pyobo 0.12.0__py3-none-any.whl → 0.12.1__py3-none-any.whl

pyobo/identifier_utils/preprocessing.json

@@ -1,8 +1,10 @@
 {
-  "blacklists": {
+  "blocklists": {
     "full": [
       ":",
       "ADL:FTT",
+      "BGEE:curator",
+      "BSPO:PATO_mtg_2009",
       "Bgee:curator",
       "BioGRID:curators",
       "CGP:curators",
@@ -16,8 +18,10 @@
       "Europe:\\:260",
       "FBC:Autogenerated",
       "Follicular:fluid",
+      "GO:curator",
       "GOC:TermGenie",
       "GOC:go_curators",
+      "GOC:mtg_cell_cycle",
       "GOC:mtg_kidney_jan10",
       "GOC:pamgo_curators",
       "GROUP:OBI",
@@ -30,13 +34,16 @@
       "KEGG",
       "Lamina:propria",
       "Lymph:node",
+      "MIM:OMIM",
+      "MeSH:MeSH",
       "NIFSTD:NeuroNames_abbrevSource",
       "NIST",
       "PLATY:A.H.L.Fischer",
       "POC:curators",
       "Pituitary:gland",
       "PomBane:vw",
-      "PomBase\\:mah",
+      "RGD:www.rgd.mcw.edu",
+      "SGD:curators",
       "STRUCTURE_Formula",
       "South:Korea",
       "TAIR:TED",
@@ -74,8 +81,10 @@
       "STRUCTURE_Formula",
       "SUBMITTER",
       "TEMP:",
+      "http://wiki.geneontology.org/index.php",
       "stedman",
-      "synonym:"
+      "synonym:",
+      "urn:lsid\\:globalnames.org\\:index\\:"
     ],
     "resource_full": {
       "ceph": [
@@ -303,9 +312,9 @@
   },
   "rewrites": {
     "full": {
-      "OBO_REL:is_a": "rdfs:subClassOf",
-      ":has_start_point": "has_start_point",
       "ABBREVIATION": "omo:0003000",
+      "BSPO:cjm": "orcid:0000-0002-6601-2165",
+      "BSPO:mah": "orcid:0000-0003-4148-4606",
       "CHEBI:133245 MetaCyc:quercetin 3-rhamnoside-7-rhamnoside": "CHEBI:133245",
       "CHEBI:16531 MetaCyc:renillar luciferin": "CHEBI:16531",
       "CHEBI:49553 PDBeChem:Copper(II) chloride": "CHEBI:49553",
@@ -319,23 +328,42 @@
       "FOBI_050091": "FOBI:050091",
       "GIOC:vw": "GOC:vw",
       "GOC:MAH": "orcid:0000-0003-4148-4606",
+      "HAO:attached_to": "ro:0002371",
       "HPO:SKOEHLER": "orcid:0000-0002-5316-1399",
       "HPO:skoehler": "orcid:0000-0002-5316-1399",
       "LIPIDMAPSLMFA01030141": "LIPIDMAPS:LMFA01030141",
       "LIPIDMAPSLMFA01030152": "LIPIDMAPS:LMFA01030152",
       "MimicDB:KatalinParej": "orcid:0000-0002-2567-6061",
       "OBO_REL2:has_role": "ro:0000087",
+      "OBO_REL:adjacent_to": "ro:0002220",
+      "OBO_REL:has_participant": "ro:0000057",
+      "OBO_REL:has_quality": "bfo:0000086",
+      "OBO_REL:has_role": "ro:0000087",
+      "OBO_REL:has_vector": "ro:0002460",
+      "OBO_REL:inheres_in": "ro:0004096",
+      "OBO_REL:is_a": "rdfs:subClassOf",
+      "OBO_REL:located_in": "ro:0001025",
+      "OBO_REL:location_of": "ro:0001015",
+      "OBO_REL:part_of": "bfo:0000050",
+      "OBO_REL:participates_in": "ro:0000056",
+      "OBO_REL:preceded_by": "bfo:0000062",
+      "OBO_REL:precedes": "bfo:0000063",
+      "OBO_REL:proper_part_of": "bfo:0000050",
+      "OBO_REL:transformation_of": "ro:0002494",
       "PATOC:CJM": "orcid:0000-0002-6601-2165",
       "PATOC:MAH": "orcid:0000-0003-4148-4606",
       "PHI-base:AlayneCuzick": "orcid:0000-0001-8941-3984",
       "PMI:17498297": "PMID:17498297",
+      "POMBASE:mah": "orcid:0000-0003-4148-4606",
+      "PomBase\\:mah": "orcid:0000-0003-4148-4606",
       "Property:P1659": "wikidata:P1659",
+      "RO:has_part": "bfo:0000051",
+      "RO:part_of": "BFO:0000050",
       "SBN:9780070316607": "ISBN:9780070316607",
       "SIB:PG": "orcid:0000-0003-1813-6857",
       "SIB:PG xsd:string": "orcid:0000-0003-1813-6857",
       "SNOMEDCT274897005": "SNOMEDCT:274897005",
       "UBERON:cjm": "orcid:0000-0002-6601-2165",
-      "\\:has_start_point": "has_start_point",
       "bearer:of": "RO:0000053",
       "broadMatch": "skos:broadMatch",
       "connected_to": "ro:0002170",
@@ -368,7 +396,6 @@
       "hasNarrowSynonym": "oboinowl:hasNarrowSynonym",
       "hasRelatedSynonym": "oboinowl:hasRelatedSynonym",
       "has_part": "bfo:0000051",
-      "has_start_point:": "has_start_point",
       "http://creativecommons.org/licenses/by/3.0/": "spdx:CC-BY-3.0",
       "http://creativecommons.org/licenses/by/4.0/": "spdx:CC-BY-4.0",
       "http://creativecommons.org/publicdomain/zero/1.0/": "spdx:CC0-1.0",
@@ -565,6 +592,10 @@
       "is_a": "rdfs:subClassOf",
       "isa": "rdfs:subClassOf",
       "narrowMatch": "skos:narrowMatch",
+      "obo:aism#dcterms-license": "dcterms:license",
+      "obo:caro#dcterms-license": "dcterms:license",
+      "obo:sasap#closeMatch": "skos:closeMatch",
+      "obo:sasap#relatedMatch": "skos:relatedMatch",
       "part:of": "BFO:0000050",
       "part_of": "bfo:0000050",
       "provenance_notes": "ubprop:0000004",
@@ -590,7 +621,7 @@
       "CREDIT_00": "CREDIT:00",
       "CVCL_": "cellosaurus:CVCL_",
       "DC:0000": "diseaseclass:0000",
-      "DrugNames:DB": "drugbank:DB:",
+      "DrugNames:DB": "drugbank:DB",
       "ECGOntology:<new dbxref> \"": "ECGOntology:",
       "EGA:EGAD": "ega.study:EGAD",
       "EGA:EGAS": "ega.study:EGAS",
@@ -604,12 +635,14 @@
       "From_Merriam-Webster's_Online_Dictionary_at_www.Merriam-Webster.com:http\\://www.merriam-webster.com/dictionary/": "merriamwebster:",
       "GEMET:http\\://www.eionet.europa.eu/gemet/concept/": "GEMET:",
       "GNOme: \"GNO:": "glygen",
+      "GO:GO\\:": "go:",
       "IEDB:RV": "orcid:0000-0001-8957-7612",
       "IEDB:RandiVita": "orcid:0000-0001-8957-7612",
       "IEDB:RandiVita xsd:string": "orcid:0000-0001-8957-7612",
       "KCB:KCB ": "KCB:",
       "KEGG COMPOUND": "KEGG.COMPOUND",
       "KEGG DRUG": "KEGG.DRUG",
+      "KEGG.COMPOUND:c": "KEGG.COMPOUND:C",
       "LIPID MAPS:": "LIPIDMAPS:",
       "MONDOLEX:": "MONDO:",
       "MedlinePlus: ": "MedlinePlus:",
@@ -635,9 +668,13 @@
       "PANTHER:PTHR": "panther.family:PTHR",
       "PDR:PMID:": "pubmed:",
       "PMID: ": "PMID:",
+      "PMID:ID\\:": "pubmed:",
+      "PMID:_": "pubmed:",
+      "Pubmed:PMID\\:": "pubmed:",
       "SNOMEDCT: ": "SNOMEDCT:",
       "TKG:TKG ": "TKG:",
       "TS-": "caloha:",
+      "UM-BBD_enzymeID:r": "umbbd.reaction:r",
       "UMLS CUI:": "UMLS:",
       "URL: ": "URL:",
       "URL: http\\://": "http://",
@@ -652,8 +689,10 @@
       "chembl target:CHEMBL": "chembl.target:CHEMBL",
       "detail?JGLOBAL:ID=": "iobc",
       "doi:/": "doi:",
+      "edamontology:topic_": "edam.topic:",
       "has:": "has_",
       "http://en.wikipedia.org/wiki/": "wikipedia.en:",
+      "http://https://orcid.org/": "orcid:",
       "http://linkedlifedata.com/resource/umls/id/": "UMLS:",
       "http://orcid.org/": "orcid:",
       "http:en.wikipedia.org/wiki/": "wikipedia.en:",
@@ -671,6 +710,7 @@
       "resource:SIO_": "SIO:",
       "scipion:CRYOEM_": "cryoem:",
       "snap#": "snap:",
+      "subject:SRAO_": "srao:",
       "terms1": "dcterms",
       "unirot:": "uniprot:",
       "url: \"https://en.wikipedia.org/wiki/": "wikipedia.en:",
@@ -691,7 +731,16 @@
       "vo/ontorat/PR:": "PR:",
       "xsd\\:": "xsd:"
     },
-    "resource_full": {},
+    "resource_full": {
+      "bspo": {
+        ":has_start_point": "BSPO:0020002",
+        "has_start_point": "BSPO:0020002"
+      },
+      "cteno": {
+        ":has_start_point": "BSPO:0020002",
+        "has_start_point": "BSPO:0020002"
+      }
+    },
     "resource_prefix": {
       "biolink": {
         "active:in": "biolink:active_in",
@@ -710,7 +759,8 @@
         "coexists:with": "biolink:coexists_with",
         "coexpressed:with": "biolink:coexpressed_with",
         "colocalizes:with": "biolink:colocalizes_with",
-        "completed:by": "biolink:completed_by"
+        "completed:by": "biolink:completed_by",
+        "os:": "owlstar:"
       },
       "biomodels.teddy": {
         "TR:": "biomodels.teddy:"
@@ -723,18 +773,21 @@
         "pgx:CVCL_": "cellosaurus:"
       },
       "chebi": {
-        "DrugBank:DBSALT": "drugbank.salt:"
+        "DrugBank:DBSALT": "drugbank.salt:DBSALT"
       },
       "chmo": {
         "Orange:": "orangebook:",
         "Orange: ": "orangebook:"
       },
-      "ehdaa2": {
-        "CS": "carnegie.stage:"
+      "classyfire": {
+        "LIPIDMAPS:": "lipidmaps:LM"
       },
       "doid": {
         "MIM:PS": "omim.ps:"
       },
+      "ehdaa2": {
+        "CS": "carnegie.stage:"
+      },
       "emapa": {
         "TS:": "theiler:"
       },
@@ -760,6 +813,10 @@
       "mdm": {
         "drugbank:DB:": "drugbank:DB"
       },
+      "ncro": {
+        "miRBase:MIPF": "mirbase.family:MIPF",
+        "mirbase:MIMAT": "mirbase.mature:MIMAT"
+      },
       "phipo": {
         "created:by": "dcterms:creator",
         "created:date": "dcterms:created",
@@ -769,6 +826,10 @@
         "OMA:": "uniprot:",
         "iPTMnet:": "uniprot:"
       },
+      "pw": {
+        "KEGG:": "kegg.pathway:",
+        "PID:": "pid.pathway:"
+      },
       "senso": {
         "odo:SENSO_": "senso:"
       },

pyobo/identifier_utils/preprocessing.py

@@ -1,18 +1,14 @@
 """Load the manually curated metaregistry."""
 
-import json
 from functools import lru_cache
 from pathlib import Path
 
-from bioregistry import NormalizedNamableReference
+from curies.preprocessing import PreprocessingRules, _load_rules
 
-from .model import Rules
 from ..resources.goc import load_goc_map
 
 __all__ = [
-    "remap_full",
-    "remap_prefix",
-    "str_is_blacklisted",
+    "get_rules",
 ]
 
 HERE = Path(__file__).parent.resolve()
@@ -20,42 +16,12 @@ RULES_PATH = HERE.joinpath("preprocessing.json")
 
 
 @lru_cache(1)
-def get_rules() -> Rules:
+def get_rules() -> PreprocessingRules:
     """Get the CURIE/URI string preprocessing rules."""
-    rules = Rules.model_validate_json(RULES_PATH.read_text())
+    rules = _load_rules(RULES_PATH)
     rules.rewrites.full.update(load_goc_map())
     return rules
 
 
-def remap_full(
-    str_or_curie_or_uri: str, *, ontology_prefix: str | None = None
-) -> NormalizedNamableReference | None:
-    """Remap the string if possible otherwise return it."""
-    return get_rules().remap_full(
-        str_or_curie_or_uri, cls=NormalizedNamableReference, ontology_prefix=ontology_prefix
-    )
-
-
-def remap_prefix(str_or_curie_or_uri: str, ontology_prefix: str | None = None) -> str:
-    """Remap a prefix."""
-    return get_rules().remap_prefix(str_or_curie_or_uri, ontology_prefix=ontology_prefix)
-
-
-def _lint() -> None:
-    rules = Rules.model_validate_json(RULES_PATH.read_text())
-    rules.blacklists._sort()
-    RULES_PATH.write_text(json.dumps(rules.model_dump(), sort_keys=True, indent=2))
-
-
-def str_is_blacklisted(str_or_curie_or_uri: str, *, ontology_prefix: str | None = None) -> bool:
-    """Check if the full CURIE string is blacklisted."""
-    rules = get_rules()
-    return (
-        rules.str_is_blacklisted_full(str_or_curie_or_uri, ontology_prefix=ontology_prefix)
-        or rules.str_has_blacklisted_prefix(str_or_curie_or_uri, ontology_prefix=ontology_prefix)
-        or rules.str_has_blacklisted_suffix(str_or_curie_or_uri)
-    )
-
-
 if __name__ == "__main__":
-    _lint()
+    PreprocessingRules.lint_file(RULES_PATH)

pyobo/obographs.py

@@ -41,7 +41,11 @@ def graph_from_obo(obo: Obo, use_tqdm: bool = True) -> Graph:
     nodes: list[Node] = []
     edges: list[Edge] = []
     for term in tqdm(
-        obo, disable=not use_tqdm, unit="term", unit_scale=True, desc=f"[{obo.ontology}] to JSON"
+        obo,
+        disable=not use_tqdm,
+        unit="term",
+        unit_scale=True,
+        desc=f"[{obo._prefix_version}] to OBO Graph JSON",
     ):
         nodes.append(_get_class_node(term))
         edges.extend(_iter_edges(term))

pyobo/reader.py

@@ -15,20 +15,19 @@ from typing import Any
 import bioregistry
 import networkx as nx
 from curies import ReferenceTuple
+from curies.preprocessing import BlocklistError
 from curies.vocabulary import SynonymScope
 from more_itertools import pairwise
 from tqdm.auto import tqdm
 
 from .constants import DATE_FORMAT, PROVENANCE_PREFIXES
 from .identifier_utils import (
-    BlacklistedError,
     NotCURIEError,
     ParseError,
     UnparsableIRIError,
     _is_valid_identifier,
     _parse_str_or_curie_or_uri_helper,
-    remap_prefix,
-    str_is_blacklisted,
+    get_rules,
 )
 from .reader_utils import (
     _chomp_axioms,
@@ -53,6 +52,7 @@ from .struct.struct_utils import Annotation, Stanza
 from .struct.typedef import comment as has_comment
 from .struct.typedef import default_typedefs, has_ontology_root_term
 from .utils.cache import write_gzipped_graph
+from .utils.io import safe_open
 from .utils.misc import STATIC_VERSION_REWRITES, cleanup_version
 
 __all__ = [
@@ -76,13 +76,7 @@ def from_obo_path(
 ) -> Obo:
     """Get the OBO graph from a path."""
     path = Path(path).expanduser().resolve()
-    if path.suffix.endswith(".gz"):
-        import gzip
-
-        logger.info("[%s] parsing gzipped OBO with obonet from %s", prefix or "<unknown>", path)
-        with gzip.open(path, "rt") as file:
-            graph = _read_obo(file, prefix, ignore_obsolete=ignore_obsolete, use_tqdm=use_tqdm)
-    elif path.suffix.endswith(".zip"):
+    if path.suffix.endswith(".zip"):
         import io
         import zipfile
 
@@ -95,7 +89,7 @@ def from_obo_path(
                 )
     else:
         logger.info("[%s] parsing OBO with obonet from %s", prefix or "<unknown>", path)
-        with open(path) as file:
+        with safe_open(path, read=True) as file:
             graph = _read_obo(file, prefix, ignore_obsolete=ignore_obsolete, use_tqdm=use_tqdm)
 
     if prefix:
@@ -1262,7 +1256,7 @@ def _handle_prop(
         ):
             case Reference() as datatype_:
                 datatype = datatype_
-            case BlacklistedError():
+            case BlocklistError():
                 return None
             case ParseError() as exc:
                 if strict:
@@ -1304,7 +1298,7 @@ def _handle_prop(
         ):
             case Reference() as obj_reference:
                 return Annotation(prop_reference, obj_reference)
-            case BlacklistedError():
+            case BlocklistError():
                 return None
             case UnparsableIRIError():
                 return Annotation(prop_reference, OBOLiteral.uri(value))
@@ -1330,7 +1324,7 @@ def _handle_prop(
         ):
             case Reference() as obj_reference:
                 return Annotation(prop_reference, obj_reference)
-            case BlacklistedError():
+            case BlocklistError():
                 return None
             case ParseError():
                 if datatype:
@@ -1535,10 +1529,12 @@ def _parse_xref_line(
 ) -> tuple[Reference, list[Reference | OBOLiteral]] | None:
     xref, _, rest = line.partition(" [")
 
-    if str_is_blacklisted(xref, ontology_prefix=ontology_prefix) or ":" not in xref:
+    rules = get_rules()
+
+    if rules.str_is_blocked(xref, context=ontology_prefix) or ":" not in xref:
         return None  # sometimes xref to self... weird
 
-    xref = remap_prefix(xref, ontology_prefix=ontology_prefix)
+    xref = rules.remap_prefix(xref, context=ontology_prefix)
 
     split_space = " " in xref
     if split_space:
@@ -1552,7 +1548,7 @@ def _parse_xref_line(
         xref, ontology_prefix=ontology_prefix, node=node, line=line, context="xref", upgrade=upgrade
     )
     match xref_ref:
-        case BlacklistedError():
+        case BlocklistError():
             return None
         case ParseError() as exc:
             if strict:

pyobo/sources/cgnc.py

@@ -45,7 +45,15 @@ HEADER = [
 
 def get_terms(force: bool = False) -> Iterable[Term]:
     """Get CGNC terms."""
-    df = ensure_df(PREFIX, url=URL, name=f"{PREFIX}.tsv", force=force, header=0, names=HEADER)
+    df = ensure_df(
+        PREFIX,
+        url=URL,
+        name=f"{PREFIX}.tsv",
+        force=force,
+        header=0,
+        names=HEADER,
+        on_bad_lines="skip",
+    )
     for i, (cgnc_id, entrez_id, ensembl_id, name, synonym_1, synoynm_2, _, _) in enumerate(
         df.values
     ):

pyobo/sources/flybase.py

@@ -18,7 +18,7 @@ __all__ = [
 
 logger = logging.getLogger(__name__)
 
-BASE_URL = "http://ftp.flybase.net/releases"
+BASE_URL = "https://s3ftp.flybase.org/releases"
 PREFIX = "flybase"
 NAME = "FlyBase"
 
@@ -51,7 +51,7 @@ def _get_names(version: str, force: bool = False) -> pd.DataFrame:
 
 def _get_organisms(version: str, force: bool = False) -> Mapping[str, str]:
     """Get mapping from abbreviation column to NCBI taxonomy ID column."""
-    url = f"http://ftp.flybase.net/releases/FB{version}/precomputed_files/species/organism_list_fb_{version}.tsv.gz"
+    url = f"{BASE_URL}/FB{version}/precomputed_files/species/organism_list_fb_{version}.tsv.gz"
     df = ensure_df(
         PREFIX, url=url, force=force, version=version, skiprows=4, header=None, usecols=[2, 4]
     )
@@ -60,7 +60,7 @@ def _get_organisms(version: str, force: bool = False) -> Mapping[str, str]:
 
 
 def _get_definitions(version: str, force: bool = False) -> Mapping[str, str]:
-    url = f"http://ftp.flybase.net/releases/FB{version}/precomputed_files/genes/automated_gene_summaries.tsv.gz"
+    url = f"{BASE_URL}/FB{version}/precomputed_files/genes/automated_gene_summaries.tsv.gz"
     df = ensure_df(
         PREFIX, url=url, force=force, version=version, skiprows=2, header=None, usecols=[0, 1]
     )
@@ -69,7 +69,7 @@ def _get_definitions(version: str, force: bool = False) -> Mapping[str, str]:
 
 def _get_human_orthologs(version: str, force: bool = False) -> Mapping[str, set[str]]:
     url = (
-        f"http://ftp.flybase.net/releases/FB{version}/precomputed_files/"
+        f"{BASE_URL}/FB{version}/precomputed_files/"
         f"orthologs/dmel_human_orthologs_disease_fb_{version}.tsv.gz"
     )
     df = ensure_df(
@@ -86,7 +86,7 @@ def _get_human_orthologs(version: str, force: bool = False) -> Mapping[str, set[
 
 
 def _get_synonyms(version, force):
-    url = f"http://ftp.flybase.net/releases/FB{version}/precomputed_files/synonyms/fb_synonym_fb_{version}.tsv.gz"
+    url = f"{BASE_URL}/FB{version}/precomputed_files/synonyms/fb_synonym_fb_{version}.tsv.gz"
     df = ensure_df(PREFIX, url=url, force=force, version=version, skiprows=4, usecols=[0, 2])
     return df  # TODO use this
 

pyobo/sources/omim_ps.py

@@ -13,7 +13,7 @@ __all__ = [
 
 logger = logging.getLogger(__name__)
 PREFIX = "omim.ps"
-URL = "https://omim.org/phenotypicSeriesTitles/all"
+URL = "https://omim.org/phenotypicSeriesTitles/"
 
 
 class OMIMPSGetter(Obo):
@@ -26,13 +26,13 @@ class OMIMPSGetter(Obo):
         soup = get_soup(URL, user_agent="Mozilla/5.0")
         content = soup.find(id="mimContent")
         if content is None:
-            raise ValueError
+            raise ValueError("omim.ps failed - scraper could not find id='mimContent' in HTML")
         table = content.find("table")  # type:ignore[attr-defined]
         if table is None:
-            raise ValueError
+            raise ValueError("omim.ps failed - scraper could not find table in HTML")
         tbody = table.find("tbody")
         if tbody is None:
-            raise ValueError
+            raise ValueError("omim.ps failed - scraper could not find table body in HTML")
         for row in tbody.find_all("tr"):
             anchor = row.find("td").find("a")
             name = anchor.text.strip()

pyobo/sources/pharmgkb/pharmgkb_gene.py

@@ -105,4 +105,4 @@ def iter_terms(force: bool = False) -> Iterable[Term]:
 
 
 if __name__ == "__main__":
-    PharmGKBGeneGetter().write_default(force=True, write_obo=True, use_tqdm=True)
+    PharmGKBGeneGetter.cli()

pyobo/struct/functional/ontology.py

@@ -16,6 +16,7 @@ from pyobo.struct.functional.utils import (
     FunctionalOWLSerializable,
     list_to_funowl,
 )
+from pyobo.utils.io import safe_open
 
 __all__ = [
     "Document",
@@ -109,7 +110,8 @@ class Document:
     def write_funowl(self, path: str | Path) -> None:
         """Write functional OWL to a file.."""
         path = Path(path).expanduser().resolve()
-        path.write_text(self.to_funowl())
+        with safe_open(path, read=False) as file:
+            file.write(self.to_funowl())
 
     def to_funowl(self) -> str:
         """Get the document as a functional OWL string."""

pyobo/struct/reference.py

@@ -14,9 +14,9 @@ import dateutil.parser
 import pytz
 from bioregistry import NormalizedNamableReference as Reference
 from curies import ReferenceTuple
+from curies.preprocessing import BlocklistError
 
 from ..identifier_utils import (
-    BlacklistedError,
     NotCURIEError,
     ParseError,
     UnparsableIRIError,
@@ -62,7 +62,7 @@ def _parse_str_or_curie_or_uri(
     match reference:
         case Reference():
             return reference
-        case BlacklistedError():
+        case BlocklistError():
             return None
         case ParseError():
             if strict:
@@ -224,7 +224,7 @@ def _obo_parse_identifier(
     ):
         case Reference() as reference:
             return reference
-        case BlacklistedError():
+        case BlocklistError():
             return None
         case NotCURIEError() as exc:
             # this means there's no colon `:`
@@ -272,7 +272,7 @@ def _parse_reference_or_uri_literal(
     ):
         case Reference() as reference:
             return reference
-        case BlacklistedError():
+        case BlocklistError():
             return None
         case UnparsableIRIError():
             # this means that it's defininitely a URI,