Index

_

__download_gff_file() (bkbit.data_translators.genome_annotation_translator.Gff3 method) __get_attribute() (bkbit.data_translators.genome_annotation_translator.Gff3 method) __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) __resolve_ncbi_gene_annotation() (bkbit.data_translators.genome_annotation_translator.Gff3 method)

A

Activity (class in bkbit.models.genome_annotation) ActivityAndBehavior (class in bkbit.models.genome_annotation) adding_template() (in module bkbit.model_converters.sheets_converter) AnatomicalAnnotationSet (class in bkbit.models.anatomical_structure) ANATOMICALDIRECTION (class in bkbit.models.anatomical_structure) AnatomicalSpace (class in bkbit.models.anatomical_structure) Annotation (class in bkbit.models.genome_annotation) AnnotationCollection (class in bkbit.models.genome_annotation) annotations (bkbit.models.genome_annotation.AnnotationCollection attribute)

AnS (class in bkbit.data_translators.anatomical_structure_translator) anterior_to_posterior (bkbit.models.anatomical_structure.ANATOMICALDIRECTION attribute) assembly_accession (bkbit.data_translators.genome_annotation_translator.Gff3 attribute) assembly_strain (bkbit.data_translators.genome_annotation_translator.Gff3 attribute) assign_authority_type() (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] assign_func_header() (bkbit.data_translators.anatomical_structure_translator.AnS class method) Attribute (class in bkbit.models.genome_annotation) authority (bkbit.models.genome_annotation.GenomeAnnotation attribute) AuthorityType (class in bkbit.models.genome_annotation)

B

bican_fix() (in module bkbit.model_converters.sheets_converter) BiologicalEntity (class in bkbit.models.genome_annotation) BioType (class in bkbit.models.genome_annotation) bkbit module bkbit.data_translators module bkbit.data_translators.anatomical_structure_translator module bkbit.data_translators.genome_annotation_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.genome_annotation module bkbit.utils module bkbit.utils.get_ncbi_taxonomy module bkbit.utils.load_json module bkbit.utils.nimp_api_endpoints module bkbit.utils.setup_logger module

C

category (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.NamedThing 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.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)

Checksum (class in bkbit.models.genome_annotation) checksum_algorithm (bkbit.models.genome_annotation.Checksum attribute) ChemicalEntityOrGeneOrGeneProduct (class in bkbit.models.genome_annotation) color (bkbit.models.anatomical_structure.ParcellationColorAssignment attribute) ConfiguredBaseModel (class in bkbit.models.anatomical_structure) (class in bkbit.models.genome_annotation) content_url (bkbit.data_translators.genome_annotation_translator.Gff3 attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) 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.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute)

D

Dataset (class in bkbit.models.genome_annotation) deprecated (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) description (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.NamedThing 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.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)

digest (bkbit.models.genome_annotation.GenomeAnnotation attribute) DigestType (class in bkbit.models.genome_annotation) DISTANCEUNIT (class in bkbit.models.anatomical_structure) download_and_extract_zip_in_memory() (in module bkbit.utils.get_ncbi_taxonomy) download_google_sheet_as_tsv() (in module bkbit.model_converters.sheets_converter) download_gsheets() (in module bkbit.model_converters.sheets_converter)

E

ENSEMBL (bkbit.models.genome_annotation.AuthorityType attribute)

Entity (class in bkbit.models.genome_annotation) extract_specimen_ids() (in module bkbit.data_translators.specimen_metadata_translator)

F

fix_tsv_files() (in module bkbit.model_converters.sheets_converter) format (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) full_name (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)

G

Gene (class in bkbit.models.genome_annotation) GeneAnnotation (class in bkbit.models.genome_annotation) GeneOrGeneProduct (class in bkbit.models.genome_annotation) generate_anatomical_annotation_set() (bkbit.data_translators.anatomical_structure_translator.AnS method) generate_anatomical_space() (bkbit.data_translators.anatomical_structure_translator.AnS method) 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_organism_taxon() (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] 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) Genome (class in bkbit.models.genome_annotation) genome_annotations (bkbit.models.genome_annotation.AnnotationCollection attribute) genome_assemblies (bkbit.models.genome_annotation.AnnotationCollection attribute) GenomeAnnotation (class in bkbit.models.genome_annotation) GenomeAssembly (class in bkbit.models.genome_annotation) GenomicEntity (class in bkbit.models.genome_annotation) 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) Gff3 (class in bkbit.data_translators.genome_annotation_translator)

H

has_anatomical_annotation_set (bkbit.models.anatomical_structure.ParcellationAtlas attribute) has_anatomical_space (bkbit.models.anatomical_structure.ParcellationAtlas attribute) has_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)

has_attribute_type (bkbit.models.genome_annotation.Attribute attribute) has_biological_sequence (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) has_numeric_value (bkbit.models.genome_annotation.QuantityValue attribute) has_parcellation_terminology (bkbit.models.anatomical_structure.ParcellationAtlas attribute) has_parent_parcellation_term (bkbit.models.anatomical_structure.ParcellationTerm attribute) has_parent_parcellation_term_set (bkbit.models.anatomical_structure.ParcellationTermSet attribute) has_qualitative_value (bkbit.models.genome_annotation.Attribute attribute) has_quantitative_value (bkbit.models.genome_annotation.Attribute attribute) has_taxonomic_rank (bkbit.models.genome_annotation.OrganismTaxon attribute) has_unit (bkbit.models.genome_annotation.QuantityValue attribute)

I

id (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.NamedThing 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.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) ImageDataset (class in bkbit.models.anatomical_structure) in_taxon (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)

in_taxon_label (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) inferior_to_superior (bkbit.models.anatomical_structure.ANATOMICALDIRECTION attribute) InformationContentEntity (class in bkbit.models.genome_annotation) internal_identifier (bkbit.models.anatomical_structure.ParcellationAnnotation attribute) iri (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)

L

left_to_right (bkbit.models.anatomical_structure.ANATOMICALDIRECTION attribute) license (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) linkml_meta (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.NamedThing 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.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)

LinkMLMeta (class in bkbit.models.anatomical_structure) (class in bkbit.models.genome_annotation) load_json() (in module bkbit.utils.get_ncbi_taxonomy) (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)

M

MacromolecularMachineMixin (class in bkbit.models.genome_annotation) MaterialSample (class in bkbit.models.genome_annotation) MD5 (bkbit.models.genome_annotation.DigestType attribute) measures (bkbit.models.anatomical_structure.AnatomicalSpace attribute) meter (bkbit.models.anatomical_structure.DISTANCEUNIT attribute) micrometer (bkbit.models.anatomical_structure.DISTANCEUNIT attribute) millimeter (bkbit.models.anatomical_structure.DISTANCEUNIT attribute) model_computed_fields (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.ConfiguredBaseModel attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.LinkMLMeta attribute) (bkbit.models.anatomical_structure.NamedThing 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.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) model_config (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.ConfiguredBaseModel attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.LinkMLMeta attribute) (bkbit.models.anatomical_structure.NamedThing 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.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)

model_fields (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.ConfiguredBaseModel attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.LinkMLMeta attribute) (bkbit.models.anatomical_structure.NamedThing 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.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) module bkbit bkbit.data_translators bkbit.data_translators.anatomical_structure_translator bkbit.data_translators.genome_annotation_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.genome_annotation bkbit.utils bkbit.utils.get_ncbi_taxonomy bkbit.utils.load_json bkbit.utils.nimp_api_endpoints bkbit.utils.setup_logger molecular_type (bkbit.models.genome_annotation.GeneAnnotation attribute)

N

name (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) (bkbit.models.anatomical_structure.AnatomicalSpace attribute) (bkbit.models.anatomical_structure.ImageDataset attribute) (bkbit.models.anatomical_structure.NamedThing 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.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)

NamedThing (class in bkbit.models.anatomical_structure) (class in bkbit.models.genome_annotation) NCBI (bkbit.models.genome_annotation.AuthorityType attribute) noncoding (bkbit.models.genome_annotation.BioType attribute)

O

Occurrent (class in bkbit.models.genome_annotation) OntologyClass (class in bkbit.models.genome_annotation)

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

P

parameterizes (bkbit.models.anatomical_structure.AnatomicalAnnotationSet attribute) ParcellationAnnotation (class in bkbit.models.anatomical_structure) ParcellationAnnotationTermMap (class in bkbit.models.anatomical_structure) ParcellationAtlas (class in bkbit.models.anatomical_structure) ParcellationColorAssignment (class in bkbit.models.anatomical_structure) ParcellationColorScheme (class in bkbit.models.anatomical_structure) ParcellationTerm (class in bkbit.models.anatomical_structure) ParcellationTerminology (class in bkbit.models.anatomical_structure) ParcellationTermSet (class in bkbit.models.anatomical_structure) parse() (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] parse_dmp_content() (in module bkbit.utils.get_ncbi_taxonomy) parse_url() (bkbit.data_translators.genome_annotation_translator.Gff3 method), [1] part_of_anatomical_annotation_set (bkbit.models.anatomical_structure.ParcellationAnnotation attribute) part_of_parcellation_color_scheme (bkbit.models.anatomical_structure.ParcellationColorAssignment attribute) part_of_parcellation_term_set (bkbit.models.anatomical_structure.ParcellationTerm attribute) part_of_parcellation_terminology (bkbit.models.anatomical_structure.ParcellationTermSet attribute) PhysicalEntity (class in bkbit.models.genome_annotation) PhysicalEssence (class in bkbit.models.genome_annotation) PhysicalEssenceOrOccurrent (class in bkbit.models.genome_annotation)

posterior_to_anterior (bkbit.models.anatomical_structure.ANATOMICALDIRECTION attribute) Procedure (class in bkbit.models.genome_annotation) process_and_save_taxdmp_in_memory() (in module bkbit.utils.get_ncbi_taxonomy) protein_coding (bkbit.models.genome_annotation.BioType attribute) provide_data() (bkbit.data_translators.anatomical_structure_translator.AnS method) provided_by (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)

Q

QuantityValue (class in bkbit.models.genome_annotation)

R

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.genome_annotation.GenomeAnnotation attribute) referenced_in (bkbit.models.genome_annotation.GeneAnnotation attribute) 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.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute)

rights (bkbit.models.genome_annotation.Dataset attribute) (bkbit.models.genome_annotation.InformationContentEntity attribute) root (bkbit.models.anatomical_structure.LinkMLMeta attribute) (bkbit.models.genome_annotation.LinkMLMeta attribute)

S

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] setup_logger() (in module bkbit.utils.setup_logger) SHA1 (bkbit.models.genome_annotation.DigestType attribute) SHA256 (bkbit.models.genome_annotation.DigestType attribute) source_id (bkbit.models.genome_annotation.GeneAnnotation attribute) specialization_of (bkbit.models.anatomical_structure.ParcellationAtlas attribute) strain (bkbit.models.genome_annotation.GenomeAssembly attribute) subject_parcellation_annotation (bkbit.models.anatomical_structure.ParcellationAnnotationTermMap attribute) subject_parcellation_term (bkbit.models.anatomical_structure.ParcellationAnnotationTermMap attribute) (bkbit.models.anatomical_structure.ParcellationColorAssignment attribute) subject_parcellation_terminology (bkbit.models.anatomical_structure.ParcellationColorScheme attribute) SubjectOfInvestigation (class in bkbit.models.genome_annotation) superior_to_inferior (bkbit.models.anatomical_structure.ANATOMICALDIRECTION attribute) symbol (bkbit.models.anatomical_structure.ParcellationTerm attribute) (bkbit.models.genome_annotation.Gene attribute) (bkbit.models.genome_annotation.GeneAnnotation attribute)

synonym (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)

T

TaxonomicRank (class in bkbit.models.genome_annotation) ThingWithTaxon (class in bkbit.models.genome_annotation) trim_model() (bkbit.model_editors.linkml_trimmer.YamlTrimmer method) type (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)

U

unit (bkbit.models.anatomical_structure.ImageDataset attribute)

V

value (bkbit.models.genome_annotation.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.ParcellationTerminology attribute) (bkbit.models.anatomical_structure.VersionedNamedThing attribute) (bkbit.models.genome_annotation.GenomeAnnotation attribute) (bkbit.models.genome_annotation.GenomeAssembly attribute)

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

X

x_direction (bkbit.models.anatomical_structure.ImageDataset attribute) x_resolution (bkbit.models.anatomical_structure.ImageDataset attribute) x_size (bkbit.models.anatomical_structure.ImageDataset attribute) xref (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)

Y

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

y_size (bkbit.models.anatomical_structure.ImageDataset attribute) YamlTrimmer (class in bkbit.model_editors.linkml_trimmer)

Z

z_direction (bkbit.models.anatomical_structure.ImageDataset attribute)

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