Index

_

__version__ (in module wc_kb) (in module wc_kb._version) _append_metadata_entries() (wc_kb.core.KnowledgeBaseObject method) (wc_kb.KnowledgeBaseObject method) _default() (wc_kb.__main__.BaseController method) (wc_kb.__main__.ConvertController method) (wc_kb.__main__.CreateTemplateController method) (wc_kb.__main__.DifferenceController method) (wc_kb.__main__.NormalizeController method) (wc_kb.__main__.UpdateVersionMetadataController method) (wc_kb.__main__.ValidateController method)

_parse_EviNExperiment() (wc_kb.core.KnowledgeBaseObject method) (wc_kb.KnowledgeBaseObject method) _serialize() (wc_kb.core.Identifier static method) (wc_kb.core.SpeciesCoefficient static method) (wc_kb.core.SpeciesTypeCoefficient static method) (wc_kb.eukaryote.GenericLocus static method) (wc_kb.eukaryote.TranscriptionFactorRegulation static method) (wc_kb.SpeciesCoefficient static method) (wc_kb.SpeciesTypeCoefficient static method)

A

activation (wc_kb.eukaryote.RegulatoryDirection attribute) active (wc_kb.eukaryote.ActivityLevel attribute) activity (wc_kb.eukaryote.RegulatoryModule attribute), [1] ActivityLevel (class in wc_kb.eukaryote) analysis_type (wc_kb.core.Experiment attribute), [1] (wc_kb.Experiment attribute), [1] App (class in wc_kb.__main__) App.Meta (class in wc_kb.__main__) arguments (wc_kb.__main__.BaseController.Meta attribute) (wc_kb.__main__.ConvertController.Meta attribute) (wc_kb.__main__.CreateTemplateController.Meta attribute) (wc_kb.__main__.DifferenceController.Meta attribute) (wc_kb.__main__.NormalizeController.Meta attribute) (wc_kb.__main__.UpdateVersionMetadataController.Meta attribute) (wc_kb.__main__.ValidateController.Meta attribute) attribute_order (wc_kb.Cell.Meta attribute) (wc_kb.ChromosomeFeature.Meta attribute) (wc_kb.Compartment.Meta attribute) (wc_kb.ComplexSpeciesType.Meta attribute) (wc_kb.Concentration.Meta attribute) (wc_kb.core.Cell.Meta attribute) (wc_kb.core.ChromosomeFeature.Meta attribute) (wc_kb.core.Compartment.Meta attribute) (wc_kb.core.ComplexSpeciesType.Meta attribute) (wc_kb.core.Concentration.Meta attribute) (wc_kb.core.DnaSpeciesType.Meta attribute) (wc_kb.core.Evidence.Meta attribute) (wc_kb.core.Experiment.Meta attribute) (wc_kb.core.Identifier.Meta attribute) (wc_kb.core.KnowledgeBase.Meta attribute) (wc_kb.core.MetaboliteSpeciesType.Meta attribute) (wc_kb.core.Observable.Meta attribute) (wc_kb.core.Parameter.Meta attribute) (wc_kb.core.PolymerLocus.Meta attribute) (wc_kb.core.PolymerSpeciesType.Meta attribute) (wc_kb.core.RateLaw.Meta attribute) (wc_kb.core.RateLawExpression.Meta attribute) (wc_kb.core.Reaction.Meta attribute) (wc_kb.core.Reference.Meta attribute) (wc_kb.core.Species.Meta attribute) (wc_kb.core.SpeciesCoefficient.Meta attribute) (wc_kb.core.SpeciesType.Meta attribute) (wc_kb.core.SpeciesTypeCoefficient.Meta attribute) (wc_kb.core.SpeciesTypeProperty.Meta attribute) (wc_kb.DnaSpeciesType.Meta attribute) (wc_kb.eukaryote.GeneLocus.Meta attribute) (wc_kb.eukaryote.GenericLocus.Meta attribute) (wc_kb.eukaryote.ProteinSpeciesType.Meta attribute) (wc_kb.eukaryote.PtmSite.Meta attribute) (wc_kb.eukaryote.RegulatoryModule.Meta attribute) (wc_kb.eukaryote.TranscriptionFactorRegulation.Meta attribute) (wc_kb.eukaryote.TranscriptSpeciesType.Meta attribute) (wc_kb.Evidence.Meta attribute) (wc_kb.Experiment.Meta attribute) (wc_kb.KnowledgeBase.Meta attribute) (wc_kb.MetaboliteSpeciesType.Meta attribute) (wc_kb.Observable.Meta attribute) (wc_kb.Parameter.Meta attribute) (wc_kb.PolymerLocus.Meta attribute) (wc_kb.PolymerSpeciesType.Meta attribute) (wc_kb.RateLaw.Meta attribute) (wc_kb.RateLawExpression.Meta attribute) (wc_kb.Reaction.Meta attribute) (wc_kb.Reference.Meta attribute) (wc_kb.Species.Meta attribute) (wc_kb.SpeciesCoefficient.Meta attribute) (wc_kb.SpeciesType.Meta attribute) (wc_kb.SpeciesTypeCoefficient.Meta attribute) (wc_kb.SpeciesTypeProperty.Meta attribute)

authors (wc_kb.core.Reference attribute), [1] (wc_kb.Reference attribute), [1]

B

backward (wc_kb.core.RateLawDirection attribute) (wc_kb.RateLawDirection attribute) base_controller (wc_kb.__main__.App.Meta attribute)

BaseController (class in wc_kb.__main__) BaseController.Meta (class in wc_kb.__main__) branch (wc_kb.core.KnowledgeBase attribute), [1] (wc_kb.KnowledgeBase attribute), [1]

C

calc_charge() (wc_kb.core.MetaboliteSpeciesType method) (wc_kb.MetaboliteSpeciesType method) calc_empirical_formula() (wc_kb.core.MetaboliteSpeciesType method) (wc_kb.MetaboliteSpeciesType method) calc_structure() (wc_kb.core.MetaboliteSpeciesType method) (wc_kb.MetaboliteSpeciesType method) Cell (class in wc_kb) (class in wc_kb.core) cell (wc_kb.ChromosomeFeature attribute) (wc_kb.Compartment attribute), [1] (wc_kb.Concentration attribute), [1] (wc_kb.core.ChromosomeFeature attribute) (wc_kb.core.Compartment attribute), [1] (wc_kb.core.Concentration attribute), [1] (wc_kb.core.Evidence attribute), [1] (wc_kb.core.Observable attribute), [1] (wc_kb.core.Parameter attribute), [1] (wc_kb.core.PolymerLocus attribute) (wc_kb.core.Reaction attribute), [1] (wc_kb.core.Reference attribute), [1] (wc_kb.core.SpeciesType attribute), [1] (wc_kb.Evidence attribute), [1] (wc_kb.Observable attribute), [1] (wc_kb.Parameter attribute), [1] (wc_kb.PolymerLocus attribute) (wc_kb.Reaction attribute), [1] (wc_kb.Reference attribute), [1] (wc_kb.SpeciesType attribute), [1] Cell.Meta (class in wc_kb) (class in wc_kb.core) ChromosomeFeature (class in wc_kb) (class in wc_kb.core) ChromosomeFeature.Meta (class in wc_kb) (class in wc_kb.core) circular (wc_kb.core.PolymerSpeciesType attribute), [1] (wc_kb.PolymerSpeciesType attribute), [1] coding_regions (wc_kb.eukaryote.ProteinSpeciesType attribute), [1] coefficient (wc_kb.core.SpeciesCoefficient attribute), [1] (wc_kb.core.SpeciesTypeCoefficient attribute), [1] (wc_kb.SpeciesCoefficient attribute), [1] (wc_kb.SpeciesTypeCoefficient attribute), [1]

coenzymes (wc_kb.core.Reaction attribute), [1] (wc_kb.Reaction attribute), [1] comments (wc_kb.Concentration attribute) (wc_kb.core.Concentration attribute) (wc_kb.core.Evidence attribute), [1] (wc_kb.core.Experiment attribute), [1] (wc_kb.core.KnowledgeBaseObject attribute), [1] (wc_kb.core.Reference attribute), [1] (wc_kb.eukaryote.RegulatoryModule attribute), [1] (wc_kb.Evidence attribute), [1] (wc_kb.Experiment attribute), [1] (wc_kb.KnowledgeBaseObject attribute), [1] (wc_kb.Reference attribute), [1] Compartment (class in wc_kb) (class in wc_kb.core) compartment (wc_kb.core.Species attribute), [1] (wc_kb.Species attribute), [1] Compartment.Meta (class in wc_kb) (class in wc_kb.core) ComplexSpeciesType (class in wc_kb) (class in wc_kb.core) ComplexSpeciesType.Meta (class in wc_kb) (class in wc_kb.core) Concentration (class in wc_kb) (class in wc_kb.core) Concentration.Meta (class in wc_kb) (class in wc_kb.core) convert() (in module wc_kb.io) ConvertController (class in wc_kb.__main__) ConvertController.Meta (class in wc_kb.__main__) coordinate (wc_kb.ChromosomeFeature attribute) (wc_kb.core.ChromosomeFeature attribute) create_template() (in module wc_kb.io) CreateTemplateController (class in wc_kb.__main__) CreateTemplateController.Meta (class in wc_kb.__main__)

D

description (wc_kb.__main__.BaseController.Meta attribute) (wc_kb.__main__.ConvertController.Meta attribute) (wc_kb.__main__.CreateTemplateController.Meta attribute) (wc_kb.__main__.DifferenceController.Meta attribute) (wc_kb.__main__.NormalizeController.Meta attribute) (wc_kb.__main__.UpdateVersionMetadataController.Meta attribute) (wc_kb.__main__.ValidateController.Meta attribute) (wc_kb.core.KnowledgeBase.Meta attribute) (wc_kb.KnowledgeBase.Meta attribute) deserialize() (wc_kb.core.IdentifierAttribute method) (wc_kb.core.Observable method) (wc_kb.core.ObservableExpression class method) (wc_kb.core.OneToOneSpeciesAttribute method) (wc_kb.core.RateLaw method) (wc_kb.core.RateLawExpression class method) (wc_kb.core.ReactionParticipantAttribute method) (wc_kb.core.Species class method) (wc_kb.core.SpeciesCoefficient class method) (wc_kb.core.SpeciesTypeCoefficient class method) (wc_kb.core.SubunitAttribute method) (wc_kb.eukaryote.LocusAttribute method) (wc_kb.eukaryote.RegDirectionAttribute method) (wc_kb.eukaryote.TranscriptionFactorRegulation class method) (wc_kb.IdentifierAttribute method) (wc_kb.Observable method) (wc_kb.ObservableExpression class method) (wc_kb.OneToOneSpeciesAttribute method) (wc_kb.RateLaw method) (wc_kb.RateLawExpression class method) (wc_kb.ReactionParticipantAttribute method) (wc_kb.Species class method) (wc_kb.SpeciesCoefficient class method) (wc_kb.SpeciesTypeCoefficient class method) (wc_kb.SubunitAttribute method)

deserialize_side() (wc_kb.core.ReactionParticipantAttribute method) (wc_kb.ReactionParticipantAttribute method) DifferenceController (class in wc_kb.__main__) DifferenceController.Meta (class in wc_kb.__main__) direction (wc_kb.core.RateLaw attribute), [1] (wc_kb.eukaryote.TranscriptionFactorRegulation attribute), [1] (wc_kb.RateLaw attribute), [1] distal (wc_kb.eukaryote.RegulationType attribute) DnaSpeciesType (class in wc_kb) (class in wc_kb.core) DnaSpeciesType.Meta (class in wc_kb) (class in wc_kb.core) double_stranded (wc_kb.core.PolymerSpeciesType attribute), [1] (wc_kb.PolymerSpeciesType attribute), [1]

E

end (wc_kb.ChromosomeFeature attribute) (wc_kb.core.ChromosomeFeature attribute) (wc_kb.core.PolymerLocus attribute), [1] (wc_kb.eukaryote.GenericLocus attribute), [1] (wc_kb.PolymerLocus attribute), [1] enzymes (wc_kb.core.Reaction attribute), [1] (wc_kb.Reaction attribute), [1] error (wc_kb.ChromosomeFeature attribute) (wc_kb.core.ChromosomeFeature attribute) (wc_kb.core.Parameter attribute), [1] (wc_kb.Parameter attribute), [1] EUKARYOTE_MODELS (in module wc_kb.io) Evidence (class in wc_kb) (class in wc_kb.core) evidence (wc_kb.ChromosomeFeature attribute) (wc_kb.Concentration attribute), [1] (wc_kb.core.ChromosomeFeature attribute) (wc_kb.core.Concentration attribute), [1] (wc_kb.core.Parameter attribute), [1] (wc_kb.core.Reaction attribute), [1] (wc_kb.core.SpeciesTypeProperty attribute), [1] (wc_kb.Parameter attribute), [1] (wc_kb.Reaction attribute), [1] (wc_kb.SpeciesTypeProperty attribute), [1] Evidence.Meta (class in wc_kb) (class in wc_kb.core) exons (wc_kb.eukaryote.TranscriptSpeciesType attribute), [1] Experiment (class in wc_kb) (class in wc_kb.core) experiment (wc_kb.core.Evidence attribute), [1] (wc_kb.Evidence attribute), [1] Experiment.Meta (class in wc_kb) (class in wc_kb.core) experiment_design (wc_kb.core.Experiment attribute), [1] (wc_kb.Experiment attribute), [1]

expression (wc_kb.core.Observable attribute), [1] (wc_kb.core.ObservableExpression attribute), [1] (wc_kb.core.RateLaw attribute), [1] (wc_kb.core.RateLawExpression attribute), [1] (wc_kb.Observable attribute), [1] (wc_kb.ObservableExpression attribute), [1] (wc_kb.RateLaw attribute), [1] (wc_kb.RateLawExpression attribute), [1] expression_is_linear (wc_kb.core.ObservableExpression.Meta attribute) (wc_kb.ObservableExpression.Meta attribute) expression_term_model (wc_kb.core.Observable.Meta attribute) (wc_kb.core.RateLaw.Meta attribute) (wc_kb.Observable.Meta attribute) (wc_kb.RateLaw.Meta attribute) expression_term_models (wc_kb.core.ObservableExpression.Meta attribute) (wc_kb.core.RateLawExpression.Meta attribute) (wc_kb.ObservableExpression.Meta attribute) (wc_kb.RateLawExpression.Meta attribute) expression_term_token_pattern (wc_kb.ChromosomeFeature.Meta attribute) (wc_kb.core.ChromosomeFeature.Meta attribute) (wc_kb.core.Parameter.Meta attribute) (wc_kb.core.Species.Meta attribute) (wc_kb.Parameter.Meta attribute) (wc_kb.Species.Meta attribute) expression_term_units (wc_kb.core.Observable.Meta attribute) (wc_kb.core.RateLaw.Meta attribute) (wc_kb.Observable.Meta attribute) (wc_kb.RateLaw.Meta attribute) expression_unit_registry (wc_kb.core.ObservableExpression.Meta attribute) (wc_kb.core.RateLawExpression.Meta attribute) (wc_kb.ObservableExpression.Meta attribute) (wc_kb.RateLawExpression.Meta attribute) external_media (wc_kb.core.Experiment attribute), [1] (wc_kb.Experiment attribute), [1]

F

formation_process (wc_kb.ComplexSpeciesType attribute), [1] (wc_kb.core.ComplexSpeciesType attribute), [1] forward (wc_kb.core.RateLawDirection attribute) (wc_kb.RateLawDirection attribute) fractional_abundance (wc_kb.eukaryote.PtmSite attribute), [1] frozen_columns (wc_kb.Concentration.Meta attribute) (wc_kb.core.Concentration.Meta attribute) (wc_kb.core.Species.Meta attribute) (wc_kb.core.SpeciesCoefficient.Meta attribute) (wc_kb.core.SpeciesTypeCoefficient.Meta attribute) (wc_kb.eukaryote.TranscriptionFactorRegulation.Meta attribute) (wc_kb.Species.Meta attribute) (wc_kb.SpeciesCoefficient.Meta attribute) (wc_kb.SpeciesTypeCoefficient.Meta attribute)

G

gen_id() (wc_kb.core.RateLaw method) (wc_kb.core.Species static method) (wc_kb.core.SpeciesTypeProperty method) (wc_kb.RateLaw method) (wc_kb.Species static method) (wc_kb.SpeciesTypeProperty method) gene (wc_kb.eukaryote.RegulatoryModule attribute), [1] (wc_kb.eukaryote.TranscriptSpeciesType attribute), [1] GeneLocus (class in wc_kb.eukaryote) GeneLocus.Meta (class in wc_kb.eukaryote) GenericLocus (class in wc_kb.eukaryote) GenericLocus.Meta (class in wc_kb.eukaryote) genetic_variant (wc_kb.core.Experiment attribute), [1] (wc_kb.Experiment attribute), [1] get_charge() (wc_kb.ComplexSpeciesType method) (wc_kb.core.ComplexSpeciesType method) (wc_kb.core.DnaSpeciesType method) (wc_kb.core.MetaboliteSpeciesType method) (wc_kb.core.SpeciesType method) (wc_kb.DnaSpeciesType method) (wc_kb.eukaryote.ProteinSpeciesType method) (wc_kb.eukaryote.TranscriptSpeciesType method) (wc_kb.MetaboliteSpeciesType method) (wc_kb.SpeciesType method) get_config() (in module wc_kb.config) (in module wc_kb.config.core) get_direction() (wc_kb.ChromosomeFeature method) (wc_kb.core.ChromosomeFeature method) (wc_kb.core.PolymerLocus method) (wc_kb.PolymerLocus method) get_empirical_formula() (wc_kb.ComplexSpeciesType method) (wc_kb.core.ComplexSpeciesType method) (wc_kb.core.DnaSpeciesType method) (wc_kb.core.MetaboliteSpeciesType method) (wc_kb.core.SpeciesType method) (wc_kb.DnaSpeciesType method) (wc_kb.eukaryote.ProteinSpeciesType method) (wc_kb.eukaryote.TranscriptSpeciesType method) (wc_kb.MetaboliteSpeciesType method) (wc_kb.SpeciesType method)

get_len() (wc_kb.core.PolymerLocus method) (wc_kb.core.PolymerSpeciesType method) (wc_kb.PolymerLocus method) (wc_kb.PolymerSpeciesType method) get_models() (in module wc_kb.util) get_mol_wt() (wc_kb.ComplexSpeciesType method) (wc_kb.core.ComplexSpeciesType method) (wc_kb.core.DnaSpeciesType method) (wc_kb.core.MetaboliteSpeciesType method) (wc_kb.core.SpeciesType method) (wc_kb.DnaSpeciesType method) (wc_kb.eukaryote.ProteinSpeciesType method) (wc_kb.eukaryote.TranscriptSpeciesType method) (wc_kb.MetaboliteSpeciesType method) (wc_kb.SpeciesType method) get_nested_metadata() (wc_kb.core.KnowledgeBaseObject method) (wc_kb.KnowledgeBaseObject method) get_seq() (wc_kb.core.DnaSpeciesType method) (wc_kb.core.PolymerLocus method) (wc_kb.core.PolymerSpeciesType method) (wc_kb.DnaSpeciesType method) (wc_kb.eukaryote.ProteinSpeciesType method) (wc_kb.eukaryote.TranscriptSpeciesType method) (wc_kb.PolymerLocus method) (wc_kb.PolymerSpeciesType method) get_seq_and_start_codon() (wc_kb.eukaryote.ProteinSpeciesType method) get_structure() (wc_kb.core.MetaboliteSpeciesType method) (wc_kb.MetaboliteSpeciesType method) get_subseq() (wc_kb.core.PolymerSpeciesType method) (wc_kb.PolymerSpeciesType method) get_value() (wc_kb.core.SpeciesTypeProperty method) (wc_kb.SpeciesTypeProperty method)

H

handlers (wc_kb.__main__.App.Meta attribute) help (wc_kb.__main__.BaseController.Meta attribute) (wc_kb.__main__.ConvertController.Meta attribute) (wc_kb.__main__.CreateTemplateController.Meta attribute) (wc_kb.__main__.DifferenceController.Meta attribute) (wc_kb.__main__.NormalizeController.Meta attribute) (wc_kb.__main__.UpdateVersionMetadataController.Meta attribute) (wc_kb.__main__.ValidateController.Meta attribute)

homologs (wc_kb.eukaryote.GeneLocus attribute)

I

id (wc_kb.Compartment attribute) (wc_kb.core.Compartment attribute) (wc_kb.core.Evidence attribute) (wc_kb.core.Experiment attribute) (wc_kb.core.Identifier attribute), [1] (wc_kb.core.KnowledgeBaseObject attribute), [1] (wc_kb.core.Reference attribute), [1] (wc_kb.core.Species attribute) (wc_kb.core.SpeciesType attribute) (wc_kb.eukaryote.RegulatoryModule attribute), [1] (wc_kb.Evidence attribute) (wc_kb.Experiment attribute) (wc_kb.KnowledgeBaseObject attribute), [1] (wc_kb.Reference attribute), [1] (wc_kb.Species attribute) (wc_kb.SpeciesType attribute) id() (wc_kb.core.Species method) (wc_kb.Species method) Identifier (class in wc_kb.core) Identifier.Meta (class in wc_kb.core) IdentifierAttribute (class in wc_kb) (class in wc_kb.core) identifiers (wc_kb.ChromosomeFeature attribute), [1] (wc_kb.Compartment attribute), [1] (wc_kb.Concentration attribute), [1] (wc_kb.core.ChromosomeFeature attribute), [1] (wc_kb.core.Compartment attribute), [1] (wc_kb.core.Concentration attribute), [1] (wc_kb.core.Evidence attribute), [1] (wc_kb.core.Experiment attribute), [1] (wc_kb.core.Observable attribute), [1] (wc_kb.core.Parameter attribute) (wc_kb.core.PolymerLocus attribute), [1] (wc_kb.core.RateLaw attribute), [1] (wc_kb.core.Reaction attribute), [1] (wc_kb.core.Reference attribute), [1] (wc_kb.core.SpeciesType attribute), [1] (wc_kb.core.SpeciesTypeProperty attribute), [1] (wc_kb.eukaryote.RegulatoryModule attribute), [1] (wc_kb.Evidence attribute), [1] (wc_kb.Experiment attribute), [1] (wc_kb.Observable attribute), [1] (wc_kb.Parameter attribute) (wc_kb.PolymerLocus attribute), [1] (wc_kb.RateLaw attribute), [1] (wc_kb.Reaction attribute), [1] (wc_kb.Reference attribute), [1] (wc_kb.SpeciesType attribute), [1] (wc_kb.SpeciesTypeProperty attribute), [1]

identifierss (wc_kb.core.Parameter attribute) (wc_kb.Parameter attribute) inactive (wc_kb.eukaryote.ActivityLevel attribute) intensity (wc_kb.ChromosomeFeature attribute) (wc_kb.core.ChromosomeFeature attribute) issue (wc_kb.core.Reference attribute), [1] (wc_kb.Reference attribute), [1] itRna (wc_kb.eukaryote.TranscriptType attribute)

J

journal (wc_kb.core.Reference attribute), [1] (wc_kb.Reference attribute), [1]

K

knowledge_base (wc_kb.Cell attribute), [1] (wc_kb.core.Cell attribute), [1] KnowledgeBase (class in wc_kb) (class in wc_kb.core)

KnowledgeBase.Meta (class in wc_kb) (class in wc_kb.core) KnowledgeBaseObject (class in wc_kb) (class in wc_kb.core)

L

label (wc_kb.__main__.App.Meta attribute) (wc_kb.__main__.BaseController.Meta attribute) (wc_kb.__main__.ConvertController.Meta attribute) (wc_kb.__main__.CreateTemplateController.Meta attribute) (wc_kb.__main__.DifferenceController.Meta attribute) (wc_kb.__main__.NormalizeController.Meta attribute) (wc_kb.__main__.UpdateVersionMetadataController.Meta attribute) (wc_kb.__main__.ValidateController.Meta attribute)

LocusAttribute (class in wc_kb.eukaryote)

M

main() (in module wc_kb.__main__) measurement_technology (wc_kb.core.Experiment attribute), [1] (wc_kb.Experiment attribute), [1] medium (wc_kb.Concentration attribute), [1] (wc_kb.core.Concentration attribute), [1] MetaboliteSpeciesType (class in wc_kb) (class in wc_kb.core) MetaboliteSpeciesType.Meta (class in wc_kb) (class in wc_kb.core) modified_protein (wc_kb.eukaryote.PtmSite attribute), [1] modified_residue (wc_kb.eukaryote.PtmSite attribute), [1]

module wc_kb wc_kb.__main__ wc_kb._version wc_kb.config wc_kb.config.core wc_kb.core wc_kb.eukaryote wc_kb.io wc_kb.util mRna (wc_kb.eukaryote.TranscriptType attribute)

N

na (wc_kb.eukaryote.ActivityLevel attribute) name (wc_kb.core.KnowledgeBaseObject attribute), [1] (wc_kb.core.Reference attribute), [1] (wc_kb.eukaryote.RegulatoryModule attribute), [1] (wc_kb.KnowledgeBaseObject attribute), [1] (wc_kb.Reference attribute), [1]

namespace (wc_kb.core.Identifier attribute), [1] NormalizeController (class in wc_kb.__main__) NormalizeController.Meta (class in wc_kb.__main__)

O

object (wc_kb.core.Evidence attribute), [1] (wc_kb.Evidence attribute), [1] Observable (class in wc_kb) (class in wc_kb.core) Observable.Meta (class in wc_kb) (class in wc_kb.core) ObservableExpression (class in wc_kb) (class in wc_kb.core) ObservableExpression.Meta (class in wc_kb) (class in wc_kb.core) observables (wc_kb.core.ObservableExpression attribute), [1] (wc_kb.core.RateLawExpression attribute), [1] (wc_kb.ObservableExpression attribute), [1] (wc_kb.RateLawExpression attribute), [1]

OneToOneSpeciesAttribute (class in wc_kb) (class in wc_kb.core) ordering (wc_kb.Concentration.Meta attribute) (wc_kb.core.Concentration.Meta attribute) (wc_kb.core.Identifier.Meta attribute) (wc_kb.core.RateLawExpression.Meta attribute) (wc_kb.core.Species.Meta attribute) (wc_kb.core.SpeciesCoefficient.Meta attribute) (wc_kb.core.SpeciesTypeCoefficient.Meta attribute) (wc_kb.eukaryote.GenericLocus.Meta attribute) (wc_kb.eukaryote.TranscriptionFactorRegulation.Meta attribute) (wc_kb.RateLawExpression.Meta attribute) (wc_kb.Species.Meta attribute) (wc_kb.SpeciesCoefficient.Meta attribute) (wc_kb.SpeciesTypeCoefficient.Meta attribute)

P

pages (wc_kb.core.Reference attribute) (wc_kb.Reference attribute) Parameter (class in wc_kb) (class in wc_kb.core) Parameter.Meta (class in wc_kb) (class in wc_kb.core) parameters (wc_kb.core.RateLawExpression attribute), [1] (wc_kb.core.Reaction attribute), [1] (wc_kb.RateLawExpression attribute), [1] (wc_kb.Reaction attribute), [1] participants (wc_kb.core.Reaction attribute), [1] (wc_kb.Reaction attribute), [1] ph (wc_kb.core.Experiment attribute), [1] (wc_kb.Experiment attribute), [1] ploidy (wc_kb.core.DnaSpeciesType attribute), [1] (wc_kb.DnaSpeciesType attribute), [1] poised (wc_kb.eukaryote.ActivityLevel attribute) polymer (wc_kb.ChromosomeFeature attribute) (wc_kb.core.ChromosomeFeature attribute) (wc_kb.core.PolymerLocus attribute), [1] (wc_kb.PolymerLocus attribute), [1]

PolymerDirection (in module wc_kb.core) PolymerLocus (class in wc_kb) (class in wc_kb.core) PolymerLocus.Meta (class in wc_kb) (class in wc_kb.core) PolymerSpeciesType (class in wc_kb) (class in wc_kb.core) PolymerSpeciesType.Meta (class in wc_kb) (class in wc_kb.core) PolymerStrand (in module wc_kb.core) promoter (wc_kb.eukaryote.RegulatoryModule attribute), [1] property (wc_kb.core.Evidence attribute), [1] (wc_kb.core.SpeciesTypeProperty attribute), [1] (wc_kb.Evidence attribute), [1] (wc_kb.SpeciesTypeProperty attribute), [1] ProteinSpeciesType (class in wc_kb.eukaryote) ProteinSpeciesType.Meta (class in wc_kb.eukaryote) proximal (wc_kb.eukaryote.RegulationType attribute) PtmSite (class in wc_kb.eukaryote) PtmSite.Meta (class in wc_kb.eukaryote)

R

RateLaw (class in wc_kb) (class in wc_kb.core) RateLaw.Meta (class in wc_kb) (class in wc_kb.core) RateLawDirection (class in wc_kb) (class in wc_kb.core) RateLawExpression (class in wc_kb) (class in wc_kb.core) RateLawExpression.Meta (class in wc_kb) (class in wc_kb.core) Reaction (class in wc_kb) (class in wc_kb.core) reaction (wc_kb.core.RateLaw attribute), [1] (wc_kb.RateLaw attribute), [1] Reaction.Meta (class in wc_kb) (class in wc_kb.core) ReactionParticipantAttribute (class in wc_kb) (class in wc_kb.core) Reader (class in wc_kb.io) Reference (class in wc_kb) (class in wc_kb.core) Reference.Meta (class in wc_kb) (class in wc_kb.core) references (wc_kb.ChromosomeFeature attribute), [1] (wc_kb.Compartment attribute), [1] (wc_kb.Concentration attribute), [1] (wc_kb.core.ChromosomeFeature attribute), [1] (wc_kb.core.Compartment attribute), [1] (wc_kb.core.Concentration attribute), [1] (wc_kb.core.Evidence attribute), [1] (wc_kb.core.Experiment attribute), [1] (wc_kb.core.Observable attribute), [1] (wc_kb.core.Parameter attribute), [1] (wc_kb.core.PolymerLocus attribute), [1] (wc_kb.core.RateLaw attribute), [1] (wc_kb.core.Reaction attribute), [1] (wc_kb.core.SpeciesType attribute), [1] (wc_kb.core.SpeciesTypeProperty attribute), [1] (wc_kb.eukaryote.RegulatoryModule attribute), [1] (wc_kb.Evidence attribute), [1] (wc_kb.Experiment attribute), [1] (wc_kb.Observable attribute), [1] (wc_kb.Parameter attribute), [1] (wc_kb.PolymerLocus attribute), [1] (wc_kb.RateLaw attribute), [1] (wc_kb.Reaction attribute), [1] (wc_kb.SpeciesType attribute), [1] (wc_kb.SpeciesTypeProperty attribute), [1]

RegDirectionAttribute (class in wc_kb.eukaryote) RegulationType (class in wc_kb.eukaryote) RegulatoryDirection (class in wc_kb.eukaryote) RegulatoryModule (class in wc_kb.eukaryote) RegulatoryModule.Meta (class in wc_kb.eukaryote) remove_metadata() (wc_kb.__main__.DifferenceController static method) repressed (wc_kb.eukaryote.ActivityLevel attribute) repression (wc_kb.eukaryote.RegulatoryDirection attribute) reversible (wc_kb.core.Reaction attribute), [1] (wc_kb.Reaction attribute), [1] revision (wc_kb.core.KnowledgeBase attribute), [1] (wc_kb.KnowledgeBase attribute), [1] rRna (wc_kb.eukaryote.TranscriptType attribute) run() (wc_kb.core.Validator method) (wc_kb.io.Reader method) (wc_kb.io.Writer method)

S

seq_path (wc_kb.core.DnaSpeciesType attribute) (wc_kb.DnaSpeciesType attribute) sequence_path (wc_kb.core.DnaSpeciesType attribute) (wc_kb.DnaSpeciesType attribute) serialize() (wc_kb.Concentration method) (wc_kb.core.Concentration method) (wc_kb.core.Identifier method) (wc_kb.core.IdentifierAttribute method) (wc_kb.core.ObservableExpression method) (wc_kb.core.OneToOneSpeciesAttribute method) (wc_kb.core.RateLawExpression method) (wc_kb.core.ReactionParticipantAttribute method) (wc_kb.core.Species method) (wc_kb.core.SpeciesCoefficient method) (wc_kb.core.SpeciesTypeCoefficient method) (wc_kb.core.SubunitAttribute method) (wc_kb.eukaryote.GenericLocus method) (wc_kb.eukaryote.LocusAttribute method) (wc_kb.eukaryote.RegDirectionAttribute method) (wc_kb.eukaryote.TranscriptionFactorRegulation method) (wc_kb.IdentifierAttribute method) (wc_kb.ObservableExpression method) (wc_kb.OneToOneSpeciesAttribute method) (wc_kb.RateLawExpression method) (wc_kb.ReactionParticipantAttribute method) (wc_kb.Species method) (wc_kb.SpeciesCoefficient method) (wc_kb.SpeciesTypeCoefficient method) (wc_kb.SubunitAttribute method) Species (class in wc_kb) (class in wc_kb.core) species (wc_kb.Concentration attribute), [1] (wc_kb.core.Concentration attribute), [1] (wc_kb.core.Experiment attribute), [1] (wc_kb.core.ObservableExpression attribute), [1] (wc_kb.core.RateLawExpression attribute), [1] (wc_kb.core.SpeciesCoefficient attribute), [1] (wc_kb.Experiment attribute), [1] (wc_kb.ObservableExpression attribute), [1] (wc_kb.RateLawExpression attribute), [1] (wc_kb.SpeciesCoefficient attribute), [1] Species.Meta (class in wc_kb) (class in wc_kb.core) species_type (wc_kb.core.Species attribute), [1] (wc_kb.core.SpeciesTypeCoefficient attribute), [1] (wc_kb.core.SpeciesTypeProperty attribute), [1] (wc_kb.Species attribute), [1] (wc_kb.SpeciesTypeCoefficient attribute), [1] (wc_kb.SpeciesTypeProperty attribute), [1]

SpeciesCoefficient (class in wc_kb) (class in wc_kb.core) SpeciesCoefficient.Meta (class in wc_kb) (class in wc_kb.core) SpeciesType (class in wc_kb) (class in wc_kb.core) SpeciesType.Meta (class in wc_kb) (class in wc_kb.core) SpeciesTypeCoefficient (class in wc_kb) (class in wc_kb.core) SpeciesTypeCoefficient.Meta (class in wc_kb) (class in wc_kb.core) SpeciesTypeProperty (class in wc_kb) (class in wc_kb.core) SpeciesTypeProperty.Meta (class in wc_kb) (class in wc_kb.core) spontaneous (wc_kb.core.Reaction attribute), [1] (wc_kb.Reaction attribute), [1] stacked_on (wc_kb.__main__.ConvertController.Meta attribute) (wc_kb.__main__.CreateTemplateController.Meta attribute) (wc_kb.__main__.DifferenceController.Meta attribute) (wc_kb.__main__.NormalizeController.Meta attribute) (wc_kb.__main__.UpdateVersionMetadataController.Meta attribute) (wc_kb.__main__.ValidateController.Meta attribute) stacked_type (wc_kb.__main__.ConvertController.Meta attribute) (wc_kb.__main__.CreateTemplateController.Meta attribute) (wc_kb.__main__.DifferenceController.Meta attribute) (wc_kb.__main__.NormalizeController.Meta attribute) (wc_kb.__main__.UpdateVersionMetadataController.Meta attribute) (wc_kb.__main__.ValidateController.Meta attribute) start (wc_kb.ChromosomeFeature attribute) (wc_kb.core.ChromosomeFeature attribute) (wc_kb.core.PolymerLocus attribute), [1] (wc_kb.eukaryote.GenericLocus attribute), [1] (wc_kb.PolymerLocus attribute), [1] strand (wc_kb.core.PolymerLocus attribute), [1] (wc_kb.PolymerLocus attribute), [1] SubunitAttribute (class in wc_kb) (class in wc_kb.core) subunits (wc_kb.ComplexSpeciesType attribute), [1] (wc_kb.core.ComplexSpeciesType attribute), [1] symbol (wc_kb.eukaryote.GeneLocus attribute), [1] synonyms (wc_kb.core.KnowledgeBaseObject attribute), [1] (wc_kb.core.MetaboliteSpeciesType attribute), [1] (wc_kb.KnowledgeBaseObject attribute), [1] (wc_kb.MetaboliteSpeciesType attribute), [1]

T

table_format (wc_kb.Cell.Meta attribute) (wc_kb.core.Cell.Meta attribute) (wc_kb.core.Identifier.Meta attribute) (wc_kb.core.KnowledgeBase.Meta attribute) (wc_kb.core.ObservableExpression.Meta attribute) (wc_kb.core.RateLawExpression.Meta attribute) (wc_kb.core.Species.Meta attribute) (wc_kb.core.SpeciesCoefficient.Meta attribute) (wc_kb.core.SpeciesTypeCoefficient.Meta attribute) (wc_kb.eukaryote.GenericLocus.Meta attribute) (wc_kb.eukaryote.TranscriptionFactorRegulation.Meta attribute) (wc_kb.KnowledgeBase.Meta attribute) (wc_kb.ObservableExpression.Meta attribute) (wc_kb.RateLawExpression.Meta attribute) (wc_kb.Species.Meta attribute) (wc_kb.SpeciesCoefficient.Meta attribute) (wc_kb.SpeciesTypeCoefficient.Meta attribute) taxon (wc_kb.Cell attribute), [1] (wc_kb.core.Cell attribute), [1] temperature (wc_kb.core.Experiment attribute), [1] (wc_kb.Experiment attribute), [1] temperature_units (wc_kb.core.Experiment attribute), [1] (wc_kb.Experiment attribute), [1] title (wc_kb.core.Reference attribute), [1] (wc_kb.Reference attribute), [1] to_openbabel_mol() (wc_kb.core.MetaboliteSpeciesType method) (wc_kb.MetaboliteSpeciesType method)

transcript (wc_kb.eukaryote.ProteinSpeciesType attribute), [1] transcription_factor (wc_kb.eukaryote.TranscriptionFactorRegulation attribute), [1] transcription_factor_regulation (wc_kb.eukaryote.RegulatoryModule attribute), [1] TranscriptionFactorRegulation (class in wc_kb.eukaryote) TranscriptionFactorRegulation.Meta (class in wc_kb.eukaryote) TranscriptSpeciesType (class in wc_kb.eukaryote) TranscriptSpeciesType.Meta (class in wc_kb.eukaryote) TranscriptType (class in wc_kb.eukaryote) translation_table (wc_kb.core.KnowledgeBase attribute), [1] (wc_kb.KnowledgeBase attribute), [1] tRna (wc_kb.eukaryote.TranscriptType attribute) type (wc_kb.ChromosomeFeature attribute) (wc_kb.ComplexSpeciesType attribute), [1] (wc_kb.core.ChromosomeFeature attribute) (wc_kb.core.ComplexSpeciesType attribute), [1] (wc_kb.core.MetaboliteSpeciesType attribute), [1] (wc_kb.core.Reaction attribute), [1] (wc_kb.core.Reference attribute), [1] (wc_kb.eukaryote.GeneLocus attribute) (wc_kb.eukaryote.PtmSite attribute), [1] (wc_kb.eukaryote.RegulatoryModule attribute), [1] (wc_kb.eukaryote.TranscriptSpeciesType attribute), [1] (wc_kb.MetaboliteSpeciesType attribute), [1] (wc_kb.Reaction attribute), [1] (wc_kb.Reference attribute), [1]

U

uniprot (wc_kb.eukaryote.ProteinSpeciesType attribute), [1] unique_together (wc_kb.Concentration.Meta attribute) (wc_kb.core.Concentration.Meta attribute) (wc_kb.core.Species.Meta attribute) (wc_kb.core.SpeciesTypeProperty.Meta attribute) (wc_kb.Species.Meta attribute) (wc_kb.SpeciesTypeProperty.Meta attribute) unit (wc_kb.ChromosomeFeature attribute) (wc_kb.core.ChromosomeFeature attribute) units (wc_kb.ChromosomeFeature attribute) (wc_kb.Concentration attribute), [1] (wc_kb.core.ChromosomeFeature attribute) (wc_kb.core.Concentration attribute), [1] (wc_kb.core.Evidence attribute), [1] (wc_kb.core.Observable attribute), [1] (wc_kb.core.Parameter attribute), [1] (wc_kb.core.RateLaw attribute), [1] (wc_kb.core.SpeciesTypeProperty attribute), [1] (wc_kb.Evidence attribute), [1] (wc_kb.Observable attribute), [1] (wc_kb.Parameter attribute), [1] (wc_kb.RateLaw attribute), [1] (wc_kb.SpeciesTypeProperty attribute), [1]

unknown (wc_kb.eukaryote.RegulatoryDirection attribute) UpdateVersionMetadataController (class in wc_kb.__main__) UpdateVersionMetadataController.Meta (class in wc_kb.__main__) url (wc_kb.core.KnowledgeBase attribute), [1] (wc_kb.KnowledgeBase attribute), [1]

V

validate_implicit_relationships() (wc_kb.io.Writer class method) validate_implicit_relationships_are_set() (wc_kb.io.Writer method) ValidateController (class in wc_kb.__main__) ValidateController.Meta (class in wc_kb.__main__) Validator (class in wc_kb.core) value (wc_kb.ChromosomeFeature attribute) (wc_kb.Concentration attribute), [1] (wc_kb.core.ChromosomeFeature attribute) (wc_kb.core.Concentration attribute), [1] (wc_kb.core.Evidence attribute), [1] (wc_kb.core.Parameter attribute), [1] (wc_kb.core.SpeciesTypeProperty attribute), [1] (wc_kb.Evidence attribute), [1] (wc_kb.Parameter attribute), [1] (wc_kb.SpeciesTypeProperty attribute), [1] value_type (wc_kb.core.SpeciesTypeProperty attribute), [1] (wc_kb.SpeciesTypeProperty attribute), [1] verbose_name (wc_kb.ComplexSpeciesType.Meta attribute) (wc_kb.core.ComplexSpeciesType.Meta attribute) (wc_kb.core.DnaSpeciesType.Meta attribute) (wc_kb.core.KnowledgeBase.Meta attribute) (wc_kb.core.MetaboliteSpeciesType.Meta attribute) (wc_kb.DnaSpeciesType.Meta attribute) (wc_kb.eukaryote.GeneLocus.Meta attribute) (wc_kb.eukaryote.ProteinSpeciesType.Meta attribute) (wc_kb.eukaryote.TranscriptSpeciesType.Meta attribute) (wc_kb.KnowledgeBase.Meta attribute) (wc_kb.MetaboliteSpeciesType.Meta attribute)

verbose_name_plural (wc_kb.core.SpeciesTypeProperty.Meta attribute) (wc_kb.eukaryote.GeneLocus.Meta attribute) (wc_kb.eukaryote.ProteinSpeciesType.Meta attribute) (wc_kb.eukaryote.TranscriptSpeciesType.Meta attribute) (wc_kb.SpeciesTypeProperty.Meta attribute) version (wc_kb.core.KnowledgeBase attribute), [1], [2] (wc_kb.KnowledgeBase attribute), [1], [2] volume (wc_kb.core.Reference attribute), [1] (wc_kb.Reference attribute), [1] volumetric_fraction (wc_kb.Compartment attribute), [1] (wc_kb.core.Compartment attribute), [1]

W

wc_kb module wc_kb.__main__ module wc_kb._version module wc_kb.config module wc_kb.config.core module

wc_kb.core module wc_kb.eukaryote module wc_kb.io module wc_kb.util module wc_kb_version (wc_kb.core.KnowledgeBase attribute), [1] (wc_kb.KnowledgeBase attribute), [1] Writer (class in wc_kb.io)

Y

year (wc_kb.core.Reference attribute), [1] (wc_kb.Reference attribute), [1]