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