_type
definition: protein
has_obo_namespace: WC
id: WC:protein

Protein Modification
type: Class
subclass of: complexFormation
definition: proteinModification
has_obo_namespace: WC
id: WC:proteinModification

protein modification reaction
type: Class
subclass of: reaction
definition: protein modification reaction
has_obo_namespace: WC
id: WC:proteinModificationReaction

provenance
type: Class
subclass of: Whole-cell modeling entities
definition: provenance terms
database_cross_reference: SEPIO:0000058
has_obo_namespace: WC
id: WC:provenance

Proximal
type: Class
subclass of: regulationType
definition: Proximal
has_obo_namespace: WC
id: WC:proximal

pseudogene
type: Class
subclass of: gene
definition: pseudogene
has_obo_namespace: WC
id: WC:pseudogene

ribosomal RNA
type: Class
subclass of: RNA
definition: ribosomal RNA
has_obo_namespace: WC
id: WC:rRNA

DNA Damage Radiation Induced Base Oxidation
type: Class
subclass of: DNA damage reaction
definition: DNA Damage Radiation Induced Base Oxidation
has_obo_namespace: WC
id: WC:radiationInducedBaseOxidation

reaction
type: Class
subclass of: model element
definition: reaction
has_obo_namespace: WC
id: WC:reaction

reactive oxygen species
type: Class
subclass of: metabolite
definition: Reactive Oxygen Species
has_obo_namespace: WC
id: WC:reactiveOxygenSpecies

reference
type: Class
subclass of: provenance
definition: reference
database_cross_reference: BRO:Information_Resource
has_obo_namespace: WC
id: WC:reference

regulationType
type: Class
subclass of: model element
definition: regulationType
has_obo_namespace: WC
id: WC:regulationType

regulatory element Type
type: Class
subclass of: model element
definition: regulatory element Type
has_obo_namespace: WC
id: WC:regulatoryElement

Replication
type: Class
subclass of: complexFormation
definition: Replication
has_obo_namespace: WC
id: WC:replication

Replication Initiation
type: Class
subclass of: complexFormation
definition: Replication Initiation
has_obo_namespace: WC
id: WC:replicationInitiation

Replication Repair
type: Class
subclass of: Clusters of orthologous groups
definition: Replication Repair
has_obo_namespace: WC
id: WC:replicationRepair

Repressed
type: Class
subclass of: activity level
definition: Repressed
has_obo_namespace: WC
id: WC:repressed

revert
type: Class
subclass of: change
definition: Revert
has_obo_namespace: WC
id: WC:revert

Ribonucleotide Biphosphate
type: Class
subclass of: metabolite
definition: Ribonucleotide Biphosphate
has_obo_namespace: WC
id: WC:ribonucleotideBiphosphate

Ribonucleotide Monophosphate
type: Class
subclass of: metabolite
definition: Ribonucleotide Monophosphate
has_obo_namespace: WC
id: WC:ribonucleotideMonophosphate

Ribonucleotide Triphosphate
type: Class
subclass of: metabolite
definition: Ribonucleotide Triphosphate
has_obo_namespace: WC
id: WC:ribonucleotideTriphosphate

Ribosome Assembly
type: Class
subclass of: complexFormation
definition: Ribosome Assembly
has_obo_namespace: WC
id: WC:ribosomeAssembly

small RNA
type: Class
subclass of: RNA
definition: small RNA
has_obo_namespace: WC
id: WC:sRNA

Secondary Structure
type: Class
subclass of: Clusters of orthologous groups
definition: Secondary Structure
has_obo_namespace: WC
id: WC:secondaryStructure

secretory Signal Sequence Type
type: Class
subclass of: signal Sequence Type
definition: secretory Signal Sequence Type
has_obo_namespace: WC
id: WC:secretory

signal Sequence Type
type: Class
subclass of: model element
definition: signal Sequence Type
has_obo_namespace: WC
id: WC:signalSequence

signal sequence type
type: Class
subclass of: value type
definition: signal sequence type
has_obo_namespace: WC
id: WC:signalSequenceType

Signal Transduction
type: Class
subclass of: Clusters of orthologous groups
definition: Signal Transduction
has_obo_namespace: WC
id: WC:signalTransduction

species
type: Class
subclass of: model element
definition: species
has_obo_namespace: WC
id: WC:species

DNA Damage Spontaneous Base Deamination
type: Class
subclass of: DNA damage reaction
definition: DNA Damage Spontaneous Base Deamination
has_obo_namespace: WC
id: WC:spontaneousBaseDeamination

DNA Damage Spontaneous Base Loss
type: Class
subclass of: DNA damage reaction
definition: DNA Damage Spontaneous Base Loss
has_obo_namespace: WC
id: WC:spontaneousBaseLoss

single Strand DNA Binding Type
type: Class
subclass of: DNA binding Type
definition: single Strand DNA Binding Type
has_obo_namespace: WC
id: WC:ssDNA

DNA Damage Strand Break
type: Class
subclass of: DNA damage reaction
definition: DNA Damage Strand Break
has_obo_namespace: WC
id: WC:strandBreak

string
type: Class
subclass of: value type
definition: string
has_obo_namespace: WC
id: WC:string

submodel
type: Class
subclass of: model element
definition: submodel
has_obo_namespace: WC
id: WC:submodel

transport RNA
type: Class
subclass of: RNA
definition: transport RNA
has_obo_namespace: WC
id: WC:tRNA

taxon
type: Class
subclass of: model element
definition: taxon
has_obo_namespace: WC
id: WC:taxon

thesis
type: Class
subclass of: reference
definition: Thesis
database_cross_reference: BRO:Thesis
has_obo_namespace: WC
id: WC:thesis

Tranlsation
type: Class
subclass of: Clusters of orthologous groups
definition: Tranlsation
has_obo_namespace: WC
id: WC:tranlsation

transcription
type: Class
subclass of: Clusters of orthologous groups
definition: transcription
has_obo_namespace: WC
id: WC:transcription

transcription
type: Class
subclass of: complexFormation
definition: transcription
has_obo_namespace: WC
id: WC:transcriptionComplexFormation

transcription unit
type: Class
subclass of: loci
definition: transcription unit
has_obo_namespace: WC
id: WC:transcriptionUnit

Translation
type: Class
subclass of: complexFormation
definition: Translation
has_obo_namespace: WC
id: WC:translationComplexFormation

Transport reaction
type: Class
subclass of: reaction
definition: Transport reaction
has_obo_namespace: WC
id: WC:transportReaction

update
type: Class
subclass of: change
definition: Update
database_cross_reference: COMODI:Update
has_obo_namespace: WC
id: WC:update

DNA Damage UvB Photodimerization
type: Class
subclass of: DNA damage reaction
definition: DNA Damage UvB Photodimerization
has_obo_namespace: WC
id: WC:uvbPhotodimerization

value type
type: Class
subclass of: model element
definition: python class of ValueType
has_obo_namespace: WC
id: WC:valueType

Vitamin
type: Class
subclass of: metabolite
definition: Vitamin
has_obo_namespace: WC
id: WC:vitamin

website
type: Class
subclass of: reference
definition: website
database_cross_reference: BRO:Website
has_obo_namespace: WC
id: WC:website

Whole-cell modeling entities
type: Class
definition: Representation of an entity used in whole-cell modeling
has_obo_namespace: WC
id: WC

3D compartment
type: Class
subclass of: geometric compartment
definition: 3D compartment
has_obo_namespace: WC
id: WC:3D_compartment

Dirichlet distribution
type: Class
subclass of: random distribution
definition: Dirichlet distribution
has_obo_namespace: WC
id: WC:Dirichlet_distribution

Gumbel distribution
type: Class
subclass of: random distribution
definition: Gumbel distribution
has_obo_namespace: WC
id: WC:Gumbel_distribution

K_i
type: Class
subclass of: kinetic constant
definition: K_i
database_cross_reference: SBO:0000261
has_obo_namespace: WC
id: WC:K_i

K_m
type: Class
subclass of: kinetic constant
definition: K_m
database_cross_reference: SBO:0000027
has_obo_namespace: WC
id: WC:K_m

Laplace distribution
type: Class
subclass of: random distribution
definition: Laplace distribution
has_obo_namespace: WC
id: WC:Laplace_distribution

Michaelis-Menten rate law
type: Class
subclass of: rate law
definition: Michaelis-Menten rate law
database_cross_reference: SBO:0000029
has_obo_namespace: WC
id: WC:Michaelis_Menten_rate_law

Pareto distribution
type: Class
subclass of: random distribution
definition: Pareto distribution
has_obo_namespace: WC
id: WC:Pareto_distribution

Poisson distribution
type: Class
subclass of: random distribution
definition: Poisson distribution
has_obo_namespace: WC
id: WC:Poisson_distribution

Rayleigh distribution
type: Class
subclass of: random distribution
definition: Rayleigh distribution
has_obo_namespace: WC
id: WC:Rayleigh_distribution

Vonmises distribution
type: Class
subclass of: random distribution
definition: Vonmises distribution
has_obo_namespace: WC
id: WC:Vonmises_distribution

Wald distribution
type: Class
subclass of: random distribution
definition: Wald distribution
has_obo_namespace: WC
id: WC:Wald_distribution

Weibull distribution
type: Class
subclass of: random distribution
definition: Weibull distribution
has_obo_namespace: WC
id: WC:Weibull_distribution

Zipf distribution
type: Class
subclass of: random distribution
definition: Zipf distribution
has_obo_namespace: WC
id: WC:Zipf_distribution

abstract compartment
type: Class
subclass of: physical compartment
definition: Compartment that doesn't contain physical matter with properties like density = mass/volume; the volume is fixed
has_obo_namespace: WC
id: WC:abstract_compartment

add metadata
type: Class
subclass of: reason
definition: Add metadata to facilitate comprehension
database_cross_reference: COMODI:modelCuration
has_obo_namespace: WC
id: WC:add_metadata_reason_provenance

beta distribution
type: Class
subclass of: random distribution
definition: beta distribution
has_obo_namespace: WC
id: WC:beta_distribution

binomial distribution
type: Class
subclass of: random distribution
definition: binomial distribution
has_obo_namespace: WC
id: WC:binomial_distribution

biological compartment
type: Class
subclass of: compartment
definition: Biological compartment
has_obo_namespace: WC
id: WC:biological_compartment

cellular compartment
type: Class
subclass of: biological compartment
definition: Cellular compartment
database_cross_reference: sao1337158144
has_obo_namespace: WC
id: WC:cellular_compartment

chi square distribution
type: Class
subclass of: random distribution
definition: Chi square distribution
has_obo_namespace: WC
id: WC:chi_square_distribution

computational observation
type: Class
subclass of: observation
definition: Computational observation
has_obo_namespace: WC
id: WC:computational_observation

correct
type: Class
subclass of: intention
definition: Correct
database_cross_reference: COMODI:Correction
has_obo_namespace: WC
id: WC:correct_intention_provenance

data analysis process
type: Class
subclass of: process
definition: Data analysis process
database_cross_reference: SEPIO:0000003
database_cross_reference: SEPIO:0000037
has_obo_namespace: WC
id: WC:data_analysis_process

data generation process
type: Class
subclass of: process
definition: Data generation process
has_obo_namespace: WC
id: WC:data_generation_process

data set
type: Class
subclass of: Whole-cell modeling entities
definition: Data set
database_cross_reference: IAO:0000100
has_obo_namespace: WC
id: WC:data_set

data
type: Class
subclass of: target
definition: Data
has_obo_namespace: WC
id: WC:data_target_provenance

deletion
type: Class
subclass of: change
definition: deletion
database_cross_reference: COMODI:Deletion
has_obo_namespace: WC
id: WC:deletion_change_provenance

deterministic simulation algorithm
type: Class
subclass of: modeling framework
definition: deterministic simulation algorithm
database_cross_reference: SBO:0000295
database_cross_reference: kisao:KISAO_0000241
has_exact_synonym: DSA
has_obo_namespace: WC
id: WC:deterministic_simulation_algorithm

dFBA objective
type: Class
subclass of: dFBA terms
definition: dFBA objective
has_obo_namespace: WC
id: WC:dfba_objective

dFBA reaction
type: Class
subclass of: dFBA terms
definition: dFBA reaction
has_obo_namespace: WC
id: WC:dfba_reaction

dFBA species
type: Class
subclass of: dFBA terms
definition: dFBA species
has_obo_namespace: WC
id: WC:dfba_species

disputing evidence
type: Class
subclass of: evidence
definition: Disputing evidence
database_cross_reference: SEPIO:0000404
has_obo_namespace: WC
id: WC:disputing_evidence

dynamic flux balance analysis
type: Class
subclass of: modeling framework
definition: Dynamic flux balance analysis
database_cross_reference: SBO:0000624
database_cross_reference: kisao:KISAO_0000499
has_exact_synonym: dFBA
has_obo_namespace: WC
id: WC:dynamic_flux_balance_analysis

elaborate
type: Class
subclass of: intention
definition: Add more detail
database_cross_reference: COMODI:Elaboration
has_obo_namespace: WC
id: WC:elaborate_intention_provenance

encoding
type: Class
subclass of: target
definition: Encoding (e.g. a different or revised file format)
database_cross_reference: COMODI:modelEncoding
has_obo_namespace: WC
id: WC:encoding_target_provenance

expand
type: Class
subclass of: intention
definition: Expand the scope
database_cross_reference: COMODI:Expansion
has_obo_namespace: WC
id: WC:expand_intention_provenance

experimental observation
type: Class
subclass of: observation
definition: Experimental observation
has_obo_namespace: WC
id: WC:experimental_observation

exponential distribution
type: Class
subclass of: random distribution
definition: Exponential distribution
has_obo_namespace: WC
id: WC:exponential_distribution

extracellular compartment
type: Class
subclass of: biological compartment
definition: Extracellular compartment
has_obo_namespace: WC
id: WC:extracellular_compartment

f distribution
type: Class
subclass of: random distribution
definition: F distribution
has_obo_namespace: WC
id: WC:f_distribution

fluid compartment
type: Class
subclass of: physical compartment
definition: Fluid compartment
has_obo_namespace: WC
id: WC:fluid_compartment

gamma distribution
type: Class
subclass of: random distribution
definition: Gamma distribution
has_obo_namespace: WC
id: WC:gamma_distribution

geometric compartment
type: Class
subclass of: compartment
definition: Geometric compartment
has_obo_namespace: WC
id: WC:geometric_compartment

geometric distribution
type: Class
subclass of: random distribution
definition: Geometric distribution
has_obo_namespace: WC
id: WC:geometric_distribution

Hill rate law
type: Class
subclass of: rate law
definition: Hill rate law
database_cross_reference: SBO:0000192
has_obo_namespace: WC
id: WC:hill_rate_law

hypergeometric distribution
type: Class
subclass of: random distribution
definition: Hypergeometric distribution
has_obo_namespace: WC
id: WC:hypergeometric_distribution

implementation error
type: Class
subclass of: reason
definition: Implementation error such as a typo
database_cross_reference: COMODI:Typo
has_obo_namespace: WC
id: WC:implementation_error_reason_provenance

inconclusive evidence
type: Class
subclass of: evidence
definition: Inconclusive evidence
database_cross_reference: SEPIO:0000405
has_obo_namespace: WC
id: WC:inconclusive_evidence

incorrect interpretation of existing knowledge
type: Class
subclass of: reason
definition: Incorrect interpretation of existing knowledge
database_cross_reference: COMODI:MismatchWithPublication
has_obo_namespace: WC
id: WC:incorrect_interpretation_reason_provenance

intention
type: Class
subclass of: provenance
definition: Intention
database_cross_reference: COMODI:Intention
has_obo_namespace: WC
id: WC:intention_provenance

k_cat
type: Class
subclass of: kinetic constant
definition: k_cat
database_cross_reference: SBO:0000025
has_obo_namespace: WC
id: WC:k_cat

kinetic constant
type: Class
subclass of: parameters
definition: Kinetic constant
database_cross_reference: SBO:0000009
has_obo_namespace: WC
id: WC:kinetic_constant

log normal distribution
type: Class
subclass of: random distribution
definition: Log normal distribution
has_obo_namespace: WC
id: WC:log_normal_distribution

log series distribution
type: Class
subclass of: random distribution
definition: Log series distribution
has_obo_namespace: WC
id: WC:log_series_distribution

logisitic distribution
type: Class
subclass of: random distribution
definition: Logisitic distribution
has_obo_namespace: WC
id: WC:logisitic_distribution

Mass-action rate law
type: Class
subclass of: rate law
definition: Mass-action rate law
database_cross_reference: SBO:0000012
has_obo_namespace: WC
id: WC:mass_action_rate_law

membrane compartment
type: Class
subclass of: physical compartment
definition: Membrane compartment
has_obo_namespace: WC
id: WC:membrane_compartment

metadata
type: Class
subclass of: target
definition: Metadata
database_cross_reference: COMODI:modelAnnotation
has_obo_namespace: WC
id: WC:metadata_target_provenance

migrate to another version
type: Class
subclass of: reason
definition: Migrate object to another version of a specification
database_cross_reference: COMODI:ChangedSpecification
has_obo_namespace: WC
id: WC:migrate_version_reason_provenance

dynamics
type: Class
subclass of: model
definition: Dynamics
has_obo_namespace: WC
id: WC:model_dynamics_target_provenance

model element
type: Class
subclass of: Whole-cell modeling entities
definition: model element
has_obo_namespace: WC
id: WC:model_element

initial conditions
type: Class
subclass of: model
definition: Initial conditions
has_obo_namespace: WC
id: WC:model_initial_conditions_target_provenance

model
type: Class
subclass of: data
definition: model
database_cross_reference: COMODI:modelDefinition
has_obo_namespace: WC
id: WC:model_target_provenance

modeling framework
type: Class
subclass of: Whole-cell modeling entities
definition: modeling framework
database_cross_reference: kisao:KISAO_0000000
has_obo_namespace: WC
id: WC:modeling_framework

Modular rate law
type: Class
subclass of: rate law
definition: Modular rate law
database_cross_reference: SBO:0000527
has_obo_namespace: WC
id: WC:modular_rate_law

multinomial distribution
type: Class
subclass of: random distribution
definition: Multinomial distribution
has_obo_namespace: WC
id: WC:multinomial_distribution

multivariate-normal distribution
type: Class
subclass of: random distribution
definition: Multivariate-normal distribution
has_obo_namespace: WC
id: WC:multivariate_normal_distribution

negative-binomial distribution
type: Class
subclass of: random distribution
definition: Negative-binomial distribution
has_obo_namespace: WC
id: WC:negative_binomial_distribution

new goal for a project
type: Class
subclass of: reason
definition: New goal for a project. For example, a new phenotype that a model should predict or a new molecular mechanism that a model should account for
has_obo_namespace: WC
id: WC:new_goal_reason_provenance

new knowledge
type: Class
subclass of: reason
definition: New knowledge
database_cross_reference: COMODI:KnowledgeGain
has_obo_namespace: WC
id: WC:new_knowledge_reason_provenance

noncentral-chi square distribution
type: Class
subclass of: random distribution
definition: Noncentral-chi square distribution
has_obo_namespace: WC
id: WC:noncentral-chi_square_distribution

noncentral-f distribution
type: Class
subclass of: random distribution
definition: Noncentral-f distribution
has_obo_namespace: WC
id: WC:noncentral-f_distribution

normal distribution
type: Class
subclass of: random distribution
definition: Normal distribution
has_obo_namespace: WC
id: WC:normal_distribution

ordinary differential equations
type: Class
subclass of: modeling framework
definition: Ordinary differential equations
database_cross_reference: SBO:0000062
has_exact_synonym: ODEs
has_obo_namespace: WC
id: WC:ordinary_differential_equations

physical compartment
type: Class
subclass of: compartment
definition: Physical compartment
database_cross_reference: SBO:0000290
has_obo_namespace: WC
id: WC:physical_compartment

power distribution
type: Class
subclass of: random distribution
definition: Power distribution
has_obo_namespace: WC
id: WC:power_distribution

pseudo species
type: Class
subclass of: species_type
definition: Pseudo-species
has_obo_namespace: WC
id: WC:pseudo_species

random distribution
type: Class
subclass of: Whole-cell modeling entities
definition: random distribution
has_obo_namespace: WC
id: WC:random_distribution

rate law
type: Class
subclass of: model element
definition: rate law
database_cross_reference: SBO:0000001
has_obo_namespace: WC
id: WC:rate_law

reason
type: Class
subclass of: provenance
definition: Reason
database_cross_reference: COMODI:Reason
has_obo_namespace: WC
id: WC:reason_provenance

simplify
type: Class
subclass of: intention
definition: Simplify
database_cross_reference: COMODI:Simplification
has_obo_namespace: WC
id: WC:simplify_intention_provenance

species_type
type: Class
subclass of: model element
definition: Type of species
database_cross_reference: MATR:Compound
has_obo_namespace: WC
id: WC:species_type

standard-Cauchy distribution
type: Class
subclass of: random distribution
definition: Standard-Cauchy distribution
has_obo_namespace: WC
id: WC:standard-Cauchy_distribution

standard-exponential distribution
type: Class
subclass of: random distribution
definition: Standard-exponential distribution
has_obo_namespace: WC
id: WC:standard-exponential_distribution

standard-gamma distribution
type: Class
subclass of: random distribution
definition: Standard-gamma distribution
has_obo_namespace: WC
id: WC:standard-gamma_distribution

standard-normal distribution
type: Class
subclass of: random distribution
definition: Standard-normal distribution
has_obo_namespace: WC
id: WC:standard-normal_distribution

standard-t distribution
type: Class
subclass of: random distribution
definition: Standard-t distribution
has_obo_namespace: WC
id: WC:standard-t_distribution

stochastic simulation algorithm
type: Class
subclass of: modeling framework
definition: stochastic simulation algorithm
database_cross_reference: SBO:0000295
database_cross_reference: kisao:KISAO_0000241
has_exact_synonym: SSA
has_obo_namespace: WC
id: WC:stochastic_simulation_algorithm

stop condition
type: Class
subclass of: model element
definition: stop condition
has_obo_namespace: WC
id: WC:stop_condition

supplementary material
type: Class
subclass of: reference
definition: supplementary_material
has_obo_namespace: WC
id: WC:supplementary_material

supporting evidence
type: Class
subclass of: evidence
definition: Supporting evidence
database_cross_reference: SEPIO:0000403
has_obo_namespace: WC
id: WC:supporting_evidence

target
type: Class
subclass of: provenance
definition: Target
database_cross_reference: COMODI:Target
has_obo_namespace: WC
id: WC:target_provenance

theoretical observation
type: Class
subclass of: observation
definition: Theoretical observation
has_obo_namespace: WC
id: WC:theoretical_observation

triangular distribution
type: Class
subclass of: random distribution
definition: Triangular distribution
has_obo_namespace: WC
id: WC:triangular_distribution

uniform distribution
type: Class
subclass of: random distribution
definition: Uniform distribution
has_obo_namespace: WC
id: WC:uniform_distribution

v_max
type: Class
subclass of: kinetic constant
definition: v_max
database_cross_reference: SBO:0000186
has_obo_namespace: WC
id: WC:v_max