mondolib.datamodels package

Submodules

mondolib.datamodels.mondolib_schema module

Autogenerated Schema file.

class mondolib.datamodels.mondolib_schema.CandidateObsoletion(term=None, label=None, confidence=None, is_ordo_only=None, lexical_pattern_matches=<factory>, direct_child_terms=<factory>, is_likely_grouping=None, has_definition=None, **_kwargs)

Bases: YAMLRoot

CandidateObsoletion.

class_class_curie: ClassVar[str] = 'mondolib:CandidateObsoletion'

class_class_uri: ClassVar[URIRef] = rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/CandidateObsoletion')

class_model_uri: ClassVar[URIRef] = rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/CandidateObsoletion')

class_name: ClassVar[str] = 'CandidateObsoletion'

confidence: Optional[float] = None

direct_child_terms: Union[str, List[str], None]

has_definition: Union[bool, Bool, None] = None

is_likely_grouping: Union[bool, Bool, None] = None

is_ordo_only: Union[bool, Bool, None] = None

label: Optional[str] = None

lexical_pattern_matches: Union[dict, LexicalPattern, List[Union[dict, LexicalPattern]], None]

term: Union[str, CandidateObsoletionTerm] = None

class mondolib.datamodels.mondolib_schema.CandidateObsoletionTerm(v)

Bases: extended_str

CandidateObsoletionTerm.

class mondolib.datamodels.mondolib_schema.Configuration(lexical_patterns=<factory>, exclude_terms_with_definitions=None, **_kwargs)

Bases: YAMLRoot

Configuration.

class_class_curie: ClassVar[str] = 'mondolib:Configuration'

class_class_uri: ClassVar[URIRef] = rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/Configuration')

class_model_uri: ClassVar[URIRef] = rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/Configuration')

class_name: ClassVar[str] = 'Configuration'

exclude_terms_with_definitions: Union[bool, Bool, None] = None

lexical_patterns: Union[dict, LexicalPattern, List[Union[dict, LexicalPattern]], None]

class mondolib.datamodels.mondolib_schema.LexicalPattern(pattern=None, description=None, obsoletion_reason=None, scope=None, **_kwargs)

Bases: YAMLRoot

A lexical pattern that is matched against labels.

class_class_curie: ClassVar[str] = 'mondolib:LexicalPattern'

class_class_uri: ClassVar[URIRef] = rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/LexicalPattern')

class_model_uri: ClassVar[URIRef] = rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/LexicalPattern')

class_name: ClassVar[str] = 'LexicalPattern'

description: Optional[str] = None

obsoletion_reason: Optional[str] = None

pattern: Optional[str] = None

scope: Union[str, ValidationCheckScope, None] = None

class mondolib.datamodels.mondolib_schema.Report(candidate_obsoletions=<factory>, **_kwargs)

Bases: YAMLRoot

A pan-ontology report. This focuses on bespoke Mondo checks rather than generic OBO checks.

candidate_obsoletions: Union[Dict[Union[str, CandidateObsoletionTerm], Union[dict, CandidateObsoletion]], List[Union[dict, CandidateObsoletion]], None]

class_class_curie: ClassVar[str] = 'mondolib:Report'

class_class_uri: ClassVar[URIRef] = rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/Report')

class_model_uri: ClassVar[URIRef] = rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/Report')

class_name: ClassVar[str] = 'Report'

class mondolib.datamodels.mondolib_schema.ValidationCheckScope(code)

Bases: EnumDefinitionImpl

Some validations are only performed in particular contexts or scopes.

ORDO_ONLY = PermissibleValue(text='ORDO_ONLY', description='A scope in which the term is mapped solely to Ordo/Orphanet, and there are no mappings to other ontologies, and there have been no non-ORDO axioms added', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)

class mondolib.datamodels.mondolib_schema.slots

Bases: object

Slots.

candidateObsoletion__confidence = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/confidence'), name='candidateObsoletion__confidence', curie='mondolib:confidence', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/candidateObsoletion__confidence'), domain=None, range=typing.Optional[float], mappings=None, pattern=None)

candidateObsoletion__direct_child_terms = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/direct_child_terms'), name='candidateObsoletion__direct_child_terms', curie='mondolib:direct_child_terms', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/candidateObsoletion__direct_child_terms'), domain=None, range=typing.Union[str, typing.List[str], NoneType], mappings=None, pattern=None)

candidateObsoletion__has_definition = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/has_definition'), name='candidateObsoletion__has_definition', curie='mondolib:has_definition', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/candidateObsoletion__has_definition'), domain=None, range=typing.Union[bool, linkml_runtime.utils.metamodelcore.Bool, NoneType], mappings=None, pattern=None)

candidateObsoletion__is_likely_grouping = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/is_likely_grouping'), name='candidateObsoletion__is_likely_grouping', curie='mondolib:is_likely_grouping', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/candidateObsoletion__is_likely_grouping'), domain=None, range=typing.Union[bool, linkml_runtime.utils.metamodelcore.Bool, NoneType], mappings=None, pattern=None)

candidateObsoletion__is_ordo_only = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/is_ordo_only'), name='candidateObsoletion__is_ordo_only', curie='mondolib:is_ordo_only', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/candidateObsoletion__is_ordo_only'), domain=None, range=typing.Union[bool, linkml_runtime.utils.metamodelcore.Bool, NoneType], mappings=None, pattern=None)

candidateObsoletion__label = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/label'), name='candidateObsoletion__label', curie='mondolib:label', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/candidateObsoletion__label'), domain=None, range=typing.Optional[str], mappings=None, pattern=None)

candidateObsoletion__lexical_pattern_matches = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/lexical_pattern_matches'), name='candidateObsoletion__lexical_pattern_matches', curie='mondolib:lexical_pattern_matches', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/candidateObsoletion__lexical_pattern_matches'), domain=None, range=typing.Union[dict, mondolib.datamodels.mondolib_schema.LexicalPattern, typing.List[typing.Union[dict, mondolib.datamodels.mondolib_schema.LexicalPattern]], NoneType], mappings=None, pattern=None)

candidateObsoletion__term = Slot(uri=<bound method Namespace.term of Namespace('https://purl.obolibrary.org/obo/mondo/schema/')>, name='candidateObsoletion__term', curie='mondolib:term', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/candidateObsoletion__term'), domain=None, range=<class 'rdflib.term.URIRef'>, mappings=None, pattern=None)

configuration__exclude_terms_with_definitions = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/exclude_terms_with_definitions'), name='configuration__exclude_terms_with_definitions', curie='mondolib:exclude_terms_with_definitions', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/configuration__exclude_terms_with_definitions'), domain=None, range=typing.Union[bool, linkml_runtime.utils.metamodelcore.Bool, NoneType], mappings=None, pattern=None)

configuration__lexical_patterns = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/lexical_patterns'), name='configuration__lexical_patterns', curie='mondolib:lexical_patterns', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/configuration__lexical_patterns'), domain=None, range=typing.Union[dict, mondolib.datamodels.mondolib_schema.LexicalPattern, typing.List[typing.Union[dict, mondolib.datamodels.mondolib_schema.LexicalPattern]], NoneType], mappings=None, pattern=None)

lexicalPattern__description = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/description'), name='lexicalPattern__description', curie='mondolib:description', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/lexicalPattern__description'), domain=None, range=typing.Optional[str], mappings=None, pattern=None)

lexicalPattern__obsoletion_reason = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/obsoletion_reason'), name='lexicalPattern__obsoletion_reason', curie='mondolib:obsoletion_reason', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/lexicalPattern__obsoletion_reason'), domain=None, range=typing.Optional[str], mappings=None, pattern=None)

lexicalPattern__pattern = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/pattern'), name='lexicalPattern__pattern', curie='mondolib:pattern', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/lexicalPattern__pattern'), domain=None, range=typing.Optional[str], mappings=None, pattern=None)

lexicalPattern__scope = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/scope'), name='lexicalPattern__scope', curie='mondolib:scope', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/lexicalPattern__scope'), domain=None, range=typing.Union[str, ForwardRef('ValidationCheckScope'), NoneType], mappings=None, pattern=None)

report__candidate_obsoletions = Slot(uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/candidate_obsoletions'), name='report__candidate_obsoletions', curie='mondolib:candidate_obsoletions', model_uri=rdflib.term.URIRef('https://purl.obolibrary.org/obo/mondo/schema/report__candidate_obsoletions'), domain=None, range=typing.Union[typing.Dict[typing.Union[str, mondolib.datamodels.mondolib_schema.CandidateObsoletionTerm], typing.Union[dict, mondolib.datamodels.mondolib_schema.CandidateObsoletion]], typing.List[typing.Union[dict, mondolib.datamodels.mondolib_schema.CandidateObsoletion]], NoneType], mappings=None, pattern=None)

mondolib.datamodels.vocabulary module

mondolib datamodel vocabularies.

Module contents

mondolib datamodels.