KarrLab/wc_onto

format-version: 1.4
data-version: 0.0.1
date: 14:01:2019 13:00
saved-by: Jonathan Karr <karr@mssm.edu>
remark: distributed under the MIT License (https://github.com/KarrLab/wc_lang/blob/master/LICENSE)

default-namespace: WC

[Term]
id: WC
name: Whole-cell modeling entities
def: "Representation of an entity used in whole-cell modeling" []


[Term]
id: WC:model_element
name: model element
def: "model element" []
is_a: WC


[Term]
id: WC:species_type
name: species_type
def: "Type of species" []
is_a: WC:model_element
xref: MATR:Compound

[Term]
id: WC:species
name: species
def: "species" []
is_a: WC:model_element

[Term]
id: WC:compartment
name: compartment
def: "compartment" []
is_a: WC:model_element
xref: SBO:0000289 ! functional compartment

[Term]
id: WC:reaction
name: reaction
def: "reaction" []
is_a: WC:model_element

[Term]
id: WC:provenance
name: provenance
def: "provenance terms" []
is_a: WC
xref: SEPIO:0000058 ! provenance

[Term]
id: WC:reference
name: reference
def: "reference" []
is_a: WC:provenance
xref: BRO:Information_Resource ! Information Resource

[Term]
id: WC:model
name: model
def: "model" []
is_a: WC:model_element

[Term]
id: WC:taxon
name: taxon
def: "taxon" []
is_a: WC:model_element

[Term]
id: WC:environment
name: environment
def: "environment" []
is_a: WC:model_element

[Term]
id: WC:submodel
name: submodel
def: "submodel" []
is_a: WC:model_element

[Term]
id: WC:observable
name: observable
def: "observable" []
is_a: WC:model_element

[Term]
id: WC:function
name: function
def: "Function" []
is_a: WC:model_element
xref: SBO:0000064 ! mathematical expression

[Term]
id: WC:rate_law
name: rate law
def: "rate law" []
is_a: WC:model_element
xref: SBO:0000001 ! rate lawloci

[Term]
id: WC:dFBA
name: dFBA terms
def: "dFBA objective" []
is_a: WC:model_element

[Term]
id: WC:dfba_objective
name: dFBA objective
def: "dFBA objective" []
is_a: WC:dFBA

[Term]
id: WC:dfba_reaction
name: dFBA reaction
def: "dFBA reaction" []
is_a: WC:dFBA

[Term]
id: WC:dfba_species
name: dFBA species
def: "dFBA species" []
is_a: WC:dFBA


[Term]
id: WC:stop_condition
name: stop condition
def: "stop condition" []
is_a: WC:model_element

[Term]
id: WC:observation
name: observation
def: "observation" []
is_a: WC:provenance
xref: SEPIO:0000149 ! evidence item
xref: IAO:0000111 ! data item

[Term]
id: WC:evidence
name: evidence
def: "Evidence" []
is_a: WC:provenance
xref: SEPIO:0000002 ! evidence line

[Term]
id: WC:supporting_evidence
name: supporting evidence
def: "Supporting evidence" []
is_a: WC:evidence
xref: SEPIO:0000403 ! supporting

[Term]
id: WC:inconclusive_evidence
name: inconclusive evidence
def: "Inconclusive evidence" []
is_a: WC:evidence
xref: SEPIO:0000405 ! inconclusive

[Term]
id: WC:disputing_evidence
name: disputing evidence
def: "Disputing evidence" []
is_a: WC:evidence
xref: SEPIO:0000404 ! disputing


[Term]
id: WC:conclusion
name: conclusion
def: "Conclusion" []
is_a: WC:provenance
xref: SEPIO:0000000 ! proposition
xref: SEPIO:0000001 ! assertion

[Term]
id: WC:author
name: author
def: "Author" []
is_a: WC:provenance
xref: foaf:Person ! Person

[Term]
id: WC:change
name: change
def: "Change" []
is_a: WC:provenance
xref: COMODI:Change

[Term]
id: WC:process
name: process
def: "process" []
is_a: WC:model_element
xref: BFO:0000015 ! process


[Term]
id: WC:biological_compartment
name: biological compartment
def: "Biological compartment" []
is_a: WC:compartment

[Term]
id: WC:cellular_compartment
name: cellular compartment
def: "Cellular compartment" []
is_a: WC:biological_compartment
xref: sao1337158144 ! Cellular Component

[Term]
id: WC:extracellular_compartment
name: extracellular compartment
def: "Extracellular compartment" []
is_a: WC:biological_compartment

[Term]
id: WC:physical_compartment
name: physical compartment
def: "Physical compartment" []
is_a: WC:compartment
xref: SBO:0000290 ! physical compartment

[Term]
id: WC:fluid_compartment
name: fluid compartment
def: "Fluid compartment" []
is_a: WC:physical_compartment

[Term]
id: WC:membrane_compartment
name: membrane compartment
def: "Membrane compartment" []
is_a: WC:physical_compartment

[Term]
id: WC:abstract_compartment
name: abstract compartment
def: "Compartment that doesn't contain physical matter with properties like density = mass/volume; the volume is fixed" []
is_a: WC:physical_compartment

[Term]
id: WC:geometric_compartment
name: geometric compartment
def: "Geometric compartment" []
is_a: WC:compartment

[Term]
id: WC:3D_compartment
name: 3D compartment
def: "3D compartment" []
is_a: WC:geometric_compartment


[Term]
id: WC:metabolite
name: metabolite
def: "Metabolite" []
is_a: WC:species_type
xref: SBO:0000299 ! metabolite

[Term]
id: WC:protein
name: protein
def: "protein" []
is_a: WC:species_type

[Term]
id: WC:RNA
name: RNA
def: "RNA" []
is_a: WC:species_type
xref: SBO:0000250 ! ribonucleic acid

[Term]
id: WC:DNA
name: DNA
def: "DNA" []
is_a: WC:species_type
xref: SBO:0000251 ! deoxyribonucleic acid

[Term]
id: WC:pseudo_species
name: pseudo species
def: "Pseudo-species" []
is_a: WC:species_type


[Term]
id: WC:modeling_framework
name: modeling framework
def: "modeling framework" []
is_a: WC
xref: kisao:KISAO_0000000 ! modelling and simulation algorithm

[Term]
id: WC:next_reaction_method
name: next reaction method
def: "next reaction method" []
synonym: "NRM" EXACT []
is_a: WC:modeling_framework
xref: SBO:0000295 ! non-spatial discrete framework
xref: kisao:KISAO_0000241 ! Gillespie-like method

[Term]
id: WC:stochastic_simulation_algorithm
name: stochastic simulation algorithm
def: "stochastic simulation algorithm" []
synonym: "SSA" EXACT []
is_a: WC:modeling_framework
xref: SBO:0000295 ! non-spatial discrete framework
xref: kisao:KISAO_0000241 ! Gillespie-like method

[Term]
id: WC:deterministic_simulation_algorithm
name: deterministic simulation algorithm
def: "deterministic simulation algorithm" []
synonym: "DSA" EXACT []
is_a: WC:modeling_framework
xref: SBO:0000295 ! non-spatial discrete framework
xref: kisao:KISAO_0000241 ! Gillespie-like method

[Term]
id: WC:ordinary_differential_equations
name: ordinary differential equations
def: "Ordinary differential equations" []
synonym: "ODEs" EXACT []
is_a: WC:modeling_framework
xref: SBO:0000062 ! continuous framework

[Term]
id: WC:dynamic_flux_balance_analysis
name: dynamic flux balance analysis
def: "Dynamic flux balance analysis" []
synonym: "dFBA" EXACT []
is_a: WC:modeling_framework
xref: SBO:0000624 ! flux balance framework
xref: kisao:KISAO_0000499 ! dynamic flux balance analysis


[Term]
id: WC:hill_rate_law
name: Hill rate law
def: "Hill rate law" []
is_a: WC:rate_law
xref: SBO:0000192 ! Hill-type rate law, generalised form

[Term]
id: WC:mass_action_rate_law
name: Mass-action rate law
def: "Mass-action rate law" []
is_a: WC:rate_law
xref: SBO:0000012 ! mass action rate law

[Term]
id: WC:Michaelis_Menten_rate_law
name: Michaelis-Menten rate law
def: "Michaelis-Menten rate law" []
is_a: WC:rate_law
xref: SBO:0000029 ! Henri-Michaelis-Menten rate law

[Term]
id: WC:modular_rate_law
name: Modular rate law
def: "Modular rate law" []
is_a: WC:rate_law
xref: SBO:0000527 ! modular rate law


[Term]
id: WC:parameter
name: parameters
def: "parameters" []
is_a: WC:model_element
xref: SBO:0000002 ! quantitative systems description parameter

[Term]
id: WC:kinetic_constant
name: kinetic constant
def: "Kinetic constant" []
is_a: WC:parameter
xref: SBO:0000009 ! kinetic constant

[Term]
id: WC:K_i
name: K_i
def: "K_i" []
is_a: WC:kinetic_constant
xref: SBO:0000261 ! inhibitory constant

[Term]
id: WC:k_cat
name: k_cat
def: "k_cat" []
is_a: WC:kinetic_constant
xref: SBO:0000025 ! catalytic rate constant

[Term]
id: WC:K_m
name: K_m
def: "K_m" []
is_a: WC:kinetic_constant
xref: SBO:0000027 ! Michaelis constant

[Term]
id: WC:v_max
name: v_max
def: "v_max" []
is_a: WC:kinetic_constant
xref: SBO:0000186 ! maximal velocity

[Term]
id: WC:K_i
name: K_i
def: "K_i" []
is_a: WC:kinetic_constant
xref: SBO:0000261 ! inhibitory constant


[Term]
id: WC:experimental_observation
name: experimental observation
def: "Experimental observation" []
is_a: WC:observation

[Term]
id: WC:computational_observation
name: computational observation
def: "Computational observation" []
is_a: WC:observation

[Term]
id: WC:theoretical_observation
name: theoretical observation
def: "Theoretical observation" []
is_a: WC:observation

[Term]
id: WC:data_set
name: data set
def: "Data set" []
is_a: WC
xref: IAO:0000100 ! data set


[Term]
id: WC:assumption
name: assumption
def: "Assumption" []
is_a: WC:conclusion

[Term]
id: WC:approximation
name: approximation
def: "Approximation" []
is_a: WC:conclusion

[Term]
id: WC:computation
name: computation
def: "Computation" []
is_a: WC:conclusion

[Term]
id: WC:decision
name: decision
def: "Decision" []
is_a: WC:conclusion


[Term]
id: WC:article
name: article
def: "Article" []
is_a: WC:reference
xref: BRO:JouRNAl_Article ! JouRNAl Article
xref: IAO:0000013 ! jouRNAl article

[Term]
id: WC:book
name: book
def: "Book" []
is_a: WC:reference
xref: BRO:Book ! book

[Term]
id: WC:website
name: website
def: "website" []
is_a: WC:reference
xref: BRO:Website ! Website

[Term]
id: WC:proceedings
name: proceedings
def: "Proceedings" []
is_a: WC:reference
xref: BRO:Conference_Proceeding ! Conference Proceeding

[Term]
id: WC:thesis
name: thesis
def: "Thesis" []
is_a: WC:reference
xref: BRO:Thesis ! Thesis

[Term]
id: WC:preprint
name: preprint
def: "preprint" []
is_a: WC:reference

[Term]
id: WC:supplementary_material
name: supplementary material
def: "supplementary_material" []
is_a: WC:reference


[Term]
id: WC:random_distribution
name: random distribution
def: "random distribution" []
is_a: WC

[Term]
id: WC:beta_distribution
name: beta distribution
def: "beta distribution" []
is_a: WC:random_distribution

[Term]
id: WC:binomial_distribution
name: binomial distribution
def: "binomial distribution" []
is_a: WC:random_distribution

[Term]
id: WC:chi_square_distribution
name: chi square distribution
def: "Chi square distribution" []
is_a: WC:random_distribution

[Term]
id: WC:Dirichlet_distribution
name: Dirichlet distribution
def: "Dirichlet distribution" []
is_a: WC:random_distribution

[Term]
id: WC:exponential_distribution
name: exponential distribution
def: "Exponential distribution" []
is_a: WC:random_distribution

[Term]
id: WC:f_distribution
name: f distribution
def: "F distribution" []
is_a: WC:random_distribution

[Term]
id: WC:gamma_distribution
name: gamma distribution
def: "Gamma distribution" []
is_a: WC:random_distribution

[Term]
id: WC:geometric_distribution
name: geometric distribution
def: "Geometric distribution" []
is_a: WC:random_distribution

[Term]
id: WC:Gumbel_distribution
name: Gumbel distribution
def: "Gumbel distribution" []
is_a: WC:random_distribution

[Term]
id: WC:hypergeometric_distribution
name: hypergeometric distribution
def: "Hypergeometric distribution" []
is_a: WC:random_distribution

[Term]
id: WC:Laplace_distribution
name: Laplace distribution
def: "Laplace distribution" []
is_a: WC:random_distribution

[Term]
id: WC:logisitic_distribution
name: logisitic distribution
def: "Logisitic distribution" []
is_a: WC:random_distribution

[Term]
id: WC:log_normal_distribution
name: log normal distribution
def: "Log normal distribution" []
is_a: WC:random_distribution

[Term]
id: WC:log_series_distribution
name: log series distribution
def: "Log series distribution" []
is_a: WC:random_distribution

[Term]
id: WC:multinomial_distribution
name: multinomial distribution
def: "Multinomial distribution" []
is_a: WC:random_distribution

[Term]
id: WC:multivariate_normal_distribution
name: multivariate-normal distribution
def: "Multivariate-normal distribution" []
is_a: WC:random_distribution

[Term]
id: WC:negative_binomial_distribution
name: negative-binomial distribution
def: "Negative-binomial distribution" []
is_a: WC:random_distribution

[Term]
id: WC:noncentral-chi_square_distribution
name: noncentral-chi square distribution
def: "Noncentral-chi square distribution" []
is_a: WC:random_distribution

[Term]
id: WC:noncentral-f_distribution
name: noncentral-f distribution
def: "Noncentral-f distribution" []
is_a: WC:random_distribution

[Term]
id: WC:normal_distribution
name: normal distribution
def: "Normal distribution" []
is_a: WC:random_distribution

[Term]
id: WC:Pareto_distribution
name: Pareto distribution
def: "Pareto distribution" []
is_a: WC:random_distribution

[Term]
id: WC:Poisson_distribution
name: Poisson distribution
def: "Poisson distribution" []
is_a: WC:random_distribution

[Term]
id: WC:power_distribution
name: power distribution
def: "Power distribution" []
is_a: WC:random_distribution

[Term]
id: WC:Rayleigh_distribution
name: Rayleigh distribution
def: "Rayleigh distribution" []
is_a: WC:random_distribution

[Term]
id: WC:standard-Cauchy_distribution
name: standard-Cauchy distribution
def: "Standard-Cauchy distribution" []
is_a: WC:random_distribution

[Term]
id: WC:standard-exponential_distribution
name: standard-exponential distribution
def: "Standard-exponential distribution" []
is_a: WC:random_distribution

[Term]
id: WC:standard-gamma_distribution
name: standard-gamma distribution
def: "Standard-gamma distribution" []
is_a: WC:random_distribution

[Term]
id: WC:standard-normal_distribution
name: standard-normal distribution
def: "Standard-normal distribution" []
is_a: WC:random_distribution

[Term]
id: WC:standard-t_distribution
name: standard-t distribution
def: "Standard-t distribution" []
is_a: WC:random_distribution

[Term]
id: WC:triangular_distribution
name: triangular distribution
def: "Triangular distribution" []
is_a: WC:random_distribution

[Term]
id: WC:uniform_distribution
name: uniform distribution
def: "Uniform distribution" []
is_a: WC:random_distribution

[Term]
id: WC:Vonmises_distribution
name: Vonmises distribution
def: "Vonmises distribution" []
is_a: WC:random_distribution

[Term]
id: WC:Wald_distribution
name: Wald distribution
def: "Wald distribution" []
is_a: WC:random_distribution

[Term]
id: WC:Weibull_distribution
name: Weibull distribution
def: "Weibull distribution" []
is_a: WC:random_distribution

[Term]
id: WC:Zipf_distribution
name: Zipf distribution
def: "Zipf distribution" []
is_a: WC:random_distribution


[Term]
id: WC:change
name: change
def: "change" []
is_a: WC:provenance

[Term]
id: WC:deletion_change_provenance
name: deletion
def: "deletion" []
is_a: WC:change
xref: COMODI:Deletion

[Term]
id: WC:insertion
name: insertion
def: "Insertion" []
is_a: WC:change
xref: COMODI:Insertion

[Term]
id: WC:move
name: move
def: "Move" []
is_a: WC:change
xref: COMODI:Move

[Term]
id: WC:update
name: update
def: "Update" []
is_a: WC:change
xref: COMODI:Update

[Term]
id: WC:merge
name: merge
def: "Merge" []
is_a: WC:change

[Term]
id: WC:copy
name: copy
def: "Copy" []
is_a: WC:change

[Term]
id: WC:revert
name: revert
def: "Revert" []
is_a: WC:change

[Term]
id: WC:intention_provenance
name: intention
def: "Intention" []
is_a: WC:provenance
xref: COMODI:Intention

[Term]
id: WC:correct_intention_provenance
name: correct
def: "Correct" []
is_a: WC:intention_provenance
xref: COMODI:Correction

[Term]
id: WC:elaborate_intention_provenance
name: elaborate
def: "Add more detail" []
is_a: WC:intention_provenance
xref: COMODI:Elaboration

[Term]
id: WC:expand_intention_provenance
name: expand
def: "Expand the scope" []
is_a: WC:intention_provenance
xref: COMODI:Expansion

[Term]
id: WC:simplify_intention_provenance
name: simplify
def: "Simplify" []
is_a: WC:intention_provenance
xref: COMODI:Simplification

[Term]
id: WC:reason_provenance
name: reason
def: "Reason" []
is_a: WC:provenance
xref: COMODI:Reason

[Term]
id: WC:new_goal_reason_provenance
name: new goal for a project
def: "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" []
is_a: WC:reason_provenance

[Term]
id: WC:new_knowledge_reason_provenance
name: new knowledge
def: "New knowledge" []
is_a: WC:reason_provenance
xref: COMODI:KnowledgeGain

[Term]
id: WC:incorrect_interpretation_reason_provenance
name: incorrect interpretation of existing knowledge
def: "Incorrect interpretation of existing knowledge" []
is_a: WC:reason_provenance
xref: COMODI:MismatchWithPublication

[Term]
id: WC:implementation_error_reason_provenance
name: implementation error
def: "Implementation error such as a typo" []
is_a: WC:reason_provenance
xref: COMODI:Typo

[Term]
id: WC:migrate_version_reason_provenance
name: migrate to another version
def: "Migrate object to another version of a specification" []
is_a: WC:reason_provenance
xref: COMODI:ChangedSpecification

[Term]
id: WC:add_metadata_reason_provenance
name: add metadata
def: "Add metadata to facilitate comprehension" []
is_a: WC:reason_provenance
xref: COMODI:modelCuration

[Term]
id: WC:target_provenance
name: target
def: "Target" []
is_a: WC:provenance
xref: COMODI:Target

[Term]
id: WC:data_target_provenance
name: data
def: "Data" []
is_a: WC:target_provenance

[Term]
id: WC:model_target_provenance
name: model
def: "model" []
is_a: WC:data_target_provenance
xref: COMODI:modelDefinition

[Term]
id: WC:model_initial_conditions_target_provenance
name: initial conditions
def: "Initial conditions" []
is_a: WC:model_target_provenance

[Term]
id: WC:model_dynamics_target_provenance
name: dynamics
def: "Dynamics" []
is_a: WC:model_target_provenance

[Term]
id: WC:metadata_target_provenance
name: metadata
def: "Metadata" []
is_a: WC:target_provenance
xref: COMODI:modelAnnotation

[Term]
id: WC:encoding_target_provenance
name: encoding
def: "Encoding (e.g. a different or revised file format)" []
is_a: WC:target_provenance
xref: COMODI:modelEncoding


[Term]
id: WC:data_generation_process
name: data generation process
def: "Data generation process" []
is_a:  WC:process

[Term]
id: WC:data_analysis_process
name: data analysis process
def: "Data analysis process" []
is_a:  WC:process
xref: SEPIO:0000037 ! assertion method
xref: SEPIO:0000003 ! assertion process


[Term]
id: WC:vitamin
name: Vitamin
def: "Vitamin" []
is_a: WC:metabolite

[Term]
id: WC:aminoAcid
name: Amino Acid
def: "Amino Acid" []
is_a: WC:metabolite

[Term]
id: WC:dipeptide
name: Dipeptide
def: "Dipeptide" []
is_a: WC:metabolite

[Term]
id: WC:nucleobase
name: Nucleobase
def: "Nucleobase" []
is_a: WC:metabolite

[Term]
id: WC:modifiedNucleobase
name: Modified Nucleobase
def: "Modified Nucleobase" []
is_a: WC:metabolite

[Term]
id: WC:carbohydrateSugar
name: Carbohydrate Sugar
def: "Carbohydrate Sugar" []
is_a: WC:metabolite

[Term]
id: WC:carbohydrateSugarPhosphate
name: Carbohydrate Sugar Phosphate
def: "Carbohydrate Sugar Phosphate" []
is_a: WC:metabolite

[Term]
id: WC:ribonucleotideMonophosphate
name: Ribonucleotide Monophosphate
def: "Ribonucleotide Monophosphate" []
is_a: WC:metabolite

[Term]
id: WC:ribonucleotideBiphosphate
name: Ribonucleotide Biphosphate
def: "Ribonucleotide Biphosphate" []
is_a: WC:metabolite

[Term]
id: WC:ribonucleotideTriphosphate
name: Ribonucleotide Triphosphate
def: "Ribonucleotide Triphosphate" []
is_a: WC:metabolite

[Term]
id: WC:carboxyAcid
name: Carboxy Acid
def: "Carboxy Acid" []
is_a: WC:metabolite

[Term]
id: WC:reactiveOxygenSpecies
name: reactive oxygen species
def: "Reactive Oxygen Species" []
is_a: WC:metabolite

[Term]
id: WC:Ion
name: Ion
def: "Ion" []
is_a: WC:metabolite

[Term]
id: WC:TRNASynthClassI
name: TRNASynthClassI
def: "TRNASynthClassI" []
is_a: WC:protein

[Term]
id: WC:TRNASynthClassIB
name: TRNASynthClassIB
def: "TRNASynthClassIB" []
is_a: WC:protein

[Term]
id: WC:TRNASynthClassII
name: TRNASynthClassII
def: "TRNASynthClassII" []
is_a: WC:protein


[Term]
id: WC:complex
name: complexes
def: "complexes" []
is_a: WC:species_type

[Term]
id: WC:TRNASynthClassIIComplex
name: TRNASynthClassII
def: "TRNASynthClassII" []
is_a: WC:complex

[Term]
id: WC:fattyAcylAcpComplex
name: FattyAcylAcp
def: "FattyAcylAcp" []
is_a: WC:complex


[Term]
id: WC:complexFormation
name: complexFormation
def: "Complex Formation Type" []
is_a: WC:model_element

[Term]
id: WC:chromosomeCondensation
name: Chromosome Condensation
def: "Chromosome Condensation" []
is_a: WC:complexFormation

[Term]
id: WC:ftsZPolymerization
name: FtsZ Polymerization
def: "FtsZ Polymerization" []
is_a: WC:complexFormation

[Term]
id: WC:macromolecularComplexation
name: Macromolecular Complexation
def: "Macromolecular Complexation" []
is_a: WC:complexFormation

[Term]
id: WC:metabolism
name: Metabolism
def: "Metabolism" []
is_a: WC:complexFormation

[Term]
id: WC:proteinModification
name: Protein Modification
def: "proteinModification" []
is_a: WC:complexFormation

[Term]
id: WC:replication
name: Replication
def: "Replication" []
is_a: WC:complexFormation

[Term]
id: WC:replicationInitiation
name: Replication Initiation
def: "Replication Initiation" []
is_a: WC:complexFormation

[Term]
id: WC:ribosomeAssembly
name: Ribosome Assembly
def: "Ribosome Assembly" []
is_a: WC:complexFormation

[Term]
id: WC:transcriptionComplexFormation
name: transcription
def: "transcription" []
is_a: WC:complexFormation

[Term]
id: WC:translationComplexFormation
name: Translation
def: "Translation" []
is_a: WC:complexFormation


[Term]
id: WC:signalSequence
name: signal Sequence Type
def: "signal Sequence Type" []
is_a: WC:model_element

[Term]
id: WC:secretory
name: secretory Signal Sequence Type
def: "secretory Signal Sequence Type" []
is_a: WC:signalSequence

[Term]
id: WC:lipoProtein
name: lipo Protein Signal Sequence
def: "lipo Protein Signal Sequence Type" []
is_a: WC:signalSequence

[Term]
id: WC:DNABinding
name: DNA binding Type
def: "DNA binding Type" []
is_a: WC:model_element

[Term]
id: WC:ssDNA
name: single Strand DNA Binding Type
def: "single Strand DNA Binding Type" []
is_a: WC:DNABinding

[Term]
id: WC:dsDNA
name: double Strand DNA Binding Type
def: "double Strand DNA Binding Type" []
is_a: WC:DNABinding


[Term]
id: WC:chromosomeFeature
name: chromosomeFeature
def: "chromosomeFeature Type" []
is_a: WC:model_element

[Term]
id: WC:longStructuralRegion
name: Long Structural Region
def: "Long Structural Region" []
is_a: WC:chromosomeFeature

[Term]
id: WC:DNAMethylation
name: DNA Methylation
def: "DNA Methylation" []
is_a: WC:chromosomeFeature

[Term]
id: WC:geneWizPrediction
name: geneWiz Prediction
def: "geneWiz Prediction" []
is_a: WC:chromosomeFeature

[Term]
id: WC:DNABindingSite
name: DNA Binding Site
def: "DNA Binding Site" []
is_a: WC:chromosomeFeature

[Term]
id: WC:DNABindingSiteLon
name: DNA BindingSite Lon
def: "DNA BindingSite Lon" []
is_a: WC:chromosomeFeature

[Term]
id: WC:functionalDNAABox
name: FunctionalDNAABox
def: "FunctionalDNAABox" []
is_a: WC:chromosomeFeature

[Term]
id: WC:DNAABox
name: DNAABox
def: "DNAABox" []
is_a: WC:chromosomeFeature

[Term]
id: WC:DNAMethylationSite
name: DNA Methylation site
def: "DNA Methylation site" []
is_a: WC:chromosomeFeature


[Term]
id: WC:COG
name: Clusters of orthologous groups
def: "Clusters of Orthologous Groups" []
is_a: WC:gene

[Term]
id: WC:RNAprocessing
name: RNA processing
def: "RNA processing" []
is_a: WC:COG

[Term]
id: WC:chromatinStructureDynamics
name: Chromatin Structure Dynamics
def: "Chromatin Structure Dynamics" []
is_a: WC:COG

[Term]
id: WC:energyProductionConversion
name: Energy Production and Conversion
def: "Energy Production and Conversion" []
is_a: WC:COG

[Term]
id: WC:cellCycleControlMitosis
name: Cell Cycle Control and Mitosis
def: "Cell Cycle Control and Mitosis" []
is_a: WC:COG

[Term]
id: WC:aminoAcidMetabolismTransport
name: Amino Acid Metabolism and Transport
def: "Amino Acid Metabolism and Transport" []
is_a: WC:COG

[Term]
id: WC:nucleotideMetabolismTransport
name: Nucleotide Metabolism and Transport
def: "Nucleotide Metabolism and Transport" []
is_a: WC:COG

[Term]
id: WC:carbohydrateMetabolismTransport
name: Carbohydrate Metabolism and Transport
def: "Carbohydrate Metabolism and Transport" []
is_a: WC:COG

[Term]
id: WC:coenzymeMetabolites
name: Coenzyme Metabolites
def: "Coenzyme Metabolites" []
is_a: WC:COG

[Term]
id: WC:lipidMetabolism
name: Lipid Metabolism
def: "Lipid Metabolism" []
is_a: WC:COG

[Term]
id: WC:tranlsation
name: Tranlsation
def: "Tranlsation" []
is_a: WC:COG

[Term]
id: WC:transcription
name: transcription
def: "transcription" []
is_a: WC:COG

[Term]
id: WC:replicationRepair
name: Replication Repair
def: "Replication Repair" []
is_a: WC:COG

[Term]
id: WC:cellWallMembraneEnvelopBiogenesis
name: Cell Wall Membrane Envelope Biogenesis
def: "Cell Wall Membrane Envelope Biogenesis" []
is_a: WC:COG

[Term]
id: WC:cellMotility
name: Cell Motility
def: "Cell Motility" []
is_a: WC:COG

[Term]
id: WC:secondaryStructure
name: Secondary Structure
def: "Secondary Structure" []
is_a: WC:COG

[Term]
id: WC:postTranslationalModification
name: Post Translational Modification
def: "Post Translational Modification" []
is_a: WC:COG

[Term]
id: WC:inorganicIonTransport
name: Inorganic Ion Transport
def: "Inorganic Ion Transport" []
is_a: WC:COG

[Term]
id: WC:signalTransduction
name: Signal Transduction
def: "Signal Transduction" []
is_a: WC:COG

[Term]
id: WC:intracellularTrafficingSecretion
name: Intracellular Trafficing Secretion
def: "Intracellular Trafficing Secretion" []
is_a: WC:COG

[Term]
id: WC:nuclearStructure
name: Nuclear Structure
def: "Nuclear Structure" []
is_a: WC:COG

[Term]
id: WC:cytoskeleton
name: Cytoskeleton
def: "Cytoskeleton" []
is_a: WC:COG


[Term]
id: WC:mRNA
name: messenger RNA
def: "messenger RNA" []
is_a: WC:RNA

[Term]
id: WC:rRNA
name: ribosomal RNA
def: "ribosomal RNA" []
is_a: WC:RNA

[Term]
id: WC:sRNA
name: small RNA
def: "small RNA" []
is_a: WC:RNA

[Term]
id: WC:tRNA
name: transport RNA
def: "transport RNA" []
is_a: WC:RNA

[Term]
id: WC:asRNA
name: anti-sense RNA
def: "anti-sense RNA" []
is_a: WC:RNA

[Term]
id: WC:ncRNA
name: non-coding RNA
def: "non-coding RNA" []
is_a: WC:RNA

[Term]
id: WC:mixed
name: mixed RNA
def: "mixed RNA" []
is_a: WC:RNA

[Term]
id: WC:intergenic
name: intergenic RNA
def: "intergenic RNA" []
is_a: WC:RNA


[Term]
id: WC:chemicalReaction
name: Chemical reaction
def: "Chemical reaction" []
is_a: WC:reaction

[Term]
id: WC:transportReaction
name: Transport reaction
def: "Transport reaction" []
is_a: WC:reaction

[Term]
id: WC:modifiedBaseTransportReaction
name: Modified base transport reaction
def: "Modified base transport reaction" []
is_a: WC:reaction

[Term]
id: WC:ionTransportReaction
name: Ion transport reaction
def: "Ion transport reaction" []
is_a: WC:reaction

[Term]
id: WC:TRNATransferReaction
name: tRRNA transfer reaction
def: "TRNA Transfer reaction" []
is_a: WC:reaction

[Term]
id: WC:TRNAAminoacylationReaction
name: tRNA aminoacylation reaction
def: "TRNAAminoacylation reaction" []
is_a: WC:reaction


[Term]
id: WC:proteinModificationReaction
name: protein modification reaction
def: "protein modification reaction" []
is_a: WC:reaction


[Term]
id: WC:oxidationInactivating
name: oxidation Inactivating Protein Modification
def: "oxidation Inactivating Protein Modification" []
is_a: WC:proteinModificationReaction

[Term]
id: WC:adduction
name: protein Modification Adduction
def: "Protein Modification Adduction" []
is_a: WC:proteinModificationReaction

[Term]
id: WC:ligation
name: protein Modification Ligation
def: "Protein Modification Ligation" []
is_a: WC:proteinModificationReaction

[Term]
id: WC:inactivating
name: phosphorylation Inactivating Protein Modification
def: "Phosphorylation Inactivating Protein Modification" []
is_a: WC:proteinModificationReaction

[Term]
id: WC:dephosphorylationActivating
name: dephosphorylation Activating Protein Modification
def: "Dephosphorylation Activating Protein Modification" []
is_a: WC:proteinModificationReaction

[Term]
id: WC:glycationInactivating
name: glycation Inactivating Protein Modification
def: "Glycation Inactivating Protein Modification" []
is_a: WC:proteinModificationReaction


[Term]
id: WC:DNARepairreaction
name: DNA repair reaction
def: "DNA repair reaction" []
is_a: WC:reaction

[Term]
id: WC:baseExcisionRepair
name: Base Excision Repair
def: "Base Excision Repair" []
is_a: WC:DNARepairreaction

[Term]
id: WC:DNALigation
name: DNA Ligation
def: "DNA Ligation" []
is_a: WC:DNARepairreaction

[Term]
id: WC:DNAPolymerization
name: DNA Polymerization
def: "DNA Polymerization" []
is_a: WC:DNARepairreaction

[Term]
id: WC:DNACleavage
name: DNA Cleavage
def: "DNA Cleavage" []
is_a: WC:DNARepairreaction

[Term]
id: WC:DNARestrictionModification
name: DNA Restriction Modification
def: "DNA Restriction Modification" []
is_a: WC:DNARepairreaction

[Term]
id: WC:homologousRecombination
name: Homologous Recombinationon
def: "Homologous Recombination" []
is_a: WC:DNARepairreaction

[Term]
id: WC:nucleotideExcisionRepair
name: Nucleotide Excision Repair
def: "Nucleotide Excision Repair" []
is_a: WC:DNARepairreaction


[Term]
id: WC:DNADamage
name: DNA damage reaction
def: "DNA damage reaction" []
is_a: WC:reaction

[Term]
id: WC:baseAlkylation
name: DNA Damage Base Alkylation
def: "DNA Damage Base Alkylation" []
is_a: WC:DNADamage

[Term]
id: WC:baseEthylation
name: DNA Damage Base Ethylation
def: "DNA Damage Base Ethylation" []
is_a: WC:DNADamage

[Term]
id: WC:radiationInducedBaseOxidation
name: DNA Damage Radiation Induced Base Oxidation
def: "DNA Damage Radiation Induced Base Oxidation" []
is_a: WC:DNADamage

[Term]
id: WC:baseMethylation
name: DNA Damage Base Methylation
def: "DNA Damage Base Methylation" []
is_a: WC:DNADamage

[Term]
id: WC:baseAmination
name: DNA Damage Base Amination
def: "DNA Damage Base Amination" []
is_a: WC:DNADamage

[Term]
id: WC:uvbPhotodimerization
name: DNA Damage UvB Photodimerization
def: "DNA Damage UvB Photodimerization" []
is_a: WC:DNADamage

[Term]
id: WC:photoOxidation
name: DNA Damage Photooxidation
def: "DNA Damage Photooxidation" []
is_a: WC:DNADamage

[Term]
id: WC:strandBreak
name: DNA Damage Strand Break
def: "DNA Damage Strand Break" []
is_a: WC:DNADamage

[Term]
id: WC:baseGlucosylTransfer
name: DNA Damage Base Glucosyl Transfer
def: "DNA Damage Base Glucosyl Transfer" []
is_a: WC:DNADamage

[Term]
id: WC:spontaneousBaseDeamination
name: DNA Damage Spontaneous Base Deamination
def: "DNA Damage Spontaneous Base Deamination" []
is_a: WC:DNADamage

[Term]
id: WC:spontaneousBaseLoss
name: DNA Damage Spontaneous Base Loss
def: "DNA Damage Spontaneous Base Loss" []
is_a: WC:DNADamage

[Term]
id: WC:baseReduction
name: DNA Damage Base Reduction
def: "DNA Damage Base Reduction" []
is_a: WC:DNADamage


[Term]
id: WC:regulatoryElement
name: regulatory element Type
def: "regulatory element Type" []
is_a: WC:model_element

[Term]
id: WC:promoter
name: Promoter
def: "Promoter" []
is_a: WC:regulatoryElement

[Term]
id: WC:promoterFlankingRegion
name: Promoter Flanking Region
def: "Promoter Flanking Region" []
is_a: WC:regulatoryElement

[Term]
id: WC:enhancer
name: Enhancer
def: "Enhancer" []
is_a: WC:regulatoryElement

[Term]
id: WC:CTCFBindingSite
name: CTCF Binding Site
def: "CTCF Binding Site" []
is_a: WC:regulatoryElement

[Term]
id: WC:TFBindingSite
name: TF Binding Site
def: "TF Binding Site" []
is_a: WC:regulatoryElement

[Term]
id: WC:openChromatinRegion
name: Open Chromatin Region
def: "Open Chromatin Region" []
is_a: WC:regulatoryElement


[Term]
id: WC:activityLevel
name: activity level
def: "activity level" []
is_a: WC:model_element

[Term]
id: WC:active
name: Active
def: "Active" []
is_a: WC:activityLevel

[Term]
id: WC:poised
name: Poised
def: "Poised" []
is_a: WC:activityLevel

[Term]
id: WC:repressed
name: Repressed
def: "Repressed" []
is_a: WC:activityLevel

[Term]
id: WC:inactive
name: Inactive
def: "Inactive" []
is_a: WC:activityLevel


[Term]
id: WC:regulationType
name: regulationType
def: "regulationType" []
is_a: WC:model_element

[Term]
id: WC:proximal
name: Proximal
def: "Proximal" []
is_a: WC:regulationType

[Term]
id: WC:distal
name: Distal
def: "Distal" []
is_a: WC:regulationType


[Term]
id: WC:loci
name: loci
def: "loci" []
is_a: WC:model_element

[Term]
id: WC:gene
name: gene
def: "gene" []
is_a: WC:loci

[Term]
id: WC:transcriptionUnit
name: transcription unit
def: "transcription unit" []
is_a: WC:loci

[Term]
id: WC:promoter
name: Promoter
def: "Promoter" []
is_a: WC:loci

[Term]
id: WC:pseudogene
name: pseudogene
def: "pseudogene" []
is_a: WC:gene


[Term]
id: WC:valueType
name: value type
def: "python class of ValueType" []
is_a: WC:model_element

[Term]
id: WC:boolean
name: boolean
def: "boolean" []
is_a: WC:valueType

[Term]
id: WC:string
name: string
def: "string" []
is_a: WC:valueType

[Term]
id: WC:integer
name: integer
def: "integer" []
is_a: WC:valueType

[Term]
id: WC:float
name: float
def: "float" []
is_a: WC:valueType

[Term]
id: WC:signalSequenceType
name: signal sequence type
def: "signal sequence type" []
is_a: WC:valueType