bkbit.models.genome_annotation module

class bkbit.models.genome_annotation.Activity(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/Activity', 'biolink:Activity']] = ['biolink:Activity'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None)[source]

Bases: ActivityAndBehavior, NamedThing

An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/Activity', 'biolink:Activity']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

id: str

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:Activity', 'definition_uri': 'https://w3id.org/biolink/vocab/Activity', 'exact_mappings': ['prov:Activity', 'NCIT:C43431', 'STY:T052'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'mixins': ['activity and behavior'], 'narrow_mappings': ['STY:T056', 'STY:T057', 'STY:T064', 'STY:T066', 'STY:T062', 'STY:T065', 'STY:T058']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.ActivityAndBehavior[source]

Bases: Occurrent

Activity or behavior of any independent integral living, organization or mechanical actor in the world

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:ActivityAndBehavior', 'definition_uri': 'https://w3id.org/biolink/vocab/ActivityAndBehavior', 'exact_mappings': ['UMLSSG:ACTI'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'mixin': True})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.Annotation[source]

Bases: ConfiguredBaseModel

Biolink Model root class for entity annotations.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'abstract': True, 'class_uri': 'biolink:Annotation', 'definition_uri': 'https://w3id.org/biolink/vocab/Annotation', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema'})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.AnnotationCollection(*, annotations: List[GeneAnnotation] | None = None, genome_annotations: List[GenomeAnnotation] | None = None, genome_assemblies: List[GenomeAssembly] | None = None)[source]

Bases: ConfiguredBaseModel

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

annotations: List[GeneAnnotation] | None

genome_annotations: List[GenomeAnnotation] | None

genome_assemblies: List[GenomeAssembly] | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'from_schema': 'https://identifiers.org/brain-bican/genome-annotation-schema', 'tree_root': True})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.Attribute(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/Attribute', 'biolink:Attribute']] = ['biolink:Attribute'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None, has_attribute_type: str, has_quantitative_value: List[QuantityValue] | None = None, has_qualitative_value: str | None = None)[source]

Bases: NamedThing, OntologyClass

A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/Attribute', 'biolink:Attribute']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

has_attribute_type: str

has_qualitative_value: str | None

has_quantitative_value: List[QuantityValue] | None

id: str

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:Attribute', 'definition_uri': 'https://w3id.org/biolink/vocab/Attribute', 'exact_mappings': ['SIO:000614'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'id_prefixes': ['EDAM-DATA', 'EDAM-FORMAT', 'EDAM-OPERATION', 'EDAM-TOPIC'], 'in_subset': ['samples'], 'mixins': ['ontology class'], 'slot_usage': {'name': {'description': "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", 'name': 'name'}}})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.AuthorityType(value)[source]

Bases: str, Enum

An enumeration.

ENSEMBL = 'ENSEMBL'

NCBI = 'NCBI'

class bkbit.models.genome_annotation.BioType(value)[source]

Bases: str, Enum

An enumeration.

noncoding = 'noncoding'

protein_coding = 'protein_coding'

class bkbit.models.genome_annotation.BiologicalEntity(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/BiologicalEntity', 'biolink:BiologicalEntity']] = ['biolink:BiologicalEntity'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None, in_taxon: List[str] | None = None, in_taxon_label: str | None = None)[source]

Bases: ThingWithTaxon, NamedThing

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/BiologicalEntity', 'biolink:BiologicalEntity']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

id: str

in_taxon: List[str] | None

in_taxon_label: str | None

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'abstract': True, 'aliases': ['bioentity'], 'class_uri': 'biolink:BiologicalEntity', 'definition_uri': 'https://w3id.org/biolink/vocab/BiologicalEntity', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'mixins': ['thing with taxon'], 'narrow_mappings': ['WIKIDATA:Q28845870', 'STY:T050', 'SIO:010046', 'STY:T129']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.Checksum(*, id: str, iri: str | None = None, category: List[Literal['https://identifiers.org/brain-bican/vocab/Checksum', 'bican:Checksum']] = ['bican:Checksum'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, checksum_algorithm: DigestType | None = None, value: str | None = None)[source]

Bases: Entity

Checksum values associated with digital entities.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://identifiers.org/brain-bican/vocab/Checksum', 'bican:Checksum']]

checksum_algorithm: DigestType | None

deprecated: bool | None

description: str | None

has_attribute: List[str] | None

id: str

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'from_schema': 'https://identifiers.org/brain-bican/bican-core-schema'})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

type: List[str] | None

value: str | None

class bkbit.models.genome_annotation.ChemicalEntityOrGeneOrGeneProduct[source]

Bases: ConfiguredBaseModel

A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:ChemicalEntityOrGeneOrGeneProduct', 'definition_uri': 'https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProduct', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'mixin': True})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.ConfiguredBaseModel[source]

Bases: BaseModel

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

Bases: InformationContentEntity

an item that refers to a collection of data from a data source.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/Dataset', 'biolink:Dataset']]

creation_date: date | None

deprecated: bool | None

description: str | None

format: str | None

full_name: str | None

has_attribute: List[str] | None

id: str

iri: str | None

license: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:Dataset', 'definition_uri': 'https://w3id.org/biolink/vocab/Dataset', 'exact_mappings': ['IAO:0000100', 'dctypes:Dataset', 'schema:dataset', 'dcid:Dataset'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema'})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

rights: str | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.DigestType(value)[source]

Bases: str, Enum

An enumeration.

MD5 = 'spdx:checksumAlgorithm_md5'

SHA1 = 'spdx:checksumAlgorithm_sha1'

SHA256 = 'spdx:checksumAlgorithm_sha256'

class bkbit.models.genome_annotation.Entity(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/Entity', 'biolink:Entity']] = ['biolink:Entity'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None)[source]

Bases: ConfiguredBaseModel

Root Biolink Model class for all things and informational relationships, real or imagined.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/Entity', 'biolink:Entity']]

deprecated: bool | None

description: str | None

has_attribute: List[str] | None

id: str

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'abstract': True, 'class_uri': 'biolink:Entity', 'definition_uri': 'https://w3id.org/biolink/vocab/Entity', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema'})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

type: List[str] | None

class bkbit.models.genome_annotation.Gene(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/Gene', 'biolink:Gene']] = ['biolink:Gene'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None, in_taxon: List[str] | None = None, in_taxon_label: str | None = None, has_biological_sequence: str | None = None, symbol: str | None = None)[source]

Bases: GeneOrGeneProduct, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass

A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/Gene', 'biolink:Gene']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

has_biological_sequence: str | None

id: str

in_taxon: List[str] | None

in_taxon_label: str | None

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'broad_mappings': ['NCIT:C45822'], 'class_uri': 'biolink:Gene', 'definition_uri': 'https://w3id.org/biolink/vocab/Gene', 'exact_mappings': ['SO:0000704', 'SIO:010035', 'WIKIDATA:Q7187', 'dcid:Gene'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'id_prefixes': ['NCBIGene', 'ENSEMBL', 'HGNC', 'MGI', 'ZFIN', 'dictyBase', 'WB', 'WormBase', 'FB', 'RGD', 'SGD', 'PomBase', 'OMIM', 'KEGG.GENES', 'UMLS', 'Xenbase', 'AspGD', 'PHARMGKB.GENE'], 'in_subset': ['translator_minimal', 'model_organism_database'], 'mixins': ['gene or gene product', 'genomic entity', 'chemical entity or gene or gene product', 'physical essence', 'ontology class'], 'narrow_mappings': ['bioschemas:gene']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

symbol: str | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

Bases: Gene

An annotation describing the location, boundaries, and functions of individual genes within a genome annotation.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://identifiers.org/brain-bican/vocab/GeneAnnotation', 'bican:GeneAnnotation']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

has_biological_sequence: str | None

id: str

in_taxon: List[str] | None

in_taxon_label: str | None

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'from_schema': 'https://identifiers.org/brain-bican/genome-annotation-schema', 'id_prefixes': ['ENSEMBL', 'MGI', 'NCBIGene']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

molecular_type: BioType | str | None

name: str | None

provided_by: List[str] | None

referenced_in: GenomeAnnotation | str

source_id: str | None

symbol: str | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.GeneOrGeneProduct(*, name: str | None = None)[source]

Bases: MacromolecularMachineMixin

A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:GeneOrGeneProduct', 'definition_uri': 'https://w3id.org/biolink/vocab/GeneOrGeneProduct', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'id_prefixes': ['CHEMBL.TARGET', 'IUPHAR.FAMILY'], 'mixin': True})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

class bkbit.models.genome_annotation.Genome(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/Genome', 'biolink:Genome']] = ['biolink:Genome'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None, in_taxon: List[str] | None = None, in_taxon_label: str | None = None, has_biological_sequence: str | None = None)[source]

Bases: GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass

A genome is the sum of genetic material within a cell or virion.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/Genome', 'biolink:Genome']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

has_biological_sequence: str | None

id: str

in_taxon: List[str] | None

in_taxon_label: str | None

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:Genome', 'close_mappings': ['dcid:GenomeAssemblyUnit'], 'definition_uri': 'https://w3id.org/biolink/vocab/Genome', 'exact_mappings': ['SO:0001026', 'SIO:000984', 'WIKIDATA:Q7020'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'in_subset': ['model_organism_database'], 'mixins': ['genomic entity', 'physical essence', 'ontology class']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.GenomeAnnotation(*, id: str, iri: str | None = None, category: List[Literal['https://identifiers.org/brain-bican/vocab/GenomeAnnotation', 'bican:GenomeAnnotation']] = ['bican:GenomeAnnotation'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None, in_taxon: List[str] | None = None, in_taxon_label: str | None = None, has_biological_sequence: str | None = None, version: str | None = None, digest: List[Checksum | str] | None = None, content_url: List[str] | None = None, authority: AuthorityType | None = None, reference_assembly: GenomeAssembly | str)[source]

Bases: Genome

Location and nomenclature of genes and all of the coding regions in a genome assembly and the classification of genes and transcripts into types.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

authority: AuthorityType | None

category: List[Literal['https://identifiers.org/brain-bican/vocab/GenomeAnnotation', 'bican:GenomeAnnotation']]

content_url: List[str] | None

deprecated: bool | None

description: str | None

digest: List[Checksum | str] | None

full_name: str | None

has_attribute: List[str] | None

has_biological_sequence: str | None

id: str

in_taxon: List[str] | None

in_taxon_label: str | None

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'from_schema': 'https://identifiers.org/brain-bican/genome-annotation-schema'})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

reference_assembly: GenomeAssembly | str

synonym: List[str] | None

type: List[str] | None

version: str | None

xref: List[str] | None

class bkbit.models.genome_annotation.GenomeAssembly(*, id: str, iri: str | None = None, category: List[Literal['https://identifiers.org/brain-bican/vocab/GenomeAssembly', 'bican:GenomeAssembly']] = ['bican:GenomeAssembly'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None, in_taxon: List[str] | None = None, in_taxon_label: str | None = None, version: str | None = None, strain: str | None = None)[source]

Bases: ThingWithTaxon, NamedThing

Genome assembly to contain version and label information

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://identifiers.org/brain-bican/vocab/GenomeAssembly', 'bican:GenomeAssembly']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

id: str

in_taxon: List[str] | None

in_taxon_label: str | None

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'from_schema': 'https://identifiers.org/brain-bican/genome-annotation-schema', 'mixins': ['thing with taxon']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

strain: str | None

synonym: List[str] | None

type: List[str] | None

version: str | None

xref: List[str] | None

class bkbit.models.genome_annotation.GenomicEntity(*, has_biological_sequence: str | None = None)[source]

Bases: ConfiguredBaseModel

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

has_biological_sequence: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:GenomicEntity', 'definition_uri': 'https://w3id.org/biolink/vocab/GenomicEntity', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'in_subset': ['translator_minimal'], 'mixin': True, 'narrow_mappings': ['STY:T028', 'GENO:0000897']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.InformationContentEntity(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/InformationContentEntity', 'biolink:InformationContentEntity']] = ['biolink:InformationContentEntity'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None, license: str | None = None, rights: str | None = None, format: str | None = None, creation_date: date | None = None)[source]

Bases: NamedThing

a piece of information that typically describes some topic of discourse or is used as support.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/InformationContentEntity', 'biolink:InformationContentEntity']]

creation_date: date | None

deprecated: bool | None

description: str | None

format: str | None

full_name: str | None

has_attribute: List[str] | None

id: str

iri: str | None

license: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'abstract': True, 'aliases': ['information', 'information artefact', 'information entity'], 'class_uri': 'biolink:InformationContentEntity', 'definition_uri': 'https://w3id.org/biolink/vocab/InformationContentEntity', 'exact_mappings': ['IAO:0000030'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'id_prefixes': ['doi'], 'narrow_mappings': ['UMLSSG:CONC', 'STY:T077', 'STY:T078', 'STY:T079', 'STY:T080', 'STY:T081', 'STY:T082', 'STY:T089', 'STY:T102', 'STY:T169', 'STY:T171', 'STY:T185']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

rights: str | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.LinkMLMeta(root: RootModelRootType = PydanticUndefined)[source]

Bases: RootModel

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'frozen': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

root: Dict[str, Any]

class bkbit.models.genome_annotation.MacromolecularMachineMixin(*, name: str | None = None)[source]

Bases: ConfiguredBaseModel

A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:MacromolecularMachineMixin', 'definition_uri': 'https://w3id.org/biolink/vocab/MacromolecularMachineMixin', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'mixin': True})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

class bkbit.models.genome_annotation.MaterialSample(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/MaterialSample', 'biolink:MaterialSample']] = ['biolink:MaterialSample'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None)[source]

Bases: SubjectOfInvestigation, PhysicalEntity

A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/MaterialSample', 'biolink:MaterialSample']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

id: str

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'aliases': ['biospecimen', 'sample', 'biosample', 'physical sample'], 'class_uri': 'biolink:MaterialSample', 'definition_uri': 'https://w3id.org/biolink/vocab/MaterialSample', 'exact_mappings': ['OBI:0000747', 'SIO:001050'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'id_prefixes': ['BIOSAMPLE', 'GOLD.META'], 'mixins': ['subject of investigation']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.NamedThing(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/NamedThing', 'biolink:NamedThing']] = ['biolink:NamedThing'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None)[source]

Bases: Entity

a databased entity or concept/class

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/NamedThing', 'biolink:NamedThing']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

id: str

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:NamedThing', 'definition_uri': 'https://w3id.org/biolink/vocab/NamedThing', 'exact_mappings': ['BFO:0000001', 'WIKIDATA:Q35120', 'UMLSSG:OBJC', 'STY:T071', 'dcid:Thing'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema'})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.Occurrent[source]

Bases: PhysicalEssenceOrOccurrent

A processual entity.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:Occurrent', 'definition_uri': 'https://w3id.org/biolink/vocab/Occurrent', 'exact_mappings': ['BFO:0000003'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'mixin': True})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.OntologyClass(*, id: str)[source]

Bases: ConfiguredBaseModel

a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

id: str

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:OntologyClass', 'comments': ["This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc", "Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity"], 'definition_uri': 'https://w3id.org/biolink/vocab/OntologyClass', 'exact_mappings': ['owl:Class', 'schema:Class'], 'examples': [{'description': "the class 'brain' from the Uberon anatomy ontology", 'value': 'UBERON:0000955'}], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'id_prefixes': ['MESH', 'UMLS', 'KEGG.BRITE'], 'mixin': True, 'see_also': ['https://github.com/biolink/biolink-model/issues/486']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.OrganismTaxon(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/OrganismTaxon', 'biolink:OrganismTaxon']] = ['biolink:OrganismTaxon'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None, has_taxonomic_rank: str | None = None)[source]

Bases: NamedThing

A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/OrganismTaxon', 'biolink:OrganismTaxon']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

has_taxonomic_rank: str | None

id: str

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'aliases': ['taxon', 'taxonomic classification'], 'class_uri': 'biolink:OrganismTaxon', 'definition_uri': 'https://w3id.org/biolink/vocab/OrganismTaxon', 'exact_mappings': ['WIKIDATA:Q16521', 'STY:T001', 'bioschemas:Taxon'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'id_prefixes': ['NCBITaxon', 'MESH', 'UMLS'], 'in_subset': ['model_organism_database'], 'narrow_mappings': ['dcid:BiologicalSpecies'], 'values_from': ['NCBITaxon']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.PhysicalEntity(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/PhysicalEntity', 'biolink:PhysicalEntity']] = ['biolink:PhysicalEntity'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None)[source]

Bases: PhysicalEssence, NamedThing

An entity that has material reality (a.k.a. physical essence).

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/PhysicalEntity', 'biolink:PhysicalEntity']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

id: str

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:PhysicalEntity', 'definition_uri': 'https://w3id.org/biolink/vocab/PhysicalEntity', 'exact_mappings': ['STY:T072'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'mixins': ['physical essence'], 'narrow_mappings': ['STY:T073']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.PhysicalEssence[source]

Bases: PhysicalEssenceOrOccurrent

Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:PhysicalEssence', 'definition_uri': 'https://w3id.org/biolink/vocab/PhysicalEssence', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'mixin': True})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.PhysicalEssenceOrOccurrent[source]

Bases: ConfiguredBaseModel

Either a physical or processual entity.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:PhysicalEssenceOrOccurrent', 'definition_uri': 'https://w3id.org/biolink/vocab/PhysicalEssenceOrOccurrent', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'mixin': True})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.Procedure(*, id: str, iri: str | None = None, category: List[Literal['https://w3id.org/biolink/vocab/Procedure', 'biolink:Procedure']] = ['biolink:Procedure'], type: List[str] | None = None, name: str | None = None, description: str | None = None, has_attribute: List[str] | None = None, deprecated: bool | None = None, provided_by: List[str] | None = None, xref: List[str] | None = None, full_name: str | None = None, synonym: List[str] | None = None)[source]

Bases: ActivityAndBehavior, NamedThing

A series of actions conducted in a certain order or manner

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

category: List[Literal['https://w3id.org/biolink/vocab/Procedure', 'biolink:Procedure']]

deprecated: bool | None

description: str | None

full_name: str | None

has_attribute: List[str] | None

id: str

iri: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:Procedure', 'definition_uri': 'https://w3id.org/biolink/vocab/Procedure', 'exact_mappings': ['UMLSSG:PROC', 'dcid:MedicalProcedure'], 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'id_prefixes': ['CPT'], 'mixins': ['activity and behavior'], 'narrow_mappings': ['STY:T059', 'STY:T060', 'STY:T061', 'STY:T063']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: str | None

provided_by: List[str] | None

synonym: List[str] | None

type: List[str] | None

xref: List[str] | None

class bkbit.models.genome_annotation.QuantityValue(*, has_unit: str | None = None, has_numeric_value: float | None = None)[source]

Bases: Annotation

A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

has_numeric_value: float | None

has_unit: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:QuantityValue', 'definition_uri': 'https://w3id.org/biolink/vocab/QuantityValue', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema'})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.SubjectOfInvestigation[source]

Bases: ConfiguredBaseModel

An entity that has the role of being studied in an investigation, study, or experiment

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:SubjectOfInvestigation', 'definition_uri': 'https://w3id.org/biolink/vocab/SubjectOfInvestigation', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'mixin': True})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.TaxonomicRank(*, id: str)[source]

Bases: OntologyClass

A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

id: str

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:TaxonomicRank', 'definition_uri': 'https://w3id.org/biolink/vocab/TaxonomicRank', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'id_prefixes': ['TAXRANK'], 'mappings': ['WIKIDATA:Q427626']})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class bkbit.models.genome_annotation.ThingWithTaxon(*, in_taxon: List[str] | None = None, in_taxon_label: str | None = None)[source]

Bases: ConfiguredBaseModel

A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

in_taxon: List[str] | None

in_taxon_label: str | None

linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(root={'class_uri': 'biolink:ThingWithTaxon', 'definition_uri': 'https://w3id.org/biolink/vocab/ThingWithTaxon', 'from_schema': 'https://w3id.org/biolink/bican-biolink-schema', 'mixin': True})

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'strict': False, 'use_enum_values': True, 'validate_assignment': True, 'validate_default': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].