Index

_

__get_line_count() (bkbit.data_translators.genome_annotation_translator.Gff3 method) __init__() (bkbit.data_translators.genome_annotation_translator.Gff3 method)

__merge_values() (bkbit.data_translators.genome_annotation_translator.Gff3 method) _get_attribute() (bkbit.data_translators.genome_annotation_translator.Gff3 method) _resolve_ncbi_gene_annotation() (bkbit.data_translators.genome_annotation_translator.Gff3 method)

A

accession_id (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) Activity (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) ActivityAndBehavior (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) adding_template() (in module bkbit.model_converters.sheets_converter) age_at_death_description (bkbit.models.library_generation.Donor attribute) age_at_death_reference_point (bkbit.models.library_generation.Donor attribute) age_at_death_unit (bkbit.models.library_generation.Donor attribute) age_at_death_value (bkbit.models.library_generation.Donor attribute) AgeAtDeathReferencePoint (class in bkbit.models.library_generation) AgeAtDeathUnit (class in bkbit.models.library_generation) amplified_cDNA_amplified_quantity_ng (bkbit.models.library_generation.AmplifiedCdna attribute) amplified_cDNA_PCR_cycles (bkbit.models.library_generation.CdnaAmplification attribute) amplified_cDNA_percent_cDNA_longer_than_400bp (bkbit.models.library_generation.AmplifiedCdna attribute) amplified_cDNA_RNA_amplification_pass_fail (bkbit.models.library_generation.AmplifiedCdna attribute) AmplifiedCdna (class in bkbit.models.library_generation) AmplifiedCdnaRnaAmplificationPassFail (class in bkbit.models.library_generation) anatomical_region (bkbit.models.cell_taxonomy.Cell attribute) anatomical_region_ontology_term_id (bkbit.models.cell_taxonomy.Cell attribute) AnatomicalAnnotationSet (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) ANATOMICALDIRECTION (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy)

AnatomicalSpace (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) annotates (bkbit.models.library_generation.DissectionRoiPolygon attribute) Annotation (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) AnnotationCollection (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) annotations (bkbit.models.cell_taxonomy.AnnotationCollection attribute) (bkbit.models.genome_annotation.AnnotationCollection attribute) AnS (class in bkbit.data_translators.anatomical_structure_translator) anterior_to_posterior (bkbit.models.anatomical_structure.ANATOMICALDIRECTION attribute) (bkbit.models.cell_taxonomy.ANATOMICALDIRECTION attribute) assay (bkbit.models.cell_taxonomy.Cell attribute) assay_ontology_term_id (bkbit.models.cell_taxonomy.Cell attribute) assembly_accession (bkbit.data_translators.genome_annotation_translator.Gff3 attribute) assembly_strain (bkbit.data_translators.genome_annotation_translator.Gff3 attribute) assign_func_header() (bkbit.data_translators.anatomical_structure_translator.AnS class method) ATACOnly (bkbit.models.library_generation.BarcodedCellSampleTechnique attribute) Attribute (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) authority (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) AuthorityType (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation)

B

barcoded_cell_input_quantity_count (bkbit.models.library_generation.CellBarcoding attribute) barcoded_cell_sample_port_well (bkbit.models.library_generation.CellBarcoding attribute) BarcodedCellSample (class in bkbit.models.library_generation) BarcodedCellSampleTechnique (class in bkbit.models.library_generation) batch_condition (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) bican_fix() (in module bkbit.model_converters.sheets_converter) biological_sex (bkbit.models.library_generation.Donor attribute) BiologicalEntity (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) BioType (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) birth (bkbit.models.library_generation.AgeAtDeathReferencePoint attribute) bkbit module bkbit.data_translators module bkbit.data_translators.anatomical_structure_translator module bkbit.data_translators.file_manifest_translator module bkbit.data_translators.genome_annotation_translator module bkbit.data_translators.library_generation_translator module bkbit.data_translators.specimen_metadata_translator module bkbit.model_converters module bkbit.model_converters.sheets_converter module bkbit.model_converters.yaml2sheet_converter module bkbit.model_editors module bkbit.model_editors.add_dunderMethods_genomeAnnotation module

bkbit.model_editors.linkml_trimmer module bkbit.models module bkbit.models.anatomical_structure module bkbit.models.cell_taxonomy module bkbit.models.genome_annotation module bkbit.models.library_generation module bkbit.utils module bkbit.utils.generate_bkbit_id module bkbit.utils.get_ncbi_taxonomy module bkbit.utils.load_json module bkbit.utils.ncbi_taxonomy_cache module bkbit.utils.ncbi_taxonomy_data module bkbit.utils.ncbi_taxonomy_data.build_subset module bkbit.utils.nimp_api_endpoints module bkbit.utils.serialize_to_ttl module bkbit.utils.setup_logger module brain_region_ontology_term_id (bkbit.models.cell_taxonomy.Cell attribute) BrainSlab (class in bkbit.models.library_generation) build_full_cache() (in module bkbit.utils.get_ncbi_taxonomy) (in module bkbit.utils.ncbi_taxonomy_cache) build_subset() (in module bkbit.utils.ncbi_taxonomy_data.build_subset)

C

category (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Entity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.Entity attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Entity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Checksum attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Entity attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute)

cDNA_amplification_process_date (bkbit.models.library_generation.CdnaAmplification attribute) cDNA_amplification_set (bkbit.models.library_generation.CdnaAmplification attribute) CdnaAmplification (class in bkbit.models.library_generation) cell (bkbit.models.cell_taxonomy.SuspensionType attribute) Cell (class in bkbit.models.cell_taxonomy) cell_source_oligo_name (bkbit.models.library_generation.EnrichedCellSample attribute) cell_type_ontology_term_id (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) cell_type_set_type (bkbit.models.cell_taxonomy.CellTypeSet attribute) cellannotation_schema (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) CellBarcoding (class in bkbit.models.library_generation) CellDissociation (class in bkbit.models.library_generation) CellEnrichment (class in bkbit.models.library_generation) Cells (bkbit.models.library_generation.DissociatedCellSampleCellPrepType attribute) CellTypeSet (class in bkbit.models.cell_taxonomy) CellTypeSetType (class in bkbit.models.cell_taxonomy) CellTypeTaxon (class in bkbit.models.cell_taxonomy) CellTypeTaxonomy (class in bkbit.models.cell_taxonomy) Checksum (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) checksum_algorithm (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.library_generation.Checksum attribute) ChemicalEntityOrGeneOrGeneProduct (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) Cluster (class in bkbit.models.cell_taxonomy) cluster_algorithm (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) cluster_id (bkbit.models.cell_taxonomy.Cell attribute) cluster_info (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) ClusterSet (class in bkbit.models.cell_taxonomy) CMO301 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) CMO302 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) CMO303 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) CMO304 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) CMO305 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) CMO306 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) CMO307 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) CMO308 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) CMO309 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) CMO310 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) CMO311 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) CMO312 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) color (bkbit.models.anatomical_structure.ParcellationColorAssignment attribute) (bkbit.models.cell_taxonomy.ParcellationColorAssignment attribute) conception (bkbit.models.library_generation.AgeAtDeathReferencePoint attribute) ConfiguredBaseModel (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) content_url (bkbit.data_translators.genome_annotation_translator.Gff3 attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.library_generation.DigitalAsset attribute) convert_jsonld_to_ttl() (in module bkbit.utils.serialize_to_ttl) create_classes_slots_cvs() (in module bkbit.model_converters.yaml2sheet_converter) create_enums_cvs() (in module bkbit.model_converters.yaml2sheet_converter) create_prefix_headers_csv() (in module bkbit.model_converters.yaml2sheet_converter) creation_date (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.InformationContentEntity attribute) curated_markers_to_mouse (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) curated_markers_to_primates (bkbit.models.cell_taxonomy.CellTypeTaxon attribute)

D

data_dir() (in module bkbit.utils.ncbi_taxonomy_cache) data_type (bkbit.models.library_generation.DigitalAsset attribute) Dataset (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) days (bkbit.models.library_generation.AgeAtDeathUnit attribute) DBiT_ATAC_seq (bkbit.models.library_generation.LibraryTechnique attribute) DBiT_RNA_seq (bkbit.models.library_generation.LibraryTechnique attribute) default_embedding (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) dendrogram (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) deprecated (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Entity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.Entity attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Entity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Checksum attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Entity attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute) description (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Entity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.Entity attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Entity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Checksum attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Entity attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute)

digest (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.library_generation.DigitalAsset attribute) DigestType (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) DigitalAsset (class in bkbit.models.library_generation) dissection_was_guided_by (bkbit.models.library_generation.TissueSample attribute) DissectionRoiDelineation (class in bkbit.models.library_generation) DissectionRoiPolygon (class in bkbit.models.library_generation) dissociated_cell_oligo_tag_name (bkbit.models.library_generation.DissociatedCellSample attribute) dissociated_cell_sample_cell_prep_type (bkbit.models.library_generation.DissociatedCellSample attribute) DissociatedCellSample (class in bkbit.models.library_generation) DissociatedCellSampleCellLabelBarcode (class in bkbit.models.library_generation) DissociatedCellSampleCellPrepType (class in bkbit.models.library_generation) DISTANCEUNIT (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) Donor (class in bkbit.models.library_generation) donor_species (bkbit.models.library_generation.Donor attribute) download_and_extract_zip_in_memory() (in module bkbit.utils.get_ncbi_taxonomy) (in module bkbit.utils.ncbi_taxonomy_cache) download_gff_file() (bkbit.data_translators.genome_annotation_translator.Gff3 method) (bkbit.data_translators.genome_annotation_translator.Gff3 static method) download_google_sheet_as_tsv() (in module bkbit.model_converters.sheets_converter) download_gsheets() (in module bkbit.model_converters.sheets_converter)

E

Embedding (class in bkbit.models.cell_taxonomy) embedding_key (bkbit.models.cell_taxonomy.Embedding attribute) embedding_matrix (bkbit.models.cell_taxonomy.Embedding attribute) EnrichedCellSample (class in bkbit.models.library_generation) EnrichedCellSampleSplitting (class in bkbit.models.library_generation) enrichment_population (bkbit.models.library_generation.EnrichedCellSample attribute) ENSEMBL (bkbit.models.cell_taxonomy.AuthorityType attribute) (bkbit.models.genome_annotation.AuthorityType attribute) ensure_full_cache() (in module bkbit.utils.ncbi_taxonomy_cache) Entity (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) equivalent_identifiers (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute)

expected_cell_capture (bkbit.models.library_generation.BarcodedCellSample attribute) ExpressionMatrix (class in bkbit.models.cell_taxonomy) ExpressionMatrixType (class in bkbit.models.cell_taxonomy) extract_specimen_ids() (in module bkbit.data_translators.specimen_metadata_translator)

F

Fail (bkbit.models.library_generation.AmplifiedCdnaRnaAmplificationPassFail attribute) (bkbit.models.library_generation.LibraryPrepPassFail attribute) filter (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) fix_tsv_files() (in module bkbit.model_converters.sheets_converter) format (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.InformationContentEntity attribute) full_cache_paths() (in module bkbit.utils.ncbi_taxonomy_cache) full_name (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute)

G

Gene (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) GeneAnnotation (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) GeneOrGeneProduct (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) generate_anatomical_annotation_set() (bkbit.data_translators.anatomical_structure_translator.AnS method) generate_anatomical_space() (bkbit.data_translators.anatomical_structure_translator.AnS method) generate_bican_object() (bkbit.data_translators.library_generation_translator.SpecimenPortal method), [1] generate_digest() (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] generate_ensembl_gene_annotation() (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] generate_genome_annotation() (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] generate_genome_assembly() (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] generate_image_dataset() (bkbit.data_translators.anatomical_structure_translator.AnS method) generate_ncbi_gene_annotation() (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] generate_object_id() (in module bkbit.utils.generate_bkbit_id) generate_organism_taxon() (bkbit.data_translators.genome_annotation_translator.Gff3 class method) (bkbit.data_translators.genome_annotation_translator.Gff3 method) generate_parcellation_annotation() (bkbit.data_translators.anatomical_structure_translator.AnS method) generate_parcellation_annotation_term_map() (bkbit.data_translators.anatomical_structure_translator.AnS method) generate_parcellation_atlas() (bkbit.data_translators.anatomical_structure_translator.AnS method) generate_parcellation_color_assignment() (bkbit.data_translators.anatomical_structure_translator.AnS method) generate_parcellation_color_scheme() (bkbit.data_translators.anatomical_structure_translator.AnS method)

generate_parcellation_term() (bkbit.data_translators.anatomical_structure_translator.AnS method) generate_parcellation_term_set() (bkbit.data_translators.anatomical_structure_translator.AnS method) generate_parcellation_terminology() (bkbit.data_translators.anatomical_structure_translator.AnS method) generated_objects (bkbit.data_translators.library_generation_translator.SpecimenPortal attribute) Genome (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) genome_annotations (bkbit.models.cell_taxonomy.AnnotationCollection attribute) (bkbit.models.genome_annotation.AnnotationCollection attribute) genome_assemblies (bkbit.models.cell_taxonomy.AnnotationCollection attribute) (bkbit.models.genome_annotation.AnnotationCollection attribute) GenomeAnnotation (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) GenomeAssembly (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) GenomicEntity (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) get_ancestors() (in module bkbit.utils.nimp_api_endpoints) get_data() (in module bkbit.utils.nimp_api_endpoints) get_descendants() (in module bkbit.utils.nimp_api_endpoints) get_donor() (in module bkbit.utils.nimp_api_endpoints) get_field_type() (bkbit.data_translators.library_generation_translator.SpecimenPortal method) (bkbit.data_translators.library_generation_translator.SpecimenPortal static method) GEXOnly (bkbit.models.library_generation.BarcodedCellSampleTechnique attribute) Gff3 (class in bkbit.data_translators.genome_annotation_translator)

H

has_anatomical_annotation_set (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) has_anatomical_space (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) has_attribute (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Entity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.Entity attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Entity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Checksum attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Entity attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute)

has_attribute_type (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.library_generation.Attribute attribute) has_biological_sequence (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.GenomicEntity attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomicEntity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomicEntity attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.GenomicEntity attribute) has_embedding (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) has_expression_matrix (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) has_numeric_value (bkbit.models.anatomical_structure.QuantityValue attribute) (bkbit.models.cell_taxonomy.QuantityValue attribute) (bkbit.models.genome_annotation.QuantityValue attribute) (bkbit.models.library_generation.QuantityValue attribute) has_parcellation_terminology (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) has_parent (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.Cluster attribute) has_parent_parcellation_term (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) has_parent_parcellation_term_set (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) has_qualitative_value (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.library_generation.Attribute attribute) has_quantitative_value (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.library_generation.Attribute attribute) has_taxonomic_rank (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.library_generation.OrganismTaxon attribute) has_unit (bkbit.models.anatomical_structure.QuantityValue attribute) (bkbit.models.cell_taxonomy.QuantityValue attribute) (bkbit.models.genome_annotation.QuantityValue attribute) (bkbit.models.library_generation.QuantityValue attribute) has_variable (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) hierarchy (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) histone_modification_marker (bkbit.models.library_generation.EnrichedCellSample attribute)

I

id (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Entity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OntologyClass attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.TaxonomicRank attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.Entity attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OntologyClass attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.TaxonomicRank attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Entity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OntologyClass attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.TaxonomicRank attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Checksum attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Entity attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OntologyClass attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TaxonomicRank attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute) ImageDataset (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) in_taxon (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ThingWithTaxon attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ThingWithTaxon attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.ThingWithTaxon attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.ThingWithTaxon attribute) in_taxon_label (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ThingWithTaxon attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ThingWithTaxon attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.ThingWithTaxon attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.ThingWithTaxon attribute)

inferior_to_superior (bkbit.models.anatomical_structure.ANATOMICALDIRECTION attribute) (bkbit.models.cell_taxonomy.ANATOMICALDIRECTION attribute) information_content (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) InformationContentEntity (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) internal_identifier (bkbit.models.anatomical_structure.ParcellationAnnotation attribute) (bkbit.models.cell_taxonomy.ParcellationAnnotation attribute) iri (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Entity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.Entity attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Entity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Checksum attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Entity attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute) is_primary_data (bkbit.models.cell_taxonomy.Cell attribute)

J

jwt_token (bkbit.data_translators.library_generation_translator.SpecimenPortal attribute)

L

left_to_right (bkbit.models.anatomical_structure.ANATOMICALDIRECTION attribute) (bkbit.models.cell_taxonomy.ANATOMICALDIRECTION attribute) Library (class in bkbit.models.library_generation) library_avg_size_bp (bkbit.models.library_generation.Library attribute) library_concentration_nm (bkbit.models.library_generation.Library attribute) library_creation_date (bkbit.models.library_generation.LibraryConstruction attribute) library_input_ng (bkbit.models.library_generation.LibraryConstruction attribute) library_method (bkbit.models.library_generation.LibraryConstruction attribute) library_pool_tube_internal_label (bkbit.models.library_generation.LibraryPool attribute) library_prep_pass_fail (bkbit.models.library_generation.Library attribute) library_prep_set (bkbit.models.library_generation.LibraryConstruction attribute) library_quantification_fmol (bkbit.models.library_generation.Library attribute) library_quantification_ng (bkbit.models.library_generation.Library attribute) LibraryAliquot (class in bkbit.models.library_generation) LibraryConstruction (class in bkbit.models.library_generation) LibraryPool (class in bkbit.models.library_generation) LibraryPooling (class in bkbit.models.library_generation) LibraryPrepPassFail (class in bkbit.models.library_generation) LibraryR1R2Index (class in bkbit.models.library_generation) LibraryTechnique (class in bkbit.models.library_generation) license (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.InformationContentEntity attribute) linkml_meta (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.ActivityAndBehavior attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Annotation attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.anatomical_structure.ChemicalEntityOrGeneOrGeneProduct attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Entity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.GeneOrGeneProduct attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.GenomicEntity attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MacromolecularMachineMixin attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.Occurrent attribute) (bkbit.models.anatomical_structure.OntologyClass attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAnnotation attribute) (bkbit.models.anatomical_structure.ParcellationAnnotationTermMap attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorAssignment attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.PhysicalEssence attribute) (bkbit.models.anatomical_structure.PhysicalEssenceOrOccurrent attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.QuantityValue attribute) (bkbit.models.anatomical_structure.SubjectOfInvestigation attribute) (bkbit.models.anatomical_structure.TaxonomicRank attribute) (bkbit.models.anatomical_structure.ThingWithTaxon attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.ActivityAndBehavior attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Annotation attribute) (bkbit.models.cell_taxonomy.AnnotationCollection attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.cell_taxonomy.ChemicalEntityOrGeneOrGeneProduct attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.Entity attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.GeneOrGeneProduct attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.GenomicEntity attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MacromolecularMachineMixin attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.Occurrent attribute) (bkbit.models.cell_taxonomy.OntologyClass attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAnnotation attribute) (bkbit.models.cell_taxonomy.ParcellationAnnotationTermMap attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorAssignment attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.PhysicalEssence attribute) (bkbit.models.cell_taxonomy.PhysicalEssenceOrOccurrent attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.ProvActivity attribute) (bkbit.models.cell_taxonomy.ProvEntity attribute) (bkbit.models.cell_taxonomy.QuantityValue attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.SubjectOfInvestigation attribute) (bkbit.models.cell_taxonomy.TaxonomicRank attribute) (bkbit.models.cell_taxonomy.ThingWithTaxon attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.ActivityAndBehavior attribute) (bkbit.models.genome_annotation.Annotation attribute) (bkbit.models.genome_annotation.AnnotationCollection attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.genome_annotation.ChemicalEntityOrGeneOrGeneProduct attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Entity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.GeneOrGeneProduct attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.GenomicEntity attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MacromolecularMachineMixin attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.Occurrent attribute) (bkbit.models.genome_annotation.OntologyClass attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.PhysicalEssence attribute) (bkbit.models.genome_annotation.PhysicalEssenceOrOccurrent attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.QuantityValue attribute) (bkbit.models.genome_annotation.SubjectOfInvestigation attribute) (bkbit.models.genome_annotation.TaxonomicRank attribute) (bkbit.models.genome_annotation.ThingWithTaxon attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.ActivityAndBehavior attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Annotation attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Checksum attribute) (bkbit.models.library_generation.ChemicalEntityOrGeneOrGeneProduct attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Entity attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.GeneOrGeneProduct attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.GenomicEntity attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MacromolecularMachineMixin attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.Occurrent attribute) (bkbit.models.library_generation.OntologyClass attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.PhysicalEssence attribute) (bkbit.models.library_generation.PhysicalEssenceOrOccurrent attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.ProvActivity attribute) (bkbit.models.library_generation.ProvEntity attribute) (bkbit.models.library_generation.QuantityValue attribute) (bkbit.models.library_generation.SubjectOfInvestigation attribute) (bkbit.models.library_generation.TaxonomicRank attribute) (bkbit.models.library_generation.ThingWithTaxon attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute)

LinkMLMeta (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) load_id (bkbit.models.cell_taxonomy.Cell attribute) load_json() (in module bkbit.utils.load_json) log_level (bkbit.data_translators.genome_annotation_translator.Gff3 attribute) LOG_LEVELS (in module bkbit.utils.setup_logger) log_to_file (bkbit.data_translators.genome_annotation_translator.Gff3 attribute) lookup_common_name() (in module bkbit.utils.ncbi_taxonomy_cache) lookup_scientific_name() (in module bkbit.utils.ncbi_taxonomy_cache) lookup_taxid() (in module bkbit.utils.ncbi_taxonomy_cache) Low_QC (bkbit.models.library_generation.AmplifiedCdnaRnaAmplificationPassFail attribute) (bkbit.models.library_generation.LibraryPrepPassFail attribute)

M

MacromolecularMachineMixin (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) MaterialSample (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) matrix_type (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) MD5 (bkbit.models.anatomical_structure.DigestType attribute) (bkbit.models.cell_taxonomy.DigestType attribute) (bkbit.models.genome_annotation.DigestType attribute) (bkbit.models.library_generation.DigestType attribute) measures (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) MERFISH (bkbit.models.library_generation.LibraryTechnique attribute) meter (bkbit.models.anatomical_structure.DISTANCEUNIT attribute) (bkbit.models.cell_taxonomy.DISTANCEUNIT attribute) method (bkbit.models.library_generation.CellBarcoding attribute) MethylC_Seq (bkbit.models.library_generation.LibraryTechnique attribute) micrometer (bkbit.models.anatomical_structure.DISTANCEUNIT attribute) (bkbit.models.cell_taxonomy.DISTANCEUNIT attribute) millimeter (bkbit.models.anatomical_structure.DISTANCEUNIT attribute) (bkbit.models.cell_taxonomy.DISTANCEUNIT attribute) mode (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) model_config (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.ActivityAndBehavior attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Annotation attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.anatomical_structure.ChemicalEntityOrGeneOrGeneProduct attribute) (bkbit.models.anatomical_structure.ConfiguredBaseModel attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Entity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.GeneOrGeneProduct attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.GenomicEntity attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.LinkMLMeta attribute) (bkbit.models.anatomical_structure.MacromolecularMachineMixin attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.Occurrent attribute) (bkbit.models.anatomical_structure.OntologyClass attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAnnotation attribute) (bkbit.models.anatomical_structure.ParcellationAnnotationTermMap attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorAssignment attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.PhysicalEssence attribute) (bkbit.models.anatomical_structure.PhysicalEssenceOrOccurrent attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.QuantityValue attribute) (bkbit.models.anatomical_structure.SubjectOfInvestigation attribute) (bkbit.models.anatomical_structure.TaxonomicRank attribute) (bkbit.models.anatomical_structure.ThingWithTaxon attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.ActivityAndBehavior attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Annotation attribute) (bkbit.models.cell_taxonomy.AnnotationCollection attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.cell_taxonomy.ChemicalEntityOrGeneOrGeneProduct attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.ConfiguredBaseModel attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.Entity attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.GeneOrGeneProduct attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.GenomicEntity attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.LinkMLMeta attribute) (bkbit.models.cell_taxonomy.MacromolecularMachineMixin attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.Occurrent attribute) (bkbit.models.cell_taxonomy.OntologyClass attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAnnotation attribute) (bkbit.models.cell_taxonomy.ParcellationAnnotationTermMap attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorAssignment attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.PhysicalEssence attribute) (bkbit.models.cell_taxonomy.PhysicalEssenceOrOccurrent attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.ProvActivity attribute) (bkbit.models.cell_taxonomy.ProvEntity attribute) (bkbit.models.cell_taxonomy.QuantityValue attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.SubjectOfInvestigation attribute) (bkbit.models.cell_taxonomy.TaxonomicRank attribute) (bkbit.models.cell_taxonomy.ThingWithTaxon attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.ActivityAndBehavior attribute) (bkbit.models.genome_annotation.Annotation attribute) (bkbit.models.genome_annotation.AnnotationCollection attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.genome_annotation.ChemicalEntityOrGeneOrGeneProduct attribute) (bkbit.models.genome_annotation.ConfiguredBaseModel attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Entity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.GeneOrGeneProduct attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.GenomicEntity attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.LinkMLMeta attribute) (bkbit.models.genome_annotation.MacromolecularMachineMixin attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.Occurrent attribute) (bkbit.models.genome_annotation.OntologyClass attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.PhysicalEssence attribute) (bkbit.models.genome_annotation.PhysicalEssenceOrOccurrent attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.QuantityValue attribute) (bkbit.models.genome_annotation.SubjectOfInvestigation attribute) (bkbit.models.genome_annotation.TaxonomicRank attribute) (bkbit.models.genome_annotation.ThingWithTaxon attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.ActivityAndBehavior attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Annotation attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Checksum attribute) (bkbit.models.library_generation.ChemicalEntityOrGeneOrGeneProduct attribute) (bkbit.models.library_generation.ConfiguredBaseModel attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Entity attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.GeneOrGeneProduct attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.GenomicEntity attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.LinkMLMeta attribute) (bkbit.models.library_generation.MacromolecularMachineMixin attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.Occurrent attribute) (bkbit.models.library_generation.OntologyClass attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.PhysicalEssence attribute) (bkbit.models.library_generation.PhysicalEssenceOrOccurrent attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.ProvActivity attribute) (bkbit.models.library_generation.ProvEntity attribute) (bkbit.models.library_generation.QuantityValue attribute) (bkbit.models.library_generation.SubjectOfInvestigation attribute) (bkbit.models.library_generation.TaxonomicRank attribute) (bkbit.models.library_generation.ThingWithTaxon attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute)

module bkbit bkbit.data_translators bkbit.data_translators.anatomical_structure_translator bkbit.data_translators.file_manifest_translator bkbit.data_translators.genome_annotation_translator bkbit.data_translators.library_generation_translator bkbit.data_translators.specimen_metadata_translator bkbit.model_converters bkbit.model_converters.sheets_converter bkbit.model_converters.yaml2sheet_converter bkbit.model_editors bkbit.model_editors.add_dunderMethods_genomeAnnotation bkbit.model_editors.linkml_trimmer bkbit.models bkbit.models.anatomical_structure bkbit.models.cell_taxonomy bkbit.models.genome_annotation bkbit.models.library_generation bkbit.utils bkbit.utils.generate_bkbit_id bkbit.utils.get_ncbi_taxonomy bkbit.utils.load_json bkbit.utils.ncbi_taxonomy_cache bkbit.utils.ncbi_taxonomy_data bkbit.utils.ncbi_taxonomy_data.build_subset bkbit.utils.nimp_api_endpoints bkbit.utils.serialize_to_ttl bkbit.utils.setup_logger molecular_type (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) months (bkbit.models.library_generation.AgeAtDeathUnit attribute) Multiome (bkbit.models.library_generation.BarcodedCellSampleTechnique attribute)

N

na (bkbit.models.cell_taxonomy.SuspensionType attribute) name (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Entity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.GeneOrGeneProduct attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MacromolecularMachineMixin attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.Entity attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.GeneOrGeneProduct attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MacromolecularMachineMixin attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Entity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.GeneOrGeneProduct attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MacromolecularMachineMixin attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Checksum attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Entity attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.GeneOrGeneProduct attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MacromolecularMachineMixin attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute)

NamedThing (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) NCBI (bkbit.models.cell_taxonomy.AuthorityType attribute) (bkbit.models.genome_annotation.AuthorityType attribute) neighborhood (bkbit.models.cell_taxonomy.CellTypeSetType attribute) noncoding (bkbit.models.cell_taxonomy.BioType attribute) (bkbit.models.genome_annotation.BioType attribute) normalized (bkbit.models.cell_taxonomy.ExpressionMatrixType attribute) Not_evaluated (bkbit.models.library_generation.AmplifiedCdnaRnaAmplificationPassFail attribute) (bkbit.models.library_generation.LibraryPrepPassFail attribute) Nuclei (bkbit.models.library_generation.DissociatedCellSampleCellPrepType attribute) nucleus (bkbit.models.cell_taxonomy.SuspensionType attribute) number_1 (bkbit.models.library_generation.Sex attribute) number_10xATAC_V2FULL_STOP0 (bkbit.models.library_generation.LibraryTechnique attribute) number_10XMultiome_Cell_HashingSEMICOLONBarcode (bkbit.models.library_generation.LibraryTechnique attribute) number_10XMultiome_CellHashingSEMICOLONATAC (bkbit.models.library_generation.LibraryTechnique attribute) number_10XMultiome_CellHashingSEMICOLONGEX (bkbit.models.library_generation.LibraryTechnique attribute) number_10xMultiomeSEMICOLONATAC (bkbit.models.library_generation.LibraryTechnique attribute) number_10xMultiomeSEMICOLONGEX (bkbit.models.library_generation.LibraryTechnique attribute) number_10xV3FULL_STOP1 (bkbit.models.library_generation.LibraryTechnique attribute) number_10xV3FULL_STOP1_CellPlexSEMICOLONBarcode (bkbit.models.library_generation.LibraryTechnique attribute) number_10xV3FULL_STOP1_CellPlexSEMICOLONGEX (bkbit.models.library_generation.LibraryTechnique attribute) number_10xV3FULL_STOP1_HT (bkbit.models.library_generation.LibraryTechnique attribute) number_10xV3FULL_STOP1_HT_CellPlexSEMICOLONBarcode (bkbit.models.library_generation.LibraryTechnique attribute) number_10xV3FULL_STOP1_HT_CellPlexSEMICOLONGEX (bkbit.models.library_generation.LibraryTechnique attribute) number_2 (bkbit.models.library_generation.Sex attribute) number_2nt_001 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) number_2nt_002 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) number_2nt_003 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) number_2nt_004 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) number_3nt_001 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) number_3nt_002 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) number_3nt_003 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) number_3nt_004 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) number_3nt_005 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) number_3nt_006 (bkbit.models.library_generation.DissociatedCellSampleCellLabelBarcode attribute) number_7 (bkbit.models.library_generation.Sex attribute) number_8 (bkbit.models.library_generation.Sex attribute) number_9 (bkbit.models.library_generation.Sex attribute) number_of_cells (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) number_of_observations (bkbit.models.cell_taxonomy.Cluster attribute)

O

Occurrent (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) OntologyClass (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) order (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute)

ordinal (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) OrganismTaxon (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation)

P

parameterizes (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) ParcellationAnnotation (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) ParcellationAnnotationTermMap (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) ParcellationAtlas (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) ParcellationColorAssignment (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) ParcellationColorScheme (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) ParcellationTerm (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) ParcellationTerminology (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) ParcellationTermSet (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) parse() (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] parse_dmp_content() (in module bkbit.utils.get_ncbi_taxonomy) (in module bkbit.utils.ncbi_taxonomy_cache) parse_gff3_file() (bkbit.data_translators.genome_annotation_translator.Gff3 method) parse_multiple_nashids() (bkbit.data_translators.library_generation_translator.SpecimenPortal method) (in module bkbit.data_translators.library_generation_translator) parse_nhash_id_bottom_up() (bkbit.data_translators.library_generation_translator.SpecimenPortal method), [1] parse_nhash_id_top_down() (bkbit.data_translators.library_generation_translator.SpecimenPortal method), [1] parse_single_nashid() (bkbit.data_translators.library_generation_translator.SpecimenPortal method) (in module bkbit.data_translators.library_generation_translator) parse_url() (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] part_of_anatomical_annotation_set (bkbit.models.anatomical_structure.ParcellationAnnotation attribute) (bkbit.models.cell_taxonomy.ParcellationAnnotation attribute) part_of_cluster (bkbit.models.cell_taxonomy.Cell attribute) part_of_parcellation_color_scheme (bkbit.models.anatomical_structure.ParcellationColorAssignment attribute) (bkbit.models.cell_taxonomy.ParcellationColorAssignment attribute) part_of_parcellation_term_set (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) part_of_parcellation_terminology (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) part_of_set (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.Cluster attribute) part_of_taxonomy (bkbit.models.cell_taxonomy.CellTypeSet attribute) Pass (bkbit.models.library_generation.AmplifiedCdnaRnaAmplificationPassFail attribute) (bkbit.models.library_generation.LibraryPrepPassFail attribute) pattern_category() (bkbit.models.library_generation.AmplifiedCdna class method) (bkbit.models.library_generation.BarcodedCellSample class method) (bkbit.models.library_generation.BrainSlab class method) (bkbit.models.library_generation.CdnaAmplification class method) (bkbit.models.library_generation.CellBarcoding class method) (bkbit.models.library_generation.CellDissociation class method) (bkbit.models.library_generation.CellEnrichment class method) (bkbit.models.library_generation.DigitalAsset class method) (bkbit.models.library_generation.DissectionRoiDelineation class method) (bkbit.models.library_generation.DissectionRoiPolygon class method) (bkbit.models.library_generation.DissociatedCellSample class method) (bkbit.models.library_generation.Donor class method) (bkbit.models.library_generation.EnrichedCellSample class method) (bkbit.models.library_generation.EnrichedCellSampleSplitting class method) (bkbit.models.library_generation.Library class method) (bkbit.models.library_generation.LibraryAliquot class method) (bkbit.models.library_generation.LibraryConstruction class method) (bkbit.models.library_generation.LibraryPool class method) (bkbit.models.library_generation.LibraryPooling class method) (bkbit.models.library_generation.TissueDissection class method) (bkbit.models.library_generation.TissueSample class method) PhysicalEntity (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) PhysicalEssence (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) PhysicalEssenceOrOccurrent (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) posterior_to_anterior (bkbit.models.anatomical_structure.ANATOMICALDIRECTION attribute) (bkbit.models.cell_taxonomy.ANATOMICALDIRECTION attribute) Procedure (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) process_and_save_taxdmp_in_memory() (in module bkbit.utils.get_ncbi_taxonomy) process_csv() (in module bkbit.data_translators.file_manifest_translator) process_date (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.LibraryPooling attribute) process_row() (in module bkbit.data_translators.file_manifest_translator) protein_coding (bkbit.models.cell_taxonomy.BioType attribute) (bkbit.models.genome_annotation.BioType attribute) ProvActivity (class in bkbit.models.cell_taxonomy) (class in bkbit.models.library_generation) ProvEntity (class in bkbit.models.cell_taxonomy) (class in bkbit.models.library_generation) provide_data() (bkbit.data_translators.anatomical_structure_translator.AnS method) provided_by (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute)

Q

quality_control_markers (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) QuantityValue (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation)

R

R1_R2_index_name (bkbit.models.library_generation.Library attribute) raw_count (bkbit.models.cell_taxonomy.ExpressionMatrixType attribute) read_and_parse_gsheet_yaml() (in module bkbit.model_converters.sheets_converter) read_data() (bkbit.data_translators.anatomical_structure_translator.AnS method) reference_assembly (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) referenced_in (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) RelativeFrequencyAnalysisResult (class in bkbit.models.cell_taxonomy) revision_of (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute)

rights (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.InformationContentEntity attribute) root (bkbit.models.anatomical_structure.LinkMLMeta attribute) (bkbit.models.cell_taxonomy.LinkMLMeta attribute) (bkbit.models.genome_annotation.LinkMLMeta attribute) (bkbit.models.library_generation.LinkMLMeta attribute)

S

scATAC_seq (bkbit.models.library_generation.LibraryTechnique attribute) schema_version (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) schemaview (bkbit.model_editors.linkml_trimmer.YamlTrimmer attribute) serialize() (bkbit.model_editors.linkml_trimmer.YamlTrimmer method), [1] serialize_to_jsonld() (bkbit.data_translators.anatomical_structure_translator.AnS method) (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] (bkbit.data_translators.library_generation_translator.SpecimenPortal method), [1] (in module bkbit.data_translators.file_manifest_translator) SetB_A1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A13 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A14 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A15 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A16 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A17 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A18 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A19 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A20 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A21 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A22 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A23 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A24 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_A9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B13 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B14 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B15 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B16 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B17 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B18 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B19 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B20 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B21 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B22 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B23 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B24 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_B9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C13 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C14 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C15 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C16 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C17 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C18 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C19 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C20 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C21 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C22 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C23 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C24 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_C9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D13 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D14 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D15 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D16 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D17 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D18 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D19 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D20 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D21 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D22 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D23 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D24 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_D9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E13 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E14 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E15 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E16 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E17 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E18 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E19 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E20 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E21 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E22 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E23 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E24 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_E9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F13 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F14 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F15 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F16 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F17 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F18 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F19 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F20 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F21 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F22 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F23 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F24 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_F9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G13 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G14 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G15 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G16 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G17 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G18 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G19 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G20 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G21 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G22 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G23 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G24 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_G9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H13 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H14 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H15 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H16 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H17 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H18 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H19 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H20 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H21 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H22 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H23 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H24 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_H9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I13 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I14 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I15 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I16 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I17 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I18 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I19 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I20 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I21 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I22 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I23 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I24 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SetB_I8 (bkbit.models.library_generation.LibraryR1R2Index attribute) setup() (bkbit.data_translators.genome_annotation_translator.Gff3 method) setup_logger() (in module bkbit.utils.setup_logger) Sex (class in bkbit.models.library_generation) SHA1 (bkbit.models.anatomical_structure.DigestType attribute) (bkbit.models.cell_taxonomy.DigestType attribute) (bkbit.models.genome_annotation.DigestType attribute) (bkbit.models.library_generation.DigestType attribute) SHA256 (bkbit.models.anatomical_structure.DigestType attribute) (bkbit.models.cell_taxonomy.DigestType attribute) (bkbit.models.genome_annotation.DigestType attribute) (bkbit.models.library_generation.DigestType attribute) SI_NA_A1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_A10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_A11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_A12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_A2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_A3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_A4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_A5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_A6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_A7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_A8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_A9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_B9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_C9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_D9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_E9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_F9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_G9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NA_H9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_A1 (bkbit.models.library_generation.LibraryR1R2Index attribute)

SI_NN_A10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_A11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_A12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_A2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_A3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_A4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_A5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_A6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_A7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_A8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_A9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_B9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_C9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_D9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_E9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_F9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_G9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_NN_H9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_A9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_B9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_C9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_D9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_E9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_F9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_G9 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H1 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H10 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H11 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H12 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H2 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H3 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H4 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H5 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H6 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H7 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H8 (bkbit.models.library_generation.LibraryR1R2Index attribute) SI_TT_H9 (bkbit.models.library_generation.LibraryR1R2Index attribute) Slide_seq_MERFISH (bkbit.models.library_generation.LibraryTechnique attribute) SmartSeq3 (bkbit.models.library_generation.LibraryTechnique attribute) SMARTSeqSC (bkbit.models.library_generation.LibraryTechnique attribute) snm3C_seq (bkbit.models.library_generation.BarcodedCellSampleTechnique attribute) (bkbit.models.library_generation.LibraryTechnique attribute) snmCT_seq (bkbit.models.library_generation.LibraryTechnique attribute) source_id (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) specialization_of (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) SpecimenPortal (class in bkbit.data_translators.library_generation_translator) strain (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) StudyResult (class in bkbit.models.cell_taxonomy) subject_parcellation_annotation (bkbit.models.anatomical_structure.ParcellationAnnotationTermMap attribute) (bkbit.models.cell_taxonomy.ParcellationAnnotationTermMap attribute) subject_parcellation_term (bkbit.models.anatomical_structure.ParcellationAnnotationTermMap attribute) (bkbit.models.anatomical_structure.ParcellationColorAssignment attribute) (bkbit.models.cell_taxonomy.ParcellationAnnotationTermMap attribute) (bkbit.models.cell_taxonomy.ParcellationColorAssignment attribute) subject_parcellation_terminology (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) SubjectOfInvestigation (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) superior_to_inferior (bkbit.models.anatomical_structure.ANATOMICALDIRECTION attribute) (bkbit.models.cell_taxonomy.ANATOMICALDIRECTION attribute) suspension_type (bkbit.models.cell_taxonomy.Cell attribute) SuspensionType (class in bkbit.models.cell_taxonomy) symbol (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.library_generation.Gene attribute) synonym (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute)

T

taxonomic_level (bkbit.models.cell_taxonomy.CellTypeSetType attribute) TaxonomicRank (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) ThingWithTaxon (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) (class in bkbit.models.library_generation) tissue_sample_structure (bkbit.models.library_generation.TissueSample attribute) TissueDissection (class in bkbit.models.library_generation) TissueSample (class in bkbit.models.library_generation) title (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) trim_model() (bkbit.model_editors.linkml_trimmer.YamlTrimmer method) type (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Entity attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.Entity attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Entity attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Checksum attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Entity attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute)

U

unit (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) used (bkbit.models.cell_taxonomy.ProvActivity attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.ProvActivity attribute) (bkbit.models.library_generation.TissueDissection attribute)

V

value (bkbit.models.anatomical_structure.Checksum attribute) (bkbit.models.cell_taxonomy.Checksum attribute) (bkbit.models.genome_annotation.Checksum attribute) (bkbit.models.library_generation.Checksum attribute) version (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute)

VersionedNamedThing (class in bkbit.models.anatomical_structure) (class in bkbit.models.cell_taxonomy) (class in bkbit.models.genome_annotation) voxel_count (bkbit.models.anatomical_structure.ParcellationAnnotation attribute) (bkbit.models.cell_taxonomy.ParcellationAnnotation attribute)

W

was_derived_from (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.ProvEntity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.ProvEntity attribute) (bkbit.models.library_generation.TissueSample attribute) was_generated_by (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.ProvEntity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiPolygon attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.ProvEntity attribute) (bkbit.models.library_generation.TissueSample attribute)

was_guided_by (bkbit.models.library_generation.TissueDissection attribute) whole_brain_MERFISH (bkbit.models.library_generation.LibraryTechnique attribute)

X

x_direction (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) x_resolution (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) x_size (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) xref (bkbit.models.anatomical_structure.Activity attribute) (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.Attribute attribute) (bkbit.models.anatomical_structure.BiologicalEntity attribute) (bkbit.models.anatomical_structure.Dataset attribute) (bkbit.models.anatomical_structure.Gene attribute) (bkbit.models.anatomical_structure.Genome attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.InformationContentEntity attribute) (bkbit.models.anatomical_structure.MaterialSample attribute) (bkbit.models.anatomical_structure.NamedThing attribute) (bkbit.models.anatomical_structure.OrganismTaxon attribute) (bkbit.models.anatomical_structure.ParcellationAtlas attribute) (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.anatomical_structure.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.ParcellationTermSet attribute) (bkbit.models.anatomical_structure.PhysicalEntity attribute) (bkbit.models.anatomical_structure.Procedure attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.cell_taxonomy.Activity attribute) (bkbit.models.cell_taxonomy.AnatomicalAnnotationSet attribute) (bkbit.models.cell_taxonomy.AnatomicalSpace attribute) (bkbit.models.cell_taxonomy.Attribute attribute) (bkbit.models.cell_taxonomy.BiologicalEntity attribute) (bkbit.models.cell_taxonomy.Cell attribute) (bkbit.models.cell_taxonomy.CellTypeSet attribute) (bkbit.models.cell_taxonomy.CellTypeTaxon attribute) (bkbit.models.cell_taxonomy.CellTypeTaxonomy attribute) (bkbit.models.cell_taxonomy.Cluster attribute) (bkbit.models.cell_taxonomy.ClusterSet attribute) (bkbit.models.cell_taxonomy.Dataset attribute) (bkbit.models.cell_taxonomy.Embedding attribute) (bkbit.models.cell_taxonomy.ExpressionMatrix attribute) (bkbit.models.cell_taxonomy.Gene attribute) (bkbit.models.cell_taxonomy.GeneAnnotation attribute) (bkbit.models.cell_taxonomy.Genome attribute) (bkbit.models.cell_taxonomy.GenomeAnnotation attribute) (bkbit.models.cell_taxonomy.GenomeAssembly attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) (bkbit.models.cell_taxonomy.InformationContentEntity attribute) (bkbit.models.cell_taxonomy.MaterialSample attribute) (bkbit.models.cell_taxonomy.NamedThing attribute) (bkbit.models.cell_taxonomy.OrganismTaxon attribute) (bkbit.models.cell_taxonomy.ParcellationAtlas attribute) (bkbit.models.cell_taxonomy.ParcellationColorScheme attribute) (bkbit.models.cell_taxonomy.ParcellationTerm attribute) (bkbit.models.cell_taxonomy.ParcellationTerminology attribute) (bkbit.models.cell_taxonomy.ParcellationTermSet attribute) (bkbit.models.cell_taxonomy.PhysicalEntity attribute) (bkbit.models.cell_taxonomy.Procedure attribute) (bkbit.models.cell_taxonomy.RelativeFrequencyAnalysisResult attribute) (bkbit.models.cell_taxonomy.StudyResult attribute) (bkbit.models.cell_taxonomy.VersionedNamedThing attribute) (bkbit.models.genome_annotation.Activity attribute) (bkbit.models.genome_annotation.Attribute attribute) (bkbit.models.genome_annotation.BiologicalEntity attribute) (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute) (bkbit.models.genome_annotation.Genome attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) (bkbit.models.genome_annotation.MaterialSample attribute) (bkbit.models.genome_annotation.NamedThing attribute) (bkbit.models.genome_annotation.OrganismTaxon attribute) (bkbit.models.genome_annotation.PhysicalEntity attribute) (bkbit.models.genome_annotation.Procedure attribute) (bkbit.models.genome_annotation.VersionedNamedThing attribute) (bkbit.models.library_generation.Activity attribute) (bkbit.models.library_generation.AmplifiedCdna attribute) (bkbit.models.library_generation.Attribute attribute) (bkbit.models.library_generation.BarcodedCellSample attribute) (bkbit.models.library_generation.BiologicalEntity attribute) (bkbit.models.library_generation.BrainSlab attribute) (bkbit.models.library_generation.CdnaAmplification attribute) (bkbit.models.library_generation.CellBarcoding attribute) (bkbit.models.library_generation.CellDissociation attribute) (bkbit.models.library_generation.CellEnrichment attribute) (bkbit.models.library_generation.Dataset attribute) (bkbit.models.library_generation.DigitalAsset attribute) (bkbit.models.library_generation.DissectionRoiDelineation attribute) (bkbit.models.library_generation.DissociatedCellSample attribute) (bkbit.models.library_generation.Donor attribute) (bkbit.models.library_generation.EnrichedCellSample attribute) (bkbit.models.library_generation.EnrichedCellSampleSplitting attribute) (bkbit.models.library_generation.Gene attribute) (bkbit.models.library_generation.Genome attribute) (bkbit.models.library_generation.InformationContentEntity attribute) (bkbit.models.library_generation.Library attribute) (bkbit.models.library_generation.LibraryAliquot attribute) (bkbit.models.library_generation.LibraryConstruction attribute) (bkbit.models.library_generation.LibraryPool attribute) (bkbit.models.library_generation.LibraryPooling attribute) (bkbit.models.library_generation.MaterialSample attribute) (bkbit.models.library_generation.NamedThing attribute) (bkbit.models.library_generation.OrganismTaxon attribute) (bkbit.models.library_generation.PhysicalEntity attribute) (bkbit.models.library_generation.Procedure attribute) (bkbit.models.library_generation.TissueDissection attribute) (bkbit.models.library_generation.TissueSample attribute)

Y

y_direction (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) y_resolution (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute)

y_size (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) YamlTrimmer (class in bkbit.model_editors.linkml_trimmer) years (bkbit.models.library_generation.AgeAtDeathUnit attribute)

Z

z_direction (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute) z_resolution (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute)

z_size (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.cell_taxonomy.ImageDataset attribute)