pyobo 0.10.5__py3-none-any.whl → 0.10.7__py3-none-any.whl

pyobo/sources/umls/synonym_types.tsv

@@ -1,242 +1,243 @@
-key	name
-AA	Attribute type abbreviation
-AB	Abbreviation in any source vocabulary
-ACR	Acronym
-AC	Activities
-AD	Adjective
-AM	Short form of modifier
-AS	Attribute type synonym
-AT	Attribute type
-AUN	Authority name
-BD	Fully-specified drug brand name that can be prescribed
-BN	Fully-specified drug brand name that can not be prescribed
-BPCK	Branded Drug Delivery Device
-BR	Binding realm
-CA2	ISO 3166-1 standard country code in alpha-2 (two-letter) format
-CA3	ISO 3166-1 standard country code in alpha-3 (three-letter) format
-CCN	Chemical code name
-CCS	FIPS 10-4 country code
-CC	Trimmed ICPC component process
-CDA	Clinical drug name in abbreviated format
-CDC	Clinical drug name in concatenated format (NDDF), Clinical drug name (NDFRT)
-CDD	Clinical drug name in delimited format
-CDO	Concept domain
-CD	Clinical Drug
-CE	Entry term for a Supplementary Concept
-CHN	Chemical structure name
-CL	Class
-CMN	Common name
-CN	LOINC official component name
-CO	Component name (these are hierarchical terms, as opposed to the LOINC component names which are analytes)
-CPR	Concept property
-CP	ICPC component process (in original form)
-CR	Concept relationship
-CSN	Chemical Structure Name
-CSY	Code system
-CS	Short component process in ICPC, i.e. include some abbreviations
-CU	Common usage
-CV	Content view
-CX	Component, with abbreviations expanded.
-DC10	Diagnostic criteria for ICD10 code
-DC9	Diagnostic criteria for ICD9 code
-DEV	Descriptor entry version
-DE	Descriptor
-DFG	Dose Form Group
-DF	Dose Form
-DI	Disease name
-DN	Display Name
-DO	Domain
-DP	Drug Product
-DSV	Descriptor sort version
-DS	Short form of descriptor
-DT	Definitional term, present in the Metathesaurus because of its connection to a Dorland's definition or to a definition created especially for the Metathesaurus
-EP	Print entry term
-EQ	Equivalent name
-ES	Short form of entry term
-ETAL	Entry Term Alias
-ETCF	Entry term, consumer friendly description
-ETCLIN	Entry term, clinician description
-ET	Entry term
-EX	Expanded form of entry term
-FBD	Foreign brand name
-FI	Finding name
-FN	Full form of descriptor
-FSY	Foreign Synonym
-GLP	Global period
-GN	Generic drug name
-GO	Goal
-GPCK	Generic Drug Delivery Device
-GT	Glossary term
-HC	Hierarchical class
-HD	Hierarchical descriptor
-HGJKN1	Japanese High Level Group Term (kana1)
-HGJKN	Japanese High Level Group Term (kana)
-HG	High Level Group Term
-HS	Short or alternate version of hierarchical term
-HTJKN1	Japanese Hierarchical term (kana1)
-HTJKN	Japanese Hierarchical term (kana)
-HTN	HL7 Table Name
-HT	Hierarchical term
-HX	Expanded version of short hierarchical term
-ID	Nursing indicator
-IN	Name for an ingredient
-IS	Obsolete Synonym
-IT	Index term
-IVC	Intervention categories
-IV	Intervention
-LA	LOINC answer
-LC	Long common name
-LG	LOINC group
-LLTJKN1	Japanese Lower Level Term (kana1)
-LLTJKN	Japanese Lower Level Term (kana)
-LLT	Lower Level Term
-LN	LOINC official fully specified name
-LO	Obsolete official fully specified name
-LPDN	LOINC parts display name
-LPN	LOINC parts name
-LS	Expanded system/sample type (The expanded version was created for the Metathesaurus and includes the full name of some abbreviations.)
-LVDN	Linguistic variant display name
-LV	Lexical variant
-MD	CCS multi-level diagnosis categories
-MH	Main heading
-MIN	name for a multi-ingredient
-MP	Preferred names of modifiers
-MS	Multum names of branded and generic supplies or supplements
-MTH_ACR	MTH acronym
-MTH_CN	MTH Component, with abbreviations expanded.
-MTH_ET	Metathesaurus entry term
-MTH_FN	MTH Full form of descriptor
-MTH_HG	MTH High Level Group Term
-MTH_HT	MTH Hierarchical term
-MTH_HX	MTH Hierarchical term expanded
-MTH_IS	Metathesaurus-supplied form of obsolete synonym
-MTH_LLT	MTH Lower Level Term
-MTH_LN	MTH Official fully specified name with expanded abbreviations
-MTH_LO	MTH Expanded LOINC obsolete fully specified name
-MTH_OAF	Metathesaurus-supplied form of obsolete active fully specified name
-MTH_OAP	Metathesaurus-supplied form of obsolete active preferred term
-MTH_OAS	Metathesaurus-supplied form of obsolete active synonym
-MTH_OET	Metathesaurus obsolete entry term
-MTH_OF	Metathesaurus-supplied form of obsolete fully specified name
-MTH_OL	MTH Non-current Lower Level Term
-MTH_OPN	Metathesaurus obsolete preferred term, natural language form
-MTH_OP	Metathesaurus obsolete preferred term
-MTH_OS	MTH System-organ class
-MTH_PTGB	Metathesaurus-supplied form of British preferred term
-MTH_PTN	Metathesaurus preferred term, natural language form
-MTH_PT	Metathesaurus preferred term
-MTH_RXN_BD	RxNorm Created BD
-MTH_RXN_CDC	RxNorm Created CDC
-MTH_RXN_CD	RxNorm Created CD
-MTH_RXN_DP	RxNorm Created DP
-MTH_SI	MTH Sign or symptom of
-MTH_SMQ	Metathesaurus version of Standardised MedDRA Query
-MTH_SYGB	Metathesaurus-supplied form of British synonym
-MTH_SY	MTH Designated synonym
-MV	Multi-level procedure category
-N1	Chemical Abstracts Service Type 1 name of a chemical
-NA	Name aliases
-NM	Name of Supplementary Concept
-NPT	HL7 non-preferred for language term
-NP	Non-preferred term
-NS	Short form of non-preferred term
-NX	Expanded form of non-preferred term
-OAF	Obsolete active fully specified name
-OAM	Obsolete Modifier Abbreviation
-OAP	Obsolete active preferred term
-OAS	Obsolete active synonym
-OA	Obsolete abbreviation
-OC	Nursing outcomes
-OET	Obsolete entry term
-OF	Obsolete fully specified name
-OLC	Obsolete Long common name
-OLG	Obsolete LOINC group name
-OLJKN1	Japanese Non-current Lower Level Term (kana1)
-OLJKN	Japanese Non-current Lower Level Term (kana)
-OL	Non-current Lower Level Term
-OM	Obsolete modifiers in HCPCS
-ONP	Obsolete non-preferred for language term
-OOSN	Obsolete official short name
-OPN	Obsolete preferred term, natural language form
-OP	Obsolete preferred name
-OR	Orders
-OSJKN1	Japanese System-organ class in the WHO Adverse Reaction Terminology (kana1)
-OSJKN	Japanese System-organ class in the WHO Adverse Reaction Terminology (kana)
-OSN	Official short name
-OS	System-organ class
-PCE	Preferred entry term for Supplementary Concept
-PC	"Preferred ""trimmed term"" in ICPC"
-PEP	Preferred entry term
-PHENO_ET	Phenotype entry term
-PHENO	Phenotype
-PIN	Name from a precise ingredient
-PM	Machine permutation
-PN	Metathesaurus preferred name
-POS	Place of service
-PQ	Qualifier for a problem
-PR	Name of a problem
-PSC	Protocol selection criteria
-PSN	Prescribable Names
-PS	Short forms that needed full specification
-PTAV	Preferred Allelic Variant
-PTCS	Preferred Clinical Synopsis
-PTGB	British preferred term
-PTJKN1	Japanese Designated preferred name (kana1)
-PTJKN	Japanese Designated preferred name (kana)
-PTN	Preferred term, natural language form
-PT	Designated preferred name
-PXQ	Preferred qualifier term
-PX	Expanded preferred terms (pair with PS)
-QAB	Qualifier abbreviation
-QEV	Qualifier entry version
-QSV	Qualifier sort version
-RAB	Root abbreviation
-RHT	Root hierarchical term
-RPT	Root preferred term
-RSY	Root synonym
-RS	Extracted related names in SNOMED2
-RT	Term that is related to, but often considered non-synonymous with, the preferred term
-RXN_IN	Rxnorm Preferred Ingredient
-RXN_PT	Rxnorm Preferred
-SBDC	Semantic Branded Drug Component
-SBDF	Semantic branded drug and form
-SBDG	Semantic branded drug group
-SBD	Semantic branded drug
-SB	Named subset of a source
-SCALE	Scale
-SCDC	Semantic Drug Component
-SCDF	Semantic clinical drug and form
-SCDG	Semantic clinical drug group
-SCD	Semantic Clinical Drug
-SCN	Scientific name
-SC	Special Category term
-SD	CCS single-level diagnosis categories
-SI	Name of a sign or symptom of a problem
-SMQ	Standardised MedDRA Query
-SP	CCS single-level procedure categories
-SSN	Source short name, used in the UMLS Knowledge Source Server
-SS	"Synonymous ""short"" forms"
-ST	Step
-SU	Active Substance
-SX	Mixed-case component synonym with expanded abbreviations
-SYGB	British synonym
-SYN	Designated alias
-SY	Designated synonym
-TA	Task
-TC	Term class
-TG	Name of the target of an intervention
-TMSY	Tall Man synonym
-TQ	Topical qualifier
-TX	CCPSS synthesized problems for TC termgroup
-UAUN	Unique authority name
-UCN	Unique common name
-UE	Unique equivalent name
-USN	Unique scientific name
-USY	Unique synonym
-VAB	Versioned abbreviation
-VPT	Versioned preferred term
-VSY	Versioned synonym
-VS	Value Set
-XD	Expanded descriptor in AOD
-XM	Cross mapping set
-XQ	Alternate name for a qualifier
+key	name
+AA	Attribute type abbreviation
+AB	Abbreviation in any source vocabulary
+AC	Activities
+ACR	Acronym
+AD	Adjective
+AM	Short form of modifier
+AS	Attribute type synonym
+AT	Attribute type
+BD	Fully-specified drug brand name that can be prescribed
+BN	Fully-specified drug brand name that can not be prescribed
+BPCK	Branded Drug Delivery Device
+BR	Binding realm
+CA2	ISO 3166-1 standard country code in alpha-2 (two-letter) format
+CA3	ISO 3166-1 standard country code in alpha-3 (three-letter) format
+CC	Trimmed ICPC component process
+CCN	Chemical code name
+CCS	FIPS 10-4 country code
+CD	Clinical Drug
+CDA	Clinical drug name in abbreviated format
+CDC	Clinical drug name in concatenated format (NDDF)
+CDD	Clinical drug name in delimited format
+CDO	Concept domain
+CE	Entry term for a Supplementary Concept
+CHN	Chemical structure name
+CL	Class
+CMN	Common name
+CN	LOINC official component name
+CO	Component name (these are hierarchical terms, as opposed to the LOINC component names which are analytes)
+CP	ICPC component process (in original form)
+CPR	Concept property
+CR	Concept relationship
+CS	Short component process in ICPC, i.e. include some abbreviations
+CSN	Chemical Structure Name
+CSY	Code system
+CU	Common usage
+CV	Content view
+CX	Component, with abbreviations expanded.
+DC10	Diagnostic criteria for ICD10 code
+DC9	Diagnostic criteria for ICD9 code
+DE	Descriptor
+DEV	Descriptor entry version
+DF	Dose Form
+DFG	Dose Form Group
+DI	Disease name
+DN	Display Name
+DO	Domain
+DP	Drug Product
+DS	Short form of descriptor
+DSV	Descriptor sort version
+DT	Definitional term, present in the Metathesaurus because of its connection to a Dorland's definition or to a definition created especially for the Metathesaurus
+EP	Print entry term
+EQ	Equivalent name
+ES	Short form of entry term
+ET	Entry term
+ETAL	Entry Term Alias
+ETCF	Entry term, consumer friendly description
+ETCLIN	Entry term, clinician description
+EX	Expanded form of entry term
+FBD	Foreign brand name
+FI	Finding name
+FN	Full form of descriptor
+FSY	Foreign Synonym
+GLP	Global period
+GN	Generic drug name
+GO	Goal
+GPCK	Generic Drug Delivery Device
+GT	Glossary term
+HC	Hierarchical class
+HD	Hierarchical descriptor
+HG	High Level Group Term
+HGJKN	Japanese High Level Group Term (kana)
+HGJKN1	Japanese High Level Group Term (kana1)
+HS	Short or alternate version of hierarchical term
+HT	Hierarchical term
+HTJKN	Japanese Hierarchical term (kana)
+HTJKN1	Japanese Hierarchical term (kana1)
+HTN	HL7 Table Name
+HX	Expanded version of short hierarchical term
+ID	Nursing indicator
+IN	Name for an ingredient
+IS	Obsolete Synonym
+IT	Index term
+IV	Intervention
+IVC	Intervention categories
+LA	LOINC answer
+LC	Long common name
+LG	LOINC group
+LLT	Lower Level Term
+LLTJKN	Japanese Lower Level Term (kana)
+LLTJKN1	Japanese Lower Level Term (kana1)
+LN	LOINC official fully specified name
+LO	Obsolete official fully specified name
+LPDN	LOINC parts display name
+LPN	LOINC parts name
+LS	Expanded system/sample type (The expanded version was created for the Metathesaurus and includes the full name of some abbreviations.)
+LV	Lexical variant
+LVDN	Linguistic variant display name
+MD	CCS multi-level diagnosis categories
+MH	Main heading
+MIN	name for a multi-ingredient
+MP	Preferred names of modifiers
+MS	Multum names of branded and generic supplies or supplements
+MTH_ACR	MTH acronym
+MTH_CN	MTH Component, with abbreviations expanded.
+MTH_ET	Metathesaurus entry term
+MTH_FN	MTH Full form of descriptor
+MTH_HG	MTH High Level Group Term
+MTH_HT	MTH Hierarchical term
+MTH_HX	MTH Hierarchical term expanded
+MTH_IS	Metathesaurus-supplied form of obsolete synonym
+MTH_LLT	MTH Lower Level Term
+MTH_LN	MTH Official fully specified name with expanded abbreviations
+MTH_LO	MTH Expanded LOINC obsolete fully specified name
+MTH_OAF	Metathesaurus-supplied form of obsolete active fully specified name
+MTH_OAP	Metathesaurus-supplied form of obsolete active preferred term
+MTH_OAS	Metathesaurus-supplied form of obsolete active synonym
+MTH_OET	Metathesaurus obsolete entry term
+MTH_OF	Metathesaurus-supplied form of obsolete fully specified name
+MTH_OL	MTH Non-current Lower Level Term
+MTH_OP	Metathesaurus obsolete preferred term
+MTH_OPN	Metathesaurus obsolete preferred term, natural language form
+MTH_OS	MTH System-organ class
+MTH_PT	Metathesaurus preferred term
+MTH_PTGB	Metathesaurus-supplied form of British preferred term
+MTH_PTN	Metathesaurus preferred term, natural language form
+MTH_RXN_BD	RxNorm Created BD
+MTH_RXN_CD	RxNorm Created CD
+MTH_RXN_CDC	RxNorm Created CDC
+MTH_RXN_DP	RxNorm Created DP
+MTH_SI	MTH Sign or symptom of
+MTH_SMQ	Metathesaurus version of Standardised MedDRA Query
+MTH_SY	MTH Designated synonym
+MTH_SYGB	Metathesaurus-supplied form of British synonym
+MV	Multi-level procedure category
+N1	Chemical Abstracts Service Type 1 name of a chemical
+NA	Name aliases
+NM	Name of Supplementary Concept
+NP	Non-preferred term
+NPT	HL7 non-preferred for language term
+NS	Short form of non-preferred term
+NX	Expanded form of non-preferred term
+OA	Obsolete abbreviation
+OAF	Obsolete active fully specified name
+OAM	Obsolete Modifier Abbreviation
+OAP	Obsolete active preferred term
+OAS	Obsolete active synonym
+OC	Nursing outcomes
+OET	Obsolete entry term
+OF	Obsolete fully specified name
+OL	Non-current Lower Level Term
+OLC	Obsolete Long common name
+OLG	Obsolete LOINC group name
+OLJKN	Japanese Non-current Lower Level Term (kana)
+OLJKN1	Japanese Non-current Lower Level Term (kana1)
+OM	Obsolete modifiers in HCPCS
+ONP	Obsolete non-preferred for language term
+OOSN	Obsolete official short name
+OP	Obsolete preferred name
+OPN	Obsolete preferred term, natural language form
+OR	Orders
+OS	System-organ class
+OSJKN	Japanese System-organ class in the WHO Adverse Reaction Terminology (kana)
+OSJKN1	Japanese System-organ class in the WHO Adverse Reaction Terminology (kana1)
+OSN	Official short name
+PC	"Preferred ""trimmed term"" in ICPC"
+PCE	Preferred entry term for Supplementary Concept
+PEP	Preferred entry term
+PHENO	Phenotype
+PHENO_ET	Phenotype entry term
+PIN	Name from a precise ingredient
+PM	Machine permutation
+PN	Metathesaurus preferred name
+POS	Place of service
+PQ	Qualifier for a problem
+PR	Name of a problem
+PS	Short forms that needed full specification
+PSC	Protocol selection criteria
+PSN	Prescribable Names
+PT	Designated preferred name
+PTAV	Preferred Allelic Variant
+PTCS	Preferred Clinical Synopsis
+PTGB	British preferred term
+PTJKN	Japanese Designated preferred name (kana)
+PTJKN1	Japanese Designated preferred name (kana1)
+PTN	Preferred term, natural language form
+PX	Expanded preferred terms (pair with PS)
+PXQ	Preferred qualifier term
+QAB	Qualifier abbreviation
+QEV	Qualifier entry version
+QSV	Qualifier sort version
+RAB	Root abbreviation
+RHT	Root hierarchical term
+RPT	Root preferred term
+RS	Extracted related names in SNOMED2
+RSY	Root synonym
+RT	Term that is related to, but often considered non-synonymous with, the preferred term
+RXN_IN	Rxnorm Preferred Ingredient
+RXN_PT	Rxnorm Preferred
+SB	Named subset of a source
+SBD	Semantic branded drug
+SBDC	Semantic Branded Drug Component
+SBDF	Semantic branded drug and form
+SBDFP	Semantic branded drug and form with precise ingredient as basis of strength
+SBDG	Semantic branded drug group
+SC	Special Category term
+SCALE	Scale
+SCD	Semantic Clinical Drug
+SCDC	Semantic Drug Component
+SCDF	Semantic clinical drug and form
+SCDFP	Semantic clinical drug and form with precise ingredient as basis of strength
+SCDG	Semantic clinical drug group
+SCDGP	Semantic clinical drug group with precise ingredient as basis of strength
+SCN	Scientific name
+SD	CCS diagnosis categories
+SI	Name of a sign or symptom of a problem
+SMQ	Standardised MedDRA Query
+SP	CCS procedure categories
+SS	"Synonymous ""short"" forms"
+SSN	Source short name, used in the UMLS Knowledge Source Server
+ST	Step
+SU	Active Substance
+SX	Mixed-case component synonym with expanded abbreviations
+SY	Designated synonym
+SYGB	British synonym
+SYN	Designated alias
+TA	Task
+TC	Term class
+TG	Name of the target of an intervention
+TMSY	Tall Man synonym
+TQ	Topical qualifier
+TX	CCPSS synthesized problems for TC termgroup
+UCN	Unique common name
+UE	Unique equivalent name
+USN	Unique scientific name
+USY	Unique synonym
+VAB	Versioned abbreviation
+VPT	Versioned preferred term
+VS	Value Set
+VSY	Versioned synonym
+XD	Expanded descriptor in AOD
+XM	Cross mapping set
+XQ	Alternate name for a qualifier

pyobo/sources/umls/umls.py

@@ -7,7 +7,6 @@ Run with ``python -m pyobo.sources.umls``
 
 import itertools as itt
 import operator
-import os
 from typing import Iterable
 
 import bioregistry
@@ -16,14 +15,13 @@ from tqdm.auto import tqdm
 from umls_downloader import open_umls
 
 from pyobo import Obo, Reference, Synonym, SynonymTypeDef, Term
-from pyobo.utils.io import open_map_tsv
+
+from .get_synonym_types import get_umls_synonyms
 
 __all__ = [
     "UMLSGetter",
 ]
 
-HERE = os.path.abspath(os.path.dirname(__file__))
-SYNONYM_TYPE_PATH = os.path.join(HERE, "synonym_types.tsv")
 
 RRF_COLUMNS = [
     "CUI",
@@ -48,10 +46,8 @@ RRF_COLUMNS = [
 ]
 
 PREFIX = "umls"
-
 SOURCE_VOCAB_URL = "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html"
-
-SYNONYM_ABB = open_map_tsv(SYNONYM_TYPE_PATH)
+SYNONYM_ABB = get_umls_synonyms()
 
 
 class UMLSGetter(Obo):

pyobo/sources/uniprot/uniprot.py

@@ -30,7 +30,7 @@ class UniProtGetter(Obo):
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
-        yield from iter_terms(force=force, version=self._version_or_raise)
+        yield from iter_terms(version=self._version_or_raise)
 
 
 def get_obo(force: bool = False) -> Obo:
@@ -38,9 +38,9 @@ def get_obo(force: bool = False) -> Obo:
     return UniProtGetter(force=force)
 
 
-def iter_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Term]:
+def iter_terms(version: Optional[str] = None) -> Iterable[Term]:
     """Iterate over UniProt Terms."""
-    with open_reader(ensure(version=version, force=force)) as reader:
+    with open_reader(ensure(version=version)) as reader:
         _ = next(reader)  # header
         for uniprot_id, name, taxonomy_id, _synonyms, ecs, pubmeds, pdbs in tqdm(
             reader, desc="Mapping UniProt", unit_scale=True
@@ -63,11 +63,11 @@ def iter_terms(version: Optional[str] = None, force: bool = False) -> Iterable[T
             yield term
 
 
-def ensure(version: Optional[str] = None, force: bool = False) -> Path:
+def ensure(version: Optional[str] = None) -> Path:
     """Ensure the reviewed uniprot names are available."""
     if version is None:
         version = bioversions.get_version("uniprot")
-    return RAW_MODULE.ensure(PREFIX, version, name="reviewed.tsv.gz", url=REVIEWED_URL, force=force)
+    return RAW_MODULE.ensure(PREFIX, version, name="reviewed.tsv.gz", url=REVIEWED_URL)
 
 
 if __name__ == "__main__":

pyobo/sources/zfin.py

@@ -16,6 +16,7 @@ from pyobo.struct import (
     has_gene_product,
     orthologous,
 )
+from pyobo.struct.typedef import exact_match
 from pyobo.utils.io import multidict, multisetdict
 from pyobo.utils.path import ensure_df
 
@@ -40,7 +41,7 @@ class ZFINGetter(Obo):
     """An ontology representation of ZFIN's zebrafish database."""
 
     bioversions_key = ontology = PREFIX
-    typedefs = [from_species, has_gene_product, orthologous]
+    typedefs = [from_species, has_gene_product, orthologous, exact_match]
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in ZFIN."""

pyobo/struct/reference.py

@@ -31,6 +31,16 @@ class Reference(curies.Reference):
             raise ExpansionError(f"Unknown prefix: {v}")
         return norm_prefix
 
+    @property
+    def preferred_prefix(self) -> str:
+        """Get the preferred curie for this reference."""
+        return bioregistry.get_preferred_prefix(self.prefix) or self.prefix
+
+    @property
+    def preferred_curie(self) -> str:
+        """Get the preferred curie for this reference."""
+        return f"{self.preferred_prefix}:{self.identifier}"
+
     @root_validator(pre=True)
     def validate_identifier(cls, values):  # noqa
         """Validate the identifier."""
@@ -48,7 +58,7 @@ class Reference(curies.Reference):
 
     @classmethod
     def auto(cls, prefix: str, identifier: str) -> "Reference":
-        """Create a reference and auto-populate its name."""
+        """Create a reference and autopopulate its name."""
         from ..api import get_name
 
         name = get_name(prefix, identifier)
@@ -119,7 +129,7 @@ class Reference(curies.Reference):
         if identifier_lower.startswith(f"{self.prefix.lower()}:"):
             rv = identifier_lower
         else:
-            rv = f"{self.prefix}:{self._escaped_identifier}"
+            rv = f"{self.preferred_prefix}:{self._escaped_identifier}"
         if self.name:
             rv = f"{rv} ! {self.name}"
         return rv
@@ -153,6 +163,11 @@ class Referenced:
         """The CURIE for this typedef."""  # noqa: D401
         return self.reference.curie
 
+    @property
+    def preferred_curie(self) -> str:
+        """The preferred CURIE for this typedef."""  # noqa: D401
+        return self.reference.preferred_curie
+
     @property
     def pair(self) -> Tuple[str, str]:
         """The pair of namespace/identifier."""  # noqa: D401