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Fixed annot schema to use OntologyClass rather than the ControlledTer…
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…mValue holder object, see #184
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@cmungall
cmungall committed Dec 22, 2020
1 parent 06a345d commit 84232ee
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Showing 4 changed files with 176 additions and 93 deletions.
6 changes: 3 additions & 3 deletions schema/annotation.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ classes:
range: string ## make this an object
required: true
type:
range: controlled term value
range: ontology class
description: >-
A type from the sequence ontology
slot_uri: rdf:type
Expand Down Expand Up @@ -77,7 +77,7 @@ classes:
aliases:
- function
- functional annotation
is_a: controlled term value
is_a: ontology class
description: >-
Abstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex).
abstract: true
Expand Down Expand Up @@ -176,7 +176,7 @@ classes:
- chemical substance
- chemical compound
- chemical
is_a: controlled term value
is_a: ontology class
description: >-
An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs.
There may be different terms for distinct acid-base forms, protonation states
Expand Down
108 changes: 77 additions & 31 deletions schema/nmdc.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Auto generated from nmdc.yaml by pythongen.py version: 0.9.0
# Generation date: 2020-12-17 13:39
# Generation date: 2020-12-22 10:17
# Schema: NMDC
#
# id: https://microbiomedata/schema
Expand Down Expand Up @@ -179,7 +179,23 @@ class MetaproteomicsAnalysisActivityActivityId(WorkflowExecutionActivityActivity
pass


class ChemicalEntityInchi(extended_str):
class FunctionalAnnotationTermId(OntologyClassId):
pass


class PathwayId(FunctionalAnnotationTermId):
pass


class ReactionId(FunctionalAnnotationTermId):
pass


class OrthologyGroupId(FunctionalAnnotationTermId):
pass


class ChemicalEntityId(OntologyClassId):
pass


Expand Down Expand Up @@ -249,12 +265,12 @@ class MetaboliteQuantification(YAMLRoot):
class_name: ClassVar[str] = "metabolite quantification"
class_model_uri: ClassVar[URIRef] = NMDC.MetaboliteQuantification

metabolite_quantified: Optional[Union[str, ChemicalEntityInchi]] = None
metabolite_quantified: Optional[Union[str, ChemicalEntityId]] = None
highest_similarity_score: Optional[float] = None

def __post_init__(self, **kwargs: Dict[str, Any]):
if self.metabolite_quantified is not None and not isinstance(self.metabolite_quantified, ChemicalEntityInchi):
self.metabolite_quantified = ChemicalEntityInchi(self.metabolite_quantified)
if self.metabolite_quantified is not None and not isinstance(self.metabolite_quantified, ChemicalEntityId):
self.metabolite_quantified = ChemicalEntityId(self.metabolite_quantified)

if self.highest_similarity_score is not None and not isinstance(self.highest_similarity_score, float):
self.highest_similarity_score = float(self.highest_similarity_score)
Expand Down Expand Up @@ -1536,7 +1552,7 @@ class GenomeFeature(YAMLRoot):
seqid: str = None
start: int = None
end: int = None
type: Optional[Union[dict, ControlledTermValue]] = None
type: Optional[Union[str, OntologyClassId]] = None
strand: Optional[str] = None
phase: Optional[int] = None
encodes: Optional[Union[dict, "GeneProduct"]] = None
Expand All @@ -1557,8 +1573,8 @@ def __post_init__(self, **kwargs: Dict[str, Any]):
if not isinstance(self.end, int):
self.end = int(self.end)

if self.type is not None and not isinstance(self.type, ControlledTermValue):
self.type = ControlledTermValue(**self.type)
if self.type is not None and not isinstance(self.type, OntologyClassId):
self.type = OntologyClassId(self.type)

if self.strand is not None and not isinstance(self.strand, str):
self.strand = str(self.strand)
Expand All @@ -1572,7 +1588,8 @@ def __post_init__(self, **kwargs: Dict[str, Any]):
super().__post_init__(**kwargs)


class FunctionalAnnotationTerm(ControlledTermValue):
@dataclass
class FunctionalAnnotationTerm(OntologyClass):
"""
Abstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein,
ncRNA, complex).
Expand All @@ -1584,6 +1601,7 @@ class FunctionalAnnotationTerm(ControlledTermValue):
class_name: ClassVar[str] = "functional annotation term"
class_model_uri: ClassVar[URIRef] = NMDC.FunctionalAnnotationTerm

id: Union[str, FunctionalAnnotationTermId] = None

@dataclass
class Pathway(FunctionalAnnotationTerm):
Expand All @@ -1597,14 +1615,20 @@ class Pathway(FunctionalAnnotationTerm):
class_name: ClassVar[str] = "pathway"
class_model_uri: ClassVar[URIRef] = NMDC.Pathway

has_part: Optional[Union[Union[dict, "Reaction"], List[Union[dict, "Reaction"]]]] = empty_list()
id: Union[str, PathwayId] = None
has_part: Optional[Union[Union[str, ReactionId], List[Union[str, ReactionId]]]] = empty_list()

def __post_init__(self, **kwargs: Dict[str, Any]):
if self.id is None:
raise ValueError("id must be supplied")
if not isinstance(self.id, PathwayId):
self.id = PathwayId(self.id)

if self.has_part is None:
self.has_part = []
if not isinstance(self.has_part, list):
self.has_part = [self.has_part]
self.has_part = [v if isinstance(v, Reaction) else Reaction(**v) for v in self.has_part]
self.has_part = [v if isinstance(v, ReactionId) else ReactionId(v) for v in self.has_part]

super().__post_init__(**kwargs)

Expand All @@ -1622,6 +1646,7 @@ class Reaction(FunctionalAnnotationTerm):
class_name: ClassVar[str] = "reaction"
class_model_uri: ClassVar[URIRef] = NMDC.Reaction

id: Union[str, ReactionId] = None
left_participants: Optional[Union[Union[dict, "ReactionParticipant"], List[Union[dict, "ReactionParticipant"]]]] = empty_list()
right_participants: Optional[Union[Union[dict, "ReactionParticipant"], List[Union[dict, "ReactionParticipant"]]]] = empty_list()
direction: Optional[str] = None
Expand All @@ -1633,6 +1658,11 @@ class Reaction(FunctionalAnnotationTerm):
is_fully_characterized: Optional[Bool] = None

def __post_init__(self, **kwargs: Dict[str, Any]):
if self.id is None:
raise ValueError("id must be supplied")
if not isinstance(self.id, ReactionId):
self.id = ReactionId(self.id)

if self.left_participants is None:
self.left_participants = []
if not isinstance(self.left_participants, list):
Expand Down Expand Up @@ -1681,19 +1711,20 @@ class ReactionParticipant(YAMLRoot):
class_name: ClassVar[str] = "reaction participant"
class_model_uri: ClassVar[URIRef] = NMDC.ReactionParticipant

chemical: Optional[Union[str, ChemicalEntityInchi]] = None
chemical: Optional[Union[str, ChemicalEntityId]] = None
stoichiometry: Optional[int] = None

def __post_init__(self, **kwargs: Dict[str, Any]):
if self.chemical is not None and not isinstance(self.chemical, ChemicalEntityInchi):
self.chemical = ChemicalEntityInchi(self.chemical)
if self.chemical is not None and not isinstance(self.chemical, ChemicalEntityId):
self.chemical = ChemicalEntityId(self.chemical)

if self.stoichiometry is not None and not isinstance(self.stoichiometry, int):
self.stoichiometry = int(self.stoichiometry)

super().__post_init__(**kwargs)


@dataclass
class OrthologyGroup(FunctionalAnnotationTerm):
"""
A set of genes or gene products in which all members are orthologous
Expand All @@ -1705,9 +1736,19 @@ class OrthologyGroup(FunctionalAnnotationTerm):
class_name: ClassVar[str] = "orthology group"
class_model_uri: ClassVar[URIRef] = NMDC.OrthologyGroup

id: Union[str, OrthologyGroupId] = None

def __post_init__(self, **kwargs: Dict[str, Any]):
if self.id is None:
raise ValueError("id must be supplied")
if not isinstance(self.id, OrthologyGroupId):
self.id = OrthologyGroupId(self.id)

super().__post_init__(**kwargs)


@dataclass
class ChemicalEntity(ControlledTermValue):
class ChemicalEntity(OntologyClass):
"""
An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products,
drugs. There may be different terms for distinct acid-base forms, protonation states
Expand All @@ -1719,16 +1760,21 @@ class ChemicalEntity(ControlledTermValue):
class_name: ClassVar[str] = "chemical entity"
class_model_uri: ClassVar[URIRef] = NMDC.ChemicalEntity

inchi: Union[str, ChemicalEntityInchi] = None
id: Union[str, ChemicalEntityId] = None
inchi_key: Optional[str] = None
smiles: Optional[Union[str, List[str]]] = empty_list()
chemical_formula: Optional[str] = None

def __post_init__(self, **kwargs: Dict[str, Any]):
if self.id is None:
raise ValueError("id must be supplied")
if not isinstance(self.id, ChemicalEntityId):
self.id = ChemicalEntityId(self.id)

if self.inchi is None:
raise ValueError("inchi must be supplied")
if not isinstance(self.inchi, ChemicalEntityInchi):
self.inchi = ChemicalEntityInchi(self.inchi)
if not isinstance(self.inchi, ChemicalEntityId):
self.inchi = ChemicalEntityId(self.inchi)

if self.inchi_key is not None and not isinstance(self.inchi_key, str):
self.inchi_key = str(self.inchi_key)
Expand Down Expand Up @@ -1774,7 +1820,7 @@ class FunctionalAnnotation(YAMLRoot):

was_generated_by: Optional[Union[str, ActivityActivityId]] = None
subject: Optional[Union[dict, GeneProduct]] = None
has_function: Optional[Union[dict, FunctionalAnnotationTerm]] = None
has_function: Optional[Union[str, FunctionalAnnotationTermId]] = None

def __post_init__(self, **kwargs: Dict[str, Any]):
if self.was_generated_by is not None and not isinstance(self.was_generated_by, ActivityActivityId):
Expand All @@ -1783,8 +1829,8 @@ def __post_init__(self, **kwargs: Dict[str, Any]):
if self.subject is not None and not isinstance(self.subject, GeneProduct):
self.subject = GeneProduct()

if self.has_function is not None and not isinstance(self.has_function, FunctionalAnnotationTerm):
self.has_function = FunctionalAnnotationTerm(**self.has_function)
if self.has_function is not None and not isinstance(self.has_function, FunctionalAnnotationTermId):
self.has_function = FunctionalAnnotationTermId(self.has_function)

super().__post_init__(**kwargs)

Expand Down Expand Up @@ -4258,7 +4304,7 @@ class slots:
model_uri=NMDC.has_peptide_quantifications, domain=None, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]])

slots.metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="metabolite quantified", curie=NMDC.curie('metabolite_quantified'),
model_uri=NMDC.metabolite_quantified, domain=None, range=Optional[Union[str, ChemicalEntityInchi]])
model_uri=NMDC.metabolite_quantified, domain=None, range=Optional[Union[str, ChemicalEntityId]])

slots.highest_similarity_score = Slot(uri=NMDC.highest_similarity_score, name="highest similarity score", curie=NMDC.curie('highest_similarity_score'),
model_uri=NMDC.highest_similarity_score, domain=None, range=Optional[float])
Expand Down Expand Up @@ -4300,7 +4346,7 @@ class slots:
model_uri=NMDC.encodes, domain=None, range=Optional[Union[dict, GeneProduct]])

slots.has_part = Slot(uri=NMDC.has_part, name="has_part", curie=NMDC.curie('has_part'),
model_uri=NMDC.has_part, domain=None, range=Optional[Union[Union[dict, Reaction], List[Union[dict, Reaction]]]])
model_uri=NMDC.has_part, domain=None, range=Optional[Union[Union[str, ReactionId], List[Union[str, ReactionId]]]])

slots.left_participants = Slot(uri=NMDC.left_participants, name="left participants", curie=NMDC.curie('left_participants'),
model_uri=NMDC.left_participants, domain=None, range=Optional[Union[Union[dict, ReactionParticipant], List[Union[dict, ReactionParticipant]]]])
Expand Down Expand Up @@ -4330,7 +4376,7 @@ class slots:
model_uri=NMDC.is_fully_characterized, domain=None, range=Optional[Bool])

slots.chemical = Slot(uri=NMDC.chemical, name="chemical", curie=NMDC.curie('chemical'),
model_uri=NMDC.chemical, domain=None, range=Optional[Union[str, ChemicalEntityInchi]])
model_uri=NMDC.chemical, domain=None, range=Optional[Union[str, ChemicalEntityId]])

slots.stoichiometry = Slot(uri=NMDC.stoichiometry, name="stoichiometry", curie=NMDC.curie('stoichiometry'),
model_uri=NMDC.stoichiometry, domain=None, range=Optional[int])
Expand All @@ -4351,7 +4397,7 @@ class slots:
model_uri=NMDC.subject, domain=None, range=Optional[Union[dict, GeneProduct]])

slots.has_function = Slot(uri=NMDC.has_function, name="has function", curie=NMDC.curie('has_function'),
model_uri=NMDC.has_function, domain=None, range=Optional[Union[dict, FunctionalAnnotationTerm]])
model_uri=NMDC.has_function, domain=None, range=Optional[Union[str, FunctionalAnnotationTermId]])

slots.data_object_was_generated_by = Slot(uri=NMDC.was_generated_by, name="data object_was generated by", curie=NMDC.curie('was_generated_by'),
model_uri=NMDC.data_object_was_generated_by, domain=DataObject, range=Optional[Union[dict, "WorkflowExecutionActivity"]])
Expand Down Expand Up @@ -4424,7 +4470,7 @@ class slots:
model_uri=NMDC.omics_processing_has_output, domain=OmicsProcessing, range=Optional[Union[Union[str, DataObjectId], List[Union[str, DataObjectId]]]])

slots.metabolite_quantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="metabolite quantification_metabolite quantified", curie=NMDC.curie('metabolite_quantified'),
model_uri=NMDC.metabolite_quantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityInchi]])
model_uri=NMDC.metabolite_quantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]])

slots.metabolite_quantification_highest_similarity_score = Slot(uri=NMDC.highest_similarity_score, name="metabolite quantification_highest similarity score", curie=NMDC.curie('highest_similarity_score'),
model_uri=NMDC.metabolite_quantification_highest_similarity_score, domain=MetaboliteQuantification, range=Optional[float])
Expand Down Expand Up @@ -4469,7 +4515,7 @@ class slots:
model_uri=NMDC.genome_feature_seqid, domain=GenomeFeature, range=str)

slots.genome_feature_type = Slot(uri=RDF.type, name="genome feature_type", curie=RDF.curie('type'),
model_uri=NMDC.genome_feature_type, domain=GenomeFeature, range=Optional[Union[dict, ControlledTermValue]])
model_uri=NMDC.genome_feature_type, domain=GenomeFeature, range=Optional[Union[str, OntologyClassId]])

slots.genome_feature_start = Slot(uri=NMDC.start, name="genome feature_start", curie=NMDC.curie('start'),
model_uri=NMDC.genome_feature_start, domain=GenomeFeature, range=int)
Expand All @@ -4487,7 +4533,7 @@ class slots:
model_uri=NMDC.genome_feature_encodes, domain=GenomeFeature, range=Optional[Union[dict, "GeneProduct"]])

slots.pathway_has_part = Slot(uri=NMDC.has_part, name="pathway_has_part", curie=NMDC.curie('has_part'),
model_uri=NMDC.pathway_has_part, domain=Pathway, range=Optional[Union[Union[dict, "Reaction"], List[Union[dict, "Reaction"]]]])
model_uri=NMDC.pathway_has_part, domain=Pathway, range=Optional[Union[Union[str, ReactionId], List[Union[str, ReactionId]]]])

slots.reaction_left_participants = Slot(uri=NMDC.left_participants, name="reaction_left participants", curie=NMDC.curie('left_participants'),
model_uri=NMDC.reaction_left_participants, domain=Reaction, range=Optional[Union[Union[dict, "ReactionParticipant"], List[Union[dict, "ReactionParticipant"]]]])
Expand Down Expand Up @@ -4517,13 +4563,13 @@ class slots:
model_uri=NMDC.reaction_is_fully_characterized, domain=Reaction, range=Optional[Bool])

slots.reaction_participant_chemical = Slot(uri=NMDC.chemical, name="reaction participant_chemical", curie=NMDC.curie('chemical'),
model_uri=NMDC.reaction_participant_chemical, domain=ReactionParticipant, range=Optional[Union[str, ChemicalEntityInchi]])
model_uri=NMDC.reaction_participant_chemical, domain=ReactionParticipant, range=Optional[Union[str, ChemicalEntityId]])

slots.reaction_participant_stoichiometry = Slot(uri=NMDC.stoichiometry, name="reaction participant_stoichiometry", curie=NMDC.curie('stoichiometry'),
model_uri=NMDC.reaction_participant_stoichiometry, domain=ReactionParticipant, range=Optional[int])

slots.chemical_entity_inchi = Slot(uri=NMDC.inchi, name="chemical entity_inchi", curie=NMDC.curie('inchi'),
model_uri=NMDC.chemical_entity_inchi, domain=ChemicalEntity, range=Union[str, ChemicalEntityInchi])
model_uri=NMDC.chemical_entity_inchi, domain=ChemicalEntity, range=Union[str, ChemicalEntityId])

slots.chemical_entity_inchi_key = Slot(uri=NMDC.inchi_key, name="chemical entity_inchi key", curie=NMDC.curie('inchi_key'),
model_uri=NMDC.chemical_entity_inchi_key, domain=ChemicalEntity, range=Optional[str])
Expand All @@ -4538,7 +4584,7 @@ class slots:
model_uri=NMDC.functional_annotation_subject, domain=FunctionalAnnotation, range=Optional[Union[dict, GeneProduct]])

slots.functional_annotation_has_function = Slot(uri=NMDC.has_function, name="functional annotation_has function", curie=NMDC.curie('has_function'),
model_uri=NMDC.functional_annotation_has_function, domain=FunctionalAnnotation, range=Optional[Union[dict, FunctionalAnnotationTerm]])
model_uri=NMDC.functional_annotation_has_function, domain=FunctionalAnnotation, range=Optional[Union[str, FunctionalAnnotationTermId]])

slots.functional_annotation_was_generated_by = Slot(uri=NMDC.was_generated_by, name="functional annotation_was generated by", curie=NMDC.curie('was_generated_by'),
model_uri=NMDC.functional_annotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, ActivityActivityId]])
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