diff --git a/src/pyobo/api/alts.py b/src/pyobo/api/alts.py
index ee90519c..2d46ab04 100644
--- a/src/pyobo/api/alts.py
+++ b/src/pyobo/api/alts.py
@@ -11,7 +11,7 @@
 from .utils import _get_pi, get_version_from_kwargs
 from ..constants import GetOntologyKwargs, check_should_cache, check_should_force
 from ..getters import get_ontology
-from ..identifier_utils import wrap_norm_prefix
+from ..identifier_utils import Reference, wrap_norm_prefix
 from ..utils.cache import cached_multidict
 from ..utils.path import CacheArtifact, get_cache_path
 
@@ -67,7 +67,7 @@ def get_primary_reference(
     identifier: str | None = None,
     /,
     **kwargs: Unpack[GetOntologyKwargs],
-) -> curies.ReferenceTuple | None:
+) -> Reference | None:
     """Get the primary reference for an entity."""
     reference = _get_pi(prefix, identifier)
     try:
@@ -77,7 +77,7 @@ def get_primary_reference(
             raise
         # this happens on invalid prefix. maybe revise?
         return None
-    return curies.ReferenceTuple(reference.prefix, primary_identifier)
+    return Reference(prefix=reference.prefix, identifier=primary_identifier)
 
 
 def get_primary_curie(
diff --git a/src/pyobo/api/hierarchy.py b/src/pyobo/api/hierarchy.py
index df0649ef..c45b0776 100644
--- a/src/pyobo/api/hierarchy.py
+++ b/src/pyobo/api/hierarchy.py
@@ -17,8 +17,8 @@
 from .properties import get_literal_properties
 from .utils import _get_pi
 from ..constants import GetOntologyKwargs
+from ..identifier_utils import Reference
 from ..struct import has_member, has_part, is_a, member_of, part_of
-from ..struct.reference import Reference
 from ..struct.struct_utils import ReferenceHint, _ensure_ref
 
 __all__ = [
diff --git a/src/pyobo/api/relations.py b/src/pyobo/api/relations.py
index a5338d1d..de086c5c 100644
--- a/src/pyobo/api/relations.py
+++ b/src/pyobo/api/relations.py
@@ -22,8 +22,7 @@
     check_should_use_tqdm,
 )
 from ..getters import get_ontology
-from ..identifier_utils import wrap_norm_prefix
-from ..struct.reference import Reference
+from ..identifier_utils import Reference, wrap_norm_prefix
 from ..struct.struct_utils import ReferenceHint, _ensure_ref
 from ..utils.cache import cached_df
 from ..utils.path import CacheArtifact, get_cache_path, get_relation_cache_path
diff --git a/src/pyobo/api/utils.py b/src/pyobo/api/utils.py
index 3bbf01d2..e5e6c646 100644
--- a/src/pyobo/api/utils.py
+++ b/src/pyobo/api/utils.py
@@ -1,11 +1,9 @@
 """Utilities for high-level API."""
 
-import warnings
-
 import curies
-from bioregistry import NormalizedNamableReference as Reference
 from curies import ReferenceTuple
 
+from ..identifier_utils import Reference
 from ..utils.ver import (
     VersionError,
     get_version,
@@ -24,21 +22,14 @@
 
 
 def _get_pi(
-    prefix: str | curies.Reference | ReferenceTuple, identifier: str | None = None, /
+    reference: str | curies.Reference | ReferenceTuple, _unused: str | None = None, /
 ) -> Reference:
-    if isinstance(prefix, ReferenceTuple | curies.Reference):
-        if identifier is not None:
-            raise ValueError("unexpected non-none value passed as second positional argument")
-        return Reference(prefix=prefix.prefix, identifier=prefix.identifier)
-    if isinstance(prefix, str) and identifier is None:
-        return Reference.from_curie(prefix)
-    if identifier is None:
-        raise ValueError(
-            "prefix was given as a string, so an identifier was expected to be passed as a string as well"
-        )
-    warnings.warn(
-        "Passing a prefix and identifier as seperate arguments is deprecated. Please pass a curies.Reference or curies.ReferenceTuple in the first positional-only argument instead.",
-        DeprecationWarning,
-        stacklevel=4,  # this is 4 since this is (always?) called from inside a decorator
-    )
-    return Reference(prefix=prefix, identifier=identifier)
+    if _unused is not None:
+        raise ValueError("unexpected non-none value passed as second positional argument")
+    if isinstance(reference, Reference):
+        return reference
+    if isinstance(reference, ReferenceTuple | curies.Reference):
+        return Reference.from_reference(reference)
+    if isinstance(reference, str):
+        return Reference.from_curie(reference)
+    raise TypeError(f"unexpected type {type(reference)}")
diff --git a/src/pyobo/cli/lookup.py b/src/pyobo/cli/lookup.py
index a91aad03..4bee8d6f 100644
--- a/src/pyobo/cli/lookup.py
+++ b/src/pyobo/cli/lookup.py
@@ -21,7 +21,7 @@
 from ..constants import GetOntologyKwargs
 
 if TYPE_CHECKING:
-    from curies import Reference
+    import curies
 
 __all__ = [
     "lookup",
@@ -306,7 +306,7 @@ def descendants(curie: str, **kwargs: Unpack[GetOntologyKwargs]) -> None:
 
 
 def _list_curies(
-    references: Iterable[Reference] | None, **kwargs: Unpack[GetOntologyKwargs]
+    references: Iterable[curies.Reference] | None, **kwargs: Unpack[GetOntologyKwargs]
 ) -> None:
     if not references:
         return
diff --git a/src/pyobo/identifier_utils/__init__.py b/src/pyobo/identifier_utils/__init__.py
index 8333bfdc..e0790d21 100644
--- a/src/pyobo/identifier_utils/__init__.py
+++ b/src/pyobo/identifier_utils/__init__.py
@@ -8,6 +8,7 @@
     NotCURIEError,
     ParseError,
     ParseValidationError,
+    Reference,
     UnparsableIRIError,
     UnregisteredPrefixError,
     _is_valid_identifier,
@@ -24,6 +25,7 @@
     "NotCURIEError",
     "ParseError",
     "ParseValidationError",
+    "Reference",
     "UnparsableIRIError",
     "UnregisteredPrefixError",
     "_is_valid_identifier",
diff --git a/src/pyobo/identifier_utils/api.py b/src/pyobo/identifier_utils/api.py
index 3c56f0c7..58975f97 100644
--- a/src/pyobo/identifier_utils/api.py
+++ b/src/pyobo/identifier_utils/api.py
@@ -9,13 +9,13 @@
 
 import bioregistry
 import click
-from bioregistry import NormalizedNamableReference as Reference
 from bioregistry.constants import FailureReturnType
 from curies.preprocessing import BlocklistError, PreprocessingConverter
 from curies_processing import get_rules
 from pydantic import ValidationError
 from typing_extensions import Doc
 
+from .reference import Reference
 from .relations import ground_relation
 
 __all__ = [
@@ -24,6 +24,7 @@
     "NotCURIEError",
     "ParseError",
     "ParseValidationError",
+    "Reference",
     "UnparsableIRIError",
     "UnregisteredPrefixError",
     "_parse_str_or_curie_or_uri_helper",
diff --git a/src/pyobo/identifier_utils/reference.py b/src/pyobo/identifier_utils/reference.py
new file mode 100644
index 00000000..1c548244
--- /dev/null
+++ b/src/pyobo/identifier_utils/reference.py
@@ -0,0 +1,5 @@
+"""Defines a PyOBO reference."""
+
+from bioregistry import NormalizedNamableReference as Reference
+
+__all__ = ["Reference"]
diff --git a/src/pyobo/identifier_utils/relations/api.py b/src/pyobo/identifier_utils/relations/api.py
index f851ced9..01f735de 100644
--- a/src/pyobo/identifier_utils/relations/api.py
+++ b/src/pyobo/identifier_utils/relations/api.py
@@ -6,9 +6,10 @@
 from pathlib import Path
 
 import requests
-from bioregistry import NormalizedNamedReference
 from tqdm import tqdm
 
+from ..reference import Reference
+
 __all__ = [
     "get_normalized_label",
     "ground_relation",
@@ -65,7 +66,7 @@ def _norm(s: str) -> str:
     return s.replace(" ", "").replace("_", "").replace(":", "").lower()
 
 
-def ground_relation(s: str) -> NormalizedNamedReference | None:
+def ground_relation(s: str) -> Reference | None:
     """Ground a string to a RO property."""
     return get_lookups().get(_norm(s))
 
@@ -82,14 +83,14 @@ def get_normalized_label(curie_or_uri: str) -> str | None:
 
 
 @lru_cache(1)
-def get_lookups() -> Mapping[str, NormalizedNamedReference]:
+def get_lookups() -> Mapping[str, Reference]:
     """Get lookups for relation ontology properties."""
     d = {}
     for record in json.loads(PATH.read_text()):
         prefix, identifier, label = record["prefix"], record["identifier"], record["label"]
-        d[_norm(label)] = NormalizedNamedReference(prefix=prefix, identifier=identifier, name=label)
+        d[_norm(label)] = Reference(prefix=prefix, identifier=identifier, name=label)
         for s in record.get("synonyms", []):
-            d[_norm(s)] = NormalizedNamedReference(prefix=prefix, identifier=identifier, name=label)
+            d[_norm(s)] = Reference(prefix=prefix, identifier=identifier, name=label)
     return d
 
 
diff --git a/src/pyobo/ner/normalizer.py b/src/pyobo/ner/normalizer.py
index d3d7e54f..18f6dd7a 100644
--- a/src/pyobo/ner/normalizer.py
+++ b/src/pyobo/ner/normalizer.py
@@ -58,5 +58,5 @@ def ground(
         #  can be type annotated with the right reference
         return Reference.from_reference(match.reference)
     if strict_match:
-        raise ValueError
+        raise ValueError(f"no match found for query: {query} against prefixes: {prefix}")
     return None
diff --git a/src/pyobo/struct/__init__.py b/src/pyobo/struct/__init__.py
index 7924d96e..f1723bee 100644
--- a/src/pyobo/struct/__init__.py
+++ b/src/pyobo/struct/__init__.py
@@ -1,12 +1,6 @@
 """Data structures for OBO."""
 
-from .reference import (
-    OBOLiteral,
-    Reference,
-    Referenced,
-    _parse_str_or_curie_or_uri,
-    default_reference,
-)
+from .reference import OBOLiteral, Referenced, _parse_str_or_curie_or_uri, default_reference
 from .struct import (
     CHARLIE_TERM,
     HUMAN_TERM,
@@ -41,6 +35,7 @@
     transcribes_to,
     translates_to,
 )
+from ..identifier_utils import Reference
 
 __all__ = [
     "CHARLIE_TERM",
@@ -50,6 +45,7 @@
     "OBOLiteral",
     "Obo",
     "Reference",
+    "Reference",
     "Referenced",
     "Stanza",
     "StanzaType",
diff --git a/src/pyobo/struct/functional.py b/src/pyobo/struct/functional.py
index a115d395..751eec10 100644
--- a/src/pyobo/struct/functional.py
+++ b/src/pyobo/struct/functional.py
@@ -14,8 +14,9 @@
 from rdflib import XSD
 
 from . import vocabulary as pv
-from .reference import OBOLiteral, Reference, _parse_datetime
+from .reference import OBOLiteral, _parse_datetime
 from .struct import get_iris
+from ..identifier_utils import Reference
 
 if TYPE_CHECKING:
     from .reference import Referenced
diff --git a/src/pyobo/struct/obo/reader.py b/src/pyobo/struct/obo/reader.py
index aa2fe48a..2dcc4c26 100644
--- a/src/pyobo/struct/obo/reader.py
+++ b/src/pyobo/struct/obo/reader.py
@@ -14,7 +14,6 @@
 
 import bioregistry
 import networkx as nx
-from bioregistry import NormalizedNamableReference as Reference
 from curies import ReferenceTuple
 from curies.preprocessing import BlocklistError
 from curies.vocabulary import SynonymScope
@@ -45,6 +44,7 @@
 from ...identifier_utils import (
     NotCURIEError,
     ParseError,
+    Reference,
     UnparsableIRIError,
     _is_valid_identifier,
     _parse_str_or_curie_or_uri_helper,
diff --git a/src/pyobo/struct/obo/reader_utils.py b/src/pyobo/struct/obo/reader_utils.py
index e2d4cbae..4b24f527 100644
--- a/src/pyobo/struct/obo/reader_utils.py
+++ b/src/pyobo/struct/obo/reader_utils.py
@@ -8,10 +8,10 @@
 from collections.abc import Mapping, Sequence
 
 import click
-from bioregistry import NormalizedNamableReference as Reference
 from curies import ReferenceTuple
 from curies import vocabulary as v
 
+from pyobo.identifier_utils import Reference
 from pyobo.struct.reference import (
     OBOLiteral,
     _obo_parse_identifier,
diff --git a/src/pyobo/struct/obograph/utils.py b/src/pyobo/struct/obograph/utils.py
index 88965a95..eb249367 100644
--- a/src/pyobo/struct/obograph/utils.py
+++ b/src/pyobo/struct/obograph/utils.py
@@ -4,10 +4,10 @@
 from typing import cast
 
 import obographs as og
-from curies import Reference
 from obographs import StandardizedGraph, StandardizedMeta
 
 from pyobo.constants import TypeDefType
+from pyobo.identifier_utils import Reference
 
 __all__ = [
     "assert_graph_equal",
diff --git a/src/pyobo/struct/reference.py b/src/pyobo/struct/reference.py
index 805734f6..0f77633b 100644
--- a/src/pyobo/struct/reference.py
+++ b/src/pyobo/struct/reference.py
@@ -14,7 +14,6 @@
 import curies
 import dateutil.parser
 import pytz
-from bioregistry import NormalizedNamableReference as Reference
 from curies import ReferenceTuple
 from curies import vocabulary as v
 from curies.preprocessing import BlocklistError
@@ -22,6 +21,7 @@
 from ..identifier_utils import (
     NotCURIEError,
     ParseError,
+    Reference,
     UnparsableIRIError,
     _is_valid_identifier,
     _parse_str_or_curie_or_uri_helper,
@@ -29,7 +29,6 @@
 
 __all__ = [
     "OBOLiteral",
-    "Reference",
     "Referenced",
     "default_reference",
     "get_preferred_curie",
@@ -158,9 +157,13 @@ def default_reference(prefix: str, identifier: str, name: str | None = None) ->
 
     >>> default_reference("chebi", "conjugate_base_of")
     Reference(prefix="obo", identifier="chebi#conjugate_base_of", name=None)
+
+    >>> default_reference("CHEBI", "conjugate_base_of")
+    Reference(prefix="obo", identifier="chebi#conjugate_base_of", name=None)
     """
     if not identifier.strip():
         raise ValueError("default identifier is empty")
+    prefix = bioregistry.normalize_prefix(prefix) or prefix.lower()
     return Reference(prefix="obo", identifier=f"{prefix}#{identifier}", name=name)
 
 
diff --git a/src/pyobo/struct/skos/export.py b/src/pyobo/struct/skos/export.py
index 4879f1e8..2c6ca560 100644
--- a/src/pyobo/struct/skos/export.py
+++ b/src/pyobo/struct/skos/export.py
@@ -6,7 +6,8 @@
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
-    from curies import Converter, Reference
+    import curies
+    from curies import Converter
     from rdflib import Graph, Node, URIRef
 
     from pyobo.struct import Obo
@@ -29,7 +30,7 @@ def write_skos(
     graph.serialize(path, format=format or "ttl")
 
 
-def _expand_rdflib(converter: Converter, reference: Reference) -> URIRef:
+def _expand_rdflib(converter: Converter, reference: curies.Reference) -> URIRef:
     import rdflib
 
     return rdflib.URIRef(converter.expand_reference(reference, strict=True))
diff --git a/src/pyobo/struct/skos/reader.py b/src/pyobo/struct/skos/reader.py
index 51677411..f90e3628 100644
--- a/src/pyobo/struct/skos/reader.py
+++ b/src/pyobo/struct/skos/reader.py
@@ -6,14 +6,12 @@
 
 import curies
 import rdflib
-from bioregistry import NormalizedNamableReference, NormalizedNamedReference
-from curies import Reference
 from curies import vocabulary as v
 from rdflib import DCTERMS, RDF, RDFS, SKOS, VANN, Graph, Node, URIRef
 from tqdm import tqdm
 
 from pyobo import Annotation
-from pyobo.identifier_utils import get_converter
+from pyobo.identifier_utils import Reference, get_converter
 from pyobo.struct import Obo, Term, build_ontology
 from pyobo.struct.vocabulary import has_source
 
@@ -73,12 +71,10 @@ def _get_scheme_object_literal(p: Node) -> str | None:
         raise ValueError(f"no prefix given nor found using {VANN.preferredNamespacePrefix}")
 
     root_terms = [
-        NormalizedNamableReference.from_reference(
-            converter.parse_uri(str(subject), strict=True).to_pydantic()
-        )
+        Reference.from_reference(converter.parse_uri(str(subject), strict=True).to_pydantic())
         for subject in graph.objects(scheme, SKOS.hasTopConcept)
     ]
-    terms: dict[Reference, Term] = {}
+    terms: dict[curies.Reference, Term] = {}
     for concept in tqdm(
         graph.subjects(RDF.type, SKOS.Concept),
         desc=f"[{prefix}] SKOS concepts to OWL",
@@ -129,10 +125,10 @@ def _get_scheme_object_literal(p: Node) -> str | None:
     )
 
 
-def _cleanup_narrow_matches(terms: dict[Reference, Term]) -> None:
+def _cleanup_narrow_matches(terms: dict[curies.Reference, Term]) -> None:
     for parent in terms.values():
         for child in parent.get_property_objects(v.narrow_match):
-            if not isinstance(child, Reference):
+            if not isinstance(child, curies.Reference):
                 continue
             if child not in terms:
                 continue
@@ -174,7 +170,7 @@ def get_term(
     labels = _literal_objects(graph, node, SKOS.prefLabel, language_priority)
     definitions = _literal_objects(graph, node, SKOS.definition, language_priority)
     term = Term(
-        reference=NormalizedNamedReference(
+        reference=Reference(
             prefix=reference_tuple.prefix,
             identifier=reference_tuple.identifier,
             name=labels[0] if labels else None,
diff --git a/src/pyobo/struct/struct.py b/src/pyobo/struct/struct.py
index 0f630ad8..d27c98ff 100644
--- a/src/pyobo/struct/struct.py
+++ b/src/pyobo/struct/struct.py
@@ -34,7 +34,6 @@
 from . import vocabulary as v
 from .reference import (
     OBOLiteral,
-    Reference,
     Referenced,
     _reference_list_tag,
     comma_separate_references,
@@ -73,6 +72,7 @@
     TypeDefType,
     get_semantic_mapping_metadata,
 )
+from ..identifier_utils import Reference
 from ..utils.cache import write_gzipped_graph
 from ..utils.io import multidict, write_iterable_tsv
 from ..utils.path import (
@@ -466,7 +466,7 @@ def get_species(
             if species.prefix == prefix:
                 return species
         if strict:
-            raise ValueError
+            raise ValueError(f"no species found with prefix {prefix}")
         return None
 
     def extend_relationship(self, typedef: ReferenceHint, references: Iterable[Reference]) -> None:
diff --git a/src/pyobo/struct/struct_utils.py b/src/pyobo/struct/struct_utils.py
index 699d8b26..ff678735 100644
--- a/src/pyobo/struct/struct_utils.py
+++ b/src/pyobo/struct/struct_utils.py
@@ -20,7 +20,6 @@
 from . import vocabulary as v
 from .reference import (
     OBOLiteral,
-    Reference,
     Referenced,
     comma_separate_references,
     default_reference,
@@ -34,6 +33,7 @@
 from ..identifier_utils import (
     NotCURIEError,
     ParseError,
+    Reference,
     _is_valid_identifier,
     _parse_str_or_curie_or_uri_helper,
 )
diff --git a/src/pyobo/struct/typedef.py b/src/pyobo/struct/typedef.py
index 031077de..0e099f58 100644
--- a/src/pyobo/struct/typedef.py
+++ b/src/pyobo/struct/typedef.py
@@ -7,8 +7,9 @@
 from curies import ReferenceTuple
 
 from . import vocabulary as v
-from .reference import Reference, default_reference
+from .reference import default_reference
 from .struct import TypeDef
+from ..identifier_utils import Reference
 from ..resources.ro import load_ro
 
 __all__ = [
diff --git a/src/pyobo/struct/vocabulary.py b/src/pyobo/struct/vocabulary.py
index 1e607159..dd172157 100644
--- a/src/pyobo/struct/vocabulary.py
+++ b/src/pyobo/struct/vocabulary.py
@@ -5,7 +5,7 @@
 import curies
 from curies import vocabulary as _v
 
-from .reference import Reference
+from ..identifier_utils import Reference
 
 __all__ = [
     "equivalent_class",
diff --git a/src/pyobo/utils/path.py b/src/pyobo/utils/path.py
index 8e3e3f13..01a6b7d8 100644
--- a/src/pyobo/utils/path.py
+++ b/src/pyobo/utils/path.py
@@ -8,8 +8,8 @@
 from pathlib import Path
 from typing import TYPE_CHECKING, Any
 
+import curies
 import pandas as pd
-from curies import Reference
 from pystow import VersionHint
 from pystow.utils.download import DownloadKwargs
 from typing_extensions import Unpack
@@ -166,7 +166,7 @@ def get_cache_path(
 
 def get_relation_cache_path(
     ontology: str,
-    reference: Reference,
+    reference: curies.Reference,
     *,
     version: str | None = None,
 ) -> Path:
diff --git a/tests/test_api.py b/tests/test_api.py
index 52bb6126..094d64be 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -16,8 +16,8 @@
 from sssom_pydantic.testing import assert_semantic_mapping_equal
 
 import pyobo
-from pyobo import Reference as PyOBOReference
 from pyobo import (
+    Reference,
     default_reference,
     get_name,
     get_name_by_curie,
@@ -97,34 +97,40 @@ def test_get_primary(self, _: Any, __: Any) -> None:
         self.assertIsNotNone(primary_id)
         self.assertEqual("0003700", primary_id)
         self.assertIsNone(get_name(ReferenceTuple("go", "0001071"), upgrade_identifier=False))
-        name = get_name(ReferenceTuple("go", "0001071"), upgrade_identifier=True)
-        self.assertIsNotNone(name)
-        self.assertEqual("DNA-binding transcription factor activity", name)
+        self.assertEqual(
+            "DNA-binding transcription factor activity",
+            get_name(ReferenceTuple("go", "0001071"), upgrade_identifier=True),
+        )
 
     @mock_id_alts_mapping
     @mock_id_names_mapping
     def test_get_primary_by_curie(self, _: Any, __: Any) -> None:
         """Test upgrading an obsolete CURIE."""
-        primary_curie = get_primary_curie("go:0001071")
+        secondary_curie = "go:0001071"
+        expected_primary_curie = "go:0003700"
+
+        primary_curie = get_primary_curie(secondary_curie)
         self.assertIsNotNone(primary_curie)
-        self.assertEqual("go:0003700", primary_curie)
+        self.assertEqual(expected_primary_curie, primary_curie)
 
-        primary_reference = get_primary_reference("go:0001071")
+        primary_reference = get_primary_reference(secondary_curie)
         self.assertIsNotNone(primary_reference)
-        self.assertEqual(ReferenceTuple("go", "0003700"), primary_reference)
+        self.assertEqual(Reference.from_curie(expected_primary_curie), primary_reference)
 
-        self.assertIsNone(get_name_by_curie("go:0001071", upgrade_identifier=False))
+        self.assertIsNone(get_name_by_curie(secondary_curie, upgrade_identifier=False))
 
         # if set explicitly to true, then it will do it eagerly
-        name = get_name_by_curie("go:0001071", upgrade_identifier=True)
-        self.assertIsNotNone(name)
-        self.assertEqual("DNA-binding transcription factor activity", name)
+        self.assertEqual(
+            "DNA-binding transcription factor activity",
+            get_name_by_curie(secondary_curie, upgrade_identifier=True),
+        )
 
         # if not set, or left as default, then it will do it only if there's no
         # original name
-        name = get_name_by_curie("go:0001071", upgrade_identifier=None)
-        self.assertIsNotNone(name)
-        self.assertEqual("DNA-binding transcription factor activity", name)
+        self.assertEqual(
+            "DNA-binding transcription factor activity",
+            get_name_by_curie(secondary_curie, upgrade_identifier=None),
+        )
 
     @mock_id_alts_mapping
     @mock_id_names_mapping
@@ -134,15 +140,12 @@ def test_already_primary(self, _: Any, __: Any) -> None:
         self.assertIsNotNone(primary_id)
         self.assertEqual("0003700", primary_id)
         name = get_name(ReferenceTuple("go", "0003700"))
-        self.assertIsNotNone(name)
         self.assertEqual("DNA-binding transcription factor activity", name)
 
         name = get_name(ReferenceTuple("go", "0003700"))
-        self.assertIsNotNone(name)
         self.assertEqual("DNA-binding transcription factor activity", name)
 
         name = get_name(curies.Reference(prefix="go", identifier="0003700"))
-        self.assertIsNotNone(name)
         self.assertEqual("DNA-binding transcription factor activity", name)
 
     @mock_id_alts_mapping
@@ -157,12 +160,11 @@ def test_get_primary_on_reference(self, _: Any, __: Any) -> None:
     @mock_id_names_mapping
     def test_already_primary_by_curie(self, _: Any, __: Any) -> None:
         """Test when you give a primary CURIE."""
-        primary_curie = get_primary_curie("go:0003700")
-        self.assertIsNotNone(primary_curie)
-        self.assertEqual("go:0003700", primary_curie)
-        name = get_name_by_curie("go:0003700")
-        self.assertIsNotNone(name)
-        self.assertEqual("DNA-binding transcription factor activity", name)
+        for curie in ["go:0003700", "GO:0003700"]:
+            primary_reference = get_primary_reference(curie)
+            self.assertEqual(Reference.from_curie(curie), primary_reference)
+            name = get_name_by_curie(curie)
+            self.assertEqual("DNA-binding transcription factor activity", name)
 
     @mock_id_alts_mapping
     @mock_id_names_mapping
@@ -183,11 +185,11 @@ def test_api(self) -> None:
         """
         tr1 = default_reference(TEST_P1, "r1")
         td1 = TypeDef(reference=tr1)
-        r1 = PyOBOReference(prefix=TEST_P1, identifier="1", name="test name")
-        r2 = PyOBOReference(prefix=TEST_P1, identifier="2")
-        r3 = PyOBOReference(prefix=TEST_P1, identifier="3")
-        r2_1 = PyOBOReference(prefix=TEST_P2, identifier="X")
-        r2_2 = PyOBOReference(prefix=TEST_P2, identifier="Y")
+        r1 = Reference(prefix=TEST_P1, identifier="1", name="test name")
+        r2 = Reference(prefix=TEST_P1, identifier="2")
+        r3 = Reference(prefix=TEST_P1, identifier="3")
+        r2_1 = Reference(prefix=TEST_P2, identifier="X")
+        r2_2 = Reference(prefix=TEST_P2, identifier="Y")
         syn1 = "ttt1"
         t1 = Term(reference=r1).append_alt(r2).append_synonym(syn1).append_xref(r2_1)
         t1.append_comment("test comment")
@@ -261,12 +263,12 @@ def test_api(self) -> None:
                 )
             )
             self.assertEqual(3, len(semantic_mappings))
-            subject_source = PyOBOReference(prefix="bioregistry", identifier=r1.prefix)
+            subject_source = Reference(prefix="bioregistry", identifier=r1.prefix)
             expected_semantic_mappings = [
                 SemanticMapping(
                     subject=r1,
                     subject_type=_v.owl_class,
-                    predicate=PyOBOReference.from_reference(_v.alternative_term),
+                    predicate=Reference.from_reference(_v.alternative_term),
                     object=r2,
                     justification=_v.unspecified_matching_process.without_name(),
                     source=subject_source,
@@ -275,7 +277,7 @@ def test_api(self) -> None:
                 SemanticMapping(
                     subject=r1,
                     subject_type=_v.owl_class,
-                    predicate=PyOBOReference.from_reference(_v.has_dbxref),
+                    predicate=Reference.from_reference(_v.has_dbxref),
                     object=r2_1,
                     justification=_v.unspecified_matching_process.without_name(),
                     source=subject_source,
@@ -284,7 +286,7 @@ def test_api(self) -> None:
                 SemanticMapping(
                     subject=r3,
                     subject_type=_v.owl_class,
-                    predicate=PyOBOReference.from_reference(_v.exact_match),
+                    predicate=Reference.from_reference(_v.exact_match),
                     object=r2_2,
                     justification=_v.unspecified_matching_process.without_name(),
                     source=subject_source,
@@ -300,13 +302,13 @@ def test_api(self) -> None:
                 LiteralMapping(
                     text="ttt1",
                     reference=r1,
-                    predicate=PyOBOReference.from_reference(_v.has_related_synonym),
+                    predicate=Reference.from_reference(_v.has_related_synonym),
                     source=TEST_P1,
                 ),
                 LiteralMapping(
                     text="test name",
                     reference=r1,
-                    predicate=PyOBOReference.from_reference(_v.has_label),
+                    predicate=Reference.from_reference(_v.has_label),
                     source=TEST_P1,
                 ),
             ]
diff --git a/tests/test_obo_reader/test_get.py b/tests/test_obo_reader/test_get.py
index 52517f43..a1f5a02b 100644
--- a/tests/test_obo_reader/test_get.py
+++ b/tests/test_obo_reader/test_get.py
@@ -272,11 +272,11 @@ def test_get_node_relations(self) -> None:
 
         self.assertIsNotNone(target)
         self.assertIsInstance(target, Reference)
-        self.assertEqual(("chebi", "29228"), target.pair)
+        self.assertEqual(ReferenceTuple("chebi", "29228"), target.pair)
 
         self.assertIsNotNone(typedef)
         self.assertIsInstance(typedef, Reference)
-        self.assertEqual(("obo", "chebi#is_conjugate_base_of"), typedef.pair)
+        self.assertEqual(ReferenceTuple("obo", "chebi#is_conjugate_base_of"), typedef.pair)
 
 
 class TestGet(unittest.TestCase):
@@ -299,6 +299,7 @@ def test_get_id_alts_mapping(self) -> None:
             alt_id: CHEBI:14384
         """
         id_alts_mapping = self.ontology.get_id_alts_mapping()
+        self.assertNotEqual({}, id_alts_mapping, msg="alternate ID dictionary unexpectedly empty")
         self.assertNotIn("C00462", id_alts_mapping)
         self.assertIn("16042", id_alts_mapping, msg="halide anion alt_id fields not parsed")
         self.assertEqual({"5605", "14384"}, set(id_alts_mapping["16042"]))
@@ -308,4 +309,4 @@ def test_typedefs(self) -> None:
         xx = default_reference("chebi", "has_major_microspecies_at_pH_7_3")
         td = self.ontology._index_typedefs()
         self.assertIn(xx.pair, td)
-        self.assertIn(ReferenceTuple("ro", "0018033"), td)
+        self.assertIn(ReferenceTuple("ro", "0018033"), set(td))
diff --git a/tests/test_obo_reader/test_reader.py b/tests/test_obo_reader/test_reader.py
index c9eedcff..0b92ec2b 100644
--- a/tests/test_obo_reader/test_reader.py
+++ b/tests/test_obo_reader/test_reader.py
@@ -1416,8 +1416,5 @@ def test_get_grounder(self) -> None:
         """)
         r1 = Reference(prefix="CHEBI", identifier="16236", name="ethanol")
         grounder = ontology.get_grounder()
-        match = grounder.get_best_match("Ethanol")
-        self.assertIsNotNone(match)
-        if match is None:
-            raise ValueError
+        match = grounder.get_best_match("Ethanol", strict=True)
         self.assertEqual(r1, match.reference)
diff --git a/tests/test_struct/test_obo/test_struct_term.py b/tests/test_struct/test_obo/test_struct_term.py
index f77f2155..c8d2c559 100644
--- a/tests/test_struct/test_obo/test_struct_term.py
+++ b/tests/test_struct/test_obo/test_struct_term.py
@@ -78,33 +78,6 @@ def test_invalid_prefix(self) -> None:
         with self.assertRaises(BioregistryError):
             Nope()
 
-    def test_reference_validation(self) -> None:
-        """Test validation of prefix."""
-        with self.assertRaises(ValueError):
-            Reference(prefix="nope", identifier="also_nope")
-
-        # For when we want to do regex checking
-        # with self.assertRaises(ValueError):
-        #     Reference(prefix="go", identifier="nope")
-        # with self.assertRaises(ValueError):
-        #     Reference(prefix="go", identifier="12345")
-
-        r1 = Reference(prefix="go", identifier="1234567")
-        self.assertEqual("go", r1.prefix)
-        self.assertEqual("1234567", r1.identifier)
-
-        r2 = Reference(prefix="GO", identifier="1234567")
-        self.assertEqual("go", r2.prefix)
-        self.assertEqual("1234567", r2.identifier)
-
-        r3 = Reference(prefix="go", identifier="GO:1234567")
-        self.assertEqual("go", r3.prefix)
-        self.assertEqual("1234567", r3.identifier)
-
-        r4 = Reference(prefix="GO", identifier="GO:1234567")
-        self.assertEqual("go", r4.prefix)
-        self.assertEqual("1234567", r4.identifier)
-
     def test_synonym_typedef(self) -> None:
         """Test synonym type definition serialization."""
         r1 = Reference(prefix="OMO", identifier="0003012", name="acronym")
diff --git a/tests/test_struct/test_obo/test_typedef.py b/tests/test_struct/test_obo/test_typedef.py
index d72b89be..eac30726 100644
--- a/tests/test_struct/test_obo/test_typedef.py
+++ b/tests/test_struct/test_obo/test_typedef.py
@@ -5,16 +5,11 @@
 from textwrap import dedent
 
 import bioregistry
-from bioregistry import NormalizedNamedReference
 from curies import vocabulary as v
 
 from pyobo import Obo, Reference, default_reference
 from pyobo.struct.reference import OBOLiteral
-from pyobo.struct.struct import (
-    Synonym,
-    TypeDef,
-    build_ontology,
-)
+from pyobo.struct.struct import Synonym, TypeDef, build_ontology
 from pyobo.struct.typedef import (
     exact_match,
     has_contributor,
@@ -318,9 +313,7 @@ def test_9_synonym(self) -> None:
 
         typedef = TypeDef(
             reference=REF,
-            synonyms=[
-                Synonym("bears role", type=NormalizedNamedReference.from_reference(v.previous_name))
-            ],
+            synonyms=[Synonym("bears role", type=Reference.from_reference(v.previous_name))],
         )
         self.assert_obo_stanza(
             """\
@@ -343,7 +336,7 @@ def test_9_synonym(self) -> None:
             synonyms=[
                 Synonym(
                     "bears role",
-                    type=NormalizedNamedReference.from_reference(v.previous_name),
+                    type=Reference.from_reference(v.previous_name),
                     specificity="EXACT",
                 )
             ],
@@ -388,7 +381,7 @@ def test_11_property_value(self) -> None:
         typedef = TypeDef(
             reference=REF,
             properties={
-                has_contributor.reference: [NormalizedNamedReference.from_reference(v.charlie)],
+                has_contributor.reference: [Reference.from_reference(v.charlie)],
                 has_inchi.reference: [OBOLiteral.string("abc")],
             },
         )
diff --git a/tests/test_utils/test_utils.py b/tests/test_utils/test_utils.py
index 2dcd2955..4987b5ce 100644
--- a/tests/test_utils/test_utils.py
+++ b/tests/test_utils/test_utils.py
@@ -2,7 +2,7 @@
 
 import unittest
 
-from curies import Reference
+import curies
 
 from pyobo.identifier_utils import (
     NotCURIEError,
@@ -21,7 +21,7 @@ def assert_pair(
     ) -> None:
         """Test a pair is parsed properly."""
         xx = _parse_str_or_curie_or_uri_helper(curie, ontology_prefix=ontology_prefix)
-        if not isinstance(xx, Reference):
+        if not isinstance(xx, curies.Reference):
             raise self.fail()
         self.assertEqual(expected, xx.pair)