datanator
0.1.20
1. Overview
1.1. Motivation
1.2. Methodology
1.3. Supported data types and data sources
1.4. Advantages of
datanator
versus manual data aggregation
2. Installation
2.1. Install dependencies
2.2. Install
datanator
2.3. Run
datanator
3. Tutorial - Getting Familiar With datanator’s Command Line Interface
3.1. Generate Template Doc
3.2. Collecting Kinetic Data
3.3. Entering Reactions Into datanator
3.4. Set Maximum Proximity Limit
4. API documentation
4.1. datanator package
4.1.1. Subpackages
4.1.1.1. datanator.api package
4.1.1.2. datanator.builds package
4.1.1.3. datanator.config package
4.1.1.4. datanator.core package
4.1.1.5. datanator.data_source package
4.1.1.6. datanator.rest package
4.1.1.7. datanator.util package
4.1.2. Submodules
4.1.3. datanator.__main__ module
4.1.4. datanator.datanator module
4.1.5. datanator.io module
4.1.6. Module contents
5. About
5.1. License
5.2. Development team
5.3. Acknowledgements
5.4. Questions and comments
6. References
datanator
Docs
»
Index
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Y
_
__str__() (datanator.util.molecule_util.InchiMolecule method)
_id (datanator.core.models.Resource attribute)
_is_modifier (datanator.core.models.Reaction attribute)
_is_name_ambiguous (datanator.data_source.sabio_rk.Compound attribute)
_is_product (datanator.core.models.Reaction attribute)
_is_reactant (datanator.core.models.Reaction attribute)
_metadata_id (datanator.core.models.Observation attribute)
_structure_formula_connectivity (datanator.core.models.Structure attribute)
(datanator.data_source.ecmdb.Compound attribute)
_value_inchi (datanator.core.models.Structure attribute)
(datanator.data_source.sabio_rk.CompoundStructure attribute)
_value_inchi_formula_connectivity (datanator.data_source.sabio_rk.CompoundStructure attribute)
_value_smiles (datanator.core.models.Structure attribute)
A
abundance (datanator.core.models.AbundanceData attribute)
,
[1]
(datanator.data_source.pax.Observation attribute)
,
[1]
abundance_data (datanator.core.models.AbundanceDataSet attribute)
abundance_id (datanator.core.models.AbundanceData attribute)
AbundanceData (class in datanator.core.models)
AbundanceDataSet (class in datanator.core.models)
ACC (datanator.data_source.jaspar.Protein attribute)
access_dict_by_index() (datanator.util.file_util.FileUtil method)
accession_number (datanator.core.models.RNASeqExperiment attribute)
accessions (datanator.data_source.refseq.ReferenceGenome attribute)
add_complexes() (datanator.data_source.intact.IntAct method)
(datanator.data_source.intact_nosql.IntActNoSQL method)
add_deprot_inchi() (datanator.data_source.sabio_rk_nosql.SabioRkNoSQL method)
add_interactions() (datanator.data_source.intact.IntAct method)
(datanator.data_source.intact_nosql.IntActNoSQL 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__)
all_observed_results (datanator.core.data_query.FilterResult attribute)
all_scores (datanator.core.data_query.FilterResult attribute)
amount_loaded (datanator.core.models.Progress attribute)
,
[1]
Annotation (class in datanator.data_source.jaspar)
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__.DbController.Meta attribute)
(datanator.__main__.DbRestoreController.Meta attribute)
(datanator.__main__.DownloadController.Meta attribute)
(datanator.__main__.GenerateRNASeqTemplate.Meta attribute)
(datanator.__main__.GenerateTemplateController.Meta attribute)
(datanator.__main__.GetDataController.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__.UploadRNASeqExperiment.Meta attribute)
(datanator.__main__.UploadReferenceGenome.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)
ArrayExpress (class in datanator.data_source.array_express)
ask() (datanator.core.query_nosql.DataQuery method)
assay (datanator.core.models.RNASeqDataSet attribute)
(datanator.data_source.array_express.Sample attribute)
,
[1]
assignment_method (datanator.core.data_model.Resource attribute)
,
[1]
attribute (datanator.core.data_query.ExponentialFilter attribute)
(datanator.core.data_query.Filter attribute)
(datanator.core.data_query.NormalFilter attribute)
(datanator.core.data_query.OptionsFilter attribute)
(datanator.core.data_query.RangeFilter attribute)
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
Base (class in datanator.data_source.corum)
(class in datanator.data_source.pax)
base_controller (datanator.__main__.App.Meta attribute)
(datanator.data_source.process_rna_seq.command_line_core.App.Meta attribute)
BASE_ID (datanator.data_source.jaspar.Matrix attribute)
(datanator.data_source.jaspar.Tffm attribute)
base_model (datanator.core.common_schema.CommonSchema attribute)
(datanator.core.data_source.CachedDataSource attribute)
(datanator.core.data_source.PostgresDataSource attribute)
(datanator.data_source.array_express.ArrayExpress attribute)
(datanator.data_source.corum.Corum attribute)
(datanator.data_source.ecmdb.Ecmdb attribute)
(datanator.data_source.ensembl.GetGenes attribute)
(datanator.data_source.intact.IntAct attribute)
(datanator.data_source.jaspar.Jaspar attribute)
(datanator.data_source.kegg.Kegg attribute)
(datanator.data_source.pax.Pax attribute)
(datanator.data_source.refseq.Refseq attribute)
(datanator.data_source.sabio_rk.SabioRk attribute)
(datanator.data_source.uniprot.Uniprot attribute)
BaseConfig (class in datanator.config.config)
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)
BaseManager (class in datanator.api.lib.data_manager)
BCRYPT_LOG_ROUNDS (datanator.config.config.BaseConfig attribute)
(datanator.config.config.BuildConfig attribute)
(datanator.config.config.CircleTestingConfig attribute)
(datanator.config.config.LocalDevelopmentConfig attribute)
(datanator.config.config.ProductionConfig attribute)
binding_matrix (datanator.core.data_model.DnaSpecie attribute)
,
[1]
bio_assay_data_cubes (datanator.core.models.DataFormat attribute)
,
[1]
(datanator.data_source.array_express.DataFormat attribute)
,
[1]
BioPortal (class in datanator.data_source.bio_portal)
BIOPORTAL_ENDPOINT (datanator.data_source.bio_portal.BioPortal attribute)
,
[1]
build() (in module datanator.builds.full)
(in module datanator.builds.med)
(in module datanator.builds.test)
(in module datanator.builds.test_log)
build_array_express() (datanator.core.common_schema.CommonSchema method)
build_corum() (datanator.core.common_schema.CommonSchema method)
build_ecmdb() (datanator.core.common_schema.CommonSchema method)
build_intact_complexes() (datanator.core.common_schema.CommonSchema method)
build_intact_interactions() (datanator.core.common_schema.CommonSchema method)
build_jaspar() (datanator.core.common_schema.CommonSchema method)
build_ncbi() (datanator.core.common_schema.CommonSchema method)
build_pax() (datanator.core.common_schema.CommonSchema method)
build_sabio() (datanator.core.common_schema.CommonSchema method)
build_uniprot() (datanator.core.common_schema.CommonSchema method)
BuildConfig (class in datanator.config.config)
BuildController (class in datanator.__main__)
BuildController.Meta (class in datanator.__main__)
C
cache_dirname (datanator.core.data_source.CachedDataSource attribute)
(datanator.core.data_source.PostgresDataSource attribute)
CachedDataSource (class in datanator.core.data_source)
CachedDataSourceQueryGenerator (class in datanator.core.data_query)
calc_average() (datanator.core.data_query.ConsensusGenerator method)
calc_enzyme_molecular_weights() (datanator.data_source.sabio_rk.SabioRk method)
calc_inchi_formula_connectivity() (datanator.data_source.sabio_rk.CompoundStructure 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)
canonical_sequence (datanator.core.models.ProteinSubunit attribute)
(datanator.data_source.uniprot.UniprotData attribute)
category (datanator.core.models.Characteristic attribute)
(datanator.core.models.Variable attribute)
(datanator.data_source.array_express.Characteristic attribute)
,
[1]
(datanator.data_source.ensembl.GeneIdentifier attribute)
CCO_DOWNLOAD_URL (datanator.data_source.bio_portal.BioPortal attribute)
,
[1]
cell_compartment (datanator.core.models.Metadata attribute)
cell_line (datanator.core.models.Metadata attribute)
(datanator.data_source.corum.Observation attribute)
CellCompartment (class in datanator.core.models)
CellCompartmentSerializer (class in datanator.api.serializer)
CellCompartmentSerializer.Meta (class in datanator.api.serializer)
CellLine (class in datanator.core.models)
center (datanator.core.data_query.ExponentialFilter attribute)
chapter (datanator.core.data_model.Reference attribute)
,
[1]
Characteristic (class in datanator.core.models)
(class in datanator.data_source.array_express)
characteristic (datanator.core.models.Metadata attribute)
characteristics (datanator.data_source.array_express.Sample attribute)
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)
CircleTestingConfig (class in datanator.config.config)
class_name (datanator.core.data_model.ProteinComplexSpecie attribute)
(datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.core.models.ProteinSubunit attribute)
,
[1]
clear_content() (datanator.core.data_source.CachedDataSource method)
(datanator.core.data_source.PostgresDataSource method)
(datanator.data_source.bio_portal.BioPortal method)
clear_requests_cache() (datanator.core.data_source.HttpDataSource method)
close_db() (in module datanator.rest.db_2)
coefficient (datanator.core.data_model.ReactionParticipant attribute)
,
[1]
(datanator.core.models.ProteinSubunit attribute)
,
[1]
(datanator.core.models.Reaction attribute)
,
[1]
(datanator.data_source.sabio_rk.EnzymeSubunit attribute)
,
[1]
(datanator.data_source.sabio_rk.ReactionParticipant attribute)
,
[1]
col (datanator.data_source.jaspar.Data attribute)
COLLECTION (datanator.data_source.jaspar.Matrix attribute)
collection_str (datanator.util.mongo_util.MongoUtil attribute)
comment (datanator.core.models.Metabolite attribute)
(datanator.data_source.ecmdb.Compound attribute)
,
[1]
comments (datanator.core.models.Characteristic attribute)
(datanator.core.models.Method attribute)
,
[1]
(datanator.core.models.Variable attribute)
commit_intermediate_results (datanator.core.data_source.CachedDataSource attribute)
CommonSchema (class in datanator.core.common_schema)
compare_observed_value_with_target_component() (datanator.core.data_query.Filter method)
(datanator.core.data_query.ReactionParticipantFilter method)
(datanator.core.data_query.ReactionSimilarityFilter method)
(datanator.core.data_query.SpecieSequenceSimilarityFilter method)
(datanator.core.data_query.SpecieStructuralSimilarityFilter method)
(datanator.core.data_query.TaxonomicDistanceFilter method)
Compartment (class in datanator.core.data_model)
(class in datanator.data_source.ecmdb)
(class in datanator.data_source.sabio_rk)
compartment (datanator.core.data_model.Observable attribute)
,
[1]
(datanator.core.data_model.ReactionParticipant attribute)
,
[1]
(datanator.core.models.Reaction attribute)
(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.core.models.Reaction attribute)
(datanator.data_source.sabio_rk.Parameter attribute)
(datanator.data_source.sabio_rk.ReactionParticipant attribute)
compartments (datanator.data_source.ecmdb.Compound attribute)
,
[1]
Complex (class in datanator.data_source.corum)
complex (datanator.data_source.corum.Observation attribute)
(datanator.data_source.corum.Subunit attribute)
complex_cmt (datanator.core.data_model.ProteinComplexSpecie attribute)
(datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.data_source.corum.Complex attribute)
,
[1]
complex_id (datanator.core.models.DNABindingDataset attribute)
,
[1]
(datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.data_source.corum.Complex attribute)
,
[1]
(datanator.data_source.corum.Subunit attribute)
,
[1]
complex_name (datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.data_source.corum.Complex attribute)
,
[1]
complex_search_vector (datanator.core.models.Metabolite attribute)
(datanator.core.models.ProteinSubunit attribute)
Compound (class in datanator.data_source.ecmdb)
(class in datanator.data_source.sabio_rk)
compound (datanator.data_source.ecmdb.Concentration attribute)
,
[1]
(datanator.data_source.sabio_rk.Parameter attribute)
,
[1]
(datanator.data_source.sabio_rk.ReactionParticipant attribute)
,
[1]
compound_id (datanator.data_source.ecmdb.Concentration attribute)
(datanator.data_source.sabio_rk.Parameter attribute)
(datanator.data_source.sabio_rk.ReactionParticipant attribute)
compounds (datanator.data_source.ecmdb.Compartment attribute)
,
[1]
(datanator.data_source.ecmdb.Resource attribute)
,
[1]
(datanator.data_source.ecmdb.Synonym attribute)
(datanator.data_source.sabio_rk.CompoundStructure attribute)
,
[1]
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)
Concentration (class in datanator.core.models)
(class in datanator.data_source.ecmdb)
concentration (datanator.core.models.Metabolite attribute)
concentration_id (datanator.core.models.Concentration attribute)
concentrations (datanator.data_source.ecmdb.Compound attribute)
,
[1]
(datanator.data_source.ecmdb.Resource attribute)
,
[1]
Conditions (class in datanator.core.models)
conditions (datanator.core.models.Metadata attribute)
confidence (datanator.core.data_model.Interaction attribute)
(datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
connections (datanator.util.molecule_util.InchiMolecule attribute)
Consensus (class in datanator.core.data_model)
Consensus.Meta (class in datanator.core.data_model)
ConsensusGenerator (class in datanator.core.data_query)
ConsensusMethod (class in datanator.core.data_model)
continuousload() (in module datanator.util.build_util)
convert_rxn_to_data_model() (datanator.api.query.reaction_kinetics.ReactionKineticsQuery method)
correct_protein_name_list() (in module datanator.data_source.corum)
(in module datanator.data_source.corum_nosql)
Corum (class in datanator.data_source.corum)
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)
coverage (datanator.core.models.AbundanceDataSet attribute)
,
[1]
(datanator.data_source.pax.Dataset attribute)
,
[1]
create() (datanator.__main__.DbController method)
create_app() (in module datanator.rest)
create_compartment_from_sbml() (datanator.data_source.sabio_rk.SabioRk method)
create_cross_references_from_sbml() (datanator.data_source.sabio_rk.SabioRk method)
create_kinetic_law_from_sbml() (datanator.data_source.sabio_rk.SabioRk method)
create_kinetic_laws_from_sbml() (datanator.data_source.sabio_rk.SabioRk method)
create_orm() (in module datanator.data_source.refseq)
create_specie_from_sbml() (datanator.data_source.sabio_rk.SabioRk method)
create_taxon() (in module datanator.__main__)
created (datanator.data_source.ecmdb.Compound 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)
cross_references (datanator.core.data_model.EntityInteractionOrProperty attribute)
,
[1]
(datanator.core.data_model.ObservedResultMetadata attribute)
(datanator.data_source.ecmdb.Compound 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.util.molecule_util.Molecule attribute)
(datanator.util.taxonomy_util.Taxon attribute)
D
Data (class in datanator.data_source.jaspar)
data_files (datanator.data_source.pax.Pax attribute)
data_folder (datanator.data_source.pax.Pax attribute)
data_formats (datanator.data_source.array_express.Experiment attribute)
,
[1]
data_source (datanator.core.data_query.CachedDataSourceQueryGenerator attribute)
database_name (datanator.core.models.Progress attribute)
DataFormat (class in datanator.core.models)
(class in datanator.data_source.array_express)
Datanator (class in datanator.datanator)
datanator (module)
datanator.__main__ (module)
datanator.api (module)
datanator.api.lib (module)
datanator.api.lib.complex (module)
datanator.api.lib.complex.manager (module)
datanator.api.lib.data_manager (module)
datanator.api.lib.filter (module)
datanator.api.lib.filter.manager (module)
datanator.api.lib.metabolite (module)
datanator.api.lib.metabolite.manager (module)
datanator.api.lib.reaction (module)
datanator.api.lib.reaction.manager (module)
datanator.api.lib.search (module)
datanator.api.lib.search.manager (module)
datanator.api.lib.subunit (module)
datanator.api.lib.subunit.manager (module)
datanator.api.query (module)
datanator.api.query.dna_protein_interactions (module)
datanator.api.query.metabolite_concentrations (module)
datanator.api.query.protein_abundance (module)
datanator.api.query.protein_protein_interactions (module)
datanator.api.query.reaction_kinetics (module)
datanator.api.query.text_search (module)
datanator.api.serializer (module)
datanator.api.urls (module)
datanator.api.views (module)
datanator.builds (module)
datanator.builds.full (module)
datanator.builds.med (module)
datanator.builds.test (module)
datanator.builds.test_log (module)
datanator.config (module)
datanator.config.config (module)
datanator.config.core (module)
datanator.core (module)
datanator.core.common_schema (module)
datanator.core.data_model (module)
datanator.core.data_query (module)
datanator.core.data_source (module)
datanator.core.models (module)
datanator.core.query_nosql (module)
datanator.core.render_form (module)
datanator.core.render_form.render_html_from_schema (module)
datanator.core.upload_data (module)
datanator.data_source (module)
datanator.data_source.array_express (module)
datanator.data_source.array_express_tools (module)
datanator.data_source.array_express_tools.ensembl_tools (module)
datanator.data_source.bio_portal (module)
datanator.data_source.corum (module)
datanator.data_source.corum_nosql (module)
datanator.data_source.cron_aggregate (module)
datanator.data_source.ecmdb (module)
datanator.data_source.ensembl (module)
datanator.data_source.ezyme (module)
datanator.data_source.intact (module)
datanator.data_source.intact_nosql (module)
datanator.data_source.jaspar (module)
datanator.data_source.kegg (module)
datanator.data_source.kegg_orthology (module)
datanator.data_source.kegg_reaction_class (module)
datanator.data_source.metabolites_meta_collection (module)
datanator.data_source.pax (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.refseq (module)
datanator.data_source.sabio_rk (module)
datanator.data_source.sabio_rk_nosql (module)
datanator.data_source.sqlite_to_json (module)
datanator.data_source.taxon_tree (module)
datanator.data_source.uniprot (module)
datanator.datanator (module)
datanator.io (module)
datanator.rest (module)
datanator.rest.auth (module)
datanator.rest.db_2 (module)
datanator.rest.query (module)
datanator.rest.query.front_end_query (module)
datanator.rest.search (module)
datanator.util (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_seq_util (module)
datanator.util.server_util (module)
datanator.util.standardize_util (module)
datanator.util.taxonomy_util (module)
datanator.util.warning_util (module)
DataQuery (class in datanator.core.query_nosql)
DataQueryGenerator (class in datanator.core.data_query)
Dataset (class in datanator.data_source.pax)
dataset (datanator.core.models.AbundanceData attribute)
(datanator.core.models.DNABindingData attribute)
(datanator.data_source.pax.Observation attribute)
dataset_id (datanator.core.models.AbundanceData attribute)
,
[1]
(datanator.core.models.AbundanceDataSet attribute)
(datanator.core.models.DNABindingData attribute)
,
[1]
(datanator.core.models.DNABindingDataset attribute)
(datanator.data_source.pax.Observation attribute)
,
[1]
datasets (datanator.data_source.pax.Taxon attribute)
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)
db_cache_dirname (datanator.api.lib.search.manager.SearchManager attribute)
(datanator.api.query.text_search.TextSearchSession attribute)
DbController (class in datanator.__main__)
DbController.Meta (class in datanator.__main__)
DbRestoreController (class in datanator.__main__)
DbRestoreController.Meta (class in datanator.__main__)
DEBUG (datanator.config.config.BaseConfig attribute)
(datanator.config.config.BuildConfig attribute)
(datanator.config.config.CircleTestingConfig attribute)
(datanator.config.config.LocalDevelopmentConfig attribute)
(datanator.config.config.ProductionConfig attribute)
DEBUG_TB_ENABLED (datanator.config.config.BaseConfig attribute)
(datanator.config.config.BuildConfig attribute)
(datanator.config.config.CircleTestingConfig attribute)
(datanator.config.config.LocalDevelopmentConfig attribute)
DEBUG_TB_INTERCEPT_REDIRECTS (datanator.config.config.BaseConfig attribute)
DEFAULT_ONTOLOGIES (datanator.data_source.bio_portal.BioPortal attribute)
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)
desc (datanator.data_source.intact.ProteinComplex attribute)
,
[1]
description (datanator.__main__.AggregateBuildController.Meta attribute)
(datanator.__main__.BaseController.Meta attribute)
(datanator.__main__.BuildController.Meta attribute)
(datanator.__main__.DbController.Meta attribute)
(datanator.__main__.DbRestoreController.Meta attribute)
(datanator.__main__.DownloadController.Meta attribute)
(datanator.__main__.GenerateRNASeqTemplate.Meta attribute)
(datanator.__main__.GenerateTemplateController.Meta attribute)
(datanator.__main__.GetDataController.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__.UploadRNASeqExperiment.Meta attribute)
(datanator.__main__.UploadReferenceGenome.Meta attribute)
(datanator.core.data_model.Method attribute)
,
[1]
(datanator.core.models.ExperimentMetadata attribute)
(datanator.core.models.Metabolite attribute)
,
[1]
(datanator.data_source.array_express.Experiment attribute)
,
[1]
(datanator.data_source.ecmdb.Compound attribute)
,
[1]
(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)
designs (datanator.data_source.array_express.Experiment attribute)
,
[1]
disable_warnings() (in module datanator.util.warning_util)
disease_cmt (datanator.core.data_model.ProteinComplexSpecie attribute)
(datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.data_source.corum.Complex attribute)
,
[1]
distance_from_nearest_ncbi_taxon (datanator.util.taxonomy_util.Taxon attribute)
dna_binding_data (datanator.core.models.DNABindingDataset attribute)
dna_binding_dataset (datanator.core.models.ProteinComplex attribute)
(datanator.core.models.ProteinSubunit attribute)
DNABindingData (class in datanator.core.models)
DNABindingDataset (class in datanator.core.models)
DnaSpecie (class in datanator.core.data_model)
DnaSpecie.Meta (class in datanator.core.data_model)
DNAtoProteinInteractionQuery (class in datanator.api.query.dna_protein_interactions)
doc_feeder() (datanator.core.query_nosql.DataQuery method)
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_COMPOUND_STRUCTURE_URL (datanator.data_source.ecmdb.Ecmdb attribute)
DOWNLOAD_COMPOUND_URL (datanator.data_source.ecmdb.Ecmdb attribute)
,
[1]
download_content() (datanator.data_source.intact.IntAct method)
(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_INDEX_URL (datanator.data_source.ecmdb.Ecmdb attribute)
,
[1]
download_ko() (datanator.data_source.kegg_orthology.KeggOrthology method)
download_ontologies() (datanator.data_source.bio_portal.BioPortal method)
download_ontology() (datanator.data_source.bio_portal.BioPortal 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.core.models.ReferenceGenome attribute)
(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__)
downloaded (datanator.data_source.ecmdb.Compound attribute)
,
[1]
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)
drop() (datanator.__main__.DbController method)
dump_database() (datanator.core.data_source.PostgresDataSource method)
E
ec_number (datanator.core.models.ProteinSubunit attribute)
(datanator.data_source.ezyme.EzymeResult attribute)
(datanator.data_source.refseq.EcNumber attribute)
(datanator.data_source.uniprot.UniprotData attribute)
ec_numbers (datanator.data_source.refseq.Gene attribute)
EC_PREDICTION_URL (datanator.data_source.ezyme.Ezyme attribute)
,
[1]
Ecmdb (class in datanator.data_source.ecmdb)
ecmdb() (datanator.__main__.BuildController method)
(datanator.__main__.DownloadController method)
EcNumber (class in datanator.data_source.refseq)
editor (datanator.core.data_model.Reference attribute)
,
[1]
enable_warnings() (in module datanator.util.warning_util)
end (datanator.data_source.refseq.Location attribute)
endpoint (datanator.api.views.Metabolite attribute)
(datanator.api.views.MetaboliteConcentration attribute)
(datanator.api.views.MetaboliteSearch attribute)
(datanator.api.views.ProteinAbundance attribute)
(datanator.api.views.ProteinComplex attribute)
(datanator.api.views.ProteinComplexSearch attribute)
(datanator.api.views.ProteinInteraction attribute)
(datanator.api.views.ProteinSubunit attribute)
(datanator.api.views.ProteinSubunitSearch attribute)
(datanator.api.views.Reaction attribute)
(datanator.api.views.ReactionParameter attribute)
(datanator.api.views.Search 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.array_express.ArrayExpress attribute)
(datanator.data_source.corum.Corum attribute)
(datanator.data_source.ecmdb.Ecmdb attribute)
(datanator.data_source.ezyme.Ezyme attribute)
(datanator.data_source.intact.IntAct attribute)
(datanator.data_source.jaspar.Jaspar attribute)
(datanator.data_source.kegg.Kegg attribute)
(datanator.data_source.pax.Pax attribute)
(datanator.data_source.sabio_rk.SabioRk attribute)
(datanator.data_source.uniprot.Uniprot 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)
ensembl_info (datanator.data_source.array_express.Sample attribute)
ensembl_organism_strain (datanator.core.models.RNASeqDataSet attribute)
(datanator.data_source.array_express.Sample attribute)
,
[1]
EnsemblInfo (class in datanator.data_source.array_express)
EntityInteractionOrProperty (class in datanator.core.data_model)
EntityInteractionOrProperty.Meta (class in datanator.core.data_model)
EntityInteractionOrPropertySerializer (class in datanator.api.serializer)
EntityInteractionOrPropertySerializer.Meta (class in datanator.api.serializer)
entrez_id (datanator.core.data_model.ProteinSpecie attribute)
,
[1]
(datanator.core.models.ProteinSubunit attribute)
,
[1]
(datanator.data_source.uniprot.UniprotData attribute)
entries (datanator.data_source.sabio_rk.Resource attribute)
,
[1]
(datanator.data_source.sabio_rk.Synonym attribute)
,
[1]
Entry (class in datanator.data_source.sabio_rk)
entry_name (datanator.data_source.uniprot.UniprotData attribute)
Environment (class in datanator.core.data_model)
environment (datanator.core.data_model.ObservedResultMetadata attribute)
,
[1]
Environment.Meta (class in datanator.core.data_model)
EnvironmentSerializer (class in datanator.api.serializer)
EnvironmentSerializer.Meta (class in datanator.api.serializer)
Enzyme (class in datanator.data_source.sabio_rk)
enzyme (datanator.core.models.KineticLaw attribute)
(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.core.models.KineticLaw attribute)
,
[1]
(datanator.data_source.sabio_rk.EnzymeSubunit attribute)
(datanator.data_source.sabio_rk.KineticLaw attribute)
(datanator.data_source.sabio_rk.Parameter attribute)
enzyme_type (datanator.core.models.KineticLaw attribute)
(datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
EnzymeSubunit (class in datanator.data_source.sabio_rk)
equation (datanator.core.models.KineticLaw attribute)
(datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
error (datanator.core.data_model.Consensus attribute)
,
[1]
(datanator.core.data_model.ObservedValue attribute)
,
[1]
(datanator.core.models.Concentration attribute)
,
[1]
(datanator.core.models.Parameter attribute)
,
[1]
(datanator.data_source.ecmdb.Concentration attribute)
,
[1]
(datanator.data_source.sabio_rk.Parameter attribute)
,
[1]
essentiality (datanator.data_source.refseq.Gene attribute)
Evidence (class in datanator.core.data_model)
evidence (datanator.core.data_model.Consensus attribute)
,
[1]
(datanator.data_source.intact.ProteinComplex attribute)
,
[1]
Evidence.Meta (class in datanator.core.data_model)
excel_batch_size (datanator.data_source.sabio_rk.SabioRk attribute)
exclude (datanator.api.serializer.CellCompartmentSerializer.Meta attribute)
(datanator.api.serializer.MetaboliteSerializer.Meta attribute)
(datanator.api.serializer.ProteinComplexSerializer.Meta attribute)
(datanator.api.serializer.ProteinSubunitSerializer.Meta attribute)
(datanator.api.serializer.SpecieSerializer.Meta attribute)
(datanator.api.serializer.StructureSerializer.Meta attribute)
(datanator.api.serializer.TaxonSerializer.Meta attribute)
exp_id (datanator.data_source.ensembl.GeneEntry attribute)
exp_name (datanator.core.models.RNASeqExperiment attribute)
Experiment (class in datanator.core.models)
(class in datanator.data_source.array_express)
experiment (datanator.core.models.ExperimentMetadata attribute)
(datanator.core.models.RNASeqDataSet attribute)
(datanator.data_source.array_express.Sample attribute)
,
[1]
experiment_accession_number (datanator.core.models.RNASeqDataSet attribute)
experiment_design (datanator.core.models.ExperimentMetadata attribute)
experiment_id (datanator.core.models.RNASeqExperiment attribute)
(datanator.data_source.array_express.Sample attribute)
,
[1]
EXPERIMENT_NAME (datanator.data_source.jaspar.Tffm attribute)
experiment_type (datanator.core.models.ExperimentMetadata attribute)
ExperimentalMethod (class in datanator.core.data_model)
ExperimentalMethod.Meta (class in datanator.core.data_model)
ExperimentDesign (class in datanator.core.models)
(class in datanator.data_source.array_express)
ExperimentMetadata (class in datanator.core.models)
experiments (datanator.data_source.array_express.DataFormat attribute)
(datanator.data_source.array_express.ExperimentDesign attribute)
(datanator.data_source.array_express.ExperimentType attribute)
(datanator.data_source.array_express.Organism attribute)
(datanator.data_source.array_express.Protocol attribute)
,
[1]
ExperimentType (class in datanator.core.models)
(class in datanator.data_source.array_express)
ExponentialFilter (class in datanator.core.data_query)
export_stats() (datanator.data_source.sabio_rk.SabioRk method)
Extract (class in datanator.data_source.array_express)
extract_values() (datanator.util.file_util.FileUtil method)
extracts (datanator.data_source.array_express.Sample attribute)
Ezyme (class in datanator.data_source.ezyme)
EzymeResult (class in datanator.data_source.ezyme)
F
family_name (datanator.core.data_model.ProteinComplexSpecie attribute)
(datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.core.models.ProteinSubunit attribute)
,
[1]
fastq_urls (datanator.data_source.array_express.Sample attribute)
,
[1]
feature_a (datanator.data_source.intact.ProteinInteraction attribute)
,
[1]
(datanator.data_source.uniprot.UniprotData attribute)
feature_b (datanator.data_source.intact.ProteinInteraction attribute)
,
[1]
(datanator.data_source.uniprot.UniprotData attribute)
fields (datanator.api.serializer.EntityInteractionOrPropertySerializer.Meta attribute)
(datanator.api.serializer.EnvironmentSerializer.Meta attribute)
(datanator.api.serializer.GeneticsSerializer.Meta attribute)
(datanator.api.serializer.InteractionSerializer.Meta attribute)
(datanator.api.serializer.MetadataSerializer.Meta attribute)
(datanator.api.serializer.ObservableSerializer.Meta attribute)
(datanator.api.serializer.ObservedComplexSpecieSerializer.Meta attribute)
(datanator.api.serializer.ObservedInteractionSerializer.Meta attribute)
(datanator.api.serializer.ObservedProteinSpecieSerializer.Meta attribute)
(datanator.api.serializer.ObservedResultMetadataSerializer.Meta attribute)
(datanator.api.serializer.ObservedResultSerializer.Meta attribute)
(datanator.api.serializer.ObservedSpecieSerializer.Meta attribute)
(datanator.api.serializer.ObservedValueSerializer.Meta attribute)
(datanator.api.serializer.PolymerSpecieSerializer.Meta attribute)
(datanator.api.serializer.ProteinComplexSpecieSerializer.Meta attribute)
(datanator.api.serializer.ProteinSpecieSerializer.Meta attribute)
(datanator.api.serializer.ReactionParticipantSerializer.Meta attribute)
(datanator.api.serializer.ReactionSerializer.Meta attribute)
(datanator.api.serializer.ResourceSerializer.Meta attribute)
(datanator.api.serializer.SpecieSerializer.Meta attribute)
file_id (datanator.data_source.pax.Pax attribute)
file_name (datanator.core.models.AbundanceDataSet attribute)
,
[1]
(datanator.data_source.pax.Dataset attribute)
,
[1]
filename (datanator.core.data_source.CachedDataSource attribute)
FileUtil (class in datanator.util.file_util)
fill_db() (datanator.util.mongo_util.MongoUtil method)
fill_metabolite_fields() (datanator.data_source.metabolites_meta_collection.MetabolitesMeta method)
Filter (class in datanator.core.data_query)
filter() (datanator.core.data_query.FilterRunner method)
filter_observed_results() (datanator.core.data_query.DataQueryGenerator method)
FilterManager (class in datanator.api.lib.filter.manager)
FilterResult (class in datanator.core.data_query)
FilterRunner (class in datanator.core.data_query)
filters (datanator.core.data_query.DataQueryGenerator attribute)
(datanator.core.data_query.FilterRunner attribute)
find_between() (datanator.data_source.intact.IntAct method)
(datanator.data_source.intact_nosql.IntActNoSQL method)
find_between_psi_mi_parentheses() (datanator.data_source.intact.IntAct method)
(datanator.data_source.intact_nosql.IntActNoSQL method)
find_files() (in module datanator.data_source.pax)
(in module datanator.data_source.pax_nosql)
find_nth() (datanator.data_source.refseq.Refseq method)
(in module datanator.data_source.array_express_tools.ensembl_tools)
find_protein_gene() (datanator.data_source.intact.IntAct method)
(datanator.data_source.intact_nosql.IntActNoSQL method)
find_pubmed_id() (datanator.data_source.intact.IntAct method)
(datanator.data_source.intact_nosql.IntActNoSQL method)
find_reaction_participants() (datanator.core.query_nosql.QuerySabio method)
find_text() (datanator.core.query_nosql.DataQuery 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)
frequency_a (datanator.core.models.DNABindingData attribute)
,
[1]
frequency_c (datanator.core.models.DNABindingData attribute)
,
[1]
frequency_g (datanator.core.models.DNABindingData attribute)
,
[1]
frequency_t (datanator.core.models.DNABindingData attribute)
,
[1]
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.core.models.RNASeqDataSet attribute)
(datanator.data_source.array_express.Sample attribute)
,
[1]
(datanator.data_source.array_express_tools.ensembl_tools.StrainInfo attribute)
FullTextQuery (class in datanator.core.models)
funcat_dsc (datanator.core.data_model.ProteinComplexSpecie attribute)
(datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.data_source.corum.Complex attribute)
,
[1]
funcat_id (datanator.core.data_model.ProteinComplexSpecie attribute)
(datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.data_source.corum.Complex attribute)
,
[1]
G
Gene (class in datanator.data_source.refseq)
gene (datanator.data_source.refseq.EcNumber attribute)
(datanator.data_source.refseq.GeneSynonym attribute)
(datanator.data_source.refseq.Identifier attribute)
(datanator.data_source.refseq.Location attribute)
(datanator.data_source.refseq.Qualifier attribute)
gene_a (datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
gene_b (datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
gene_name (datanator.core.data_model.ProteinSpecie attribute)
,
[1]
(datanator.core.models.ProteinSubunit attribute)
,
[1]
(datanator.data_source.corum.Subunit attribute)
,
[1]
(datanator.data_source.uniprot.UniprotData attribute)
gene_syn (datanator.core.models.ProteinSubunit attribute)
,
[1]
(datanator.data_source.corum.Subunit attribute)
,
[1]
gene_synonyms (datanator.data_source.refseq.Gene attribute)
GeneEntry (class in datanator.data_source.ensembl)
GeneIdentifier (class in datanator.data_source.ensembl)
GenerateRNASeqTemplate (class in datanator.__main__)
GenerateRNASeqTemplate.Meta (class in datanator.__main__)
GenerateTemplateController (class in datanator.__main__)
GenerateTemplateController.Meta (class in datanator.__main__)
genes (datanator.data_source.refseq.ReferenceGenome attribute)
GeneSynonym (class in datanator.data_source.refseq)
Genetics (class in datanator.core.data_model)
genetics (datanator.core.data_model.ObservedResultMetadata attribute)
,
[1]
Genetics.Meta (class in datanator.core.data_model)
GeneticsSerializer (class in datanator.api.serializer)
GeneticsSerializer.Meta (class in datanator.api.serializer)
get() (datanator.api.views.Metabolite method)
(datanator.api.views.MetaboliteConcentration method)
(datanator.api.views.MetaboliteSearch method)
(datanator.api.views.ProteinAbundance method)
(datanator.api.views.ProteinComplex method)
(datanator.api.views.ProteinComplexSearch method)
(datanator.api.views.ProteinInteraction method)
(datanator.api.views.ProteinSubunit method)
(datanator.api.views.ProteinSubunitSearch method)
(datanator.api.views.Reaction method)
(datanator.api.views.ReactionParameter method)
(datanator.api.views.Search method)
get_abundance_by_entrez() (datanator.api.query.protein_abundance.ProteinAbundanceQuery method)
get_abundance_by_gene_name() (datanator.api.lib.subunit.manager.ProteinSubunitManager method)
(datanator.api.query.protein_abundance.ProteinAbundanceQuery method)
get_abundance_by_length() (datanator.api.lib.subunit.manager.ProteinSubunitManager method)
(datanator.api.query.protein_abundance.ProteinAbundanceQuery method)
get_abundance_by_mass() (datanator.api.lib.subunit.manager.ProteinSubunitManager method)
(datanator.api.query.protein_abundance.ProteinAbundanceQuery method)
get_abundance_by_sequence() (datanator.api.lib.subunit.manager.ProteinSubunitManager method)
(datanator.api.query.protein_abundance.ProteinAbundanceQuery method)
get_abundance_by_uniprot() (datanator.api.lib.subunit.manager.ProteinSubunitManager method)
(datanator.api.query.protein_abundance.ProteinAbundanceQuery method)
get_anc_by_id() (datanator.core.query_nosql.QueryTaxonTree method)
get_anc_by_name() (datanator.core.query_nosql.QueryTaxonTree method)
get_api_key() (datanator.data_source.bio_portal.BioPortal method)
get_attribute_of_observed_value() (datanator.core.data_query.Filter method)
get_common() (datanator.util.file_util.FileUtil method)
get_common_ancestor() (datanator.core.query_nosql.QueryTaxonTree method)
(datanator.util.taxonomy_util.Taxon method)
get_complex_by_id() (datanator.api.lib.complex.manager.ProteinComplexManager method)
get_conc_ids() (datanator.rest.query.front_end_query.QueryFrontEnd method)
get_concentration_by_structure() (datanator.api.lib.metabolite.manager.MetaboliteManager method)
(datanator.api.query.metabolite_concentrations.MetaboliteConcentrationQuery method)
get_config() (in module datanator.config.core)
get_consensus() (datanator.core.data_query.DataQueryGenerator method)
get_db() (in module datanator.rest.db_2)
get_debug_logs_config() (in module datanator.config.core)
get_dict_of_new_objects() (datanator.core.upload_data.UploadData method)
get_distance_to_common_ancestor() (datanator.util.taxonomy_util.Taxon method)
get_distance_to_root() (datanator.util.taxonomy_util.Taxon method)
get_DNA_by_protein() (datanator.api.query.dna_protein_interactions.ProteintoDNAInteractionQuery method)
get_ec_number() (datanator.core.data_model.Reaction method)
get_ec_numbers() (datanator.core.data_model.Reaction method)
get_ecmdb_entries() (datanator.rest.query.front_end_query.QueryFrontEnd method)
get_engine() (datanator.core.data_source.CachedDataSource method)
(datanator.core.data_source.PostgresDataSource method)
(datanator.data_source.bio_portal.BioPortal 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_generic_concs() (datanator.rest.query.front_end_query.QueryFrontEnd method)
get_ids_from_hash() (datanator.core.query_nosql.QueryMetabolitesMeta method)
get_inchi_structures() (datanator.data_source.sabio_rk.Compound method)
get_interaction_by_subunit() (datanator.api.lib.subunit.manager.ProteinSubunitManager method)
(datanator.api.query.protein_protein_interactions.ProteinInteractionandComplexQuery method)
get_json_ends() (datanator.data_source.refseq.Refseq method)
(in module datanator.data_source.array_express_tools.ensembl_tools)
get_kinetic_laws_by_ec_numbers() (datanator.api.lib.reaction.manager.ReactionManager method)
(datanator.api.query.reaction_kinetics.ReactionKineticsQuery method)
get_kinetic_laws_by_metabolite() (datanator.api.lib.reaction.manager.ReactionManager method)
(datanator.api.query.reaction_kinetics.ReactionKineticsQuery method)
get_kinetic_laws_by_participants() (datanator.api.lib.reaction.manager.ReactionManager method)
(datanator.api.query.reaction_kinetics.ReactionKineticsQuery method)
get_kinetic_laws_by_reaction() (datanator.api.lib.reaction.manager.ReactionManager method)
(datanator.api.query.reaction_kinetics.ReactionKineticsQuery method)
get_kinetic_laws_by_structure() (datanator.api.lib.reaction.manager.ReactionManager method)
(datanator.api.query.reaction_kinetics.ReactionKineticsQuery method)
get_kinlawid_by_inchi() (datanator.core.query_nosql.QuerySabio method)
get_kinlawid_by_inchi_slow() (datanator.core.query_nosql.QuerySabio method)
get_kinlawid_by_rxn() (datanator.core.query_nosql.QuerySabio method)
get_known_complex_by_subunit() (datanator.api.lib.complex.manager.ProteinComplexManager method)
(datanator.api.lib.subunit.manager.ProteinSubunitManager method)
(datanator.api.query.protein_protein_interactions.ProteinInteractionandComplexQuery method)
get_manual_ec_numbers() (datanator.core.data_model.Reaction method)
get_max_distance_to_common_ancestor() (datanator.util.taxonomy_util.Taxon method)
get_metabolite_by_id() (datanator.api.lib.metabolite.manager.MetaboliteManager method)
get_metabolite_by_structure() (datanator.api.lib.metabolite.manager.MetaboliteManager method)
get_metabolite_hashed_inchi() (datanator.core.query_nosql.QueryMetabolitesMeta method)
get_metabolite_inchi() (datanator.core.query_nosql.QueryMetabolitesMeta method)
get_metabolite_name_by_hash() (datanator.core.query_nosql.QueryMetabolitesMeta method)
get_metabolite_similar_compounds() (datanator.core.query_nosql.QueryMetabolitesMeta method)
get_metabolite_synonyms() (datanator.core.query_nosql.QueryMetabolitesMeta method)
get_metabolites_by_structure() (datanator.api.query.reaction_kinetics.ReactionKineticsQuery method)
get_modifiers() (datanator.core.data_model.Reaction method)
get_name_by_id() (datanator.core.query_nosql.QueryTaxonTree method)
get_ncbi_id() (datanator.util.taxonomy_util.Taxon method)
get_node_children() (datanator.data_source.ecmdb.Ecmdb method)
get_node_text() (datanator.data_source.ecmdb.Ecmdb method)
get_object_by_id() (datanator.api.lib.search.manager.SearchManager method)
get_observable_complex() (datanator.api.lib.subunit.manager.ProteinSubunitManager method)
(datanator.api.query.protein_protein_interactions.ProteinInteractionandComplexQuery method)
get_observable_interactions() (datanator.api.lib.subunit.manager.ProteinSubunitManager method)
(datanator.api.query.protein_protein_interactions.ProteinInteractionandComplexQuery method)
get_observable_subunits() (datanator.api.lib.complex.manager.ProteinComplexManager method)
(datanator.api.query.protein_protein_interactions.ProteinInteractionandComplexQuery method)
get_observed_abundances() (datanator.api.lib.subunit.manager.ProteinSubunitManager method)
get_observed_concentrations() (datanator.api.lib.metabolite.manager.MetaboliteManager method)
get_observed_parameter_value() (datanator.api.lib.reaction.manager.ReactionManager method)
get_observed_result() (datanator.api.query.dna_protein_interactions.DNAtoProteinInteractionQuery method)
(datanator.api.query.dna_protein_interactions.ProteintoDNAInteractionQuery method)
(datanator.api.query.metabolite_concentrations.MetaboliteConcentrationQuery method)
(datanator.api.query.protein_abundance.ProteinAbundanceQuery method)
(datanator.api.query.protein_protein_interactions.ProteinInteractionandComplexQuery method)
(datanator.api.query.reaction_kinetics.ReactionKineticsQuery method)
(datanator.core.data_query.DataQueryGenerator method)
get_ontologies() (datanator.data_source.bio_portal.BioPortal method)
get_ontologies_filename() (datanator.data_source.bio_portal.BioPortal method)
get_ontology() (datanator.data_source.bio_portal.BioPortal method)
get_ontology_filename() (datanator.data_source.bio_portal.BioPortal method)
get_or_create_object() (datanator.core.data_source.CachedDataSource method)
(datanator.core.data_source.PostgresDataSource method)
(datanator.data_source.array_express.ArrayExpress method)
(datanator.data_source.refseq.Refseq method)
get_or_create_object_upload() (datanator.core.upload_data.UploadData method)
get_ordered_participants() (datanator.core.data_model.Reaction method)
get_parameter_by_properties() (datanator.data_source.sabio_rk.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)
(datanator.data_source.bio_portal.BioPortal method)
(datanator.data_source.intact.IntAct method)
(datanator.data_source.refseq.Refseq method)
get_predicted_ec_numbers() (datanator.core.data_model.Reaction method)
get_primitive_fields() (datanator.core.upload_data.UploadData method)
get_processed_data_samples() (in module datanator.data_source.process_rna_seq.core)
get_products() (datanator.core.data_model.Reaction method)
get_protein_by_DNA_sequence() (datanator.api.query.dna_protein_interactions.DNAtoProteinInteractionQuery method)
get_rank() (datanator.core.query_nosql.QueryTaxonTree method)
(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_reaction_by_kinetic_law_id() (datanator.api.lib.reaction.manager.ReactionManager method)
(datanator.api.query.reaction_kinetics.ReactionKineticsQuery method)
get_reaction_by_metabolite() (datanator.api.lib.reaction.manager.ReactionManager method)
(datanator.api.query.reaction_kinetics.ReactionKineticsQuery method)
get_ref_seq_url() (datanator.data_source.refseq.Refseq method)
(in module datanator.data_source.array_express_tools.ensembl_tools)
get_requests_session() (datanator.core.data_source.HttpDataSource method)
get_session() (datanator.core.data_source.CachedDataSource method)
(datanator.core.data_source.PostgresDataSource method)
(datanator.data_source.bio_portal.BioPortal 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_reference_from_sbml() (datanator.data_source.sabio_rk.SabioRk method)
get_strain_info() (in module datanator.data_source.array_express_tools.ensembl_tools)
get_subunit_by_id() (datanator.api.lib.subunit.manager.ProteinSubunitManager method)
get_subunits_by_known_complex() (datanator.api.lib.complex.manager.ProteinComplexManager method)
(datanator.api.query.protein_protein_interactions.ProteinInteractionandComplexQuery method)
get_tanimoto() (datanator.util.calc_tanimoto.CalcTanimoto method)
get_taxonomic_lineage() (in module datanator.data_source.array_express_tools.ensembl_tools)
get_uniprot() (datanator.data_source.uniprot_nosql.UniprotNoSQL method)
get_user_config() (datanator.util.server_util.ServerUtil method)
get_version_endpoint() (in module datanator.api.urls)
get_ymdb_entries() (datanator.rest.query.front_end_query.QueryFrontEnd method)
GetDataController (class in datanator.__main__)
GetDataController.Meta (class in datanator.__main__)
GetGenes (class in datanator.data_source.ensembl)
go_annot (datanator.data_source.intact.ProteinComplex attribute)
,
[1]
go_dsc (datanator.core.data_model.ProteinComplexSpecie attribute)
(datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.data_source.corum.Complex attribute)
,
[1]
go_id (datanator.core.data_model.ProteinComplexSpecie attribute)
(datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.data_source.corum.Complex attribute)
,
[1]
group_observed_results_by_properties() (datanator.core.data_query.ConsensusGenerator method)
growth_status (datanator.core.data_model.Environment attribute)
(datanator.core.models.Conditions attribute)
,
[1]
(datanator.data_source.ecmdb.Concentration attribute)
,
[1]
growth_system (datanator.core.data_model.Environment attribute)
(datanator.core.models.Conditions attribute)
,
[1]
(datanator.data_source.ecmdb.Concentration attribute)
,
[1]
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)
(datanator.core.models.Method attribute)
(datanator.data_source.array_express.Protocol attribute)
,
[1]
has_fastq_files (datanator.core.models.RNASeqExperiment attribute)
(datanator.data_source.array_express.Experiment attribute)
,
[1]
hash_inchi() (datanator.util.chem_util.ChemUtil method)
help (datanator.__main__.AggregateBuildController.Meta attribute)
(datanator.__main__.BaseController.Meta attribute)
(datanator.__main__.BuildController.Meta attribute)
(datanator.__main__.DbController.Meta attribute)
(datanator.__main__.DbRestoreController.Meta attribute)
(datanator.__main__.DownloadController.Meta attribute)
(datanator.__main__.GenerateRNASeqTemplate.Meta attribute)
(datanator.__main__.GenerateTemplateController.Meta attribute)
(datanator.__main__.GetDataController.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__.UploadRNASeqExperiment.Meta attribute)
(datanator.__main__.UploadReferenceGenome.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.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)
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.core.models.AbundanceDataSet attribute)
(datanator.core.models.CellCompartment attribute)
(datanator.core.models.CellLine attribute)
(datanator.core.models.Characteristic attribute)
(datanator.core.models.Concentration attribute)
(datanator.core.models.Conditions attribute)
(datanator.core.models.DNABindingDataset attribute)
(datanator.core.models.Experiment attribute)
(datanator.core.models.ExperimentDesign attribute)
(datanator.core.models.ExperimentMetadata attribute)
(datanator.core.models.ExperimentType attribute)
(datanator.core.models.KineticLaw attribute)
(datanator.core.models.Metabolite attribute)
(datanator.core.models.Metadata attribute)
(datanator.core.models.Method attribute)
(datanator.core.models.Observation attribute)
,
[1]
(datanator.core.models.PhysicalEntity attribute)
(datanator.core.models.PhysicalProperty attribute)
(datanator.core.models.ProteinComplex attribute)
(datanator.core.models.ProteinInteraction attribute)
(datanator.core.models.ProteinSubunit attribute)
(datanator.core.models.RNASeqDataSet attribute)
(datanator.core.models.RNASeqExperiment attribute)
(datanator.core.models.ReferenceGenome attribute)
(datanator.core.models.Resource attribute)
(datanator.core.models.Structure attribute)
(datanator.core.models.Synonym attribute)
(datanator.core.models.Variable attribute)
(datanator.data_source.array_express.Experiment attribute)
,
[1]
(datanator.data_source.corum.Observation attribute)
(datanator.data_source.corum.Subunit attribute)
(datanator.data_source.ecmdb.Compound attribute)
,
[1]
(datanator.data_source.ecmdb.Resource attribute)
,
[1]
ID (datanator.data_source.jaspar.Annotation attribute)
(datanator.data_source.jaspar.Data attribute)
(datanator.data_source.jaspar.Matrix attribute)
(datanator.data_source.jaspar.Protein attribute)
(datanator.data_source.jaspar.Species attribute)
(datanator.data_source.jaspar.Tffm attribute)
id (datanator.data_source.pax.Dataset attribute)
(datanator.data_source.pax.Observation attribute)
(datanator.data_source.refseq.Gene attribute)
(datanator.data_source.refseq.ReferenceGenomeAccession 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.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)
Identifier (class in datanator.data_source.refseq)
identifier (datanator.data_source.intact.ProteinComplex attribute)
,
[1]
identifiers (datanator.data_source.ensembl.GeneEntry attribute)
(datanator.data_source.refseq.Gene attribute)
InchiMolecule (class in datanator.util.molecule_util)
include_variants (datanator.datanator.Datanator attribute)
index (datanator.data_source.array_express.Sample attribute)
,
[1]
Index (datanator.data_source.intact.ProteinInteraction attribute)
index (datanator.data_source.intact.ProteinInteraction attribute)
Index (datanator.data_source.uniprot.UniprotData attribute)
index (datanator.data_source.uniprot.UniprotData attribute)
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)
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)
init_app() (in module datanator.rest.db_2)
init_db() (in module datanator.rest.db_2)
InputReader (class in datanator.io)
IntAct (class in datanator.data_source.intact)
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]
(datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
(datanator.data_source.uniprot.UniprotData attribute)
Interaction.Meta (class in datanator.core.data_model)
interaction_id (datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
interaction_type (datanator.core.data_model.SpecieInteraction attribute)
(datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
InteractionSerializer (class in datanator.api.serializer)
InteractionSerializer.Meta (class in datanator.api.serializer)
interactor_a (datanator.data_source.intact.ProteinInteraction attribute)
(datanator.data_source.uniprot.UniprotData attribute)
interactor_b (datanator.data_source.intact.ProteinInteraction attribute)
(datanator.data_source.uniprot.UniprotData 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 (class in datanator.data_source.jaspar)
jaspar() (datanator.__main__.BuildController method)
(datanator.__main__.DownloadController method)
jaspar_id (datanator.core.models.DNABindingData attribute)
,
[1]
K
Kallisto (class in datanator.util.rna_seq_util)
Kegg (class in datanator.data_source.kegg)
KeggOrthology (class in datanator.data_source.kegg_orthology)
KeggReaction (class in datanator.data_source.kegg_reaction_class)
key (datanator.data_source.refseq.Qualifier attribute)
kinetic_law (datanator.core.models.Parameter attribute)
(datanator.core.models.ProteinComplex attribute)
(datanator.core.models.Reaction attribute)
(datanator.data_source.sabio_rk.Parameter attribute)
,
[1]
kinetic_law_id (datanator.core.data_model.Reaction attribute)
(datanator.core.models.KineticLaw attribute)
(datanator.core.models.Parameter attribute)
,
[1]
(datanator.core.models.Reaction attribute)
(datanator.data_source.sabio_rk.Parameter attribute)
kinetic_laws (datanator.data_source.sabio_rk.Compartment attribute)
,
[1]
(datanator.data_source.sabio_rk.Enzyme attribute)
,
[1]
(datanator.data_source.sabio_rk.Resource attribute)
,
[1]
KineticLaw (class in datanator.core.models)
(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__.DbController.Meta attribute)
(datanator.__main__.DbRestoreController.Meta attribute)
(datanator.__main__.DownloadController.Meta attribute)
(datanator.__main__.GenerateRNASeqTemplate.Meta attribute)
(datanator.__main__.GenerateTemplateController.Meta attribute)
(datanator.__main__.GetDataController.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__.UploadRNASeqExperiment.Meta attribute)
(datanator.__main__.UploadReferenceGenome.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)
LAYERS (datanator.util.molecule_util.InchiMolecule attribute)
,
[1]
length (datanator.core.data_model.ProteinSpecie attribute)
,
[1]
(datanator.core.models.ProteinSubunit attribute)
(datanator.data_source.uniprot.UniprotData attribute)
list_all_collections() (datanator.util.mongo_util.MongoUtil method)
load_compounds() (datanator.data_source.sabio_rk.SabioRk method)
load_content() (datanator.core.common_schema.CommonSchema method)
(datanator.core.data_source.CachedDataSource method)
(datanator.core.data_source.PostgresDataSource method)
(datanator.data_source.array_express.ArrayExpress method)
(datanator.data_source.bio_portal.BioPortal method)
(datanator.data_source.corum.Corum method)
(datanator.data_source.corum_nosql.CorumNoSQL method)
(datanator.data_source.ecmdb.Ecmdb method)
(datanator.data_source.ensembl.GetGenes method)
(datanator.data_source.intact.IntAct method)
(datanator.data_source.intact_nosql.IntActNoSQL method)
(datanator.data_source.jaspar.Jaspar method)
(datanator.data_source.kegg.Kegg 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.Pax method)
(datanator.data_source.pax_nosql.PaxNoSQL method)
(datanator.data_source.refseq.Refseq method)
(datanator.data_source.sabio_rk.SabioRk method)
(datanator.data_source.taxon_tree.TaxonTree method)
(datanator.data_source.uniprot.Uniprot method)
load_entire_small_dbs (datanator.core.common_schema.CommonSchema attribute)
load_experiment_metadata() (datanator.data_source.array_express.ArrayExpress method)
load_experiment_protocol() (datanator.data_source.array_express.ArrayExpress method)
load_experiment_protocols() (datanator.data_source.array_express.ArrayExpress method)
load_experiment_sample() (datanator.data_source.array_express.ArrayExpress method)
load_experiment_samples() (datanator.data_source.array_express.ArrayExpress method)
load_json() (datanator.data_source.sabio_rk_nosql.SabioRkNoSQL method)
load_kinetic_law_ids() (datanator.data_source.sabio_rk.SabioRk method)
load_kinetic_laws() (datanator.data_source.sabio_rk.SabioRk method)
load_logged_in_user() (in module datanator.rest.auth)
load_missing_enzyme_information_from_html() (datanator.data_source.sabio_rk.SabioRk method)
load_missing_kinetic_law_information_from_tsv() (datanator.data_source.sabio_rk.SabioRk method)
load_missing_kinetic_law_information_from_tsv_helper() (datanator.data_source.sabio_rk.SabioRk method)
load_small_db_switch (datanator.core.common_schema.CommonSchema attribute)
load_uniprot() (datanator.data_source.uniprot_nosql.UniprotNoSQL method)
loc_a (datanator.core.data_model.SpecieInteraction attribute)
,
[1]
(datanator.core.models.ProteinInteraction attribute)
loc_b (datanator.core.data_model.SpecieInteraction attribute)
,
[1]
(datanator.core.models.ProteinInteraction attribute)
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)
LocalDevelopmentConfig (class in datanator.config.config)
Location (class in datanator.data_source.refseq)
location (datanator.data_source.refseq.Gene attribute)
locus_tag (datanator.data_source.refseq.Gene attribute)
LOG_P_1ST_ORDER (datanator.data_source.jaspar.Tffm attribute)
LOG_P_DETAILED (datanator.data_source.jaspar.Tffm attribute)
login() (in module datanator.rest.auth)
login_required() (in module datanator.rest.auth)
logout() (in module datanator.rest.auth)
M
main() (in module datanator.__main__)
(in module datanator.data_source.corum_nosql)
(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.sabio_rk_nosql)
(in module datanator.data_source.taxon_tree)
(in module datanator.util.calc_tanimoto)
(in module datanator.util.index_collection)
make_dict() (datanator.util.file_util.FileUtil method)
make_doc() (datanator.data_source.sabio_rk_nosql.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]
(datanator.core.models.ProteinSubunit attribute)
(datanator.data_source.uniprot.UniprotData attribute)
Matrix (class in datanator.data_source.jaspar)
MATRIX_BASE_ID (datanator.data_source.jaspar.Tffm attribute)
MATRIX_VERSION (datanator.data_source.jaspar.Tffm attribute)
max (datanator.core.data_query.RangeFilter attribute)
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]
max_ph (datanator.datanator.Datanator attribute)
max_taxon_dist (datanator.datanator.Datanator attribute)
max_temp (datanator.datanator.Datanator attribute)
mean (datanator.core.data_model.ConsensusMethod attribute)
(datanator.core.data_query.NormalFilter attribute)
mechanism (datanator.core.models.KineticLaw attribute)
(datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
media (datanator.core.data_model.Environment attribute)
,
[1]
(datanator.core.models.Conditions attribute)
,
[1]
(datanator.data_source.ecmdb.Concentration attribute)
,
[1]
(datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
median (datanator.core.data_model.ConsensusMethod attribute)
mediatypes() (datanator.api.views.Metabolite method)
(datanator.api.views.MetaboliteConcentration method)
(datanator.api.views.MetaboliteSearch method)
(datanator.api.views.ProteinAbundance method)
(datanator.api.views.ProteinComplex method)
(datanator.api.views.ProteinComplexSearch method)
(datanator.api.views.ProteinInteraction method)
(datanator.api.views.ProteinSubunit method)
(datanator.api.views.ProteinSubunitSearch method)
(datanator.api.views.Reaction method)
(datanator.api.views.ReactionParameter method)
(datanator.api.views.Search method)
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)
Metabolite (class in datanator.api.views)
(class in datanator.core.models)
metabolite (datanator.core.models.Concentration attribute)
(datanator.core.models.Parameter attribute)
(datanator.core.models.Reaction attribute)
(datanator.core.models.Structure attribute)
metabolite_id (datanator.core.models.Concentration attribute)
(datanator.core.models.Metabolite attribute)
,
[1]
(datanator.core.models.Parameter attribute)
,
[1]
(datanator.core.models.Reaction attribute)
,
[1]
metabolite_name (datanator.core.models.Metabolite attribute)
,
[1]
MetaboliteConcentration (class in datanator.api.views)
MetaboliteConcentrationQuery (class in datanator.api.query.metabolite_concentrations)
MetaboliteManager (class in datanator.api.lib.metabolite.manager)
MetaboliteNoSQL (class in datanator.data_source.metabolite_nosql)
MetaboliteSearch (class in datanator.api.views)
MetaboliteSerializer (class in datanator.api.serializer)
MetaboliteSerializer.Meta (class in datanator.api.serializer)
MetabolitesMeta (class in datanator.data_source.metabolites_meta_collection)
Metadata (class in datanator.core.models)
metadata (datanator.core.data_model.ObservedResult attribute)
(datanator.data_source.corum.Base attribute)
(datanator.data_source.pax.Base attribute)
metadata_dump() (datanator.api.lib.data_manager.BaseManager method)
(datanator.core.data_query.DataQueryGenerator method)
MetadataSerializer (class in datanator.api.serializer)
MetadataSerializer.Meta (class in datanator.api.serializer)
Method (class in datanator.core.data_model)
(class in datanator.core.models)
method (datanator.core.data_model.Consensus attribute)
,
[1]
(datanator.core.data_model.ObservedResult attribute)
(datanator.core.data_model.ObservedResultMetadata attribute)
(datanator.core.models.ExperimentMetadata attribute)
(datanator.core.models.Metadata attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
Method.Meta (class in datanator.core.data_model)
methods (datanator.api.views.Metabolite attribute)
(datanator.api.views.MetaboliteConcentration attribute)
(datanator.api.views.MetaboliteSearch attribute)
(datanator.api.views.ProteinAbundance attribute)
(datanator.api.views.ProteinComplex attribute)
(datanator.api.views.ProteinComplexSearch attribute)
(datanator.api.views.ProteinInteraction attribute)
(datanator.api.views.ProteinSubunit attribute)
(datanator.api.views.ProteinSubunitSearch attribute)
(datanator.api.views.Reaction attribute)
(datanator.api.views.ReactionParameter attribute)
(datanator.api.views.Search attribute)
migrate() (datanator.__main__.DbController method)
min (datanator.core.data_query.RangeFilter attribute)
min_ec_level (datanator.core.data_query.ReactionSimilarityFilter attribute)
min_ph (datanator.datanator.Datanator attribute)
min_similarity (datanator.core.data_query.ReactionParticipantFilter attribute)
(datanator.core.data_query.SpecieSimilarityFilter attribute)
min_temp (datanator.datanator.Datanator attribute)
mode (datanator.core.data_model.ConsensusMethod attribute)
model (datanator.api.serializer.CellCompartmentSerializer.Meta attribute)
(datanator.api.serializer.MetaboliteSerializer.Meta attribute)
(datanator.api.serializer.MetadataSerializer.Meta attribute)
(datanator.api.serializer.ProteinComplexSerializer.Meta attribute)
(datanator.api.serializer.ProteinSubunitSerializer.Meta attribute)
(datanator.api.serializer.StructureSerializer.Meta attribute)
(datanator.api.serializer.TaxonSerializer.Meta 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 (datanator.data_source.sabio_rk.ReactionParticipant attribute)
modifier_kinetic_law_id (datanator.data_source.sabio_rk.ReactionParticipant attribute)
modifiers (datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
molecular_weight (datanator.core.data_model.ProteinComplexSpecie attribute)
(datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.core.models.ProteinSubunit attribute)
,
[1]
(datanator.data_source.sabio_rk.Enzyme attribute)
,
[1]
(datanator.data_source.sabio_rk.EnzymeSubunit attribute)
,
[1]
Molecule (class in datanator.util.molecule_util)
molecule_name_query() (datanator.rest.query.front_end_query.QueryFrontEnd method)
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.core.models.AbundanceDataSet attribute)
(datanator.core.models.CellCompartment attribute)
,
[1]
(datanator.core.models.CellLine attribute)
,
[1]
(datanator.core.models.Characteristic attribute)
(datanator.core.models.Concentration attribute)
(datanator.core.models.DNABindingDataset attribute)
(datanator.core.models.DataFormat attribute)
,
[1]
(datanator.core.models.ExperimentDesign attribute)
,
[1]
(datanator.core.models.ExperimentMetadata attribute)
,
[1]
(datanator.core.models.ExperimentType attribute)
,
[1]
(datanator.core.models.KineticLaw attribute)
(datanator.core.models.Metabolite attribute)
(datanator.core.models.Metadata attribute)
,
[1]
(datanator.core.models.Method attribute)
,
[1]
(datanator.core.models.PhysicalEntity attribute)
,
[1]
(datanator.core.models.PhysicalProperty attribute)
,
[1]
(datanator.core.models.ProteinComplex attribute)
(datanator.core.models.ProteinInteraction attribute)
(datanator.core.models.ProteinSubunit attribute)
(datanator.core.models.RNASeqDataSet attribute)
(datanator.core.models.ReferenceGenome attribute)
(datanator.core.models.Structure attribute)
(datanator.core.models.Synonym attribute)
,
[1]
(datanator.core.models.Taxon attribute)
,
[1]
(datanator.core.models.Variable attribute)
(datanator.data_source.array_express.DataFormat attribute)
,
[1]
(datanator.data_source.array_express.Experiment attribute)
,
[1]
(datanator.data_source.array_express.ExperimentDesign attribute)
,
[1]
(datanator.data_source.array_express.ExperimentType attribute)
,
[1]
(datanator.data_source.array_express.Extract attribute)
,
[1]
(datanator.data_source.array_express.Organism attribute)
,
[1]
(datanator.data_source.array_express.Sample attribute)
,
[1]
(datanator.data_source.array_express.Variable attribute)
,
[1]
(datanator.data_source.ecmdb.Compartment attribute)
,
[1]
(datanator.data_source.ecmdb.Compound attribute)
,
[1]
(datanator.data_source.ecmdb.Synonym attribute)
(datanator.data_source.ensembl.GeneEntry attribute)
(datanator.data_source.ensembl.GeneIdentifier attribute)
(datanator.data_source.intact.ProteinComplex attribute)
,
[1]
NAME (datanator.data_source.jaspar.Matrix attribute)
(datanator.data_source.jaspar.TaxonExtension attribute)
(datanator.data_source.jaspar.Tffm attribute)
name (datanator.data_source.refseq.Gene attribute)
(datanator.data_source.refseq.GeneSynonym attribute)
(datanator.data_source.refseq.Identifier 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)
name_2 (datanator.data_source.array_express.Experiment attribute)
,
[1]
namespace (datanator.core.data_model.Resource attribute)
,
[1]
(datanator.core.models.ReferenceGenome attribute)
(datanator.core.models.Resource attribute)
,
[1]
(datanator.data_source.ecmdb.Resource attribute)
,
[1]
(datanator.data_source.refseq.Identifier attribute)
(datanator.data_source.sabio_rk.Resource attribute)
,
[1]
ncbi (datanator.data_source.intact.ProteinComplex attribute)
,
[1]
ncbi_id (datanator.core.models.Taxon attribute)
,
[1]
(datanator.data_source.array_express.Organism attribute)
(datanator.data_source.corum.Taxon attribute)
(datanator.data_source.pax.Taxon attribute)
nofuzzy_end (datanator.data_source.refseq.Location attribute)
nofuzzy_start (datanator.data_source.refseq.Location attribute)
NormalFilter (class in datanator.core.data_query)
normalize_kinetic_laws() (datanator.data_source.sabio_rk.SabioRk method)
normalize_observed_results() (datanator.core.data_query.ConsensusGenerator method)
normalize_parameter_value() (datanator.data_source.sabio_rk.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)
ObservableSerializer (class in datanator.api.serializer)
ObservableSerializer.Meta (class in datanator.api.serializer)
Observation (class in datanator.core.models)
(class in datanator.data_source.corum)
(class in datanator.data_source.pax)
observation (datanator.core.data_model.ObservedResult attribute)
(datanator.data_source.corum.Complex attribute)
(datanator.data_source.corum.Taxon attribute)
(datanator.data_source.pax.Dataset attribute)
(datanator.data_source.pax.Protein attribute)
observation_id (datanator.core.models.AbundanceDataSet attribute)
(datanator.core.models.Concentration attribute)
(datanator.core.models.DNABindingDataset attribute)
(datanator.core.models.KineticLaw attribute)
(datanator.core.models.Metabolite attribute)
(datanator.core.models.PhysicalEntity attribute)
,
[1]
(datanator.core.models.PhysicalProperty attribute)
,
[1]
(datanator.core.models.ProteinComplex attribute)
(datanator.core.models.ProteinInteraction attribute)
(datanator.core.models.ProteinSubunit attribute)
(datanator.core.models.RNASeqDataSet attribute)
(datanator.core.models.ReferenceGenome attribute)
(datanator.core.models.Structure attribute)
(datanator.data_source.corum.Complex 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.core.models.Parameter attribute)
,
[1]
(datanator.data_source.sabio_rk.Parameter attribute)
,
[1]
observed_name (datanator.core.models.Parameter attribute)
,
[1]
(datanator.data_source.sabio_rk.Parameter attribute)
,
[1]
observed_results (datanator.core.data_query.FilterResult attribute)
observed_sabio_type (datanator.core.models.Parameter attribute)
,
[1]
observed_type (datanator.data_source.sabio_rk.Parameter attribute)
,
[1]
observed_units (datanator.core.models.Parameter attribute)
,
[1]
(datanator.data_source.sabio_rk.Parameter attribute)
,
[1]
observed_value (datanator.core.models.Parameter attribute)
,
[1]
(datanator.data_source.sabio_rk.Parameter attribute)
,
[1]
observed_value_indices (datanator.core.data_query.FilterResult attribute)
ObservedComplexSpecieSerializer (class in datanator.api.serializer)
ObservedComplexSpecieSerializer.Meta (class in datanator.api.serializer)
ObservedInteraction (class in datanator.core.data_model)
ObservedInteraction.Meta (class in datanator.core.data_model)
ObservedInteractionSerializer (class in datanator.api.serializer)
ObservedInteractionSerializer.Meta (class in datanator.api.serializer)
ObservedProteinSpecieSerializer (class in datanator.api.serializer)
ObservedProteinSpecieSerializer.Meta (class in datanator.api.serializer)
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)
ObservedResultMetadataSerializer (class in datanator.api.serializer)
ObservedResultMetadataSerializer.Meta (class in datanator.api.serializer)
ObservedResultSerializer (class in datanator.api.serializer)
ObservedResultSerializer.Meta (class in datanator.api.serializer)
ObservedSpecie (class in datanator.core.data_model)
ObservedSpecie.Meta (class in datanator.core.data_model)
ObservedSpecieSerializer (class in datanator.api.serializer)
ObservedSpecieSerializer.Meta (class in datanator.api.serializer)
ObservedValue (class in datanator.core.data_model)
ObservedValue.Meta (class in datanator.core.data_model)
ObservedValueSerializer (class in datanator.api.serializer)
ObservedValueSerializer.Meta (class in datanator.api.serializer)
one_to_many() (datanator.util.calc_tanimoto.CalcTanimoto method)
ontologies (datanator.data_source.bio_portal.BioPortal attribute)
options (datanator.core.data_query.OptionsFilter attribute)
OptionsFilter (class in datanator.core.data_query)
opts (datanator.api.serializer.CellCompartmentSerializer attribute)
(datanator.api.serializer.EntityInteractionOrPropertySerializer attribute)
(datanator.api.serializer.EnvironmentSerializer attribute)
(datanator.api.serializer.GeneticsSerializer attribute)
(datanator.api.serializer.InteractionSerializer attribute)
(datanator.api.serializer.InteractionSerializer.Meta attribute)
(datanator.api.serializer.MetaboliteSerializer attribute)
(datanator.api.serializer.MetadataSerializer attribute)
(datanator.api.serializer.ObservableSerializer attribute)
(datanator.api.serializer.ObservedComplexSpecieSerializer attribute)
(datanator.api.serializer.ObservedComplexSpecieSerializer.Meta attribute)
(datanator.api.serializer.ObservedInteractionSerializer attribute)
(datanator.api.serializer.ObservedInteractionSerializer.Meta attribute)
(datanator.api.serializer.ObservedProteinSpecieSerializer attribute)
(datanator.api.serializer.ObservedProteinSpecieSerializer.Meta attribute)
(datanator.api.serializer.ObservedResultMetadataSerializer attribute)
(datanator.api.serializer.ObservedResultSerializer attribute)
(datanator.api.serializer.ObservedSpecieSerializer attribute)
(datanator.api.serializer.ObservedSpecieSerializer.Meta attribute)
(datanator.api.serializer.ObservedValueSerializer attribute)
(datanator.api.serializer.ObservedValueSerializer.Meta attribute)
(datanator.api.serializer.PolymerSpecieSerializer attribute)
(datanator.api.serializer.ProteinComplexSerializer attribute)
(datanator.api.serializer.ProteinComplexSpecieSerializer attribute)
(datanator.api.serializer.ProteinSpecieSerializer attribute)
(datanator.api.serializer.ProteinSubunitSerializer attribute)
(datanator.api.serializer.ReactionParticipantSerializer attribute)
(datanator.api.serializer.ReactionSerializer attribute)
(datanator.api.serializer.ReactionSerializer.Meta attribute)
(datanator.api.serializer.ResourceSerializer attribute)
(datanator.api.serializer.SpecieSerializer attribute)
(datanator.api.serializer.StructureSerializer attribute)
(datanator.api.serializer.TaxonSerializer attribute)
order (datanator.core.data_model.ReactionParticipant attribute)
,
[1]
order() (datanator.core.data_query.FilterRunner method)
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 (class in datanator.data_source.array_express)
organism (datanator.data_source.ensembl.GeneEntry attribute)
(datanator.data_source.refseq.ReferenceGenome attribute)
organism_strain (datanator.core.models.ReferenceGenome attribute)
(datanator.data_source.array_express.EnsemblInfo attribute)
,
[1]
(datanator.data_source.array_express_tools.ensembl_tools.StrainInfo attribute)
organisms (datanator.data_source.array_express.Experiment attribute)
,
[1]
output_json() (in module datanator.api.views)
P
page_not_found() (in module datanator)
pages (datanator.core.data_model.Reference attribute)
,
[1]
Parameter (class in datanator.core.models)
(class in datanator.data_source.sabio_rk)
parameter (datanator.core.models.KineticLaw attribute)
(datanator.core.models.Metabolite attribute)
parameter_id (datanator.core.models.Parameter attribute)
parameters (datanator.data_source.sabio_rk.Compartment attribute)
(datanator.data_source.sabio_rk.Compound attribute)
,
[1]
(datanator.data_source.sabio_rk.Enzyme attribute)
,
[1]
(datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
parse_complex_subunit_structure() (datanator.data_source.sabio_rk.SabioRk 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)
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_ko_txt() (datanator.data_source.kegg_orthology.KeggOrthology method)
parse_list() (in module datanator.data_source.corum)
(in module datanator.data_source.corum_nosql)
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_paxDB_files() (datanator.data_source.pax.Pax method)
(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_reaction_equation() (datanator.io.InputReader 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_taxid_line() (datanator.data_source.taxon_tree.TaxonTree method)
participant_a (datanator.core.models.ProteinInteraction attribute)
participant_b (datanator.core.models.ProteinInteraction attribute)
participants (datanator.core.data_model.Reaction attribute)
,
[1]
Pax (class in datanator.data_source.pax)
pax() (datanator.__main__.BuildController method)
(datanator.__main__.DownloadController method)
pax_load (datanator.core.models.AbundanceData attribute)
(datanator.core.models.ProteinSubunit attribute)
PaxNoSQL (class in datanator.data_source.pax_nosql)
performer (datanator.core.data_model.Method attribute)
(datanator.core.models.Method attribute)
(datanator.data_source.array_express.Protocol attribute)
,
[1]
ph (datanator.core.data_model.Environment attribute)
,
[1]
(datanator.core.models.Conditions attribute)
,
[1]
(datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
PhNormalFilter (class in datanator.core.data_query)
PhRangeFilter (class in datanator.core.data_query)
PhysicalEntity (class in datanator.core.models)
PhysicalProperty (class in datanator.core.models)
PolymerSpecie (class in datanator.core.data_model)
PolymerSpecie.Meta (class in datanator.core.data_model)
PolymerSpecieSerializer (class in datanator.api.serializer)
PolymerSpecieSerializer.Meta (class in datanator.api.serializer)
position (datanator.core.data_model.Interaction attribute)
,
[1]
(datanator.core.models.DNABindingData attribute)
,
[1]
position_id (datanator.core.models.DNABindingData attribute)
PostgresDataSource (class in datanator.core.data_source)
predicted (datanator.core.data_model.ResourceAssignmentMethod attribute)
PRESERVE_CONTEXT_ON_EXCEPTION (datanator.config.config.BuildConfig attribute)
(datanator.config.config.CircleTestingConfig attribute)
(datanator.config.config.ProductionConfig 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_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)
,
[1]
product_kinetic_law_id (datanator.data_source.sabio_rk.ReactionParticipant attribute)
ProductionConfig (class in datanator.config.config)
products (datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
Progress (class in datanator.core.models)
property (datanator.core.data_model.Observable attribute)
,
[1]
Protein (class in datanator.data_source.jaspar)
(class in datanator.data_source.pax)
protein (datanator.data_source.pax.Observation attribute)
protein_a (datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
protein_b (datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
protein_id (datanator.data_source.pax.Observation attribute)
(datanator.data_source.pax.Protein attribute)
protein_name (datanator.data_source.corum.Subunit attribute)
,
[1]
(datanator.data_source.uniprot.UniprotData attribute)
protein_subunit (datanator.core.models.ProteinComplex attribute)
ProteinAbundance (class in datanator.api.views)
ProteinAbundanceQuery (class in datanator.api.query.protein_abundance)
ProteinComplex (class in datanator.api.views)
(class in datanator.core.models)
(class in datanator.data_source.intact)
proteincomplex (datanator.core.models.ProteinSubunit attribute)
proteincomplex_id (datanator.core.models.ProteinSubunit attribute)
ProteinComplexManager (class in datanator.api.lib.complex.manager)
ProteinComplexSearch (class in datanator.api.views)
ProteinComplexSerializer (class in datanator.api.serializer)
ProteinComplexSerializer.Meta (class in datanator.api.serializer)
ProteinComplexSpecie (class in datanator.core.data_model)
ProteinComplexSpecie.Meta (class in datanator.core.data_model)
ProteinComplexSpecieSerializer (class in datanator.api.serializer)
ProteinComplexSpecieSerializer.Meta (class in datanator.api.serializer)
ProteinInteraction (class in datanator.api.views)
(class in datanator.core.models)
(class in datanator.data_source.intact)
ProteinInteractionandComplexQuery (class in datanator.api.query.protein_protein_interactions)
ProteinSpecie (class in datanator.core.data_model)
ProteinSpecie.Meta (class in datanator.core.data_model)
ProteinSpecieSerializer (class in datanator.api.serializer)
ProteinSpecieSerializer.Meta (class in datanator.api.serializer)
ProteinSubunit (class in datanator.api.views)
(class in datanator.core.models)
ProteinSubunitManager (class in datanator.api.lib.subunit.manager)
ProteinSubunitSearch (class in datanator.api.views)
ProteinSubunitSerializer (class in datanator.api.serializer)
ProteinSubunitSerializer.Meta (class in datanator.api.serializer)
ProteintoDNAInteractionQuery (class in datanator.api.query.dna_protein_interactions)
Protocol (class in datanator.data_source.array_express)
protocol_accession (datanator.data_source.array_express.Protocol attribute)
,
[1]
protocol_type (datanator.data_source.array_express.Protocol attribute)
,
[1]
protocols (datanator.data_source.array_express.Experiment attribute)
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]
(datanator.data_source.intact.ProteinInteraction attribute)
(datanator.data_source.pax.Dataset attribute)
,
[1]
publication_author (datanator.data_source.intact.ProteinInteraction attribute)
publications (datanator.data_source.intact.ProteinInteraction attribute)
(datanator.data_source.uniprot.UniprotData attribute)
pubmed_id (datanator.data_source.corum.Observation attribute)
,
[1]
pur_method (datanator.data_source.corum.Observation attribute)
,
[1]
Q
Qualifier (class in datanator.data_source.refseq)
qualifiers (datanator.data_source.refseq.Gene attribute)
quant() (datanator.util.rna_seq_util.Kallisto method)
query (in module datanator.data_source.sqlite_to_json)
query_class (datanator.core.models.CellCompartment attribute)
(datanator.core.models.CellLine attribute)
(datanator.core.models.Metabolite attribute)
(datanator.core.models.Method attribute)
(datanator.core.models.ProteinComplex attribute)
(datanator.core.models.ProteinInteraction attribute)
(datanator.core.models.ProteinSubunit attribute)
(datanator.core.models.Synonym attribute)
(datanator.core.models.Taxon attribute)
query_table() (datanator.data_source.sqlite_to_json.SQLToJSON method)
QueryFrontEnd (class in datanator.rest.query.front_end_query)
QueryMetabolitesMeta (class in datanator.core.query_nosql)
QuerySabio (class in datanator.core.query_nosql)
QueryTaxonTree (class in datanator.core.query_nosql)
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)
(datanator.data_source.bio_portal.BioPortal attribute)
R
RangeFilter (class in datanator.core.data_query)
reactant_kinetic_law (datanator.data_source.sabio_rk.ReactionParticipant attribute)
,
[1]
reactant_kinetic_law_id (datanator.data_source.sabio_rk.ReactionParticipant attribute)
reactants (datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
Reaction (class in datanator.api.views)
(class in datanator.core.data_model)
(class in datanator.core.models)
reaction (datanator.core.data_query.ReactionSimilarityFilter attribute)
(datanator.core.models.CellCompartment attribute)
(datanator.core.models.KineticLaw attribute)
(datanator.core.models.Metabolite attribute)
Reaction.Meta (class in datanator.core.data_model)
reaction_id (datanator.core.models.Reaction attribute)
reaction_participants (datanator.data_source.sabio_rk.Compartment attribute)
(datanator.data_source.sabio_rk.Compound attribute)
,
[1]
ReactionController (class in datanator.__main__)
ReactionController.Meta (class in datanator.__main__)
ReactionGetEcNumberController (class in datanator.__main__)
ReactionGetEcNumberController.Meta (class in datanator.__main__)
ReactionKineticsQuery (class in datanator.api.query.reaction_kinetics)
ReactionManager (class in datanator.api.lib.reaction.manager)
ReactionParameter (class in datanator.api.views)
ReactionParticipant (class in datanator.core.data_model)
(class in datanator.data_source.sabio_rk)
ReactionParticipant.Meta (class in datanator.core.data_model)
ReactionParticipantFilter (class in datanator.core.data_query)
ReactionParticipantSerializer (class in datanator.api.serializer)
ReactionParticipantSerializer.Meta (class in datanator.api.serializer)
ReactionSerializer (class in datanator.api.serializer)
ReactionSerializer.Meta (class in datanator.api.serializer)
ReactionSimilarityFilter (class in datanator.core.data_query)
read_compartments() (datanator.io.InputReader method)
read_genetics() (datanator.io.InputReader method)
read_model() (datanator.datanator.Datanator method)
read_reactions() (datanator.io.InputReader method)
read_species() (datanator.io.InputReader method)
read_type (datanator.core.models.RNASeqDataSet attribute)
(datanator.data_source.array_express.Experiment attribute)
,
[1]
(datanator.data_source.array_express.Sample attribute)
,
[1]
reconnected_metals (datanator.util.molecule_util.InchiMolecule attribute)
ref (datanator.data_source.refseq.Location attribute)
ref_db (datanator.data_source.refseq.Location attribute)
ref_genome (datanator.data_source.array_express.EnsemblInfo attribute)
ref_genome_version (datanator.data_source.refseq.Gene attribute)
Reference (class in datanator.core.data_model)
reference (datanator.core.data_model.ObservedResultMetadata attribute)
Reference.Meta (class in datanator.core.data_model)
reference_genome (datanator.core.models.RNASeqDataSet attribute)
reference_genome_id (datanator.core.models.ReferenceGenome attribute)
ReferenceGenome (class in datanator.core.models)
(class in datanator.data_source.refseq)
referenceGenome (datanator.data_source.refseq.Gene attribute)
(datanator.data_source.refseq.ReferenceGenomeAccession attribute)
ReferenceGenomeAccession (class in datanator.data_source.refseq)
references (datanator.data_source.ecmdb.Concentration attribute)
,
[1]
(datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
Refseq (class in datanator.data_source.refseq)
register() (in module datanator.rest.auth)
register_blueprints() (in module datanator)
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)
release_date (datanator.core.models.Resource attribute)
,
[1]
(datanator.data_source.array_express.Experiment attribute)
,
[1]
relevance (datanator.core.data_model.Evidence attribute)
,
[1]
(datanator.core.data_model.Resource attribute)
,
[1]
remove_layer() (datanator.util.molecule_util.InchiMolecule method)
render() (in module datanator.core.render_form.render_html_from_schema)
replace_dict_key() (datanator.util.file_util.FileUtil method)
REQUEST_URL (datanator.data_source.ezyme.Ezyme attribute)
,
[1]
requests_cache_filename (datanator.core.data_source.HttpDataSource attribute)
requests_session (datanator.core.data_source.HttpDataSource attribute)
(datanator.core.data_source.WebserviceDataSource attribute)
Resource (class in datanator.core.data_model)
(class in datanator.core.models)
(class in datanator.data_source.ecmdb)
(class in datanator.data_source.sabio_rk)
resource (datanator.core.models.ExperimentMetadata attribute)
(datanator.core.models.Metadata attribute)
Resource.Meta (class in datanator.core.data_model)
ResourceAssignmentMethod (class in datanator.core.data_model)
ResourceSerializer (class in datanator.api.serializer)
ResourceSerializer.Meta (class in datanator.api.serializer)
restore_backup() (datanator.core.data_source.PostgresDataSource method)
restore_database() (datanator.core.data_source.PostgresDataSource method)
results() (in module datanator.rest.search)
ResultsWriter (class in datanator.io)
RETRIEVAL_URL (datanator.data_source.ezyme.Ezyme attribute)
,
[1]
return_search() (datanator.api.query.text_search.TextSearchSession method)
reversible (datanator.core.data_model.Reaction attribute)
,
[1]
RNASeqDataSet (class in datanator.core.models)
RNASeqExperiment (class in datanator.core.models)
RnaSpecie (class in datanator.core.data_model)
RnaSpecie.Meta (class in datanator.core.data_model)
role_a (datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
role_b (datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
row (datanator.data_source.jaspar.Data attribute)
run() (datanator.api.lib.filter.manager.FilterManager method)
(datanator.core.data_query.ConsensusGenerator method)
(datanator.core.data_query.DataQueryGenerator method)
(datanator.core.data_query.FilterRunner method)
(datanator.data_source.ezyme.Ezyme method)
(datanator.io.InputReader method)
(datanator.io.ResultsWriter class method)
(in module datanator.data_source.process_rna_seq.download_cdna)
run2() (datanator.io.ResultsWriter class method)
rxn_type (datanator.core.models.Reaction attribute)
,
[1]
S
sabio() (datanator.__main__.BuildController method)
(datanator.__main__.DownloadController method)
sabio_type (datanator.core.models.Parameter attribute)
,
[1]
SabioRk (class in datanator.data_source.sabio_rk)
SabioRkNoSQL (class in datanator.data_source.sabio_rk_nosql)
samp_id (datanator.data_source.ensembl.GeneEntry attribute)
Sample (class in datanator.data_source.array_express)
sample (datanator.core.models.ReferenceGenome attribute)
sample_id (datanator.core.models.RNASeqDataSet attribute)
sample_name (datanator.core.models.RNASeqDataSet attribute)
samples (datanator.core.models.RNASeqExperiment attribute)
(datanator.data_source.array_express.Characteristic attribute)
,
[1]
(datanator.data_source.array_express.EnsemblInfo attribute)
(datanator.data_source.array_express.Experiment attribute)
(datanator.data_source.array_express.Extract attribute)
,
[1]
(datanator.data_source.array_express.Url attribute)
,
[1]
(datanator.data_source.array_express.Variable attribute)
,
[1]
(datanator.data_source.ensembl.GeneIdentifier attribute)
,
[1]
scale (datanator.core.data_query.ExponentialFilter attribute)
(datanator.core.data_query.ReactionSimilarityFilter attribute)
score (datanator.core.data_model.Interaction attribute)
,
[1]
(datanator.core.models.AbundanceDataSet attribute)
,
[1]
(datanator.data_source.ezyme.EzymeResult attribute)
(datanator.data_source.pax.Dataset attribute)
,
[1]
score() (datanator.core.data_query.ExponentialFilter method)
(datanator.core.data_query.Filter method)
(datanator.core.data_query.FilterRunner method)
(datanator.core.data_query.NormalFilter method)
(datanator.core.data_query.OptionsFilter method)
(datanator.core.data_query.RangeFilter method)
(datanator.core.data_query.ReactionParticipantFilter method)
(datanator.core.data_query.ReactionSimilarityFilter method)
(datanator.core.data_query.SpecieSimilarityFilter method)
(datanator.core.data_query.TaxonomicDistanceFilter method)
scores (datanator.core.data_query.FilterResult attribute)
Search (class in datanator.api.views)
search() (datanator.api.lib.search.manager.SearchManager method)
(in module datanator.rest.search)
search_vector (datanator.core.models.CellCompartment attribute)
(datanator.core.models.CellLine attribute)
(datanator.core.models.Synonym attribute)
(datanator.core.models.Taxon attribute)
SearchManager (class in datanator.api.lib.search.manager)
SECRET_KEY (datanator.config.config.BaseConfig attribute)
sequence (datanator.core.data_model.PolymerSpecie attribute)
,
[1]
(datanator.core.models.ProteinSubunit attribute)
(datanator.data_source.sabio_rk.EnzymeSubunit attribute)
,
[1]
ServerUtil (class in datanator.util.server_util)
session (datanator.core.data_source.CachedDataSource attribute)
(datanator.core.data_source.PostgresDataSource attribute)
setup_database() (in module datanator.util.taxonomy_util)
simple_search_vector (datanator.core.models.Metabolite attribute)
(datanator.core.models.ProteinComplex attribute)
(datanator.core.models.ProteinSubunit attribute)
simplify_inchi() (datanator.util.chem_util.ChemUtil method)
site_a (datanator.core.models.ProteinInteraction attribute)
site_b (datanator.core.models.ProteinInteraction attribute)
SKIP_KINETIC_LAW_IDS (datanator.data_source.sabio_rk.SabioRk attribute)
,
[1]
software (datanator.core.data_model.Method attribute)
(datanator.core.models.Method attribute)
(datanator.data_source.array_express.Protocol attribute)
,
[1]
source (datanator.data_source.intact.ProteinComplex attribute)
,
[1]
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)
Species (class in datanator.data_source.jaspar)
SPECIES (datanator.data_source.jaspar.Taxon attribute)
species_name (datanator.data_source.corum.Taxon attribute)
(datanator.data_source.pax.Taxon attribute)
,
[1]
SpecieSequenceSimilarityFilter (class in datanator.core.data_query)
SpecieSerializer (class in datanator.api.serializer)
SpecieSerializer.Meta (class in datanator.api.serializer)
SpecieSimilarityFilter (class in datanator.core.data_query)
SpecieStructuralSimilarityFilter (class in datanator.core.data_query)
split_colon() (datanator.data_source.intact.IntAct method)
(datanator.data_source.intact_nosql.IntActNoSQL method)
split_line() (datanator.data_source.intact.IntAct method)
(datanator.data_source.intact_nosql.IntActNoSQL method)
sqla_session (datanator.api.serializer.CellCompartmentSerializer.Meta attribute)
(datanator.api.serializer.MetaboliteSerializer.Meta attribute)
(datanator.api.serializer.MetadataSerializer.Meta attribute)
(datanator.api.serializer.ProteinComplexSerializer.Meta attribute)
(datanator.api.serializer.ProteinSubunitSerializer.Meta attribute)
(datanator.api.serializer.StructureSerializer.Meta attribute)
(datanator.api.serializer.TaxonSerializer.Meta attribute)
SQLALCHEMY_DATABASE_URI (datanator.config.config.BuildConfig attribute)
(datanator.config.config.CircleTestingConfig attribute)
(datanator.config.config.LocalDevelopmentConfig attribute)
(datanator.config.config.ProductionConfig attribute)
SQLALCHEMY_TEST_DATABASE_URI (datanator.config.config.CircleTestingConfig attribute)
(datanator.config.config.LocalDevelopmentConfig attribute)
SQLALCHEMY_TRACK_MODIFICATIONS (datanator.config.config.BaseConfig attribute)
SQLToJSON (class in datanator.data_source.sqlite_to_json)
stacked_on (datanator.__main__.AggregateBuildController.Meta attribute)
(datanator.__main__.BuildController.Meta attribute)
(datanator.__main__.DbController.Meta attribute)
(datanator.__main__.DbRestoreController.Meta attribute)
(datanator.__main__.DownloadController.Meta attribute)
(datanator.__main__.GenerateRNASeqTemplate.Meta attribute)
(datanator.__main__.GenerateTemplateController.Meta attribute)
(datanator.__main__.GetDataController.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__.UploadRNASeqExperiment.Meta attribute)
(datanator.__main__.UploadReferenceGenome.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__.DbController.Meta attribute)
(datanator.__main__.DbRestoreController.Meta attribute)
(datanator.__main__.DownloadController.Meta attribute)
(datanator.__main__.GenerateRNASeqTemplate.Meta attribute)
(datanator.__main__.GenerateTemplateController.Meta attribute)
(datanator.__main__.GetDataController.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__.UploadRNASeqExperiment.Meta attribute)
(datanator.__main__.UploadReferenceGenome.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)
standardize_metabolite() (datanator.util.standardize_util.StandardizeUtil method)
standardize_sabio() (datanator.util.standardize_util.StandardizeUtil method)
StandardizeUtil (class in datanator.util.standardize_util)
start (datanator.data_source.refseq.Location attribute)
status (datanator.data_source.uniprot.UniprotData attribute)
std (datanator.core.data_query.NormalFilter attribute)
stereochemistry (datanator.util.molecule_util.InchiMolecule attribute)
stereochemistry_parity (datanator.util.molecule_util.InchiMolecule attribute)
stereochemistry_type (datanator.util.molecule_util.InchiMolecule attribute)
stoich_a (datanator.core.models.ProteinInteraction attribute)
,
[1]
(datanator.data_source.intact.ProteinInteraction attribute)
,
[1]
(datanator.data_source.uniprot.UniprotData attribute)
stoich_b (datanator.core.models.ProteinInteraction attribute)
,
[1]
(datanator.data_source.intact.ProteinInteraction attribute)
,
[1]
(datanator.data_source.uniprot.UniprotData attribute)
stoichiometry_a (datanator.core.data_model.SpecieInteraction attribute)
,
[1]
stoichiometry_b (datanator.core.data_model.SpecieInteraction attribute)
,
[1]
strain (datanator.data_source.ecmdb.Concentration attribute)
,
[1]
StrainInfo (class in datanator.data_source.array_express_tools.ensembl_tools)
strand (datanator.data_source.refseq.Location attribute)
string_id (datanator.data_source.pax.Protein attribute)
,
[1]
stringify() (datanator.core.data_model.Reaction method)
struct_id (datanator.core.models.Structure attribute)
Structure (class in datanator.core.models)
structure (datanator.core.data_model.Specie attribute)
,
[1]
(datanator.core.models.Metabolite attribute)
(datanator.data_source.ecmdb.Compound attribute)
,
[1]
(datanator.util.molecule_util.Molecule attribute)
structure_id (datanator.core.models.Metabolite attribute)
structures (datanator.data_source.sabio_rk.Compound attribute)
,
[1]
StructureSerializer (class in datanator.api.serializer)
StructureSerializer.Meta (class in datanator.api.serializer)
su_cmt (datanator.core.data_model.ProteinComplexSpecie attribute)
(datanator.core.models.ProteinComplex attribute)
,
[1]
(datanator.data_source.corum.Complex attribute)
,
[1]
su_entrezs (datanator.data_source.corum.Subunit attribute)
,
[1]
su_uniprot (datanator.data_source.corum.Subunit attribute)
,
[1]
submission_date (datanator.data_source.array_express.Experiment attribute)
,
[1]
Subunit (class in datanator.data_source.corum)
subunit (datanator.core.models.AbundanceData attribute)
(datanator.core.models.DNABindingDataset attribute)
subunit_id (datanator.core.models.AbundanceData attribute)
,
[1]
(datanator.core.models.DNABindingDataset attribute)
,
[1]
(datanator.core.models.ProteinSubunit attribute)
,
[1]
subunit_name (datanator.core.models.ProteinSubunit attribute)
,
[1]
subunits (datanator.data_source.corum.Complex attribute)
(datanator.data_source.intact.ProteinComplex attribute)
,
[1]
(datanator.data_source.sabio_rk.Enzyme attribute)
,
[1]
swissprot_id (datanator.data_source.corum.Taxon attribute)
sym_link (datanator.util.mongo_util.MongoUtil attribute)
Synonym (class in datanator.core.data_model)
(class in datanator.core.models)
(class in datanator.data_source.ecmdb)
(class in datanator.data_source.sabio_rk)
synonym (datanator.core.data_model.ObservedResultMetadata attribute)
(datanator.core.models.Metadata attribute)
Synonym.Meta (class in datanator.core.data_model)
synonyms (datanator.data_source.ecmdb.Compound 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)
T
table() (datanator.data_source.sqlite_to_json.SQLToJSON method)
tabular_orientation (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)
TAG (datanator.data_source.jaspar.Annotation attribute)
TAX_ID (datanator.data_source.jaspar.Species attribute)
(datanator.data_source.jaspar.Taxon attribute)
(datanator.data_source.jaspar.TaxonExtension attribute)
Taxon (class in datanator.core.models)
(class in datanator.data_source.corum)
(class in datanator.data_source.jaspar)
(class in datanator.data_source.pax)
(class in datanator.util.taxonomy_util)
taxon (datanator.core.data_model.Genetics attribute)
(datanator.core.data_query.TaxonomicDistanceFilter attribute)
(datanator.core.models.ExperimentMetadata attribute)
(datanator.core.models.Metadata attribute)
(datanator.data_source.corum.Observation attribute)
(datanator.data_source.pax.Dataset attribute)
(datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
taxon_ncbi_id (datanator.data_source.corum.Observation attribute)
,
[1]
(datanator.data_source.pax.Dataset attribute)
taxon_variant (datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
taxon_wildtype (datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
TaxonExtension (class in datanator.data_source.jaspar)
TaxonomicDistanceFilter (class in datanator.core.data_query)
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__)
TaxonSerializer (class in datanator.api.serializer)
TaxonSerializer.Meta (class in datanator.api.serializer)
TaxonTree (class in datanator.data_source.taxon_tree)
temperature (datanator.core.data_model.Environment attribute)
,
[1]
(datanator.core.models.Conditions attribute)
,
[1]
(datanator.data_source.ecmdb.Concentration attribute)
(datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
TemperatureNormalFilter (class in datanator.core.data_query)
temperaturer (datanator.data_source.ecmdb.Concentration attribute)
TemperatureRangeFilter (class in datanator.core.data_query)
test (datanator.core.common_schema.CommonSchema attribute)
TESTING (datanator.config.config.BuildConfig attribute)
(datanator.config.config.CircleTestingConfig attribute)
(datanator.config.config.LocalDevelopmentConfig attribute)
(datanator.config.config.ProductionConfig attribute)
text (datanator.data_source.array_express.Protocol attribute)
,
[1]
TextSearchSession (class in datanator.api.query.text_search)
tf (datanator.core.models.DNABindingDataset attribute)
Tffm (class in datanator.data_source.jaspar)
timeloadcontent() (in module datanator.util.build_util)
timemethod() (in module datanator.util.build_util)
timesofar() (datanator.core.query_nosql.DataQuery method)
tissue (datanator.core.models.KineticLaw attribute)
(datanator.data_source.sabio_rk.KineticLaw attribute)
,
[1]
title (datanator.core.data_model.Reference attribute)
,
[1]
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)
type (datanator.core.models.AbundanceDataSet attribute)
(datanator.core.models.Concentration attribute)
(datanator.core.models.DNABindingDataset attribute)
(datanator.core.models.KineticLaw attribute)
(datanator.core.models.Metabolite attribute)
(datanator.core.models.PhysicalEntity attribute)
,
[1]
(datanator.core.models.PhysicalProperty attribute)
,
[1]
(datanator.core.models.ProteinComplex attribute)
(datanator.core.models.ProteinInteraction attribute)
(datanator.core.models.ProteinSubunit attribute)
(datanator.core.models.RNASeqDataSet attribute)
(datanator.core.models.ReferenceGenome attribute)
(datanator.core.models.Structure attribute)
(datanator.data_source.sabio_rk.Parameter attribute)
,
[1]
(datanator.data_source.sabio_rk.ReactionParticipant attribute)
,
[1]
type_a (datanator.core.data_model.SpecieInteraction attribute)
(datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
type_b (datanator.core.data_model.SpecieInteraction attribute)
(datanator.core.models.ProteinInteraction attribute)
(datanator.data_source.intact.ProteinInteraction attribute)
types (datanator.data_source.array_express.Experiment attribute)
,
[1]
TYPES (datanator.data_source.sabio_rk.Parameter attribute)
U
unauthorized_page() (in module datanator)
Uniprot (class in datanator.data_source.uniprot)
uniprot() (datanator.__main__.BuildController method)
(datanator.__main__.DownloadController method)
uniprot_checked (datanator.core.models.ProteinSubunit attribute)
uniprot_id (datanator.core.data_model.ProteinSpecie attribute)
,
[1]
(datanator.core.models.AbundanceData attribute)
(datanator.core.models.ProteinSubunit attribute)
,
[1]
(datanator.data_source.pax.Protein attribute)
(datanator.data_source.uniprot.UniprotData attribute)
UniprotData (class in datanator.data_source.uniprot)
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)
unit (datanator.data_source.array_express.Variable attribute)
,
[1]
units (datanator.core.data_model.Consensus attribute)
,
[1]
(datanator.core.data_model.ObservedValue attribute)
,
[1]
(datanator.core.models.Concentration attribute)
(datanator.core.models.Parameter attribute)
,
[1]
(datanator.core.models.Variable attribute)
(datanator.data_source.sabio_rk.Parameter attribute)
,
[1]
unpack_list() (datanator.util.file_util.FileUtil method)
updated (datanator.data_source.ecmdb.Compound attribute)
,
[1]
(datanator.data_source.sabio_rk.Entry attribute)
upload_backup() (datanator.core.data_source.PostgresDataSource method)
upload_backups() (datanator.core.data_source.CachedDataSource method)
upload_data_from_kegg_org_symbol() (datanator.data_source.refseq.Refseq method)
upload_from_json() (datanator.core.upload_data.UploadData method)
upload_ref_seq_for_all_prokaryotic_kegg_org() (datanator.data_source.refseq.Refseq method)
upload_reference_genome() (datanator.core.upload_data.UploadData method)
upload_rna_rseq_experiment() (datanator.core.upload_data.UploadData method)
UploadData (class in datanator.__main__)
(class in datanator.core.upload_data)
UploadData.Meta (class in datanator.__main__)
UploadDataController (class in datanator.__main__)
UploadDataController.Meta (class in datanator.__main__)
Uploader (class in datanator.core.upload_data)
UploadReferenceGenome (class in datanator.__main__)
UploadReferenceGenome.Meta (class in datanator.__main__)
UploadRNASeqExperiment (class in datanator.__main__)
UploadRNASeqExperiment.Meta (class in datanator.__main__)
Url (class in datanator.data_source.array_express)
url (datanator.core.data_model.Reference attribute)
,
[1]
(datanator.data_source.array_express.EnsemblInfo attribute)
,
[1]
(datanator.data_source.array_express.Url attribute)
,
[1]
user (datanator.core.data_model.Consensus attribute)
,
[1]
V
VAL (datanator.data_source.jaspar.Annotation attribute)
val (datanator.data_source.jaspar.Data attribute)
value (datanator.core.data_model.Consensus attribute)
,
[1]
(datanator.core.data_model.Evidence attribute)
,
[1]
(datanator.core.data_model.ObservedValue attribute)
,
[1]
(datanator.core.models.Characteristic attribute)
(datanator.core.models.Concentration attribute)
,
[1]
(datanator.core.models.Parameter attribute)
,
[1]
(datanator.core.models.Variable attribute)
(datanator.data_source.array_express.Characteristic attribute)
,
[1]
(datanator.data_source.array_express.Variable attribute)
,
[1]
(datanator.data_source.ecmdb.Concentration attribute)
,
[1]
(datanator.data_source.ensembl.GeneIdentifier attribute)
(datanator.data_source.refseq.Qualifier attribute)
(datanator.data_source.sabio_rk.CompoundStructure attribute)
,
[1]
(datanator.data_source.sabio_rk.Parameter attribute)
,
[1]
values (datanator.core.data_model.ObservedResultMetadata attribute)
Variable (class in datanator.core.models)
(class in datanator.data_source.array_express)
variable (datanator.core.models.Metadata attribute)
variables (datanator.data_source.array_express.Sample attribute)
,
[1]
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]
(datanator.core.models.DNABindingDataset attribute)
,
[1]
VERSION (datanator.data_source.jaspar.Matrix attribute)
(datanator.data_source.jaspar.Tffm attribute)
version (datanator.data_source.refseq.ReferenceGenome attribute)
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)
weight (datanator.core.models.AbundanceDataSet attribute)
,
[1]
(datanator.data_source.pax.Dataset attribute)
,
[1]
weighted_mean (datanator.core.data_model.ConsensusMethod attribute)
weighted_median (datanator.core.data_model.ConsensusMethod attribute)
weighted_mode (datanator.core.data_model.ConsensusMethod attribute)
WildtypeFilter (class in datanator.core.data_query)
write_sabio_json() (in module datanator.data_source.cron_aggregate)
write_to_json() (datanator.data_source.metabolite_nosql.MetaboliteNoSQL method)
WTF_CSRF_ENABLED (datanator.config.config.BaseConfig attribute)
(datanator.config.config.BuildConfig attribute)
(datanator.config.config.CircleTestingConfig attribute)
(datanator.config.config.LocalDevelopmentConfig attribute)
(datanator.config.config.ProductionConfig attribute)
Y
year (datanator.core.data_model.Reference attribute)
,
[1]