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_class_curie:
- 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_class_curie:
- 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_class_curie:
- 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'
-
candidate_obsoletions:
- 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.