Update

Author: cthoyt

src/pyobo/getters.py

@@ -255,14 +255,15 @@ def _ensure_ontology_path(
             case None:
                 continue
             case AnnotatedURL() as a:
-                name = _name_from_url(a.url, ontology_format, rdf_format=a.rdf_format)
+                url = a.url
                 rdf_format = a.rdf_format
             case str() as url:
-                name = _name_from_url(url, ontology_format)
                 rdf_format = None
             case _:
                 raise TypeError
 
+        name = _name_from_url(url, ontology_format, rdf_format=rdf_format)
+
         try:
             path = ensure_path(prefix, url=url, force=force, version=version, name=name)
         except (urllib.error.HTTPError, pystow.utils.DownloadError):

src/pyobo/struct/jskos_utils.py

@@ -5,12 +5,36 @@
 import curies
 
 from .struct import Obo, build_ontology
+import jskos
+from jskos import ProcessedConcept, ProcessedKOS
 
 __all__ = [
     "read_jskos",
+    "from_pkos",
 ]
 
 
 def read_jskos(path: str | Path, *, prefix: str, converter: curies.Converter | None = None) -> Obo:
     """Read JSKOS into an ontology."""
+    if converter is None:
+        from ..identifier_utils import get_converter
+        converter = get_converter()
+    kos = jskos.read(path)
+    pkos = jskos.process(kos, converter)
+    return from_pkos(prefix=prefix, pkos=pkos)
+
+
+def from_pkos(prefix: str, pkos: ProcessedKOS) -> Obo:
+    raise NotImplementedError
     return build_ontology(prefix=prefix)
+
+
+def _iterate_concepts(pkos: ProcessedKOS) -> list[ProcessedConcept]:
+    for c in pkos.concepts:
+        yield from _iterate_concepts_inner(c)
+
+
+def _iterate_concepts_inner(concept: ProcessedConcept):
+    yield concept
+    for narrower in concept.narrower:
+        yield from _iterate_concepts_inner(concept)

src/pyobo/struct/reference.py

@@ -277,7 +277,7 @@ def _parse_reference_or_uri_literal(
         case BlocklistError():
             return None
         case UnparsableIRIError():
-            # this means that it's defininitely a URI,
+            # this means that it's definitely a URI,
             # but it couldn't be parsed with Bioregistry
             return OBOLiteral.uri(str_or_curie_or_uri)
         case NotCURIEError() as exc:

src/pyobo/utils/misc.py

@@ -8,11 +8,8 @@
 from typing import TYPE_CHECKING, TypeAlias
 
 import bioversions.utils
-
 from pyobo.constants import ONTOLOGY_GETTERS, OntologyFormat
-
-if TYPE_CHECKING:
-    from bioregistry.schema.struct import AnnotatedURL
+from bioregistry.schema.struct import AnnotatedURL
 
 __all__ = [
     "VERSION_GETTERS",
@@ -52,6 +49,8 @@
     "https://w3id.org/lehrplan/ontology/",  # like in https://w3id.org/lehrplan/ontology/1.0.0-4
     "http://www.ebi.ac.uk/swo/version/",  # http://www.ebi.ac.uk/swo/version/6.0
     "https://w3id.org/emi/version/",
+    "https://nfdi4culture.de/ontology/", # https://nfdi4culture.de/ontology/3.0.0
+    "http://purls.helmholtz-metadaten.de/mwo/mwo.owl/", # http://purls.helmholtz-metadaten.de/mwo/mwo.owl/3.0.0
 ]
 VERSION_PREFIX_SPLITS = [
     "http://www.ebi.ac.uk/efo/releases/v",
@@ -60,6 +59,7 @@
     "http://ontology.neuinfo.org/NIF/ttl/nif/version/",
     "http://nmrml.org/cv/v",  # as in http://nmrml.org/cv/v1.1.0/nmrCV
     "http://enanomapper.github.io/ontologies/releases/",  # as in http://enanomapper.github.io/ontologies/releases/10.0/enanomapper
+    "https://w3id.org/sulo/sulo-", # as in https://w3id.org/sulo/sulo-0.2.4.ttl
 ]
 BAD = {
     "http://purl.obolibrary.org/obo",

tests/test_struct/test_jskos/__init__.py

@@ -0,0 +1 @@
+"""Tests for ingestion of JSKOS."""

tests/test_struct/test_jskos/test_jskos.py

@@ -0,0 +1,22 @@
+"""Test JSKOS."""
+
+import unittest
+from pyobo.struct.jskos_utils import read_jskos
+
+import curies
+
+URL = "https://skohub.io/KDSF-FFK/kdsf-ffk/heads/main/w3id.org/kdsf-ffk/index.json"
+
+
+class TestJSKOS(unittest.TestCase):
+    """Test JSKOS."""
+
+    def test_jskos(self) -> None:
+        """Test JSKOS."""
+        converter = curies.Converter.from_prefix_map({
+            "ksdf.fkk": "https://w3id.org/kdsf-ffk/",
+        })
+        ontology = read_jskos(prefix="ksdf.fkk", path=URL, converter=converter)
+        names = ontology.get_id_name_mapping()
+        self.assertIn("ArbeitUndWirtschaft", names)
+        self.assertIn("Work and Economy", names["ArbeitUndWirtschaft"])