def test_basics(self):
BFO = CurieNamespace('bfo', "http://purl.obolibrary.org/obo/BFO_")
self.assertEqual(URIRef("http://purl.obolibrary.org/obo/BFO_test"),
BFO.test)
self.assertEqual("http://purl.obolibrary.org/obo/BFO_", BFO)
self.assertEqual("bfo:test", BFO.curie('test'))
self.assertEqual("bfo:", BFO.curie())
def parse_identifier(cls, identifier: str) -> Tuple[CurieNamespace, str]:
# trivial case of a null identifier?
if not identifier:
return CurieNamespace("", ""), ""
# check if this is a candidate URI...
if identifier.lower().startswith("http"):
# guess that perhaps it is, so try to parse it
return cls.parse_uri(identifier)
else: # attempt to parse as a CURIE
return cls.parse_curie(identifier)
def parse_curie(cls, curie: str) -> Tuple[CurieNamespace, str]:
"""
Parse a candidate CURIE
:param curie: candidate curie string
:return: CURIE namespace and object_id
"""
found = CurieNamespace("", ""), curie # default value if not a CURIE or unknown XMLNS prefix
if ':' in curie:
part = curie.split(":")
# Normalize retrieval with upper case of prefix for lookup
prefix = part[0].upper()
if prefix in cls._get_prefix_map():
found = cls._prefix_map[prefix], part[1]
return found
def parse_uri(cls, uri: str) -> Tuple[CurieNamespace, str]:
"""
Parse a candidate URI
:param uri: candidate URI string
:return: namespace and object_id
"""
found = CurieNamespace("", ""), uri # default value returned if unknown URI namespace
# TODO: is there a more efficient lookup scheme here than a linear search of namespaces?
for ns in cls._namespaces:
base_uri = str(ns)
if uri.startswith(base_uri):
# simple minded deletion of base_uri to give the object_id
object_id = uri.replace(base_uri, "")
found = ns, object_id
break
return found
from src.core.localidentifiers import CodeSystemName
from src.core.references import CodeSystemReference, CodeSystemReferenceName, CodeSystemVersionReference, CodeSystemVersionReferenceName, FormatReference, FormatReferenceName, LanguageReference, LanguageReferenceName, MapReference, MapReferenceName, MatchAlgorithmReference, MatchAlgorithmReferenceName, NameAndMeaningReference, NameAndMeaningReferenceName, OntologyLanguageReference, OntologyLanguageReferenceName, OntologySyntaxReference, OntologySyntaxReferenceName, PredicateReference, RoleReference, RoleReferenceName, ValueSetDefinitionReference, ValueSetDefinitionReferenceName, ValueSetReference, ValueSetReferenceName, VersionTagReference, VersionTagReferenceName
from src.core.resourcedescription import ResourceVersionDescription, ResourceVersionDescriptionId, SourceAndNotation
from src.core.uritypes import DocumentURI, ExternalURI, LocalURI, PersistentURI, RenderingURI
from biolinkml.utils.metamodelcore import Bool, URIorCURIE, XSDDateTime
from includes.annotations import Annotation
from includes.extensions import Extension
from includes.types import Boolean, String
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINKML = CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/')
RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#')
SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#')
TCCM = CurieNamespace('tccm', 'https://hotecosystem.org/tccm/')
DEFAULT_ = TCCM
# Types
# Class references
class SpecificEntityListNamespaceURI(EntityReferenceListNamespaceURI):
pass
class ValueSetDefinitionId(ResourceVersionDescriptionId):
pass
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from biolinkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
XSD = CurieNamespace('xsd', 'http://example.org/UNKNOWN/xsd/')
DEFAULT_ = CurieNamespace('', 'http://example.org/sample/example1/')
# Types
class String(str):
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = URIRef("http://example.org/sample/example1/String")
# Class references
class AId(extended_str):
pass
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from biolinkml.utils.metamodelcore import URIorCURIE
from includes.types import Uriorcurie
metamodel_version = "1.6.1"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
IAO = CurieNamespace('IAO', 'http://purl.obolibrary.org/obo/IAO_')
OIO = CurieNamespace('OIO', 'http://www.geneontology.org/formats/oboInOwl#')
BIOLINKML = CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/')
META = CurieNamespace('meta', 'https://w3id.org/biolink/biolinkml/meta/')
METATYPE = CurieNamespace('metatype',
'https://w3id.org/biolink/biolinkml/meta/types/')
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_ = META
# Types
# Class references
class BiolinkNameSpace:
"""
Map of BioLink Model registered URI Namespaces
"""
_namespaces = [
CurieNamespace('OIO', 'http://www.geneontology.org/formats/oboInOwl#'),
CurieNamespace('bibo', 'http://purl.org/ontology/bibo/'),
CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/'),
CurieNamespace('dcterms', 'http://purl.org/dc/terms/'),
CurieNamespace('meta', 'https://w3id.org/biolink/biolinkml/meta/'),
CurieNamespace('oslc', 'http://open-services.net/ns/core#'),
CurieNamespace('owl', 'http://www.w3.org/2002/07/owl#'),
CurieNamespace('pav', 'http://purl.org/pav/'),
CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'),
CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#'),
CurieNamespace('schema', 'http://schema.org/'),
CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#'),
CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#'),
]
# class level dictionaries
_prefix_map: Dict[str, CurieNamespace] = {}
@classmethod
def _get_prefix_map(cls):
if not cls._prefix_map:
for ns in cls._namespaces:
# index by upper case for uniformity of search
cls._prefix_map[ns.prefix.upper()] = ns
return cls._prefix_map
@classmethod
def parse_curie(cls, curie: str) -> Tuple[CurieNamespace, str]:
"""
Parse a candidate CURIE
:param curie: candidate curie string
:return: CURIE namespace and object_id
"""
found = CurieNamespace("", ""), curie # default value if not a CURIE or unknown XMLNS prefix
if ':' in curie:
part = curie.split(":")
# Normalize retrieval with upper case of prefix for lookup
prefix = part[0].upper()
if prefix in cls._get_prefix_map():
found = cls._prefix_map[prefix], part[1]
return found
@classmethod
def parse_uri(cls, uri: str) -> Tuple[CurieNamespace, str]:
"""
Parse a candidate URI
:param uri: candidate URI string
:return: namespace and object_id
"""
found = CurieNamespace("", ""), uri # default value returned if unknown URI namespace
# TODO: is there a more efficient lookup scheme here than a linear search of namespaces?
for ns in cls._namespaces:
base_uri = str(ns)
if uri.startswith(base_uri):
# simple minded deletion of base_uri to give the object_id
object_id = uri.replace(base_uri, "")
found = ns, object_id
break
return found
@classmethod
def parse_identifier(cls, identifier: str) -> Tuple[CurieNamespace, str]:
# trivial case of a null identifier?
if not identifier:
return CurieNamespace("", ""), ""
# check if this is a candidate URI...
if identifier.lower().startswith("http"):
# guess that perhaps it is, so try to parse it
return cls.parse_uri(identifier)
else: # attempt to parse as a CURIE
return cls.parse_curie(identifier)
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from biolinkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINKML = CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/')
EX = CurieNamespace('ex', 'http://example.org/')
DEFAULT_ = EX
# Types
# Class references
class MyClass(YAMLRoot):
"""
Annotations as tag value pairs. Note that altLabel is defined in the default namespace, not in the SKOS namespace
"""
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = EX.MyClass
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from biolinkml.utils.metamodelcore import Bool, ElementIdentifier, NCName, NodeIdentifier, URI, URIorCURIE, XSDDate, XSDDateTime, XSDTime
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
SHEX = CurieNamespace('shex', 'http://www.w3.org/ns/shex#')
SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#')
TEST = CurieNamespace('test', 'http://example.org/test/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = TEST
# Types
class String(str):
""" A character string """
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = TEST.String
from biolinkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
FOAF = CurieNamespace('foaf', 'http://xmlns.com/foaf/0.1/')
SAMP = CurieNamespace('samp', 'http://example.org/model/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = SAMP
# Types
class String(str):
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = SAMP.String
# Class references
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
DEFAULT_ = CurieNamespace('', 'https://hotecosystem.org/tccm/prefixes/')
# Types
# Class references
# Slots
class slots:
pass
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from biolinkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINKML = CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/')
TCCM = CurieNamespace('tccm', 'https://hotecosystem.org/tccm/')
DEFAULT_ = TCCM
# Types
# Class references
@dataclass
class IterableResolvedValueSet(YAMLRoot):
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = TCCM.IterableResolvedValueSet
class_class_curie: ClassVar[str] = "tccm:IterableResolvedValueSet"
class_name: ClassVar[str] = "IterableResolvedValueSet"
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from biolinkml.utils.metamodelcore import URIorCURIE
from includes.types import Uriorcurie
metamodel_version = "1.6.1"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
META = CurieNamespace('meta', 'https://w3id.org/biolink/biolinkml/')
RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = CurieNamespace('', 'https://example.com/test44/')
# Types
class IriType(Uriorcurie):
""" An IRI """
type_class_uri = XSD.anyURI
type_class_curie = "xsd:anyURI"
type_name = "iri type"
type_model_uri = URIRef("https://example.com/test44/IriType")
# Class references
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from includes.types import String
metamodel_version = "1.4.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#')
TEST = CurieNamespace('test', 'http://example.org/test/')
DEFAULT_ = TEST
# Types
# Class references
@dataclass
class C1(YAMLRoot):
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = TEST.C1
class_class_curie: ClassVar[str] = "test:C1"
class_name: ClassVar[str] = "c1"
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from biolinkml.utils.metamodelcore import URIorCURIE
metamodel_version = "1.4.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = CurieNamespace('', 'http://example.org/example/multi_id/')
# Types
class Uri(URIorCURIE):
type_class_uri = XSD.anyURI
type_class_curie = "xsd:anyURI"
type_name = "uri"
type_model_uri = URIRef("http://example.org/example/multi_id/Uri")
class IdentifierType(Uri):
type_class_uri = XSD.anyURI
type_class_curie = "xsd:anyURI"
type_name = "identifier type"
from biolinkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.4.4"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
XSD = CurieNamespace('xsd', 'http://example.org/UNKNOWN/xsd/')
DEFAULT_ = CurieNamespace('', 'http://example.org/sample/organization/')
# Types
class YearCount(int):
type_class_uri = XSD.int
type_class_curie = "xsd:int"
type_name = "yearCount"
type_model_uri = URIRef("http://example.org/sample/organization/YearCount")
class String(str):
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from includes.types import String
metamodel_version = "1.6.1"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINKML = CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/')
TEST = CurieNamespace('test', 'http://example.org/test/')
DEFAULT_ = CurieNamespace('', 'http://example.org/tests/namespace/')
# Types
# Class references
@dataclass
class C1(YAMLRoot):
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = URIRef(
"http://example.org/tests/namespace/C1")
class_class_curie: ClassVar[str] = None
from biolinkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = CurieNamespace('', 'http://example.com/')
# Types
class String(str):
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = URIRef("http://example.com/String")
# Class references
class C1Id(extended_str):
pass
class BiolinkNameSpace:
"""
Map of BioLink Model registered URI Namespaces
"""
_namespaces = [
CurieNamespace('APO', 'http://purl.obolibrary.org/obo/APO_'),
CurieNamespace('Aeolus', 'http://translator.ncats.nih.gov/Aeolus_'),
CurieNamespace('BIOGRID', 'http://identifiers.org/biogrid/'),
CurieNamespace('BIOSAMPLE', 'http://identifiers.org/biosample/'),
CurieNamespace('BSPO', 'http://purl.obolibrary.org/obo/BSPO_'),
CurieNamespace(
'CAID',
'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid='
),
CurieNamespace('CAS', 'http://identifiers.org/cas/'),
CurieNamespace('CATH', 'http://identifiers.org/cath/'),
CurieNamespace('CATH_SUPERFAMILY',
'http://identifiers.org/cath.superfamily/'),
CurieNamespace('CDD', 'http://identifiers.org/cdd/'),
CurieNamespace('CHADO', 'http://gmod.org/wiki/Chado/'),
CurieNamespace('CHEBI', 'http://purl.obolibrary.org/obo/CHEBI_'),
CurieNamespace('CHEMBL_COMPOUND',
'http://identifiers.org/chembl.compound/'),
CurieNamespace('CHEMBL_MECHANISM',
'https://www.ebi.ac.uk/chembl/mechanism/inspect/'),
CurieNamespace('CHEMBL_TARGET',
'http://identifiers.org/chembl.target/'),
CurieNamespace('CID', 'http://pubchem.ncbi.nlm.nih.gov/compound/'),
CurieNamespace('CL', 'http://purl.obolibrary.org/obo/CL_'),
CurieNamespace('CLINVAR', 'http://identifiers.org/clinvar/'),
CurieNamespace('CLO', 'http://purl.obolibrary.org/obo/CLO_'),
CurieNamespace('COAR_RESOURCE', 'http://purl.org/coar/resource_type/'),
CurieNamespace('CPT',
'https://www.ama-assn.org/practice-management/cpt/'),
CurieNamespace('CTD', 'http://translator.ncats.nih.gov/CTD_'),
CurieNamespace(
'ChemBank',
'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid='
),
CurieNamespace('ClinVarVariant',
'http://www.ncbi.nlm.nih.gov/clinvar/variation/'),
CurieNamespace('DBSNP', 'http://identifiers.org/dbsnp/'),
CurieNamespace('DGIdb', 'https://www.dgidb.org/interaction_types'),
CurieNamespace('DOID', 'http://purl.obolibrary.org/obo/DOID_'),
CurieNamespace('DRUGBANK', 'http://identifiers.org/drugbank/'),
CurieNamespace('DrugCentral',
'http://translator.ncats.nih.gov/DrugCentral_'),
CurieNamespace('EC', 'http://www.enzyme-database.org/query.php?ec='),
CurieNamespace('ECTO', 'http://purl.obolibrary.org/obo/ECTO_'),
CurieNamespace('EDAM-DATA', 'http://edamontology.org/data_'),
CurieNamespace('EDAM-FORMAT', 'http://edamontology.org/format_'),
CurieNamespace('EDAM-OPERATION', 'http://edamontology.org/operation_'),
CurieNamespace('EDAM-TOPIC', 'http://edamontology.org/topic_'),
CurieNamespace('EFO', 'http://www.ebi.ac.uk/efo/EFO_'),
CurieNamespace('EGGNOG', 'http://identifiers.org/eggnog/'),
CurieNamespace('ENSEMBL', 'http://identifiers.org/ensembl/'),
CurieNamespace('ExO', 'http://purl.obolibrary.org/obo/ExO_'),
CurieNamespace('FAO', 'http://purl.obolibrary.org/obo/FAO_'),
CurieNamespace('FB', 'http://identifiers.org/fb/'),
CurieNamespace('FBcv', 'http://purl.obolibrary.org/obo/FBcv_'),
CurieNamespace('GAMMA', 'http://translator.renci.org/GAMMA_'),
CurieNamespace('GO', 'http://purl.obolibrary.org/obo/GO_'),
CurieNamespace('GOLD_META', 'http://identifiers.org/gold.meta/'),
CurieNamespace('GOP', 'http://purl.obolibrary.org/obo/go#'),
CurieNamespace('GOREL', 'http://purl.obolibrary.org/obo/GOREL_'),
CurieNamespace('GSID', 'https://scholar.google.com/citations?user='******'GTEx', 'https://www.gtexportal.org/home/gene/'),
CurieNamespace(
'GTOPDB',
'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId='
),
CurieNamespace('HAMAP', 'http://identifiers.org/hamap/'),
CurieNamespace('HANCESTRO', 'http://www.ebi.ac.uk/ancestro/ancestro_'),
CurieNamespace('HCPCS', 'http://purl.bioontology.org/ontology/HCPCS/'),
CurieNamespace('HGNC', 'http://identifiers.org/hgnc/'),
CurieNamespace('HGNC_FAMILY', 'http://identifiers.org/hgnc.family/'),
CurieNamespace('HMDB', 'http://identifiers.org/hmdb/'),
CurieNamespace('HP', 'http://purl.obolibrary.org/obo/HP_'),
CurieNamespace('HsapDv', 'http://purl.obolibrary.org/obo/HsapDv_'),
CurieNamespace('ICD0', 'http://translator.ncats.nih.gov/ICD0_'),
CurieNamespace('ICD10', 'http://translator.ncats.nih.gov/ICD10_'),
CurieNamespace('ICD9', 'http://translator.ncats.nih.gov/ICD9_'),
CurieNamespace('INCHI', 'http://identifiers.org/inchi/'),
CurieNamespace('INCHIKEY', 'http://identifiers.org/inchikey/'),
CurieNamespace('INO', 'http://purl.obolibrary.org/obo/INO_'),
CurieNamespace('INTACT', 'http://identifiers.org/intact/'),
CurieNamespace('IUPHAR_FAMILY',
'http://identifiers.org/iuphar.family/'),
CurieNamespace('KEGG', 'http://identifiers.org/kegg/'),
CurieNamespace('KEGG_BRITE', 'http://www.kegg.jp/entry/'),
CurieNamespace('KEGG_COMPOUND',
'http://identifiers.org/kegg.compound/'),
CurieNamespace('KEGG_DGROUP', 'http://www.kegg.jp/entry/'),
CurieNamespace('KEGG_DISEASE', 'http://identifiers.org/kegg.disease/'),
CurieNamespace('KEGG_DRUG', 'http://identifiers.org/kegg.drug/'),
CurieNamespace('KEGG_ENVIRON', 'http://identifiers.org/kegg.environ/'),
CurieNamespace('KEGG_ENZYME', 'http://www.kegg.jp/entry/'),
CurieNamespace('KEGG_GENE', 'http://www.kegg.jp/entry/'),
CurieNamespace('KEGG_GLYCAN', 'http://identifiers.org/kegg.glycan/'),
CurieNamespace('KEGG_MODULE', 'http://identifiers.org/kegg.module/'),
CurieNamespace('KEGG_ORTHOLOGY',
'http://identifiers.org/kegg.orthology/'),
CurieNamespace('KEGG_RCLASS', 'http://www.kegg.jp/entry/'),
CurieNamespace('KEGG_REACTION',
'http://identifiers.org/kegg.reaction/'),
CurieNamespace('LOINC', 'http://loinc.org/rdf/'),
CurieNamespace('MEDDRA', 'http://identifiers.org/meddra/'),
CurieNamespace('MESH', 'http://identifiers.org/mesh/'),
CurieNamespace('MGI', 'http://identifiers.org/mgi/'),
CurieNamespace('MI', 'http://purl.obolibrary.org/obo/MI_'),
CurieNamespace('MIR', 'http://identifiers.org/mir/'),
CurieNamespace('MONDO', 'http://purl.obolibrary.org/obo/MONDO_'),
CurieNamespace('MP', 'http://purl.obolibrary.org/obo/MP_'),
CurieNamespace('MSigDB', 'https://www.gsea-msigdb.org/gsea/msigdb/'),
CurieNamespace('MetaCyc', 'http://translator.ncats.nih.gov/MetaCyc_'),
CurieNamespace('NCBIGENE', 'http://identifiers.org/ncbigene/'),
CurieNamespace('NCBITaxon',
'http://purl.obolibrary.org/obo/NCBITaxon_'),
CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_'),
CurieNamespace('NDC', 'http://identifiers.org/ndc/'),
CurieNamespace('NDDF', 'http://purl.bioontology.org/ontology/NDDF/'),
CurieNamespace('NLMID',
'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term='),
CurieNamespace('OBAN', 'http://purl.org/oban/'),
CurieNamespace('OBOREL', 'http://purl.obolibrary.org/obo/RO_'),
CurieNamespace('OIO', 'http://www.geneontology.org/formats/oboInOwl#'),
CurieNamespace('OMIM', 'http://purl.obolibrary.org/obo/OMIM_'),
CurieNamespace('ORCID', 'https://orcid.org/'),
CurieNamespace('ORPHA', 'http://www.orpha.net/ORDO/Orphanet_'),
CurieNamespace('ORPHANET', 'http://identifiers.org/orphanet/'),
CurieNamespace('PANTHER_FAMILY',
'http://identifiers.org/panther.family/'),
CurieNamespace('PANTHER_PATHWAY',
'http://identifiers.org/panther.pathway/'),
CurieNamespace('PATO', 'http://purl.obolibrary.org/obo/PATO_'),
CurieNamespace('PATO-PROPERTY',
'http://purl.obolibrary.org/obo/pato#'),
CurieNamespace('PDQ', 'https://www.cancer.gov/publications/pdq#'),
CurieNamespace('PFAM', 'http://identifiers.org/pfam/'),
CurieNamespace('PHARMGKB_DRUG',
'http://identifiers.org/pharmgkb.drug/'),
CurieNamespace('PHARMGKB_PATHWAYS',
'http://identifiers.org/pharmgkb.pathways/'),
CurieNamespace('PHAROS', 'http://pharos.nih.gov'),
CurieNamespace('PIRSF', 'http://identifiers.org/pirsf/'),
CurieNamespace('PMID', 'http://www.ncbi.nlm.nih.gov/pubmed/'),
CurieNamespace('PO', 'http://purl.obolibrary.org/obo/PO_'),
CurieNamespace('POMBASE', 'http://identifiers.org/pombase/'),
CurieNamespace('PR', 'http://purl.obolibrary.org/obo/PR_'),
CurieNamespace('PRINTS', 'http://identifiers.org/prints/'),
CurieNamespace('PRODOM', 'http://identifiers.org/prodom/'),
CurieNamespace('PROSITE', 'http://identifiers.org/prosite/'),
CurieNamespace('PUBCHEM_COMPOUND',
'http://identifiers.org/pubchem.compound/'),
CurieNamespace('PUBCHEM_SUBSTANCE',
'http://identifiers.org/pubchem.substance/'),
CurieNamespace('PathWhiz', 'http://smpdb.ca/pathways/#'),
CurieNamespace('REACT', 'http://www.reactome.org/PathwayBrowser/#/'),
CurieNamespace('REPODB', 'http://apps.chiragjpgroup.org/repoDB/'),
CurieNamespace('RFAM', 'http://identifiers.org/rfam/'),
CurieNamespace('RGD', 'http://identifiers.org/rgd/'),
CurieNamespace('RHEA', 'http://identifiers.org/rhea/'),
CurieNamespace('RNACENTRAL', 'http://identifiers.org/rnacentral/'),
CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_'),
CurieNamespace('RTXKG1', 'http://kg1endpoint.rtx.ai/'),
CurieNamespace(
'RXCUI',
'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm='),
CurieNamespace('RXNORM',
'http://purl.bioontology.org/ontology/RXNORM/'),
CurieNamespace('ResearchID', 'https://publons.com/researcher/'),
CurieNamespace('SEMMEDDB', 'https://skr3.nlm.nih.gov/SemMedDB'),
CurieNamespace('SGD', 'http://identifiers.org/sgd/'),
CurieNamespace('SIDER_DRUG', 'http://identifiers.org/sider.drug/'),
CurieNamespace('SIO', 'http://semanticscience.org/resource/SIO_'),
CurieNamespace('SMART', 'http://identifiers.org/smart/'),
CurieNamespace('SMPDB', 'http://identifiers.org/smpdb/'),
CurieNamespace('SNOMEDCT', 'http://identifiers.org/snomedct/'),
CurieNamespace('SNPEFF', 'http://translator.ncats.nih.gov/SNPEFF_'),
CurieNamespace('SUPFAM', 'http://identifiers.org/supfam/'),
CurieNamespace('ScopusID',
'https://www.scopus.com/authid/detail.uri?authorId='),
CurieNamespace('TAXRANK', 'http://purl.obolibrary.org/obo/TAXRANK_'),
CurieNamespace('TCDB', 'http://identifiers.org/tcdb/'),
CurieNamespace('TIGRFAM', 'http://identifiers.org/tigrfam/'),
CurieNamespace('UBERGRAPH',
'http://translator.renci.org/ubergraph-axioms.ofn#'),
CurieNamespace('UBERON', 'http://purl.obolibrary.org/obo/UBERON_'),
CurieNamespace('UBERON_CORE',
'http://purl.obolibrary.org/obo/uberon/core#'),
CurieNamespace('UMLS', 'http://identifiers.org/umls/'),
CurieNamespace(
'UMLSSC',
'https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt/code#'),
CurieNamespace(
'UMLSSG',
'https://metamap.nlm.nih.gov/Docs/SemGroups_2018.txt/group#'),
CurieNamespace(
'UMLSST',
'https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt/type#'),
CurieNamespace('UNII', 'http://identifiers.org/unii/'),
CurieNamespace('UNIPROT_ISOFORM',
'http://identifiers.org/uniprot.isoform/'),
CurieNamespace('UO', 'http://purl.obolibrary.org/obo/UO_'),
CurieNamespace('UPHENO', 'http://purl.obolibrary.org/obo/UPHENO_'),
CurieNamespace('UniProtKB', 'http://identifiers.org/uniprot/'),
CurieNamespace(
'VANDF',
'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'
),
CurieNamespace('VMC', 'https://github.com/ga4gh/vr-spec/'),
CurieNamespace('WB', 'http://identifiers.org/wb/'),
CurieNamespace('WBPhenotype',
'http://purl.obolibrary.org/obo/WBPhenotype_'),
CurieNamespace('WBVocab', 'http://bio2rdf.org/wormbase_vocabulary'),
CurieNamespace('WIKIDATA', 'https://www.wikidata.org/wiki/'),
CurieNamespace('WIKIDATA_PROPERTY',
'https://www.wikidata.org/wiki/Property:'),
CurieNamespace('WIKIPATHWAYS', 'http://identifiers.org/wikipathways/'),
CurieNamespace('WormBase', 'https://www.wormbase.org/get?name='),
CurieNamespace('ZFIN', 'http://identifiers.org/zfin/'),
CurieNamespace('ZP', 'http://purl.obolibrary.org/obo/ZP_'),
CurieNamespace('alliancegenome', 'https://www.alliancegenome.org/'),
CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/'),
CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/'),
CurieNamespace('chembio', 'http://translator.ncats.nih.gov/chembio_'),
CurieNamespace('dcat', 'http://www.w3.org/ns/dcat#'),
CurieNamespace('dct', 'http://purl.org/dc/terms/'),
CurieNamespace('dictyBase', 'http://dictybase.org/gene/'),
CurieNamespace('doi', 'https://doi.org/'),
CurieNamespace('fabio', 'http://purl.org/spar/fabio/'),
CurieNamespace('foaf', 'http://xmlns.com/foaf/0.1/'),
CurieNamespace('foodb_compound', 'http://foodb.ca/compounds/'),
CurieNamespace(
'gff3',
'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#'
),
CurieNamespace(
'gpi',
'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#'
),
CurieNamespace('gtpo', 'https://rdf.guidetopharmacology.org/ns/gtpo#'),
CurieNamespace('hetio', 'http://translator.ncats.nih.gov/hetio_'),
CurieNamespace('interpro', 'https://www.ebi.ac.uk/interpro/entry/'),
CurieNamespace('isbn',
'https://www.isbn-international.org/identifier/'),
CurieNamespace('isni', 'https://isni.org/isni/'),
CurieNamespace('issn', 'https://portal.issn.org/resource/ISSN/'),
CurieNamespace('medgen', 'https://www.ncbi.nlm.nih.gov/medgen/'),
CurieNamespace('oboformat',
'http://www.geneontology.org/formats/oboInOWL#'),
CurieNamespace('pav', 'http://purl.org/pav/'),
CurieNamespace('prov', 'http://www.w3.org/ns/prov#'),
CurieNamespace('qud', 'http://qudt.org/1.1/schema/qudt#'),
CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'),
CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#'),
CurieNamespace('schema', 'http://schema.org/'),
CurieNamespace('skos', 'https://www.w3.org/TR/skos-reference/#'),
CurieNamespace('wgs', 'http://www.w3.org/2003/01/geo/wgs84_pos'),
CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#'),
]
# class level dictionaries
_prefix_map: Dict[str, CurieNamespace] = {}
@classmethod
def _get_prefix_map(cls):
if not cls._prefix_map:
for ns in cls._namespaces:
# index by upper case for uniformity of search
cls._prefix_map[ns.prefix.upper()] = ns
return cls._prefix_map
@classmethod
def parse_curie(cls, curie: str) -> Tuple[CurieNamespace, str]:
"""
Parse a candidate CURIE
:param curie: candidate curie string
:return: CURIE namespace and object_id
"""
found = CurieNamespace(
"",
""), curie # default value if not a CURIE or unknown XMLNS prefix
if ':' in curie:
part = curie.split(":")
# Normalize retrieval with upper case of prefix for lookup
prefix = part[0].upper()
if prefix in cls._get_prefix_map():
found = cls._prefix_map[prefix], part[1]
return found
@classmethod
def parse_uri(cls, uri: str) -> Tuple[CurieNamespace, str]:
"""
Parse a candidate URI
:param uri: candidate URI string
:return: namespace and object_id
"""
found = CurieNamespace(
"", ""), uri # default value returned if unknown URI namespace
# TODO: is there a more efficient lookup scheme here than a linear search of namespaces?
for ns in cls._namespaces:
base_uri = str(ns)
if uri.startswith(base_uri):
# simple minded deletion of base_uri to give the object_id
object_id = uri.replace(base_uri, "")
found = ns, object_id
break
return found
@classmethod
def parse_identifier(cls, identifier: str) -> Tuple[CurieNamespace, str]:
# trivial case of a null identifier?
if not identifier:
return CurieNamespace("", ""), ""
# check if this is a candidate URI...
if identifier.lower().startswith("http"):
# guess that perhaps it is, so try to parse it
return cls.parse_uri(identifier)
else: # attempt to parse as a CURIE
return cls.parse_curie(identifier)
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from includes.types import String
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINKML = CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/')
DEFAULT_ = CurieNamespace('', 'https://microbiomedata/schema/')
# Types
# Class references
@dataclass
class Biosample(YAMLRoot):
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = URIRef(
"https://microbiomedata/schema/Biosample")
class_class_curie: ClassVar[str] = None
class_name: ClassVar[str] = "biosample"
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from biolinkml.utils.metamodelcore import URIorCURIE
from includes.types import String, Uriorcurie
metamodel_version = "1.6.1"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINKML = CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/')
META = CurieNamespace('meta', 'https://w3id.org/biolink/biolinkml/meta/')
DEFAULT_ = META
# Types
# Class references
@dataclass
class Extension(YAMLRoot):
"""
a tag/value pair used to add non-model information to an entry
"""
_inherited_slots: ClassVar[List[str]] = []
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from biolinkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from biolinkml.utils.metamodelcore import ElementIdentifier
from includes.types import Integer, Objectidentifier, String
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/')
BIOLINKML = CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/')
EX = CurieNamespace('ex', 'http://example.org/')
MODEL = CurieNamespace('model', 'https://w3id.org/biolink/')
DEFAULT_ = BIOLINK
# Types
# Class references
class PersonId(ElementIdentifier):
pass
@dataclass
class Person(YAMLRoot):
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from includes.types import String
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINKML = CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/')
TYPES = CurieNamespace('types', 'https://ccdh.org/datatypes/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = TYPES
# Types
class Literal(String):
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "literal"
type_model_uri = TYPES.Literal
# Class references
from ..core.filters import FilterComponent
from ..core.localidentifiers import CodeSystemName
from ..core.references import CodeSystemReference, CodeSystemReferenceName, CodeSystemVersionReference, CodeSystemVersionReferenceName, FormatReference, FormatReferenceName, LanguageReference, LanguageReferenceName, MapReference, MapReferenceName, MatchAlgorithmReference, MatchAlgorithmReferenceName, NameAndMeaningReference, NameAndMeaningReferenceName, OntologyLanguageReference, OntologyLanguageReferenceName, OntologySyntaxReference, OntologySyntaxReferenceName, PredicateReference, RoleReference, RoleReferenceName, ValueSetDefinitionReference, ValueSetDefinitionReferenceName, ValueSetReference, ValueSetReferenceName, VersionTagReference, VersionTagReferenceName
from ..core.resourcedescription import SourceAndNotation
from ..core.uritypes import DocumentURI, ExternalURI, LocalURI, PersistentURI, RenderingURI
from biolinkml.utils.metamodelcore import Bool, URIorCURIE, XSDDateTime
from includes.types import Boolean, String
from valuesetdefinition import AssociatedEntitiesReference, CompleteCodeSystemReference, CompleteValueSetReference, ExternalValueSetDefinition, FormalDefinition, PropertyQueryReference, SpecificEntityList, SpecificEntityListNamespaceURI, ValueSetDefinitionEntry
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINKML = CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/')
RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#')
SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#')
TCCM = CurieNamespace('tccm', 'https://hotecosystem.org/tccm/')
DEFAULT_ = TCCM
# Types
# Class references
@dataclass
class ResolvedValueSetHeader(YAMLRoot):
"""
The information required to completely resolve a value set definition.
"""
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from biolinkml.utils.metamodelcore import Bool, ElementIdentifier, NCName, NodeIdentifier, URI, URIorCURIE, XSDDate, XSDDateTime, XSDTime
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
METATYPE = CurieNamespace('metatype',
'https://w3id.org/biolink/biolinkml/meta/types/')
SHEX = CurieNamespace('shex', 'http://www.w3.org/ns/shex#')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = METATYPE
# Types
class String(str):
""" A character string """
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = METATYPE.String
class Integer(int):
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from includes.types import String
metamodel_version = "1.6.1"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
META = CurieNamespace('meta', 'https://w3id.org/biolink/biolinkml/')
DEFAULT_ = CurieNamespace('', 'https://example.com/test14/')
# Types
# Class references
class NamedThingId(extended_str):
pass
class MixinOwnerId(NamedThingId):
pass
class SubjectRange1Id(NamedThingId):
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from biolinkml.utils.metamodelcore import URIorCURIE
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
TCCM = CurieNamespace('tccm', 'https://hotecosystem.org/tccm/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = TCCM
# Types
class ValueSet(URIorCURIE):
""" A URI that can be indirectly resolved to a set of entity descriptions """
type_class_uri = XSD.anyURI
type_class_curie = "xsd:anyURI"
type_name = "ValueSet"
type_model_uri = TCCM.ValueSet
class ASSOCIATION(ValueSet):
""" A formal “semantic” assertion about a named entity, in the form of subject, predicate, and object including any
from biolinkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
XSD = CurieNamespace('xsd', 'http://example.org/UNKNOWN/xsd/')
DEFAULT_ = CurieNamespace('', 'https://issue_test/106/schema/')
# Types
class String(str):
""" A character string """
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = URIRef("https://issue_test/106/schema/String")
# Class references
if sys.version_info < (3, 7, 6):
from biolinkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from biolinkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from biolinkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from biolinkml.utils.curienamespace import CurieNamespace
from biolinkml.utils.metamodelcore import Bool, ElementIdentifier, NCName, NodeIdentifier, URI, URIorCURIE, XSDDate, XSDDateTime, XSDTime
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
SHEX = CurieNamespace('shex', 'http://www.w3.org/ns/shex#')
SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#')
TEST = CurieNamespace('test', 'http://example.org/test/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = TEST
# Types
class String(str):
""" A character string """
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = TEST.String
