-
Notifications
You must be signed in to change notification settings - Fork 13
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
6 changed files
with
285 additions
and
55 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,230 @@ | ||
| # Auto generated from information_resource_registry.yaml by pythongen.py version: 0.0.1 | ||
| # Generation date: 2024-03-08T12:38:21 | ||
| # Schema: Information-Resource-Registry-Schema | ||
| # | ||
| # id: https://w3id.org/biolink/information_resource_registry.yaml | ||
| # description: | ||
| # license: https://creativecommons.org/publicdomain/zero/1.0/ | ||
|
|
||
| import dataclasses | ||
| import re | ||
| from jsonasobj2 import JsonObj, as_dict | ||
| from typing import Optional, List, Union, Dict, ClassVar, Any | ||
| from dataclasses import dataclass | ||
| from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions | ||
|
|
||
| from linkml_runtime.utils.slot import Slot | ||
| from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode | ||
| from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int | ||
| from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs | ||
| from linkml_runtime.utils.formatutils import camelcase, underscore, sfx | ||
| from linkml_runtime.utils.enumerations import EnumDefinitionImpl | ||
| from rdflib import Namespace, URIRef | ||
| from linkml_runtime.utils.curienamespace import CurieNamespace | ||
| from linkml_runtime.linkml_model.types import String | ||
|
|
||
| metamodel_version = "1.7.0" | ||
| version = "1.0.0" | ||
|
|
||
| # Overwrite dataclasses _init_fn to add **kwargs in __init__ | ||
| dataclasses._init_fn = dataclasses_init_fn_with_kwargs | ||
|
|
||
| # Namespaces | ||
| BIOGRID = CurieNamespace('BIOGRID', 'http://identifiers.org/biogrid/') | ||
| SO = CurieNamespace('SO', 'http://purl.obolibrary.org/obo/SO_') | ||
| BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/') | ||
| INFORES = CurieNamespace('infores', 'https://w3id.org/biolink/infores/') | ||
| LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') | ||
| OBOINOWL = CurieNamespace('oboInOwl', 'http://www.geneontology.org/formats/oboInOwl#') | ||
| RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#') | ||
| RDFS = CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#') | ||
| SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#') | ||
| XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#') | ||
| DEFAULT_ = INFORES | ||
|
|
||
|
|
||
| # Types | ||
|
|
||
| # Class references | ||
|
|
||
|
|
||
|
|
||
| @dataclass | ||
| class InformationResourceContainer(YAMLRoot): | ||
| """ | ||
| A collection of information resources | ||
| """ | ||
| _inherited_slots: ClassVar[List[str]] = [] | ||
|
|
||
| class_class_uri: ClassVar[URIRef] = INFORES["InformationResourceContainer"] | ||
| class_class_curie: ClassVar[str] = "infores:InformationResourceContainer" | ||
| class_name: ClassVar[str] = "InformationResourceContainer" | ||
| class_model_uri: ClassVar[URIRef] = INFORES.InformationResourceContainer | ||
|
|
||
| information_resources: Optional[Union[Union[dict, "InformationResource"], List[Union[dict, "InformationResource"]]]] = empty_list() | ||
|
|
||
| def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): | ||
| if not isinstance(self.information_resources, list): | ||
| self.information_resources = [self.information_resources] if self.information_resources is not None else [] | ||
| self.information_resources = [v if isinstance(v, InformationResource) else InformationResource(**as_dict(v)) for v in self.information_resources] | ||
|
|
||
| super().__post_init__(**kwargs) | ||
|
|
||
|
|
||
| @dataclass | ||
| class InformationResource(YAMLRoot): | ||
| """ | ||
| A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to | ||
| consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single | ||
| Information Resource by this definition may span many different datasets or databases, and include many access | ||
| endpoints and user interfaces. Information Resources include project-specific resources such as a Translator | ||
| Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb. | ||
| """ | ||
| _inherited_slots: ClassVar[List[str]] = [] | ||
|
|
||
| class_class_uri: ClassVar[URIRef] = INFORES["InformationResource"] | ||
| class_class_curie: ClassVar[str] = "infores:InformationResource" | ||
| class_name: ClassVar[str] = "InformationResource" | ||
| class_model_uri: ClassVar[URIRef] = INFORES.InformationResource | ||
|
|
||
| id: str = None | ||
| status: Optional[Union[str, "InformationResourceStatusEnum"]] = None | ||
| name: Optional[str] = None | ||
| xref: Optional[Union[str, List[str]]] = empty_list() | ||
| synonym: Optional[Union[str, List[str]]] = empty_list() | ||
| description: Optional[str] = None | ||
| knowledge_level: Optional[Union[str, "KnowledgeLevelEnum"]] = None | ||
| agent_type: Optional[Union[str, "AgentTypeEnum"]] = None | ||
|
|
||
| def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): | ||
| if self._is_empty(self.id): | ||
| self.MissingRequiredField("id") | ||
| if not isinstance(self.id, str): | ||
| self.id = str(self.id) | ||
|
|
||
| if self.status is not None and not isinstance(self.status, InformationResourceStatusEnum): | ||
| self.status = InformationResourceStatusEnum(self.status) | ||
|
|
||
| if self.name is not None and not isinstance(self.name, str): | ||
| self.name = str(self.name) | ||
|
|
||
| if not isinstance(self.xref, list): | ||
| self.xref = [self.xref] if self.xref is not None else [] | ||
| self.xref = [v if isinstance(v, str) else str(v) for v in self.xref] | ||
|
|
||
| if not isinstance(self.synonym, list): | ||
| self.synonym = [self.synonym] if self.synonym is not None else [] | ||
| self.synonym = [v if isinstance(v, str) else str(v) for v in self.synonym] | ||
|
|
||
| if self.description is not None and not isinstance(self.description, str): | ||
| self.description = str(self.description) | ||
|
|
||
| if self.knowledge_level is not None and not isinstance(self.knowledge_level, KnowledgeLevelEnum): | ||
| self.knowledge_level = KnowledgeLevelEnum(self.knowledge_level) | ||
|
|
||
| if self.agent_type is not None and not isinstance(self.agent_type, AgentTypeEnum): | ||
| self.agent_type = AgentTypeEnum(self.agent_type) | ||
|
|
||
| super().__post_init__(**kwargs) | ||
|
|
||
|
|
||
| # Enumerations | ||
| class InformationResourceStatusEnum(EnumDefinitionImpl): | ||
| """ | ||
| The status of the infores identifier | ||
| """ | ||
| released = PermissibleValue(text="released") | ||
| deprecated = PermissibleValue(text="deprecated") | ||
| draft = PermissibleValue(text="draft") | ||
| modified = PermissibleValue(text="modified") | ||
|
|
||
| _defn = EnumDefinition( | ||
| name="InformationResourceStatusEnum", | ||
| description="The status of the infores identifier", | ||
| ) | ||
|
|
||
| class KnowledgeLevelEnum(EnumDefinitionImpl): | ||
| """ | ||
| The level of knowledge that supports an edge or node. This is a general categorization of the type of evidence | ||
| that supports a statement, and is not intended to be a comprehensive description of the evidence. For example, a | ||
| statement may be supported by a single publication, but that publication may contain multiple types of evidence, | ||
| such as a computational prediction and a manual curation. In this case, the knowledge level would be "curated", | ||
| and the evidence would be described in more detail in the evidence graph. | ||
| """ | ||
| curated = PermissibleValue( | ||
| text="curated", | ||
| description="""knowledge generated through manual curation or interpretation of data or published study results""") | ||
| predicted = PermissibleValue( | ||
| text="predicted", | ||
| description="""predictions generated computationally through inference over less direct forms of evidence (without human intervention or review)""") | ||
| text_mined = PermissibleValue( | ||
| text="text_mined", | ||
| description="knowledge extracted from published text by NLP agents (without human intervention or review)") | ||
| correlation = PermissibleValue( | ||
| text="correlation", | ||
| description="""statistical correlations calculated between variables in a clinical or omics dataset, by an automated analysis pipeline""") | ||
| observed = PermissibleValue( | ||
| text="observed", | ||
| description="""edge reports a phenomenon that was reported/observed to have occurred (and possibly some quantification, e.g. how many times, at what frequency)""") | ||
| other = PermissibleValue( | ||
| text="other", | ||
| description="knowledge level may not fit into the categories above, or is not provided/known") | ||
| mixed = PermissibleValue( | ||
| text="mixed", | ||
| description="""used for sources that might provide edges with different knowledge levels, e.g.correlations in addition to curated Edges - set tag to Curated, unless predicate rules override""") | ||
|
|
||
| _defn = EnumDefinition( | ||
| name="KnowledgeLevelEnum", | ||
| description="""The level of knowledge that supports an edge or node. This is a general categorization of the type of evidence that supports a statement, and is not intended to be a comprehensive description of the evidence. For example, a statement may be supported by a single publication, but that publication may contain multiple types of evidence, such as a computational prediction and a manual curation. In this case, the knowledge level would be \"curated\", and the evidence would be described in more detail in the evidence graph.""", | ||
| ) | ||
|
|
||
| class AgentTypeEnum(EnumDefinitionImpl): | ||
| """ | ||
| The type of agent that supports an edge or node. This is a general categorization of the type of agent that | ||
| supports a statement, and is not intended to be a comprehensive description of the agent. For example, a statement | ||
| may be supported by a single publication, but that publication may contain multiple types of evidence, such as a | ||
| computational prediction and a manual curation. In this case, the agent type would be "publication", and the | ||
| evidence would be described in more detail in the evidence graph. | ||
| """ | ||
| not_provided = PermissibleValue( | ||
| text="not_provided", | ||
| description="agent type is not provided or known") | ||
| computational_model = PermissibleValue( | ||
| text="computational_model", | ||
| description="a computational model, such as a machine learning model") | ||
|
|
||
| _defn = EnumDefinition( | ||
| name="AgentTypeEnum", | ||
| description="""The type of agent that supports an edge or node. This is a general categorization of the type of agent that supports a statement, and is not intended to be a comprehensive description of the agent. For example, a statement may be supported by a single publication, but that publication may contain multiple types of evidence, such as a computational prediction and a manual curation. In this case, the agent type would be \"publication\", and the evidence would be described in more detail in the evidence graph.""", | ||
| ) | ||
|
|
||
| # Slots | ||
| class slots: | ||
| pass | ||
|
|
||
| slots.status = Slot(uri=INFORES.status, name="status", curie=INFORES.curie('status'), | ||
| model_uri=INFORES.status, domain=None, range=Optional[Union[str, "InformationResourceStatusEnum"]]) | ||
|
|
||
| slots.information_resources = Slot(uri=INFORES.information_resources, name="information_resources", curie=INFORES.curie('information_resources'), | ||
| model_uri=INFORES.information_resources, domain=None, range=Optional[Union[Union[dict, InformationResource], List[Union[dict, InformationResource]]]]) | ||
|
|
||
| slots.name = Slot(uri=RDFS.label, name="name", curie=RDFS.curie('label'), | ||
| model_uri=INFORES.name, domain=None, range=Optional[str]) | ||
|
|
||
| slots.id = Slot(uri=INFORES.id, name="id", curie=INFORES.curie('id'), | ||
| model_uri=INFORES.id, domain=None, range=str) | ||
|
|
||
| slots.xref = Slot(uri=INFORES.xref, name="xref", curie=INFORES.curie('xref'), | ||
| model_uri=INFORES.xref, domain=None, range=Optional[Union[str, List[str]]]) | ||
|
|
||
| slots.synonym = Slot(uri=INFORES.synonym, name="synonym", curie=INFORES.curie('synonym'), | ||
| model_uri=INFORES.synonym, domain=None, range=Optional[Union[str, List[str]]]) | ||
|
|
||
| slots.description = Slot(uri=RDFS.comment, name="description", curie=RDFS.curie('comment'), | ||
| model_uri=INFORES.description, domain=None, range=Optional[str]) | ||
|
|
||
| slots.knowledge_level = Slot(uri=INFORES.knowledge_level, name="knowledge level", curie=INFORES.curie('knowledge_level'), | ||
| model_uri=INFORES.knowledge_level, domain=None, range=Optional[Union[str, "KnowledgeLevelEnum"]]) | ||
|
|
||
| slots.agent_type = Slot(uri=INFORES.agent_type, name="agent type", curie=INFORES.curie('agent_type'), | ||
| model_uri=INFORES.agent_type, domain=None, range=Optional[Union[str, "AgentTypeEnum"]]) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.