Index

_

__str__() (datanator.util.molecule_util.InchiMolecule method) _is_name_ambiguous (datanator.data_source.sabio_rk.Compound attribute)

_value_inchi (datanator.data_source.sabio_rk.CompoundStructure attribute) _value_inchi_formula_connectivity (datanator.data_source.sabio_rk.CompoundStructure attribute)

A

access_dict_by_index() (datanator.util.file_util.FileUtil method) add_complexes() (datanator.data_source.intact_nosql.IntActNoSQL method) add_inchi_hash() (datanator.data_source.sabio_rk_json_mongo.SabioRkNoSQL method) (datanator.data_source.sabio_rk_nosql.SabioRk method) add_inchi_key() (datanator.data_source.sabio_compound.SabioCompound method) add_interactions() (datanator.data_source.intact_nosql.IntActNoSQL method) add_taxon_info() (datanator.data_source.sabio_rk_json_mongo.SabioRkNoSQL method) additional_name_beyond_nearest_ncbi_taxon (datanator.util.taxonomy_util.Taxon attribute) aggregate() (datanator.__main__.DownloadController method) AggregateBuildController (class in datanator.__main__) AggregateBuildController.Meta (class in datanator.__main__) App (class in datanator.__main__) (class in datanator.data_source.process_rna_seq.command_line_core) App.Meta (class in datanator.__main__) (class in datanator.data_source.process_rna_seq.command_line_core) arguments (datanator.__main__.AggregateBuildController.Meta attribute) (datanator.__main__.BaseController.Meta attribute) (datanator.__main__.BuildController.Meta attribute) (datanator.__main__.DownloadController.Meta attribute) (datanator.__main__.GenerateRNASeqTemplate.Meta attribute) (datanator.__main__.GenerateTemplateController.Meta attribute) (datanator.__main__.MoleculeController.Meta attribute) (datanator.__main__.MoleculeConvertStructureController.Meta attribute) (datanator.__main__.MoleculeGetStructureController.Meta attribute) (datanator.__main__.ReactionController.Meta attribute) (datanator.__main__.ReactionGetEcNumberController.Meta attribute) (datanator.__main__.TaxonomyController.Meta attribute) (datanator.__main__.TaxonomyGetCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToRoot.Meta attribute) (datanator.__main__.TaxonomyGetParentsController.Meta attribute) (datanator.__main__.TaxonomyGetRankController.Meta attribute) (datanator.__main__.UploadData.Meta attribute) (datanator.__main__.UploadDataController.Meta attribute) (datanator.__main__.UploadReferenceGenome.Meta attribute) (datanator.__main__.UploadRNASeqExperiment.Meta attribute) (datanator.core.data_model.ComputationalMethod attribute), [1] (datanator.data_source.process_rna_seq.command_line_core.DeleteCDNAFiles.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DeleteFASTQFiles.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DownloadCDNA.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DownloadFASTQ.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.ProcessCDNA.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.ProcessFASTQ.Meta attribute) array_express() (datanator.__main__.BuildController method) (datanator.__main__.DownloadController method) assignment_method (datanator.core.data_model.Resource attribute), [1] attribute_order (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute)

attributes (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute) author (datanator.core.data_model.Reference attribute), [1]

B

base26_dublet_for_bits_28_to_36() (in module datanator.util.base26) base26_dublet_for_bits_56_to_64() (in module datanator.util.base26) base26_triplet_1() (in module datanator.util.base26) base26_triplet_2() (in module datanator.util.base26) base26_triplet_3() (in module datanator.util.base26) base26_triplet_4() (in module datanator.util.base26) base_controller (datanator.__main__.App.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.App.Meta attribute) base_model (datanator.core.data_source.CachedDataSource attribute) (datanator.core.data_source.PostgresDataSource attribute) (datanator.data_source.sabio_rk.SabioRk attribute) BaseController (class in datanator.__main__) (class in datanator.data_source.process_rna_seq.command_line_core) BaseController.Meta (class in datanator.__main__) (class in datanator.data_source.process_rna_seq.command_line_core)

binding_matrix (datanator.core.data_model.DnaSpecie attribute), [1] build_conc_observation() (datanator.schema_2.transform_metabolite_concentrations.TMC method) build_entity() (datanator.schema_2.transform_metabolites_meta.TransformMetabolitesMeta method) build_obs() (datanator.schema_2.transform_metabolites_meta.TransformMetabolitesMeta method) build_rna_modification_entity() (datanator.schema_2.transform.Transform method) build_rna_modification_observation() (datanator.schema_2.transform.Transform method) build_rna_observation() (datanator.schema_2.transform.Transform method) build_sabio_entity() (datanator.schema_2.transform.Transform method) build_uniprot_entity() (datanator.schema_2.transform.Transform method) build_uniprot_observation() (datanator.schema_2.transform.Transform method) BuildController (class in datanator.__main__) BuildController.Meta (class in datanator.__main__) bulk_load() (datanator.data_source.kegg_org_code.KeggOrgCode method)

C

cache_dirname (datanator.core.data_source.CachedDataSource attribute) (datanator.core.data_source.PostgresDataSource attribute) CachedDataSource (class in datanator.core.data_source) calc_enzyme_molecular_weights() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) calc_inchi_formula_connectivity() (datanator.data_source.sabio_rk.CompoundStructure method) (datanator.data_source.sabio_rk_nosql.SabioRk method) calc_reactant_product_pairs() (in module datanator.util.reaction_util) calc_stats() (datanator.data_source.sabio_rk.SabioRk method) CalcTanimoto (class in datanator.util.calc_tanimoto) chapter (datanator.core.data_model.Reference attribute), [1] charge (datanator.util.molecule_util.InchiMolecule attribute) ChemUtil (class in datanator.util.chem_util) children (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute) class_name (datanator.core.data_model.ProteinComplexSpecie attribute) clear_content() (datanator.core.data_source.CachedDataSource method) (datanator.core.data_source.PostgresDataSource method) clear_requests_cache() (datanator.core.data_source.HttpDataSource method) coefficient (datanator.core.data_model.ReactionParticipant attribute), [1] (datanator.data_source.sabio_rk.EnzymeSubunit attribute), [1] (datanator.data_source.sabio_rk.ReactionParticipant attribute), [1] commit_intermediate_results (datanator.core.data_source.CachedDataSource attribute) Compartment (class in datanator.core.data_model) (class in datanator.data_source.sabio_rk) compartment (datanator.core.data_model.Observable attribute), [1] (datanator.core.data_model.ReactionParticipant attribute), [1] (datanator.data_source.sabio_rk.Parameter attribute), [1] (datanator.data_source.sabio_rk.ReactionParticipant attribute), [1]

Compartment.Meta (class in datanator.core.data_model) compartment_id (datanator.data_source.sabio_rk.Parameter attribute) (datanator.data_source.sabio_rk.ReactionParticipant attribute) complex_cmt (datanator.core.data_model.ProteinComplexSpecie attribute) Compound (class in datanator.data_source.sabio_rk) compound (datanator.data_source.sabio_rk.Parameter attribute), [1] (datanator.data_source.sabio_rk.ReactionParticipant attribute), [1] compound_id (datanator.data_source.sabio_rk.Parameter attribute) (datanator.data_source.sabio_rk.ReactionParticipant attribute) compounds (datanator.data_source.sabio_rk.CompoundStructure attribute) CompoundStructure (class in datanator.data_source.sabio_rk) ComputationalMethod (class in datanator.core.data_model) ComputationalMethod.Meta (class in datanator.core.data_model) con_db() (datanator.util.mongo_util.MongoUtil method) confidence (datanator.core.data_model.Interaction attribute) connections (datanator.util.molecule_util.InchiMolecule attribute) Consensus (class in datanator.core.data_model) Consensus.Meta (class in datanator.core.data_model) ConsensusMethod (class in datanator.core.data_model) continuousload() (in module datanator.util.build_util) copy_uniprot() (datanator.data_source.protein_aggregate.ProteinAggregate method) correct_protein_name_list() (in module datanator.data_source.corum_nosql) corum() (datanator.__main__.BuildController method) (datanator.__main__.DownloadController method) CorumNoSQL (class in datanator.data_source.corum_nosql) count_line() (datanator.data_source.taxon_tree.TaxonTree method) create_compartment_from_sbml() (datanator.data_source.sabio_rk.SabioRk method) create_cross_references_from_sbml() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) create_kinetic_law_from_sbml() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) create_kinetic_laws_from_sbml() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) create_reactants() (datanator.data_source.sabio_reaction.RxnAggregate method) create_specie_from_sbml() (datanator.data_source.sabio_rk.SabioRk method) create_taxon() (in module datanator.__main__) created (datanator.data_source.sabio_rk.Compartment attribute) (datanator.data_source.sabio_rk.Compound attribute) (datanator.data_source.sabio_rk.Entry attribute), [1] (datanator.data_source.sabio_rk.Enzyme attribute) (datanator.data_source.sabio_rk.EnzymeSubunit attribute) (datanator.data_source.sabio_rk.KineticLaw attribute) (datanator.data_source.sabio_rk.Parameter attribute) cross_references (datanator.core.data_model.EntityInteractionOrProperty attribute), [1] (datanator.core.data_model.ObservedResultMetadata attribute) (datanator.data_source.sabio_rk.Compartment attribute) (datanator.data_source.sabio_rk.Compound attribute) (datanator.data_source.sabio_rk.Entry attribute), [1] (datanator.data_source.sabio_rk.Enzyme attribute) (datanator.data_source.sabio_rk.EnzymeSubunit attribute) (datanator.data_source.sabio_rk.KineticLaw attribute) (datanator.data_source.sabio_rk.Parameter attribute) (datanator.util.molecule_util.Molecule attribute) (datanator.util.taxonomy_util.Taxon attribute)

D

datanator (module) datanator.__main__ (module) datanator._version (module) datanator.config (module) datanator.config.core (module) datanator.core (module) datanator.core.data_model (module) datanator.core.data_source (module) datanator.data_source (module) datanator.data_source.array_express_tools (module) datanator.data_source.array_express_tools.ensembl_tools (module) datanator.data_source.builds (module) datanator.data_source.corum_nosql (module) datanator.data_source.ec (module) datanator.data_source.gene_ortholog (module) datanator.data_source.intact_nosql (module) datanator.data_source.kegg_org_code (module) datanator.data_source.kegg_orthology (module) datanator.data_source.kegg_reaction_class (module) datanator.data_source.metabolites_meta_collection (module) datanator.data_source.modomics (module) datanator.data_source.pax_nosql (module) datanator.data_source.process_rna_seq (module) datanator.data_source.process_rna_seq.command_line_core (module) datanator.data_source.process_rna_seq.core (module) datanator.data_source.process_rna_seq.download_cdna (module) datanator.data_source.protein_aggregate (module) datanator.data_source.sabio_compound (module) datanator.data_source.sabio_reaction (module) datanator.data_source.sabio_rk (module) datanator.data_source.sabio_rk_json_mongo (module) datanator.data_source.sabio_rk_nosql (module) datanator.data_source.sqlite_to_json (module) datanator.data_source.taxon_tree (module) datanator.parse_metabolite_concentration (module) datanator.schema_2 (module) datanator.schema_2.transform (module) datanator.schema_2.transform_metabolite_concentrations (module) datanator.schema_2.transform_metabolites_meta (module) datanator.util (module) datanator.util.base26 (module) datanator.util.build_util (module) datanator.util.calc_tanimoto (module) datanator.util.chem_util (module) datanator.util.constants (module) datanator.util.file_util (module) datanator.util.index_collection (module) datanator.util.molecule_util (module) datanator.util.mongo_util (module) datanator.util.reaction_util (module) datanator.util.rna_halflife_util (module) datanator.util.rna_seq_util (module) datanator.util.taxonomy_util (module) datanator.util.warning_util (module) DataSource (class in datanator.core.data_source) DataSourceWarning date (datanator.core.data_model.Consensus attribute), [1] db() (datanator.data_source.sqlite_to_json.SQLToJSON method) delete_cdna_files() (in module datanator.data_source.process_rna_seq.core) delete_fastq_files() (in module datanator.data_source.process_rna_seq.core) DeleteCDNAFiles (class in datanator.data_source.process_rna_seq.command_line_core) DeleteCDNAFiles.Meta (class in datanator.data_source.process_rna_seq.command_line_core) DeleteFASTQFiles (class in datanator.data_source.process_rna_seq.command_line_core) DeleteFASTQFiles.Meta (class in datanator.data_source.process_rna_seq.command_line_core) description (datanator.__main__.AggregateBuildController.Meta attribute) (datanator.__main__.BaseController.Meta attribute) (datanator.__main__.BuildController.Meta attribute) (datanator.__main__.DownloadController.Meta attribute) (datanator.__main__.GenerateRNASeqTemplate.Meta attribute) (datanator.__main__.GenerateTemplateController.Meta attribute) (datanator.__main__.MoleculeController.Meta attribute) (datanator.__main__.MoleculeConvertStructureController.Meta attribute) (datanator.__main__.MoleculeGetStructureController.Meta attribute) (datanator.__main__.ReactionController.Meta attribute) (datanator.__main__.ReactionGetEcNumberController.Meta attribute) (datanator.__main__.TaxonomyController.Meta attribute) (datanator.__main__.TaxonomyGetCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToRoot.Meta attribute) (datanator.__main__.TaxonomyGetParentsController.Meta attribute) (datanator.__main__.TaxonomyGetRankController.Meta attribute) (datanator.__main__.UploadData.Meta attribute) (datanator.__main__.UploadDataController.Meta attribute) (datanator.__main__.UploadReferenceGenome.Meta attribute) (datanator.__main__.UploadRNASeqExperiment.Meta attribute) (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method attribute), [1] (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.BaseController.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DeleteCDNAFiles.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DeleteFASTQFiles.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DownloadCDNA.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DownloadFASTQ.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.ProcessCDNA.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.ProcessFASTQ.Meta attribute)

disable_warnings() (in module datanator.util.warning_util) disease_cmt (datanator.core.data_model.ProteinComplexSpecie attribute) distance_from_nearest_ncbi_taxon (datanator.util.taxonomy_util.Taxon attribute) DnaSpecie (class in datanator.core.data_model) DnaSpecie.Meta (class in datanator.core.data_model) double_bonds (datanator.util.molecule_util.InchiMolecule attribute) download_backups() (datanator.core.data_source.CachedDataSource method) download_cdna() (in module datanator.data_source.process_rna_seq.core) (in module datanator.data_source.process_rna_seq.download_cdna) download_content() (datanator.data_source.intact_nosql.IntActNoSQL method) download_dump() (datanator.data_source.taxon_tree.TaxonTree method) download_fastq() (in module datanator.data_source.process_rna_seq.core) download_ko() (datanator.data_source.kegg_orthology.KeggOrthology method) download_request_backup (datanator.core.data_source.HttpDataSource attribute) download_rxn() (datanator.data_source.kegg_reaction_class.KeggReaction method) download_rxn_cls() (datanator.data_source.kegg_reaction_class.KeggReaction method) download_url (datanator.data_source.array_express_tools.ensembl_tools.StrainInfo attribute) DownloadCDNA (class in datanator.data_source.process_rna_seq.command_line_core) DownloadCDNA.Meta (class in datanator.data_source.process_rna_seq.command_line_core) DownloadController (class in datanator.__main__) DownloadController.Meta (class in datanator.__main__) DownloadFASTQ (class in datanator.data_source.process_rna_seq.command_line_core) DownloadFASTQ.Meta (class in datanator.data_source.process_rna_seq.command_line_core) dump_database() (datanator.core.data_source.PostgresDataSource method)

E

EC (class in datanator.data_source.ec) ecmdb() (datanator.__main__.BuildController method) (datanator.__main__.DownloadController method) editor (datanator.core.data_model.Reference attribute), [1] embl_helper() (datanator.data_source.uniprot_nosql.UniprotNoSQL method) enable_warnings() (in module datanator.util.warning_util) ENDPOINT (datanator.data_source.modomics.Modomics attribute) ENDPOINT_COMPOUNDS_PAGE (datanator.data_source.sabio_rk.SabioRk attribute), [1] ENDPOINT_DOMAINS (datanator.core.data_source.FtpDataSource attribute), [1] (datanator.core.data_source.HttpDataSource attribute), [1] (datanator.core.data_source.WebserviceDataSource attribute), [1] (datanator.data_source.sabio_rk.SabioRk attribute) ENDPOINT_EXCEL_EXPORT (datanator.data_source.sabio_rk.SabioRk attribute), [1] ENDPOINT_KINETIC_LAWS_PAGE (datanator.data_source.sabio_rk.SabioRk attribute) ENDPOINT_KINETIC_LAWS_SEARCH (datanator.data_source.sabio_rk.SabioRk attribute), [1] ENDPOINT_WEBSERVICE (datanator.data_source.sabio_rk.SabioRk attribute), [1] engine (datanator.core.data_source.CachedDataSource attribute) (datanator.core.data_source.PostgresDataSource attribute) EntityInteractionOrProperty (class in datanator.core.data_model) EntityInteractionOrProperty.Meta (class in datanator.core.data_model) entrez_id (datanator.core.data_model.ProteinSpecie attribute), [1] entries (datanator.data_source.sabio_rk.Resource attribute) (datanator.data_source.sabio_rk.Synonym attribute) Entry (class in datanator.data_source.sabio_rk) Environment (class in datanator.core.data_model) environment (datanator.core.data_model.ObservedResultMetadata attribute), [1] Environment.Meta (class in datanator.core.data_model)

Enzyme (class in datanator.data_source.sabio_rk) enzyme (datanator.data_source.sabio_rk.EnzymeSubunit attribute), [1] (datanator.data_source.sabio_rk.KineticLaw attribute), [1] (datanator.data_source.sabio_rk.Parameter attribute), [1] enzyme_compartment (datanator.data_source.sabio_rk.KineticLaw attribute), [1] enzyme_compartment_id (datanator.data_source.sabio_rk.KineticLaw attribute) enzyme_id (datanator.data_source.sabio_rk.EnzymeSubunit attribute) (datanator.data_source.sabio_rk.KineticLaw attribute) (datanator.data_source.sabio_rk.Parameter attribute) enzyme_type (datanator.data_source.sabio_rk.KineticLaw attribute), [1] EnzymeSubunit (class in datanator.data_source.sabio_rk) equation (datanator.data_source.sabio_rk.KineticLaw attribute), [1] error (datanator.core.data_model.Consensus attribute), [1] (datanator.core.data_model.ObservedValue attribute), [1] (datanator.data_source.sabio_rk.Parameter attribute), [1] establish_ftp() (datanator.data_source.ec.EC method) Evidence (class in datanator.core.data_model) evidence (datanator.core.data_model.Consensus attribute), [1] Evidence.Meta (class in datanator.core.data_model) excel_batch_size (datanator.data_source.sabio_rk.SabioRk attribute) exists_key_value_pair() (datanator.util.file_util.FileUtil method) ExperimentalMethod (class in datanator.core.data_model) ExperimentalMethod.Meta (class in datanator.core.data_model) export_stats() (datanator.data_source.sabio_rk.SabioRk method) extract_enzyme_names() (datanator.data_source.sabio_reaction.RxnAggregate method) extract_reactant_names() (datanator.data_source.sabio_reaction.RxnAggregate method) extract_values() (datanator.util.file_util.FileUtil method)

F

family_name (datanator.core.data_model.ProteinComplexSpecie attribute) filename (datanator.core.data_source.CachedDataSource attribute) FileUtil (class in datanator.util.file_util) fill_abundance_publication() (datanator.data_source.uniprot_nosql.UniprotNoSQL method) fill_collection() (datanator.data_source.sabio_reaction.RxnAggregate method) fill_db() (datanator.util.mongo_util.MongoUtil method) fill_ec_meta() (datanator.data_source.sabio_rk_json_mongo.SabioRkNoSQL method) fill_kegg_meta() (datanator.data_source.sabio_rk_json_mongo.SabioRkNoSQL method) fill_ko_name() (datanator.data_source.uniprot_nosql.UniprotNoSQL method) fill_metabolite_fields() (datanator.data_source.metabolites_meta_collection.MetabolitesMeta method) fill_names() (datanator.data_source.metabolites_meta_collection.MetabolitesMeta method) fill_reactant_aggregate_name() (datanator.data_source.sabio_rk_json_mongo.SabioRkNoSQL method) fill_reactions() (datanator.data_source.uniprot_nosql.UniprotNoSQL method) fill_species_info() (datanator.data_source.uniprot_nosql.UniprotNoSQL method) fill_species_name() (datanator.data_source.uniprot_nosql.UniprotNoSQL method) fill_species_name_new() (datanator.data_source.uniprot_nosql.UniprotNoSQL method) fill_standard_id() (datanator.data_source.metabolites_meta_collection.MetabolitesMeta method) fill_uniprot_by_embl() (datanator.util.rna_halflife_util.RnaHLUtil method) fill_uniprot_by_gn() (datanator.util.rna_halflife_util.RnaHLUtil method) fill_uniprot_by_oln() (datanator.util.rna_halflife_util.RnaHLUtil method) fill_uniprot_with_df() (datanator.util.rna_halflife_util.RnaHLUtil method) find_between() (datanator.data_source.intact_nosql.IntActNoSQL method) find_between_psi_mi_parentheses() (datanator.data_source.intact_nosql.IntActNoSQL method) find_files() (in module datanator.data_source.pax_nosql) find_nth() (in module datanator.data_source.array_express_tools.ensembl_tools) find_protein_gene() (datanator.data_source.intact_nosql.IntActNoSQL method) find_pubmed_id() (datanator.data_source.intact_nosql.IntActNoSQL method) fixed_hydrogens (datanator.util.molecule_util.InchiMolecule attribute) flatten_collection() (datanator.util.mongo_util.MongoUtil method) flatten_json() (datanator.util.file_util.FileUtil method) format (datanator.data_source.sabio_rk.CompoundStructure attribute), [1] format_org_name() (in module datanator.data_source.array_express_tools.ensembl_tools)

formula (datanator.util.molecule_util.InchiMolecule attribute) frozen_columns (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute) FtpDataSource (class in datanator.core.data_source) full_strain_specificity (datanator.data_source.array_express_tools.ensembl_tools.StrainInfo attribute) funcat_dsc (datanator.core.data_model.ProteinComplexSpecie attribute) funcat_id (datanator.core.data_model.ProteinComplexSpecie attribute)

G

gene_name (datanator.core.data_model.ProteinSpecie attribute), [1] GenerateRNASeqTemplate (class in datanator.__main__) GenerateRNASeqTemplate.Meta (class in datanator.__main__) GenerateTemplateController (class in datanator.__main__) GenerateTemplateController.Meta (class in datanator.__main__) Genetics (class in datanator.core.data_model) genetics (datanator.core.data_model.ObservedResultMetadata attribute), [1] Genetics.Meta (class in datanator.core.data_model) get_common() (datanator.util.file_util.FileUtil method) get_common_ancestor() (datanator.util.taxonomy_util.Taxon method) get_compartment_from_sbml() (datanator.data_source.sabio_rk_nosql.SabioRk method) get_config() (in module datanator.config.core) get_debug_logs_config() (in module datanator.config.core) get_distance_to_common_ancestor() (datanator.util.taxonomy_util.Taxon method) get_distance_to_root() (datanator.util.taxonomy_util.Taxon method) get_ec() (datanator.data_source.sabio_reaction.RxnAggregate method) get_ec_number() (datanator.core.data_model.Reaction method) get_ec_numbers() (datanator.core.data_model.Reaction method) get_engine() (datanator.core.data_source.CachedDataSource method) (datanator.core.data_source.PostgresDataSource method) get_fingerprint() (datanator.util.molecule_util.Molecule method) get_fingerprint_types() (datanator.util.molecule_util.Molecule static method) get_format() (datanator.util.molecule_util.Molecule method) get_formula_and_connectivity() (datanator.util.molecule_util.InchiMolecule method) get_ftp_url() (in module datanator.data_source.array_express_tools.ensembl_tools) get_html() (datanator.data_source.gene_ortholog.KeggGeneOrtholog method) get_inchi_structures() (datanator.data_source.sabio_rk.Compound method) get_json_ends() (in module datanator.data_source.array_express_tools.ensembl_tools) get_manual_ec_numbers() (datanator.core.data_model.Reaction method) get_max_distance_to_common_ancestor() (datanator.util.taxonomy_util.Taxon method) get_modifiers() (datanator.core.data_model.Reaction method) get_mongo_config() (in module datanator.config.core) get_ncbi_id() (datanator.data_source.kegg_org_code.KeggOrgCode method) (datanator.util.taxonomy_util.Taxon method)

get_ncbi_id_rest() (datanator.data_source.kegg_org_code.KeggOrgCode method) get_or_create_object() (datanator.core.data_source.CachedDataSource method) (datanator.core.data_source.PostgresDataSource method) get_ordered_participants() (datanator.core.data_model.Reaction method) get_parameter_by_properties() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) get_parent_taxa() (datanator.util.taxonomy_util.Taxon method) get_paths_to_backup() (datanator.core.data_source.CachedDataSource method) (datanator.core.data_source.HttpDataSource method) get_predicted_ec_numbers() (datanator.core.data_model.Reaction method) get_processed_data_samples() (in module datanator.data_source.process_rna_seq.core) get_products() (datanator.core.data_model.Reaction method) get_rank() (datanator.util.taxonomy_util.Taxon method) get_reactant_product_pairs() (datanator.core.data_model.Reaction method) get_reactants() (datanator.core.data_model.Reaction method) get_ref_seq_url() (in module datanator.data_source.array_express_tools.ensembl_tools) get_requests_session() (datanator.core.data_source.HttpDataSource method) get_rxn_id() (datanator.data_source.sabio_reaction.RxnAggregate method) get_session() (datanator.core.data_source.CachedDataSource method) (datanator.core.data_source.PostgresDataSource method) get_sha256() (datanator.util.chem_util.ChemUtil method) get_similarity() (datanator.core.data_model.Specie method) (datanator.util.molecule_util.Molecule method) get_smiles_structures() (datanator.data_source.sabio_rk.Compound method) get_specie_from_sbml() (datanator.data_source.sabio_rk_nosql.SabioRk method) get_specie_reference_from_sbml() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) get_strain_info() (in module datanator.data_source.array_express_tools.ensembl_tools) get_tanimoto() (datanator.util.calc_tanimoto.CalcTanimoto method) get_taxonomic_lineage() (in module datanator.data_source.array_express_tools.ensembl_tools) get_val_from_dict_list() (datanator.util.file_util.FileUtil method) go_dsc (datanator.core.data_model.ProteinComplexSpecie attribute) go_id (datanator.core.data_model.ProteinComplexSpecie attribute) growth_status (datanator.core.data_model.Environment attribute) growth_system (datanator.core.data_model.Environment attribute)

H

handlers (datanator.__main__.App.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.App.Meta attribute) hardware (datanator.core.data_model.Method attribute) has_align_but_no_rowspan() (datanator.data_source.kegg_org_code.KeggOrgCode method) hash_inchi() (datanator.util.chem_util.ChemUtil method) hash_null_reactants() (datanator.data_source.sabio_reaction.RxnAggregate method) help (datanator.__main__.AggregateBuildController.Meta attribute) (datanator.__main__.BaseController.Meta attribute) (datanator.__main__.BuildController.Meta attribute) (datanator.__main__.DownloadController.Meta attribute) (datanator.__main__.GenerateRNASeqTemplate.Meta attribute) (datanator.__main__.GenerateTemplateController.Meta attribute) (datanator.__main__.MoleculeController.Meta attribute) (datanator.__main__.MoleculeConvertStructureController.Meta attribute) (datanator.__main__.MoleculeGetStructureController.Meta attribute) (datanator.__main__.ReactionController.Meta attribute) (datanator.__main__.ReactionGetEcNumberController.Meta attribute) (datanator.__main__.TaxonomyController.Meta attribute) (datanator.__main__.TaxonomyGetCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToRoot.Meta attribute) (datanator.__main__.TaxonomyGetParentsController.Meta attribute) (datanator.__main__.TaxonomyGetRankController.Meta attribute) (datanator.__main__.UploadData.Meta attribute) (datanator.__main__.UploadDataController.Meta attribute) (datanator.__main__.UploadReferenceGenome.Meta attribute) (datanator.__main__.UploadRNASeqExperiment.Meta attribute)

HttpDataSource (class in datanator.core.data_source) hydrogens (datanator.util.molecule_util.InchiMolecule attribute)

I

id (datanator.core.data_model.EntityInteractionOrProperty attribute), [1] (datanator.core.data_model.Resource attribute), [1] (datanator.data_source.sabio_rk.Compartment attribute) (datanator.data_source.sabio_rk.Compound attribute) (datanator.data_source.sabio_rk.Entry attribute), [1] (datanator.data_source.sabio_rk.Enzyme attribute) (datanator.data_source.sabio_rk.EnzymeSubunit attribute) (datanator.data_source.sabio_rk.KineticLaw attribute) (datanator.data_source.sabio_rk.Parameter attribute) (datanator.data_source.sabio_rk.Resource attribute), [1] (datanator.util.molecule_util.Molecule attribute) (datanator.util.taxonomy_util.Taxon attribute) id_of_nearest_ncbi_taxon (datanator.util.taxonomy_util.Taxon attribute) inchi_to_inchikey() (datanator.util.chem_util.ChemUtil method) InchiMolecule (class in datanator.util.molecule_util) index() (datanator.util.rna_seq_util.Kallisto method) index_corum() (datanator.util.index_collection.IndexCollection method) index_intact_complex() (datanator.util.index_collection.IndexCollection method) index_metabolites_meta() (datanator.util.index_collection.IndexCollection method) index_pax() (datanator.util.index_collection.IndexCollection method) index_sabio() (datanator.util.index_collection.IndexCollection method) index_strdb() (datanator.util.index_collection.IndexCollection method) index_uniprot() (datanator.util.index_collection.IndexCollection method) IndexCollection (class in datanator.util.index_collection) indexed_attrs_tuples (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute)

infer_compound_structures_from_names() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) inheritance (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute) insert_canon_anc() (datanator.data_source.taxon_tree.TaxonTree method) intact() (datanator.__main__.BuildController method) (datanator.__main__.DownloadController method) IntActNoSQL (class in datanator.data_source.intact_nosql) Interaction (class in datanator.core.data_model) interaction (datanator.core.data_model.Observable attribute), [1] (datanator.core.data_model.ObservedInteraction attribute), [1] Interaction.Meta (class in datanator.core.data_model) interaction_type (datanator.core.data_model.SpecieInteraction attribute) is_equal() (datanator.util.molecule_util.InchiMolecule method) is_protonation_isomer() (datanator.util.molecule_util.InchiMolecule method) is_stereoisomer() (datanator.util.molecule_util.InchiMolecule method) is_tautomer() (datanator.util.molecule_util.InchiMolecule method) is_variant() (datanator.core.data_model.Genetics method) is_wildtype() (datanator.core.data_model.Genetics method) isotopes (datanator.util.molecule_util.InchiMolecule attribute)

J

jaspar() (datanator.__main__.BuildController method) (datanator.__main__.DownloadController method)

K

Kallisto (class in datanator.util.rna_seq_util) KeggGeneOrtholog (class in datanator.data_source.gene_ortholog) KeggOrgCode (class in datanator.data_source.kegg_org_code) KeggOrthology (class in datanator.data_source.kegg_orthology) KeggReaction (class in datanator.data_source.kegg_reaction_class) kinetic_law (datanator.data_source.sabio_rk.Parameter attribute)

kinetic_law_id (datanator.core.data_model.Reaction attribute) (datanator.data_source.sabio_rk.Parameter attribute) kinetic_laws (datanator.data_source.sabio_rk.Compartment attribute) (datanator.data_source.sabio_rk.Enzyme attribute) (datanator.data_source.sabio_rk.Resource attribute) KineticLaw (class in datanator.data_source.sabio_rk)

L

label (datanator.__main__.AggregateBuildController.Meta attribute) (datanator.__main__.App.Meta attribute) (datanator.__main__.BaseController.Meta attribute) (datanator.__main__.BuildController.Meta attribute) (datanator.__main__.DownloadController.Meta attribute) (datanator.__main__.GenerateRNASeqTemplate.Meta attribute) (datanator.__main__.GenerateTemplateController.Meta attribute) (datanator.__main__.MoleculeController.Meta attribute) (datanator.__main__.MoleculeConvertStructureController.Meta attribute) (datanator.__main__.MoleculeGetStructureController.Meta attribute) (datanator.__main__.ReactionController.Meta attribute) (datanator.__main__.ReactionGetEcNumberController.Meta attribute) (datanator.__main__.TaxonomyController.Meta attribute) (datanator.__main__.TaxonomyGetCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToRoot.Meta attribute) (datanator.__main__.TaxonomyGetParentsController.Meta attribute) (datanator.__main__.TaxonomyGetRankController.Meta attribute) (datanator.__main__.UploadData.Meta attribute) (datanator.__main__.UploadDataController.Meta attribute) (datanator.__main__.UploadReferenceGenome.Meta attribute) (datanator.__main__.UploadRNASeqExperiment.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.App.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.BaseController.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DeleteCDNAFiles.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DeleteFASTQFiles.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DownloadCDNA.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DownloadFASTQ.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.ProcessCDNA.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.ProcessFASTQ.Meta attribute) label_existence() (datanator.data_source.sabio_reaction.RxnAggregate method) LAYERS (datanator.util.molecule_util.InchiMolecule attribute), [1] length (datanator.core.data_model.ProteinSpecie attribute), [1] list_all_collections() (datanator.util.mongo_util.MongoUtil method) load_abundance_from_pax() (datanator.data_source.protein_aggregate.ProteinAggregate method) (datanator.data_source.uniprot_nosql.UniprotNoSQL method) load_bad_kinlaw() (datanator.data_source.protein_aggregate.ProteinAggregate method) load_compounds() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) load_content() (datanator.core.data_source.CachedDataSource method) (datanator.core.data_source.PostgresDataSource method) (datanator.data_source.corum_nosql.CorumNoSQL method) (datanator.data_source.intact_nosql.IntActNoSQL method) (datanator.data_source.kegg_orthology.KeggOrthology method) (datanator.data_source.kegg_reaction_class.KeggReaction method) (datanator.data_source.metabolites_meta_collection.MetabolitesMeta method) (datanator.data_source.pax_nosql.PaxNoSQL method) (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) (datanator.data_source.taxon_tree.TaxonTree method)

load_data() (datanator.data_source.gene_ortholog.KeggGeneOrtholog method) load_df() (datanator.data_source.uniprot_nosql.UniprotNoSQL method) load_json() (datanator.data_source.sabio_rk_json_mongo.SabioRkNoSQL method) load_kinetic_law_ids() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) load_kinetic_laws() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) load_ko() (datanator.data_source.protein_aggregate.ProteinAggregate method) load_ko_from_uniprot() (datanator.data_source.protein_aggregate.ProteinAggregate method) load_missing_enzyme_information_from_html() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) load_missing_kinetic_law_information_from_tsv() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) load_missing_kinetic_law_information_from_tsv_helper() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) load_taxon() (datanator.data_source.protein_aggregate.ProteinAggregate method) load_uniprot() (datanator.data_source.uniprot_nosql.UniprotNoSQL method) load_unreviewed_abundance() (datanator.data_source.protein_aggregate.ProteinAggregate method) loc_a (datanator.core.data_model.SpecieInteraction attribute), [1] loc_b (datanator.core.data_model.SpecieInteraction attribute), [1] local_attributes (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute)

M

main() (in module datanator.__main__) (in module datanator.data_source.corum_nosql) (in module datanator.data_source.ec) (in module datanator.data_source.gene_ortholog) (in module datanator.data_source.kegg_org_code) (in module datanator.data_source.kegg_orthology) (in module datanator.data_source.kegg_reaction_class) (in module datanator.data_source.metabolites_meta_collection) (in module datanator.data_source.process_rna_seq.command_line_core) (in module datanator.data_source.protein_aggregate) (in module datanator.data_source.sabio_compound) (in module datanator.data_source.sabio_reaction) (in module datanator.data_source.sabio_rk_json_mongo) (in module datanator.data_source.sabio_rk_nosql) (in module datanator.data_source.sqlite_to_json) (in module datanator.data_source.taxon_tree) (in module datanator.data_source.uniprot_nosql) (in module datanator.parse_metabolite_concentration) (in module datanator.schema_2.transform) (in module datanator.util.calc_tanimoto) (in module datanator.util.index_collection) make_bulk() (datanator.data_source.kegg_org_code.KeggOrgCode method) make_df() (datanator.util.rna_halflife_util.RnaHLUtil method) make_dict() (datanator.util.file_util.FileUtil method) make_doc() (datanator.data_source.ec.EC method) (datanator.data_source.sabio_rk_json_mongo.SabioRkNoSQL method) manual (datanator.core.data_model.ConsensusMethod attribute) (datanator.core.data_model.ResourceAssignmentMethod attribute) many_to_many() (datanator.util.calc_tanimoto.CalcTanimoto method) mass (datanator.core.data_model.ProteinSpecie attribute), [1] max_entries (datanator.core.data_source.CachedDataSource attribute) (datanator.core.data_source.PostgresDataSource attribute) MAX_HTTP_RETRIES (datanator.core.data_source.HttpDataSource attribute), [1] (datanator.core.data_source.WebserviceDataSource attribute), [1] mean (datanator.core.data_model.ConsensusMethod attribute) mechanism (datanator.data_source.sabio_rk.KineticLaw attribute), [1] media (datanator.core.data_model.Environment attribute), [1] (datanator.data_source.sabio_rk.KineticLaw attribute), [1] median (datanator.core.data_model.ConsensusMethod attribute) merge (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute)

merge_dict() (datanator.util.file_util.FileUtil method) MetaboliteNoSQL (class in datanator.data_source.metabolite_nosql) MetabolitesMeta (class in datanator.data_source.metabolites_meta_collection) metadata (datanator.core.data_model.ObservedResult attribute) Method (class in datanator.core.data_model) method (datanator.core.data_model.Consensus attribute), [1] (datanator.core.data_model.ObservedResult attribute) (datanator.core.data_model.ObservedResultMetadata attribute) Method.Meta (class in datanator.core.data_model) mode (datanator.core.data_model.ConsensusMethod attribute) modified (datanator.data_source.sabio_rk.Compartment attribute) (datanator.data_source.sabio_rk.Compound attribute) (datanator.data_source.sabio_rk.Entry attribute) (datanator.data_source.sabio_rk.Enzyme attribute) (datanator.data_source.sabio_rk.EnzymeSubunit attribute) (datanator.data_source.sabio_rk.KineticLaw attribute) (datanator.data_source.sabio_rk.Parameter attribute) modifier_kinetic_law_id (datanator.data_source.sabio_rk.ReactionParticipant attribute) modifiers (datanator.data_source.sabio_rk.KineticLaw attribute), [1] Modomics (class in datanator.data_source.modomics) molecular_weight (datanator.core.data_model.ProteinComplexSpecie attribute) (datanator.data_source.sabio_rk.Enzyme attribute), [1] (datanator.data_source.sabio_rk.EnzymeSubunit attribute), [1] Molecule (class in datanator.util.molecule_util) MoleculeController (class in datanator.__main__) MoleculeController.Meta (class in datanator.__main__) MoleculeConvertStructureController (class in datanator.__main__) MoleculeConvertStructureController.Meta (class in datanator.__main__) MoleculeGetStructureController (class in datanator.__main__) MoleculeGetStructureController.Meta (class in datanator.__main__) MongoUtil (class in datanator.util.mongo_util)

N

name (datanator.core.data_model.EntityInteractionOrProperty attribute), [1] (datanator.core.data_model.Method attribute), [1] (datanator.core.data_model.Synonym attribute), [1] (datanator.core.data_source.DataSource attribute) (datanator.core.data_source.PostgresDataSource attribute) (datanator.data_source.sabio_rk.Compartment attribute) (datanator.data_source.sabio_rk.Compound attribute) (datanator.data_source.sabio_rk.Entry attribute), [1] (datanator.data_source.sabio_rk.Enzyme attribute) (datanator.data_source.sabio_rk.EnzymeSubunit attribute) (datanator.data_source.sabio_rk.KineticLaw attribute) (datanator.data_source.sabio_rk.Parameter attribute) (datanator.data_source.sabio_rk.Synonym attribute), [1] (datanator.util.molecule_util.Molecule attribute) (datanator.util.taxonomy_util.Taxon attribute)

namespace (datanator.core.data_model.Resource attribute), [1] (datanator.data_source.sabio_rk.Resource attribute), [1] normalize_kinetic_laws() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) normalize_parameter_value() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) number (datanator.core.data_model.Reference attribute), [1]

O

objects (datanator.core.data_model.Compartment attribute) (datanator.core.data_model.ComputationalMethod attribute) (datanator.core.data_model.Consensus attribute) (datanator.core.data_model.DnaSpecie attribute) (datanator.core.data_model.EntityInteractionOrProperty attribute) (datanator.core.data_model.Environment attribute) (datanator.core.data_model.Evidence attribute) (datanator.core.data_model.ExperimentalMethod attribute) (datanator.core.data_model.Genetics attribute) (datanator.core.data_model.Interaction attribute) (datanator.core.data_model.Method attribute) (datanator.core.data_model.Observable attribute) (datanator.core.data_model.ObservedInteraction attribute) (datanator.core.data_model.ObservedResult attribute) (datanator.core.data_model.ObservedResultMetadata attribute) (datanator.core.data_model.ObservedSpecie attribute) (datanator.core.data_model.ObservedValue attribute) (datanator.core.data_model.PolymerSpecie attribute) (datanator.core.data_model.ProteinComplexSpecie attribute) (datanator.core.data_model.ProteinSpecie attribute) (datanator.core.data_model.Reaction attribute) (datanator.core.data_model.ReactionParticipant attribute) (datanator.core.data_model.Reference attribute) (datanator.core.data_model.Resource attribute) (datanator.core.data_model.RnaSpecie attribute) (datanator.core.data_model.Specie attribute) (datanator.core.data_model.SpecieInteraction attribute) (datanator.core.data_model.Synonym attribute) Observable (class in datanator.core.data_model) observable (datanator.core.data_model.Consensus attribute), [1] (datanator.core.data_model.ObservedValue attribute), [1] Observable.Meta (class in datanator.core.data_model) observation (datanator.core.data_model.ObservedResult attribute) observations (datanator.core.data_model.Environment attribute) (datanator.core.data_model.Genetics attribute) (datanator.core.data_model.Method attribute) (datanator.core.data_model.Reference attribute) observed_error (datanator.data_source.sabio_rk.Parameter attribute), [1] observed_name (datanator.data_source.sabio_rk.Parameter attribute), [1] observed_type (datanator.data_source.sabio_rk.Parameter attribute), [1] observed_units (datanator.data_source.sabio_rk.Parameter attribute), [1]

observed_value (datanator.data_source.sabio_rk.Parameter attribute), [1] ObservedInteraction (class in datanator.core.data_model) ObservedInteraction.Meta (class in datanator.core.data_model) ObservedResult (class in datanator.core.data_model) ObservedResult.Meta (class in datanator.core.data_model) ObservedResultMetadata (class in datanator.core.data_model) ObservedResultMetadata.Meta (class in datanator.core.data_model) ObservedSpecie (class in datanator.core.data_model) ObservedSpecie.Meta (class in datanator.core.data_model) ObservedValue (class in datanator.core.data_model) ObservedValue.Meta (class in datanator.core.data_model) one_to_many() (datanator.util.calc_tanimoto.CalcTanimoto method) order (datanator.core.data_model.ReactionParticipant attribute), [1] ordering (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute) organism_strain (datanator.data_source.array_express_tools.ensembl_tools.StrainInfo attribute)

P

pages (datanator.core.data_model.Reference attribute), [1] Parameter (class in datanator.data_source.sabio_rk) parameters (datanator.data_source.sabio_rk.Compound attribute) (datanator.data_source.sabio_rk.Enzyme attribute) (datanator.data_source.sabio_rk.KineticLaw attribute), [1] parse_complex_subunit_structure() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) parse_content() (datanator.data_source.ec.EC method) parse_definition() (datanator.data_source.kegg_orthology.KeggOrthology method) parse_division() (datanator.data_source.taxon_tree.TaxonTree method) parse_enzyme_name() (datanator.data_source.sabio_rk.SabioRk method) (datanator.data_source.sabio_rk_nosql.SabioRk method) parse_fullname_line() (datanator.data_source.taxon_tree.TaxonTree method) parse_fullname_taxid() (datanator.data_source.taxon_tree.TaxonTree method) parse_gencode() (datanator.data_source.taxon_tree.TaxonTree method) parse_gene() (datanator.data_source.kegg_orthology.KeggOrthology method) parse_gene_info() (datanator.data_source.gene_ortholog.KeggGeneOrtholog method) parse_html() (datanator.data_source.gene_ortholog.KeggGeneOrtholog method) parse_html_iter() (datanator.data_source.kegg_org_code.KeggOrgCode method) parse_ko_txt() (datanator.data_source.kegg_orthology.KeggOrthology method) parse_list() (in module datanator.data_source.corum_nosql) parse_metabolite() (datanator.parse_metabolite_concentration.ParseMetaboliteConcentration method) parse_names() (datanator.data_source.taxon_tree.TaxonTree method) parse_nodes() (datanator.data_source.taxon_tree.TaxonTree method) parse_nodes_line() (datanator.data_source.taxon_tree.TaxonTree method) parse_pathway_disease() (datanator.data_source.kegg_orthology.KeggOrthology method) parse_paxDB_files() (datanator.data_source.pax_nosql.PaxNoSQL method) parse_rc_multiline() (datanator.data_source.kegg_reaction_class.KeggReaction method) parse_rc_orthology() (datanator.data_source.kegg_reaction_class.KeggReaction method) parse_root_json() (datanator.data_source.kegg_reaction_class.KeggReaction method) parse_rxn_cls_txt() (datanator.data_source.kegg_reaction_class.KeggReaction method) parse_subunits() (in module datanator.data_source.corum_nosql) parse_taxid_line() (datanator.data_source.taxon_tree.TaxonTree method) ParseMetaboliteConcentration (class in datanator.parse_metabolite_concentration) participants (datanator.core.data_model.Reaction attribute), [1] pax() (datanator.__main__.BuildController method) (datanator.__main__.DownloadController method) PaxNoSQL (class in datanator.data_source.pax_nosql) performer (datanator.core.data_model.Method attribute) ph (datanator.core.data_model.Environment attribute), [1] (datanator.data_source.sabio_rk.KineticLaw attribute), [1] PolymerSpecie (class in datanator.core.data_model) PolymerSpecie.Meta (class in datanator.core.data_model) position (datanator.core.data_model.Interaction attribute), [1] PostgresDataSource (class in datanator.core.data_source) predicted (datanator.core.data_model.ResourceAssignmentMethod attribute) primary_attribute (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute)

print_schema() (datanator.util.mongo_util.MongoUtil method) process_cdna() (in module datanator.data_source.process_rna_seq.core) (in module datanator.data_source.process_rna_seq.download_cdna) process_docs() (datanator.schema_2.transform.Transform method) (datanator.schema_2.transform_metabolite_concentrations.TMC method) (datanator.schema_2.transform_metabolites_meta.TransformMetabolitesMeta method) process_fastq() (in module datanator.data_source.process_rna_seq.core) ProcessCDNA (class in datanator.data_source.process_rna_seq.command_line_core) ProcessCDNA.Meta (class in datanator.data_source.process_rna_seq.command_line_core) ProcessFASTQ (class in datanator.data_source.process_rna_seq.command_line_core) ProcessFASTQ.Meta (class in datanator.data_source.process_rna_seq.command_line_core) product_kinetic_law (datanator.data_source.sabio_rk.ReactionParticipant attribute) product_kinetic_law_id (datanator.data_source.sabio_rk.ReactionParticipant attribute) products (datanator.data_source.sabio_rk.KineticLaw attribute), [1] property (datanator.core.data_model.Observable attribute), [1] ProteinAggregate (class in datanator.data_source.protein_aggregate) ProteinComplexSpecie (class in datanator.core.data_model) ProteinComplexSpecie.Meta (class in datanator.core.data_model) ProteinSpecie (class in datanator.core.data_model) ProteinSpecie.Meta (class in datanator.core.data_model) protons (datanator.util.molecule_util.InchiMolecule attribute) PUBCHEM_MAX_TRIES (datanator.data_source.sabio_rk.SabioRk attribute), [1] PUBCHEM_TRY_DELAY (datanator.data_source.sabio_rk.SabioRk attribute), [1] publication (datanator.core.data_model.Reference attribute), [1]

Q

quant() (datanator.util.rna_seq_util.Kallisto method) query (in module datanator.data_source.sqlite_to_json) query_table() (datanator.data_source.sqlite_to_json.SQLToJSON method)

quilt_owner (datanator.core.data_source.CachedDataSource attribute) (datanator.core.data_source.PostgresDataSource attribute) quilt_package (datanator.core.data_source.CachedDataSource attribute), [1] (datanator.core.data_source.PostgresDataSource attribute)

R

reactant_kinetic_law (datanator.data_source.sabio_rk.ReactionParticipant attribute) reactant_kinetic_law_id (datanator.data_source.sabio_rk.ReactionParticipant attribute) reactants (datanator.data_source.sabio_rk.KineticLaw attribute), [1] Reaction (class in datanator.core.data_model) Reaction.Meta (class in datanator.core.data_model) reaction_participants (datanator.data_source.sabio_rk.Compound attribute) ReactionController (class in datanator.__main__) ReactionController.Meta (class in datanator.__main__) ReactionGetEcNumberController (class in datanator.__main__) ReactionGetEcNumberController.Meta (class in datanator.__main__) ReactionParticipant (class in datanator.core.data_model) (class in datanator.data_source.sabio_rk) ReactionParticipant.Meta (class in datanator.core.data_model) reconnected_metals (datanator.util.molecule_util.InchiMolecule attribute) Reference (class in datanator.core.data_model) reference (datanator.core.data_model.ObservedResultMetadata attribute) Reference.Meta (class in datanator.core.data_model) references (datanator.data_source.sabio_rk.KineticLaw attribute), [1] related_attributes (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute)

relevance (datanator.core.data_model.Evidence attribute), [1] (datanator.core.data_model.Resource attribute), [1] remove_dups() (datanator.data_source.metabolites_meta_collection.MetabolitesMeta method) remove_layer() (datanator.util.molecule_util.InchiMolecule method) remove_redudant_id() (datanator.data_source.uniprot_nosql.UniprotNoSQL method) replace_dict_key() (datanator.util.file_util.FileUtil method) replace_key_in_similar_compounds() (datanator.data_source.metabolites_meta_collection.MetabolitesMeta method) replace_list_dict_key() (datanator.util.file_util.FileUtil method) requests_cache_filename (datanator.core.data_source.HttpDataSource attribute) requests_session (datanator.core.data_source.HttpDataSource attribute) (datanator.core.data_source.WebserviceDataSource attribute) reset_cellular_locations() (datanator.data_source.metabolites_meta_collection.MetabolitesMeta method) Resource (class in datanator.core.data_model) (class in datanator.data_source.sabio_rk) Resource.Meta (class in datanator.core.data_model) ResourceAssignmentMethod (class in datanator.core.data_model) restore_backup() (datanator.core.data_source.PostgresDataSource method) restore_database() (datanator.core.data_source.PostgresDataSource method) retrieve_content() (datanator.data_source.ec.EC method) reversible (datanator.core.data_model.Reaction attribute), [1] RnaHLUtil (class in datanator.util.rna_halflife_util) RnaSpecie (class in datanator.core.data_model) RnaSpecie.Meta (class in datanator.core.data_model) run() (datanator.data_source.modomics.Modomics method) (in module datanator.data_source.process_rna_seq.download_cdna) RxnAggregate (class in datanator.data_source.sabio_reaction)

S

sabio() (datanator.__main__.BuildController method) (datanator.__main__.DownloadController method) SabioCompound (class in datanator.data_source.sabio_compound) SabioRk (class in datanator.data_source.sabio_rk) (class in datanator.data_source.sabio_rk_nosql) SabioRkNoSQL (class in datanator.data_source.sabio_rk_json_mongo) score (datanator.core.data_model.Interaction attribute), [1] search_dict_list() (datanator.util.file_util.FileUtil method) sequence (datanator.core.data_model.PolymerSpecie attribute), [1] (datanator.data_source.sabio_rk.EnzymeSubunit attribute), [1] session (datanator.core.data_source.CachedDataSource attribute) (datanator.core.data_source.PostgresDataSource attribute) setup_database() (in module datanator.util.taxonomy_util) simplify_inchi() (datanator.util.chem_util.ChemUtil method) SKIP_KINETIC_LAW_IDS (datanator.data_source.sabio_rk.SabioRk attribute), [1] software (datanator.core.data_model.Method attribute) Specie (class in datanator.core.data_model) specie (datanator.core.data_model.Observable attribute), [1] (datanator.core.data_model.ObservedSpecie attribute), [1] (datanator.core.data_model.ReactionParticipant attribute), [1] Specie.Meta (class in datanator.core.data_model) specie_a (datanator.core.data_model.SpecieInteraction attribute), [1] specie_b (datanator.core.data_model.SpecieInteraction attribute), [1] SpecieInteraction (class in datanator.core.data_model) SpecieInteraction.Meta (class in datanator.core.data_model) split_colon() (datanator.data_source.intact_nosql.IntActNoSQL method) split_line() (datanator.data_source.intact_nosql.IntActNoSQL method) SQLToJSON (class in datanator.data_source.sqlite_to_json) stacked_on (datanator.__main__.AggregateBuildController.Meta attribute) (datanator.__main__.BuildController.Meta attribute) (datanator.__main__.DownloadController.Meta attribute) (datanator.__main__.GenerateRNASeqTemplate.Meta attribute) (datanator.__main__.GenerateTemplateController.Meta attribute) (datanator.__main__.MoleculeController.Meta attribute) (datanator.__main__.MoleculeConvertStructureController.Meta attribute) (datanator.__main__.MoleculeGetStructureController.Meta attribute) (datanator.__main__.ReactionController.Meta attribute) (datanator.__main__.ReactionGetEcNumberController.Meta attribute) (datanator.__main__.TaxonomyController.Meta attribute) (datanator.__main__.TaxonomyGetCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToRoot.Meta attribute) (datanator.__main__.TaxonomyGetParentsController.Meta attribute) (datanator.__main__.TaxonomyGetRankController.Meta attribute) (datanator.__main__.UploadData.Meta attribute) (datanator.__main__.UploadDataController.Meta attribute) (datanator.__main__.UploadReferenceGenome.Meta attribute) (datanator.__main__.UploadRNASeqExperiment.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DeleteCDNAFiles.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DeleteFASTQFiles.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DownloadCDNA.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DownloadFASTQ.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.ProcessCDNA.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.ProcessFASTQ.Meta attribute)

stacked_type (datanator.__main__.AggregateBuildController.Meta attribute) (datanator.__main__.BuildController.Meta attribute) (datanator.__main__.DownloadController.Meta attribute) (datanator.__main__.GenerateRNASeqTemplate.Meta attribute) (datanator.__main__.GenerateTemplateController.Meta attribute) (datanator.__main__.MoleculeController.Meta attribute) (datanator.__main__.MoleculeConvertStructureController.Meta attribute) (datanator.__main__.MoleculeGetStructureController.Meta attribute) (datanator.__main__.ReactionController.Meta attribute) (datanator.__main__.ReactionGetEcNumberController.Meta attribute) (datanator.__main__.TaxonomyController.Meta attribute) (datanator.__main__.TaxonomyGetCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToCommonAncestorController.Meta attribute) (datanator.__main__.TaxonomyGetDistanceToRoot.Meta attribute) (datanator.__main__.TaxonomyGetParentsController.Meta attribute) (datanator.__main__.TaxonomyGetRankController.Meta attribute) (datanator.__main__.UploadData.Meta attribute) (datanator.__main__.UploadDataController.Meta attribute) (datanator.__main__.UploadReferenceGenome.Meta attribute) (datanator.__main__.UploadRNASeqExperiment.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DeleteCDNAFiles.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DeleteFASTQFiles.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DownloadCDNA.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.DownloadFASTQ.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.ProcessCDNA.Meta attribute) (datanator.data_source.process_rna_seq.command_line_core.ProcessFASTQ.Meta attribute) stereochemistry (datanator.util.molecule_util.InchiMolecule attribute) stereochemistry_parity (datanator.util.molecule_util.InchiMolecule attribute) stereochemistry_type (datanator.util.molecule_util.InchiMolecule attribute) stoichiometry_a (datanator.core.data_model.SpecieInteraction attribute), [1] stoichiometry_b (datanator.core.data_model.SpecieInteraction attribute), [1] StrainInfo (class in datanator.data_source.array_express_tools.ensembl_tools) stringify() (datanator.core.data_model.Reaction method) structure (datanator.core.data_model.Specie attribute), [1] (datanator.util.molecule_util.Molecule attribute) structures (datanator.data_source.sabio_rk.Compound attribute), [1] su_cmt (datanator.core.data_model.ProteinComplexSpecie attribute) subunits (datanator.data_source.sabio_rk.Enzyme attribute) Synonym (class in datanator.core.data_model) (class in datanator.data_source.sabio_rk) synonym (datanator.core.data_model.ObservedResultMetadata attribute) Synonym.Meta (class in datanator.core.data_model) synonyms (datanator.data_source.sabio_rk.Compartment attribute) (datanator.data_source.sabio_rk.Compound attribute) (datanator.data_source.sabio_rk.Entry attribute), [1] (datanator.data_source.sabio_rk.Enzyme attribute) (datanator.data_source.sabio_rk.EnzymeSubunit attribute) (datanator.data_source.sabio_rk.KineticLaw attribute) (datanator.data_source.sabio_rk.Parameter attribute)

T

table() (datanator.data_source.sqlite_to_json.SQLToJSON method) table_format (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute) Taxon (class in datanator.util.taxonomy_util) taxon (datanator.core.data_model.Genetics attribute), [1] (datanator.data_source.sabio_rk.KineticLaw attribute), [1] taxon_variant (datanator.data_source.sabio_rk.KineticLaw attribute), [1] taxon_wildtype (datanator.data_source.sabio_rk.KineticLaw attribute), [1] TaxonomyController (class in datanator.__main__) TaxonomyController.Meta (class in datanator.__main__)

TaxonomyGetCommonAncestorController (class in datanator.__main__) TaxonomyGetCommonAncestorController.Meta (class in datanator.__main__) TaxonomyGetDistanceToCommonAncestorController (class in datanator.__main__) TaxonomyGetDistanceToCommonAncestorController.Meta (class in datanator.__main__) TaxonomyGetDistanceToRoot (class in datanator.__main__) TaxonomyGetDistanceToRoot.Meta (class in datanator.__main__) TaxonomyGetParentsController (class in datanator.__main__) TaxonomyGetParentsController.Meta (class in datanator.__main__) TaxonomyGetRankController (class in datanator.__main__) TaxonomyGetRankController.Meta (class in datanator.__main__) TaxonTree (class in datanator.data_source.taxon_tree) temperature (datanator.core.data_model.Environment attribute), [1] (datanator.data_source.sabio_rk.KineticLaw attribute), [1] timeloadcontent() (in module datanator.util.build_util) timemethod() (in module datanator.util.build_util) tissue (datanator.data_source.sabio_rk.KineticLaw attribute), [1] title (datanator.core.data_model.Reference attribute), [1] TMC (class in datanator.schema_2.transform_metabolite_concentrations) to_format() (datanator.util.molecule_util.Molecule method) to_inchi() (datanator.core.data_model.Specie method) (datanator.util.molecule_util.Molecule method) to_mol() (datanator.core.data_model.Specie method) (datanator.util.molecule_util.Molecule method) to_openbabel() (datanator.core.data_model.Specie method) (datanator.util.molecule_util.Molecule method) to_pybel() (datanator.core.data_model.Specie method) (datanator.util.molecule_util.Molecule method) to_smiles() (datanator.core.data_model.Specie method) (datanator.util.molecule_util.Molecule method) Transform (class in datanator.schema_2.transform) TransformMetabolitesMeta (class in datanator.schema_2.transform_metabolites_meta) type (datanator.data_source.sabio_rk.Parameter attribute), [1] (datanator.data_source.sabio_rk.ReactionParticipant attribute), [1] type_a (datanator.core.data_model.SpecieInteraction attribute) type_b (datanator.core.data_model.SpecieInteraction attribute) TYPES (datanator.data_source.sabio_rk.Parameter attribute)

U

uniprot() (datanator.__main__.BuildController method) (datanator.__main__.DownloadController method) uniprot_id (datanator.core.data_model.ProteinSpecie attribute), [1] uniprot_names() (datanator.util.rna_halflife_util.RnaHLUtil method) uniprot_to_org_gene() (datanator.data_source.gene_ortholog.KeggGeneOrtholog method) UniprotNoSQL (class in datanator.data_source.uniprot_nosql) unique_together (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute)

units (datanator.core.data_model.Consensus attribute), [1] (datanator.core.data_model.ObservedValue attribute), [1] (datanator.data_source.sabio_rk.Parameter attribute), [1] unpack_list() (datanator.util.file_util.FileUtil method) unzip_file() (datanator.util.file_util.FileUtil method) updated (datanator.data_source.sabio_rk.Entry attribute) upload_backup() (datanator.core.data_source.PostgresDataSource method) upload_backups() (datanator.core.data_source.CachedDataSource method) UploadData (class in datanator.__main__) UploadData.Meta (class in datanator.__main__) UploadDataController (class in datanator.__main__) UploadDataController.Meta (class in datanator.__main__) UploadReferenceGenome (class in datanator.__main__) UploadReferenceGenome.Meta (class in datanator.__main__) UploadRNASeqExperiment (class in datanator.__main__) UploadRNASeqExperiment.Meta (class in datanator.__main__) url (datanator.core.data_model.Reference attribute), [1] user (datanator.core.data_model.Consensus attribute), [1]

V

value (datanator.core.data_model.Consensus attribute), [1] (datanator.core.data_model.Evidence attribute), [1] (datanator.core.data_model.ObservedValue attribute), [1] (datanator.data_source.sabio_rk.CompoundStructure attribute), [1] (datanator.data_source.sabio_rk.Parameter attribute), [1] values (datanator.core.data_model.ObservedResultMetadata attribute) variation (datanator.core.data_model.Genetics attribute), [1] verbose (datanator.core.data_source.CachedDataSource attribute) (datanator.core.data_source.PostgresDataSource attribute) verbose_name (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute)

verbose_name_plural (datanator.core.data_model.Compartment.Meta attribute) (datanator.core.data_model.ComputationalMethod.Meta attribute) (datanator.core.data_model.Consensus.Meta attribute) (datanator.core.data_model.DnaSpecie.Meta attribute) (datanator.core.data_model.EntityInteractionOrProperty.Meta attribute) (datanator.core.data_model.Environment.Meta attribute) (datanator.core.data_model.Evidence.Meta attribute) (datanator.core.data_model.ExperimentalMethod.Meta attribute) (datanator.core.data_model.Genetics.Meta attribute) (datanator.core.data_model.Interaction.Meta attribute) (datanator.core.data_model.Method.Meta attribute) (datanator.core.data_model.Observable.Meta attribute) (datanator.core.data_model.ObservedInteraction.Meta attribute) (datanator.core.data_model.ObservedResult.Meta attribute) (datanator.core.data_model.ObservedResultMetadata.Meta attribute) (datanator.core.data_model.ObservedSpecie.Meta attribute) (datanator.core.data_model.ObservedValue.Meta attribute) (datanator.core.data_model.PolymerSpecie.Meta attribute) (datanator.core.data_model.ProteinComplexSpecie.Meta attribute) (datanator.core.data_model.ProteinSpecie.Meta attribute) (datanator.core.data_model.Reaction.Meta attribute) (datanator.core.data_model.ReactionParticipant.Meta attribute) (datanator.core.data_model.Reference.Meta attribute) (datanator.core.data_model.Resource.Meta attribute) (datanator.core.data_model.RnaSpecie.Meta attribute) (datanator.core.data_model.Specie.Meta attribute) (datanator.core.data_model.SpecieInteraction.Meta attribute) (datanator.core.data_model.Synonym.Meta attribute) version (datanator.core.data_model.ComputationalMethod attribute), [1] volume (datanator.core.data_model.Reference attribute), [1] vprint() (datanator.core.data_source.DataSource method)

W

webservice_batch_size (datanator.data_source.sabio_rk.SabioRk attribute) WebserviceDataSource (class in datanator.core.data_source) weighted_mean (datanator.core.data_model.ConsensusMethod attribute)

weighted_median (datanator.core.data_model.ConsensusMethod attribute) weighted_mode (datanator.core.data_model.ConsensusMethod attribute) write_to_json() (datanator.data_source.metabolite_nosql.MetaboliteNoSQL method)

Y

year (datanator.core.data_model.Reference attribute), [1]