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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/Activity', 'biolink:Activity']], required=False, default=['biolink:Activity'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'annotations': FieldInfo(annotation=Union[List[GeneAnnotation], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'annotations', 'domain_of': ['annotation collection']}}), 'genome_annotations': FieldInfo(annotation=Union[List[GenomeAnnotation], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'genome_annotations', 'domain_of': ['annotation collection']}}), 'genome_assemblies': FieldInfo(annotation=Union[List[GenomeAssembly], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'genome_assemblies', 'domain_of': ['annotation collection']}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/Attribute', 'biolink:Attribute']], required=False, default=['biolink:Attribute'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'has_attribute_type': FieldInfo(annotation=str, required=True, description='connects an attribute to a class that describes it', json_schema_extra={'linkml_meta': {'alias': 'has_attribute_type', 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute_type', 'domain': 'attribute', 'domain_of': ['attribute'], 'in_subset': ['samples'], 'narrow_mappings': ['LOINC:has_modality_type', 'LOINC:has_view_type'], 'slot_uri': 'biolink:has_attribute_type'}}), 'has_qualitative_value': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='connects an attribute to a value', json_schema_extra={'linkml_meta': {'alias': 'has_qualitative_value', 'definition_uri': 'https://w3id.org/biolink/vocab/has_qualitative_value', 'domain': 'attribute', 'domain_of': ['attribute'], 'in_subset': ['samples'], 'slot_uri': 'biolink:has_qualitative_value'}}), 'has_quantitative_value': FieldInfo(annotation=Union[List[QuantityValue], NoneType], required=False, default=None, description='connects an attribute to a value', json_schema_extra={'linkml_meta': {'alias': 'has_quantitative_value', 'definition_uri': 'https://w3id.org/biolink/vocab/has_quantitative_value', 'domain': 'attribute', 'domain_of': ['attribute'], 'exact_mappings': ['qud:quantityValue'], 'in_subset': ['samples'], 'narrow_mappings': ['SNOMED:has_concentration_strength_numerator_value', 'SNOMED:has_presentation_strength_denominator_value', 'SNOMED:has_presentation_strength_numerator_value'], 'slot_uri': 'biolink:has_quantitative_value'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, 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.", json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/BiologicalEntity', 'biolink:BiologicalEntity']], required=False, default=['biolink:BiologicalEntity'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'in_taxon': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description="connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", json_schema_extra={'linkml_meta': {'alias': 'in_taxon', 'aliases': ['instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source'], 'annotations': {'canonical_predicate': {'tag': 'canonical_predicate', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['RO:0002162', 'WIKIDATA_PROPERTY:P703'], 'in_subset': ['translator_minimal'], 'inherited': True, 'is_a': 'related to at instance level', 'narrow_mappings': ['RO:0002160'], 'slot_uri': 'biolink:in_taxon'}}), 'in_taxon_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The human readable scientific name for the taxon of the entity.', json_schema_extra={'linkml_meta': {'alias': 'in_taxon_label', 'annotations': {'denormalized': {'tag': 'denormalized', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon_label', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P225'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'slot_uri': 'biolink:in_taxon_label'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://identifiers.org/brain-bican/vocab/Checksum', 'bican:Checksum']], required=False, default=['bican:Checksum'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'checksum_algorithm': FieldInfo(annotation=Union[DigestType, NoneType], required=False, default=None, description='The type of cryptographic hash function used to calculate the checksum value.', json_schema_extra={'linkml_meta': {'alias': 'checksum_algorithm', 'domain_of': ['checksum']}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'value': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The checksum value obtained from a specific cryotographic hash function.', json_schema_extra={'linkml_meta': {'alias': 'value', 'domain_of': ['checksum']}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/Dataset', 'biolink:Dataset']], required=False, default=['biolink:Dataset'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'creation_date': FieldInfo(annotation=Union[date, NoneType], required=False, default=None, description='date on which an entity was created. This can be applied to nodes or edges', json_schema_extra={'linkml_meta': {'alias': 'creation_date', 'aliases': ['publication date'], 'definition_uri': 'https://w3id.org/biolink/vocab/creation_date', 'domain': 'named thing', 'domain_of': ['information content entity', 'dataset'], 'exact_mappings': ['dct:createdOn', 'WIKIDATA_PROPERTY:P577'], 'is_a': 'node property', 'slot_uri': 'biolink:creation_date'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'format': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'format', 'definition_uri': 'https://w3id.org/biolink/vocab/format', 'domain': 'information content entity', 'domain_of': ['information content entity', 'dataset'], 'exact_mappings': ['dct:format', 'WIKIDATA_PROPERTY:P2701'], 'is_a': 'node property', 'slot_uri': 'biolink:format'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'license': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'license', 'definition_uri': 'https://w3id.org/biolink/vocab/license', 'domain': 'information content entity', 'domain_of': ['information content entity', 'dataset'], 'exact_mappings': ['dct:license'], 'is_a': 'node property', 'narrow_mappings': ['WIKIDATA_PROPERTY:P275'], 'slot_uri': 'biolink:license'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'rights': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'rights', 'definition_uri': 'https://w3id.org/biolink/vocab/rights', 'domain': 'information content entity', 'domain_of': ['information content entity', 'dataset'], 'exact_mappings': ['dct:rights'], 'is_a': 'node property', 'slot_uri': 'biolink:rights'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/Entity', 'biolink:Entity']], required=False, default=['biolink:Entity'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/Gene', 'biolink:Gene']], required=False, default=['biolink:Gene'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'has_biological_sequence': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='connects a genomic feature to its sequence', json_schema_extra={'linkml_meta': {'alias': 'has_biological_sequence', 'definition_uri': 'https://w3id.org/biolink/vocab/has_biological_sequence', 'domain': 'named thing', 'domain_of': ['genomic entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:has_biological_sequence'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'in_taxon': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description="connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", json_schema_extra={'linkml_meta': {'alias': 'in_taxon', 'aliases': ['instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source'], 'annotations': {'canonical_predicate': {'tag': 'canonical_predicate', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['RO:0002162', 'WIKIDATA_PROPERTY:P703'], 'in_subset': ['translator_minimal'], 'inherited': True, 'is_a': 'related to at instance level', 'narrow_mappings': ['RO:0002160'], 'slot_uri': 'biolink:in_taxon'}}), 'in_taxon_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The human readable scientific name for the taxon of the entity.', json_schema_extra={'linkml_meta': {'alias': 'in_taxon_label', 'annotations': {'denormalized': {'tag': 'denormalized', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon_label', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P225'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'slot_uri': 'biolink:in_taxon_label'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'symbol': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='Symbol for a particular thing', json_schema_extra={'linkml_meta': {'alias': 'symbol', 'definition_uri': 'https://w3id.org/biolink/vocab/symbol', 'domain': 'named thing', 'domain_of': ['gene'], 'exact_mappings': ['AGRKB:symbol', 'gpi:DB_Object_Symbol'], 'is_a': 'node property', 'slot_uri': 'biolink:symbol'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://identifiers.org/brain-bican/vocab/GeneAnnotation', 'bican:GeneAnnotation']], required=False, default=['bican:GeneAnnotation'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'has_biological_sequence': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='connects a genomic feature to its sequence', json_schema_extra={'linkml_meta': {'alias': 'has_biological_sequence', 'definition_uri': 'https://w3id.org/biolink/vocab/has_biological_sequence', 'domain': 'named thing', 'domain_of': ['genomic entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:has_biological_sequence'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'in_taxon': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description="connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", json_schema_extra={'linkml_meta': {'alias': 'in_taxon', 'aliases': ['instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source'], 'annotations': {'canonical_predicate': {'tag': 'canonical_predicate', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['RO:0002162', 'WIKIDATA_PROPERTY:P703'], 'in_subset': ['translator_minimal'], 'inherited': True, 'is_a': 'related to at instance level', 'narrow_mappings': ['RO:0002160'], 'slot_uri': 'biolink:in_taxon'}}), 'in_taxon_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The human readable scientific name for the taxon of the entity.', json_schema_extra={'linkml_meta': {'alias': 'in_taxon_label', 'annotations': {'denormalized': {'tag': 'denormalized', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon_label', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P225'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'slot_uri': 'biolink:in_taxon_label'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'molecular_type': FieldInfo(annotation=Union[BioType, str, NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'molecular_type', 'any_of': [{'range': 'BioType'}, {'range': 'string'}], 'domain_of': ['gene annotation']}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'referenced_in': FieldInfo(annotation=Union[GenomeAnnotation, str], required=True, description='The genome annotation that this gene annotation was referenced from.', json_schema_extra={'linkml_meta': {'alias': 'referenced_in', 'any_of': [{'range': 'genome annotation'}, {'range': 'string'}], 'domain_of': ['gene annotation']}}), 'source_id': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The authority specific identifier.', json_schema_extra={'linkml_meta': {'alias': 'source_id', 'domain_of': ['gene annotation'], 'slot_uri': 'schema:identifier'}}), 'symbol': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='Symbol for a particular thing', json_schema_extra={'linkml_meta': {'alias': 'symbol', 'definition_uri': 'https://w3id.org/biolink/vocab/symbol', 'domain': 'named thing', 'domain_of': ['gene'], 'exact_mappings': ['AGRKB:symbol', 'gpi:DB_Object_Symbol'], 'is_a': 'node property', 'slot_uri': 'biolink:symbol'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/Genome', 'biolink:Genome']], required=False, default=['biolink:Genome'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'has_biological_sequence': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='connects a genomic feature to its sequence', json_schema_extra={'linkml_meta': {'alias': 'has_biological_sequence', 'definition_uri': 'https://w3id.org/biolink/vocab/has_biological_sequence', 'domain': 'named thing', 'domain_of': ['genomic entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:has_biological_sequence'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'in_taxon': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description="connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", json_schema_extra={'linkml_meta': {'alias': 'in_taxon', 'aliases': ['instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source'], 'annotations': {'canonical_predicate': {'tag': 'canonical_predicate', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['RO:0002162', 'WIKIDATA_PROPERTY:P703'], 'in_subset': ['translator_minimal'], 'inherited': True, 'is_a': 'related to at instance level', 'narrow_mappings': ['RO:0002160'], 'slot_uri': 'biolink:in_taxon'}}), 'in_taxon_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The human readable scientific name for the taxon of the entity.', json_schema_extra={'linkml_meta': {'alias': 'in_taxon_label', 'annotations': {'denormalized': {'tag': 'denormalized', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon_label', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P225'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'slot_uri': 'biolink:in_taxon_label'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'authority': FieldInfo(annotation=Union[AuthorityType, NoneType], required=False, default=None, description='The organization responsible for publishing the data.', json_schema_extra={'linkml_meta': {'alias': 'authority', 'domain_of': ['genome annotation']}}), 'category': FieldInfo(annotation=List[Literal['https://identifiers.org/brain-bican/vocab/GenomeAnnotation', 'bican:GenomeAnnotation']], required=False, default=['bican:GenomeAnnotation'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'content_url': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'content_url', 'domain_of': ['genome annotation'], 'slot_uri': 'schema:url'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'digest': FieldInfo(annotation=Union[List[Union[Checksum, str]], NoneType], required=False, default=None, description='Stores checksum information.', json_schema_extra={'linkml_meta': {'alias': 'digest', 'any_of': [{'range': 'checksum'}, {'range': 'string'}], 'domain_of': ['genome annotation']}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'has_biological_sequence': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='connects a genomic feature to its sequence', json_schema_extra={'linkml_meta': {'alias': 'has_biological_sequence', 'definition_uri': 'https://w3id.org/biolink/vocab/has_biological_sequence', 'domain': 'named thing', 'domain_of': ['genomic entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:has_biological_sequence'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'in_taxon': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description="connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", json_schema_extra={'linkml_meta': {'alias': 'in_taxon', 'aliases': ['instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source'], 'annotations': {'canonical_predicate': {'tag': 'canonical_predicate', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['RO:0002162', 'WIKIDATA_PROPERTY:P703'], 'in_subset': ['translator_minimal'], 'inherited': True, 'is_a': 'related to at instance level', 'narrow_mappings': ['RO:0002160'], 'slot_uri': 'biolink:in_taxon'}}), 'in_taxon_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The human readable scientific name for the taxon of the entity.', json_schema_extra={'linkml_meta': {'alias': 'in_taxon_label', 'annotations': {'denormalized': {'tag': 'denormalized', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon_label', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P225'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'slot_uri': 'biolink:in_taxon_label'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'reference_assembly': FieldInfo(annotation=Union[GenomeAssembly, str], required=True, description='The reference genome assembly that this genome annotation was created from.', json_schema_extra={'linkml_meta': {'alias': 'reference_assembly', 'any_of': [{'range': 'genome assembly'}, {'range': 'string'}], 'domain_of': ['genome annotation']}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'version': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'version', 'broad_mappings': ['pav:version', 'owl:versionInfo'], 'definition_uri': 'https://w3id.org/biolink/vocab/version', 'domain': 'dataset', 'domain_of': ['genome annotation', 'genome assembly'], 'is_a': 'node property', 'slot_uri': 'biolink:version'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://identifiers.org/brain-bican/vocab/GenomeAssembly', 'bican:GenomeAssembly']], required=False, default=['bican:GenomeAssembly'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'in_taxon': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description="connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", json_schema_extra={'linkml_meta': {'alias': 'in_taxon', 'aliases': ['instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source'], 'annotations': {'canonical_predicate': {'tag': 'canonical_predicate', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['RO:0002162', 'WIKIDATA_PROPERTY:P703'], 'in_subset': ['translator_minimal'], 'inherited': True, 'is_a': 'related to at instance level', 'narrow_mappings': ['RO:0002160'], 'slot_uri': 'biolink:in_taxon'}}), 'in_taxon_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The human readable scientific name for the taxon of the entity.', json_schema_extra={'linkml_meta': {'alias': 'in_taxon_label', 'annotations': {'denormalized': {'tag': 'denormalized', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon_label', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P225'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'slot_uri': 'biolink:in_taxon_label'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'strain': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The genetic variant or subtype of a species or organism.', json_schema_extra={'linkml_meta': {'alias': 'strain', 'domain_of': ['genome assembly']}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'version': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'version', 'broad_mappings': ['pav:version', 'owl:versionInfo'], 'definition_uri': 'https://w3id.org/biolink/vocab/version', 'domain': 'dataset', 'domain_of': ['genome annotation', 'genome assembly'], 'is_a': 'node property', 'slot_uri': 'biolink:version'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'has_biological_sequence': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='connects a genomic feature to its sequence', json_schema_extra={'linkml_meta': {'alias': 'has_biological_sequence', 'definition_uri': 'https://w3id.org/biolink/vocab/has_biological_sequence', 'domain': 'named thing', 'domain_of': ['genomic entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:has_biological_sequence'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/InformationContentEntity', 'biolink:InformationContentEntity']], required=False, default=['biolink:InformationContentEntity'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'creation_date': FieldInfo(annotation=Union[date, NoneType], required=False, default=None, description='date on which an entity was created. This can be applied to nodes or edges', json_schema_extra={'linkml_meta': {'alias': 'creation_date', 'aliases': ['publication date'], 'definition_uri': 'https://w3id.org/biolink/vocab/creation_date', 'domain': 'named thing', 'domain_of': ['information content entity', 'dataset'], 'exact_mappings': ['dct:createdOn', 'WIKIDATA_PROPERTY:P577'], 'is_a': 'node property', 'slot_uri': 'biolink:creation_date'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'format': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'format', 'definition_uri': 'https://w3id.org/biolink/vocab/format', 'domain': 'information content entity', 'domain_of': ['information content entity', 'dataset'], 'exact_mappings': ['dct:format', 'WIKIDATA_PROPERTY:P2701'], 'is_a': 'node property', 'slot_uri': 'biolink:format'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'license': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'license', 'definition_uri': 'https://w3id.org/biolink/vocab/license', 'domain': 'information content entity', 'domain_of': ['information content entity', 'dataset'], 'exact_mappings': ['dct:license'], 'is_a': 'node property', 'narrow_mappings': ['WIKIDATA_PROPERTY:P275'], 'slot_uri': 'biolink:license'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'rights': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'rights', 'definition_uri': 'https://w3id.org/biolink/vocab/rights', 'domain': 'information content entity', 'domain_of': ['information content entity', 'dataset'], 'exact_mappings': ['dct:rights'], 'is_a': 'node property', 'slot_uri': 'biolink:rights'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'root': FieldInfo(annotation=Dict[str, Any], required=False, default={})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/MaterialSample', 'biolink:MaterialSample']], required=False, default=['biolink:MaterialSample'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/NamedThing', 'biolink:NamedThing']], required=False, default=['biolink:NamedThing'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/OrganismTaxon', 'biolink:OrganismTaxon']], required=False, default=['biolink:OrganismTaxon'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'has_taxonomic_rank': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'has_taxonomic_rank', 'definition_uri': 'https://w3id.org/biolink/vocab/has_taxonomic_rank', 'domain': 'named thing', 'domain_of': ['organism taxon'], 'is_a': 'node property', 'mappings': ['WIKIDATA:P105'], 'slot_uri': 'biolink:has_taxonomic_rank'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/PhysicalEntity', 'biolink:PhysicalEntity']], required=False, default=['biolink:PhysicalEntity'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'category': FieldInfo(annotation=List[Literal['https://w3id.org/biolink/vocab/Procedure', 'biolink:Procedure']], required=False, default=['biolink:Procedure'], description='Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}', json_schema_extra={'linkml_meta': {'alias': 'category', 'definition_uri': 'https://w3id.org/biolink/vocab/category', 'designates_type': True, 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'type', 'is_class_field': True, 'slot_uri': 'biolink:category'}}), 'deprecated': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None, description='A boolean flag indicating that an entity is no longer considered current or valid.', json_schema_extra={'linkml_meta': {'alias': 'deprecated', 'definition_uri': 'https://w3id.org/biolink/vocab/deprecated', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['oboInOwl:ObsoleteClass'], 'slot_uri': 'biolink:deprecated'}}), 'description': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a human-readable description of an entity', json_schema_extra={'linkml_meta': {'alias': 'description', 'aliases': ['definition'], 'definition_uri': 'https://w3id.org/biolink/vocab/description', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['IAO:0000115', 'skos:definitions'], 'in_subset': ['translator_minimal'], 'mappings': ['dct:description'], 'narrow_mappings': ['gff3:Description'], 'slot_uri': 'dct:description'}}), 'full_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='a long-form human readable name for a thing', json_schema_extra={'linkml_meta': {'alias': 'full_name', 'definition_uri': 'https://w3id.org/biolink/vocab/full_name', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:full_name'}}), 'has_attribute': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='connects any entity to an attribute', json_schema_extra={'linkml_meta': {'alias': 'has_attribute', 'close_mappings': ['OBI:0001927'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_attribute', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['SIO:000008'], 'in_subset': ['samples'], 'narrow_mappings': ['OBAN:association_has_subject_property', 'OBAN:association_has_object_property', 'CPT:has_possibly_included_panel_element', 'DRUGBANK:category', 'EFO:is_executed_in', 'HANCESTRO:0301', 'LOINC:has_action_guidance', 'LOINC:has_adjustment', 'LOINC:has_aggregation_view', 'LOINC:has_approach_guidance', 'LOINC:has_divisor', 'LOINC:has_exam', 'LOINC:has_method', 'LOINC:has_modality_subtype', 'LOINC:has_object_guidance', 'LOINC:has_scale', 'LOINC:has_suffix', 'LOINC:has_time_aspect', 'LOINC:has_time_modifier', 'LOINC:has_timing_of', 'NCIT:R88', 'NCIT:eo_disease_has_property_or_attribute', 'NCIT:has_data_element', 'NCIT:has_pharmaceutical_administration_method', 'NCIT:has_pharmaceutical_basic_dose_form', 'NCIT:has_pharmaceutical_intended_site', 'NCIT:has_pharmaceutical_release_characteristics', 'NCIT:has_pharmaceutical_state_of_matter', 'NCIT:has_pharmaceutical_transformation', 'NCIT:is_qualified_by', 'NCIT:qualifier_applies_to', 'NCIT:role_has_domain', 'NCIT:role_has_range', 'INO:0000154', 'HANCESTRO:0308', 'OMIM:has_inheritance_type', 'orphanet:C016', 'orphanet:C017', 'RO:0000053', 'RO:0000086', 'RO:0000087', 'SNOMED:has_access', 'SNOMED:has_clinical_course', 'SNOMED:has_count_of_base_of_active_ingredient', 'SNOMED:has_dose_form_administration_method', 'SNOMED:has_dose_form_release_characteristic', 'SNOMED:has_dose_form_transformation', 'SNOMED:has_finding_context', 'SNOMED:has_finding_informer', 'SNOMED:has_inherent_attribute', 'SNOMED:has_intent', 'SNOMED:has_interpretation', 'SNOMED:has_laterality', 'SNOMED:has_measurement_method', 'SNOMED:has_method', 'SNOMED:has_priority', 'SNOMED:has_procedure_context', 'SNOMED:has_process_duration', 'SNOMED:has_property', 'SNOMED:has_revision_status', 'SNOMED:has_scale_type', 'SNOMED:has_severity', 'SNOMED:has_specimen', 'SNOMED:has_state_of_matter', 'SNOMED:has_subject_relationship_context', 'SNOMED:has_surgical_approach', 'SNOMED:has_technique', 'SNOMED:has_temporal_context', 'SNOMED:has_time_aspect', 'SNOMED:has_units', 'UMLS:has_structural_class', 'UMLS:has_supported_concept_property', 'UMLS:has_supported_concept_relationship', 'UMLS:may_be_qualified_by'], 'slot_uri': 'biolink:has_attribute'}}), 'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}}), 'iri': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='An IRI for an entity. This is determined by the id using expansion rules.', json_schema_extra={'linkml_meta': {'alias': 'iri', 'definition_uri': 'https://w3id.org/biolink/vocab/iri', 'domain_of': ['attribute', 'entity', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P854'], 'in_subset': ['translator_minimal', 'samples'], 'slot_uri': 'biolink:iri'}}), 'name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A human-readable name for an attribute or entity.', json_schema_extra={'linkml_meta': {'alias': 'name', 'aliases': ['label', 'display name', 'title'], 'definition_uri': 'https://w3id.org/biolink/vocab/name', 'domain': 'entity', 'domain_of': ['attribute', 'entity', 'macromolecular machine mixin', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene or gene product', 'gene', 'genome'], 'exact_mappings': ['gff3:Name', 'gpi:DB_Object_Name'], 'in_subset': ['translator_minimal', 'samples'], 'mappings': ['rdfs:label'], 'narrow_mappings': ['dct:title', 'WIKIDATA_PROPERTY:P1476'], 'slot_uri': 'rdfs:label'}}), 'provided_by': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.', json_schema_extra={'linkml_meta': {'alias': 'provided_by', 'definition_uri': 'https://w3id.org/biolink/vocab/provided_by', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'is_a': 'node property', 'slot_uri': 'biolink:provided_by'}}), 'synonym': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='Alternate human-readable names for a thing', json_schema_extra={'linkml_meta': {'alias': 'synonym', 'aliases': ['alias'], 'definition_uri': 'https://w3id.org/biolink/vocab/synonym', 'domain': 'named thing', 'domain_of': ['named thing', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'narrow_mappings': ['skos:altLabel', 'gff3:Alias', 'AGRKB:synonyms', 'gpi:DB_Object_Synonyms', 'HANCESTRO:0330', 'IAO:0000136', 'RXNORM:has_tradename'], 'slot_uri': 'biolink:synonym'}}), 'type': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, json_schema_extra={'linkml_meta': {'alias': 'type', 'definition_uri': 'https://w3id.org/biolink/vocab/type', 'domain': 'entity', 'domain_of': ['entity', 'attribute', 'named thing', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['gff3:type', 'gpi:DB_Object_Type'], 'mappings': ['rdf:type'], 'slot_uri': 'rdf:type'}}), 'xref': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description='A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.', json_schema_extra={'linkml_meta': {'alias': 'xref', 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'], 'definition_uri': 'https://w3id.org/biolink/vocab/xref', 'domain': 'named thing', 'domain_of': ['named thing', 'gene', 'attribute', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'genome'], 'in_subset': ['translator_minimal'], 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'], 'slot_uri': 'biolink:xref'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'has_numeric_value': FieldInfo(annotation=Union[float, NoneType], required=False, default=None, description='connects a quantity value to a number', json_schema_extra={'linkml_meta': {'alias': 'has_numeric_value', 'definition_uri': 'https://w3id.org/biolink/vocab/has_numeric_value', 'domain': 'quantity value', 'domain_of': ['quantity value'], 'exact_mappings': ['qud:quantityValue'], 'in_subset': ['samples'], 'slot_uri': 'biolink:has_numeric_value'}}), 'has_unit': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='connects a quantity value to a unit', json_schema_extra={'linkml_meta': {'alias': 'has_unit', 'close_mappings': ['EFO:0001697', 'UO-PROPERTY:is_unit_of'], 'definition_uri': 'https://w3id.org/biolink/vocab/has_unit', 'domain': 'quantity value', 'domain_of': ['quantity value'], 'exact_mappings': ['qud:unit', 'IAO:0000039'], 'in_subset': ['samples'], 'narrow_mappings': ['SNOMED:has_concentration_strength_denominator_unit', 'SNOMED:has_concentration_strength_numerator_unit', 'SNOMED:has_presentation_strength_denominator_unit', 'SNOMED:has_presentation_strength_numerator_unit', 'SNOMED:has_unit_of_presentation'], 'slot_uri': 'biolink:has_unit'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'id': FieldInfo(annotation=str, required=True, description='A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI', json_schema_extra={'linkml_meta': {'alias': 'id', 'definition_uri': 'https://w3id.org/biolink/vocab/id', 'domain': 'entity', 'domain_of': ['ontology class', 'entity', 'attribute', 'named thing', 'taxonomic rank', 'organism taxon', 'information content entity', 'dataset', 'physical entity', 'activity', 'procedure', 'material sample', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['AGRKB:primaryId', 'gff3:ID', 'gpi:DB_Object_ID'], 'in_subset': ['translator_minimal'], 'slot_uri': 'biolink:id'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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].

model_fields: ClassVar[Dict[str, FieldInfo]] = {'in_taxon': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None, description="connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", json_schema_extra={'linkml_meta': {'alias': 'in_taxon', 'aliases': ['instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source'], 'annotations': {'canonical_predicate': {'tag': 'canonical_predicate', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['RO:0002162', 'WIKIDATA_PROPERTY:P703'], 'in_subset': ['translator_minimal'], 'inherited': True, 'is_a': 'related to at instance level', 'narrow_mappings': ['RO:0002160'], 'slot_uri': 'biolink:in_taxon'}}), 'in_taxon_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='The human readable scientific name for the taxon of the entity.', json_schema_extra={'linkml_meta': {'alias': 'in_taxon_label', 'annotations': {'denormalized': {'tag': 'denormalized', 'value': True}}, 'definition_uri': 'https://w3id.org/biolink/vocab/in_taxon_label', 'domain': 'thing with taxon', 'domain_of': ['thing with taxon', 'biological entity', 'gene', 'genome'], 'exact_mappings': ['WIKIDATA_PROPERTY:P225'], 'in_subset': ['translator_minimal'], 'is_a': 'node property', 'slot_uri': 'biolink:in_taxon_label'}})}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.