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Add template for MIRO checklist extraction
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,294 @@ | ||
| from __future__ import annotations | ||
| from datetime import ( | ||
| datetime, | ||
| date | ||
| ) | ||
| from decimal import Decimal | ||
| from enum import Enum | ||
| import re | ||
| import sys | ||
| from typing import ( | ||
| Any, | ||
| ClassVar, | ||
| List, | ||
| Literal, | ||
| Dict, | ||
| Optional, | ||
| Union | ||
| ) | ||
| from pydantic.version import VERSION as PYDANTIC_VERSION | ||
| if int(PYDANTIC_VERSION[0])>=2: | ||
| from pydantic import ( | ||
| BaseModel, | ||
| ConfigDict, | ||
| Field, | ||
| RootModel, | ||
| field_validator | ||
| ) | ||
| else: | ||
| from pydantic import ( | ||
| BaseModel, | ||
| Field, | ||
| validator | ||
| ) | ||
|
|
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| metamodel_version = "None" | ||
| version = "None" | ||
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|
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| class ConfiguredBaseModel(BaseModel): | ||
| model_config = ConfigDict( | ||
| validate_assignment = True, | ||
| validate_default = True, | ||
| extra = "forbid", | ||
| arbitrary_types_allowed = True, | ||
| use_enum_values = True, | ||
| strict = False, | ||
| ) | ||
| pass | ||
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| class LinkMLMeta(RootModel): | ||
| root: Dict[str, Any] = {} | ||
| model_config = ConfigDict(frozen=True) | ||
|
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| def __getattr__(self, key:str): | ||
| return getattr(self.root, key) | ||
|
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| def __getitem__(self, key:str): | ||
| return self.root[key] | ||
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| def __setitem__(self, key:str, value): | ||
| self.root[key] = value | ||
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| def __contains__(self, key:str) -> bool: | ||
| return key in self.root | ||
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| linkml_meta = LinkMLMeta({'default_prefix': 'miro', | ||
| 'default_range': 'string', | ||
| 'description': 'A template for extracting the minimal information for ' | ||
| 'reporting an ontology, as per the MIRO guidelines. See ' | ||
| 'doi:10.1186/s13326-017-0172-7 The target for this template ' | ||
| 'should be a report or publication describing a single ' | ||
| 'ontology.', | ||
| 'id': 'http://w3id.org/ontogpt/miro', | ||
| 'imports': ['linkml:types', 'core'], | ||
| 'license': 'https://creativecommons.org/publicdomain/zero/1.0/', | ||
| 'name': 'miro', | ||
| 'prefixes': {'linkml': {'prefix_prefix': 'linkml', | ||
| 'prefix_reference': 'https://w3id.org/linkml/'}, | ||
| 'onto_usage': {'prefix_prefix': 'onto_usage', | ||
| 'prefix_reference': 'http://w3id.org/ontogpt/onto_usage'}, | ||
| 'rdf': {'prefix_prefix': 'rdf', | ||
| 'prefix_reference': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'}}, | ||
| 'source_file': 'src/ontogpt/templates/miro.yaml', | ||
| 'title': 'MIRO Extraction Template'} ) | ||
|
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| class NullDataOptions(str, Enum): | ||
| UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" | ||
| NOT_APPLICABLE = "NOT_APPLICABLE" | ||
| NOT_MENTIONED = "NOT_MENTIONED" | ||
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| class ExtractionResult(ConfiguredBaseModel): | ||
| """ | ||
| A result of extracting knowledge on text | ||
| """ | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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| input_id: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_id', 'domain_of': ['ExtractionResult']} }) | ||
| input_title: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_title', 'domain_of': ['ExtractionResult']} }) | ||
| input_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_text', 'domain_of': ['ExtractionResult']} }) | ||
| raw_completion_output: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'raw_completion_output', 'domain_of': ['ExtractionResult']} }) | ||
| prompt: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'prompt', 'domain_of': ['ExtractionResult']} }) | ||
| extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""", json_schema_extra = { "linkml_meta": {'alias': 'extracted_object', 'domain_of': ['ExtractionResult']} }) | ||
| named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""", json_schema_extra = { "linkml_meta": {'alias': 'named_entities', 'domain_of': ['ExtractionResult']} }) | ||
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| class NamedEntity(ConfiguredBaseModel): | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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| id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', | ||
| 'comments': ['this is populated during the grounding and normalization step'], | ||
| 'domain_of': ['NamedEntity', 'Publication']} }) | ||
| label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', | ||
| 'aliases': ['name'], | ||
| 'domain_of': ['NamedEntity'], | ||
| 'slot_uri': 'rdfs:label'} }) | ||
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| class CompoundExpression(ConfiguredBaseModel): | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
|
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| pass | ||
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| class Triple(CompoundExpression): | ||
| """ | ||
| Abstract parent for Relation Extraction tasks | ||
| """ | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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| subject: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'subject', 'domain_of': ['Triple']} }) | ||
| predicate: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'predicate', 'domain_of': ['Triple']} }) | ||
| object: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object', 'domain_of': ['Triple']} }) | ||
| qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""", json_schema_extra = { "linkml_meta": {'alias': 'qualifier', 'domain_of': ['Triple']} }) | ||
| subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""", json_schema_extra = { "linkml_meta": {'alias': 'subject_qualifier', 'domain_of': ['Triple']} }) | ||
| object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""", json_schema_extra = { "linkml_meta": {'alias': 'object_qualifier', 'domain_of': ['Triple']} }) | ||
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| class TextWithTriples(ConfiguredBaseModel): | ||
| """ | ||
| A text containing one or more relations of the Triple type. | ||
| """ | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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| publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication', 'domain_of': ['TextWithTriples', 'TextWithEntity']} }) | ||
| triples: Optional[List[Triple]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'triples', 'domain_of': ['TextWithTriples']} }) | ||
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| class TextWithEntity(ConfiguredBaseModel): | ||
| """ | ||
| A text containing one or more instances of a single type of entity. | ||
| """ | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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| publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication', 'domain_of': ['TextWithTriples', 'TextWithEntity']} }) | ||
| entities: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'entities', 'domain_of': ['TextWithEntity']} }) | ||
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| class RelationshipType(NamedEntity): | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core', | ||
| 'id_prefixes': ['RO', 'biolink']}) | ||
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| id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', | ||
| 'comments': ['this is populated during the grounding and normalization step'], | ||
| 'domain_of': ['NamedEntity', 'Publication']} }) | ||
| label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', | ||
| 'aliases': ['name'], | ||
| 'domain_of': ['NamedEntity'], | ||
| 'slot_uri': 'rdfs:label'} }) | ||
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| class Publication(ConfiguredBaseModel): | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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| id: Optional[str] = Field(None, description="""The publication identifier""", json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['NamedEntity', 'Publication']} }) | ||
| title: Optional[str] = Field(None, description="""The title of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'title', 'domain_of': ['Publication']} }) | ||
| abstract: Optional[str] = Field(None, description="""The abstract of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'abstract', 'domain_of': ['Publication']} }) | ||
| combined_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'combined_text', 'domain_of': ['Publication']} }) | ||
| full_text: Optional[str] = Field(None, description="""The full text of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'full_text', 'domain_of': ['Publication']} }) | ||
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| class AnnotatorResult(ConfiguredBaseModel): | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) | ||
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| subject_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'subject_text', 'domain_of': ['AnnotatorResult']} }) | ||
| object_id: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object_id', 'domain_of': ['AnnotatorResult']} }) | ||
| object_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object_text', 'domain_of': ['AnnotatorResult']} }) | ||
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| class Ontology(NamedEntity): | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/miro', 'tree_root': True}) | ||
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| name: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['Ontology', 'Owner', 'CitedOntology']} }) | ||
| owners: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'owners', 'domain_of': ['Ontology']} }) | ||
| license: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'license', 'domain_of': ['Ontology']} }) | ||
| url: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'url', 'domain_of': ['Ontology']} }) | ||
| repository: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'repository', 'domain_of': ['Ontology']} }) | ||
| methodological_framework: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'methodological_framework', 'domain_of': ['Ontology']} }) | ||
| need: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'need', 'domain_of': ['Ontology']} }) | ||
| competition: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'competition', 'domain_of': ['Ontology']} }) | ||
| target_audience: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'target_audience', 'domain_of': ['Ontology']} }) | ||
| scope_and_coverage: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'scope_and_coverage', 'domain_of': ['Ontology']} }) | ||
| development_community: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'development_community', 'domain_of': ['Ontology']} }) | ||
| communication: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'communication', 'domain_of': ['Ontology']} }) | ||
| knowledge_acquisition_method: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'knowledge_acquisition_method', 'domain_of': ['Ontology']} }) | ||
| source_knowledge_location: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'source_knowledge_location', 'domain_of': ['Ontology']} }) | ||
| content_selection: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'content_selection', 'domain_of': ['Ontology']} }) | ||
| knowledge_representation_language: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'knowledge_representation_language', 'domain_of': ['Ontology']} }) | ||
| development_environment: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'development_environment', 'domain_of': ['Ontology']} }) | ||
| ontology_metrics: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'ontology_metrics', 'domain_of': ['Ontology']} }) | ||
| incorporation_of_ontologies: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'incorporation_of_ontologies', 'domain_of': ['Ontology']} }) | ||
| entity_naming_convention: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'entity_naming_convention', 'domain_of': ['Ontology']} }) | ||
| identifier_generation_policy: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'identifier_generation_policy', 'domain_of': ['Ontology']} }) | ||
| entity_metadata_policy: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'entity_metadata_policy', 'domain_of': ['Ontology']} }) | ||
| upper_ontology: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'upper_ontology', 'domain_of': ['Ontology']} }) | ||
| ontology_relationships: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'ontology_relationships', 'domain_of': ['Ontology']} }) | ||
| axiom_patterns: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'axiom_patterns', 'domain_of': ['Ontology']} }) | ||
| dereferencable_iri: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'dereferencable_iri', 'domain_of': ['Ontology']} }) | ||
| sustainability_plan: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'sustainability_plan', 'domain_of': ['Ontology']} }) | ||
| deprecation_strategy: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'deprecation_strategy', 'domain_of': ['Ontology']} }) | ||
| versioning_policy: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'versioning_policy', 'domain_of': ['Ontology']} }) | ||
| testing: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'testing', 'domain_of': ['Ontology']} }) | ||
| evaluation: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evaluation', 'domain_of': ['Ontology']} }) | ||
| examples_of_use: Optional[List[UseExample]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'examples_of_use', 'domain_of': ['Ontology']} }) | ||
| institutional_endorsement: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'institutional_endorsement', 'domain_of': ['Ontology']} }) | ||
| evidence_of_use: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence_of_use', 'domain_of': ['Ontology']} }) | ||
| id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', | ||
| 'comments': ['this is populated during the grounding and normalization step'], | ||
| 'domain_of': ['NamedEntity', 'Publication']} }) | ||
| label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', | ||
| 'aliases': ['name'], | ||
| 'domain_of': ['NamedEntity'], | ||
| 'slot_uri': 'rdfs:label'} }) | ||
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| class Owner(NamedEntity): | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'owl': {'tag': 'owl', 'value': 'IntersectionOf'}}, | ||
| 'from_schema': 'http://w3id.org/ontogpt/miro'}) | ||
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| name: Optional[str] = Field(None, description="""The name of a person, group of people, organization, or consortium that manages development of the ontology.""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['Ontology', 'Owner', 'CitedOntology']} }) | ||
| affiliation: Optional[str] = Field(None, description="""The name of the organization with which the owner is affiliated.""", json_schema_extra = { "linkml_meta": {'alias': 'affiliation', 'domain_of': ['Owner']} }) | ||
| contact: Optional[str] = Field(None, description="""The contact details of the owner. This is typically an email address.""", json_schema_extra = { "linkml_meta": {'alias': 'contact', 'domain_of': ['Owner']} }) | ||
| id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', | ||
| 'comments': ['this is populated during the grounding and normalization step'], | ||
| 'domain_of': ['NamedEntity', 'Publication']} }) | ||
| label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', | ||
| 'aliases': ['name'], | ||
| 'domain_of': ['NamedEntity'], | ||
| 'slot_uri': 'rdfs:label'} }) | ||
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| class CitedOntology(NamedEntity): | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/miro'}) | ||
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| name: Optional[str] = Field(None, description="""The name of the ontology being cited.""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['Ontology', 'Owner', 'CitedOntology']} }) | ||
| version: Optional[str] = Field(None, description="""The version of the ontology being cited.""", json_schema_extra = { "linkml_meta": {'alias': 'version', 'domain_of': ['CitedOntology']} }) | ||
| citation: Optional[str] = Field(None, description="""The citation for the ontology being cited.""", json_schema_extra = { "linkml_meta": {'alias': 'citation', 'domain_of': ['CitedOntology']} }) | ||
| integration: Optional[str] = Field(None, description="""A description of how the ontology being cited is integrated into the ontology being reported.""", json_schema_extra = { "linkml_meta": {'alias': 'integration', 'domain_of': ['CitedOntology']} }) | ||
| id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', | ||
| 'comments': ['this is populated during the grounding and normalization step'], | ||
| 'domain_of': ['NamedEntity', 'Publication']} }) | ||
| label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', | ||
| 'aliases': ['name'], | ||
| 'domain_of': ['NamedEntity'], | ||
| 'slot_uri': 'rdfs:label'} }) | ||
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| class UseExample(ConfiguredBaseModel): | ||
| linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/miro'}) | ||
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| example_description: Optional[str] = Field(None, description="""A description of the ontology in use in its application setting or use case.""", json_schema_extra = { "linkml_meta": {'alias': 'example_description', 'domain_of': ['UseExample']} }) | ||
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| # Model rebuild | ||
| # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model | ||
| ExtractionResult.model_rebuild() | ||
| NamedEntity.model_rebuild() | ||
| CompoundExpression.model_rebuild() | ||
| Triple.model_rebuild() | ||
| TextWithTriples.model_rebuild() | ||
| TextWithEntity.model_rebuild() | ||
| RelationshipType.model_rebuild() | ||
| Publication.model_rebuild() | ||
| AnnotatorResult.model_rebuild() | ||
| Ontology.model_rebuild() | ||
| Owner.model_rebuild() | ||
| CitedOntology.model_rebuild() | ||
| UseExample.model_rebuild() | ||
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