pyobo 0.12.9__py3-none-any.whl → 0.12.10__py3-none-any.whl

pyobo/ner/scispacy_utils.py

@@ -9,7 +9,7 @@ entity linking (also called named entity normalization (NEN) or grounding) in
 Constructing a Lexical Index
 ============================
 
-An *ad hoc* SciSpacy lexical index can be constructed on-the-fly by passing a
+An *ad hoc* ScispaCy lexical index can be constructed on-the-fly by passing a
 Bioregistry prefix to :func:`pyobo.get_scispacy_knowledgebase`. In the following
 example, the prefix ``to`` is used to construct a lexical index for the `Plant Trait
 Ontology <https://bioregistry.io/to>`_.
@@ -74,7 +74,7 @@ process in the correctly versioned folder in the PyOBO cache.
     import pyobo
     from scispacy.linking import EntityLinker
 
-    linker = pyobo.get_scispacy_entity_linker("hgnc", filter_for_definitions=False)
+    linker: EntityLinker = pyobo.get_scispacy_entity_linker("hgnc", filter_for_definitions=False)
 
 Full Workflow
 =============
@@ -128,7 +128,7 @@ highly scored groundings, the best of which, `hgnc:391
 
 .. note::
 
-    The groundings and scores are stored by SciSpacy in the hidden attribute
+    The groundings and scores are stored by ScispaCy in the hidden attribute
     ``span._.kb_ents``.
 """
 
@@ -162,12 +162,10 @@ def get_scispacy_entity_linker(
     candidate_generator_kwargs: dict[str, Any] | None = None,
     **entity_linker_kwargs: Any,
 ) -> EntityLinker:
-    """Get a knowledgebase object for usage with :mod:`scispacy`.
-
-    :param prefix :
-        The ontology's prefix, such as ``go` for Gene Ontology, ``doid`` for the Disease
-        Ontology, or more.
+    """Get an entity linker for usage with :mod:`scispacy`.
 
+    :param prefix: The ontology's prefix, such as ``go` for Gene Ontology, ``doid`` for
+        the Disease Ontology, or more.
     :param ontology_kwargs: keyword arguments to pass to :func:`pyobo.get_ontology`,
         such as ``version``.
     :param candidate_generator_kwargs: keyword arguments to pass to
@@ -199,14 +197,12 @@ def get_scispacy_entity_linker(
 
 
 def get_scispacy_knowledgebase(prefix: str, **kwargs: Unpack[GetOntologyKwargs]) -> KnowledgeBase:
-    """Get a knowledgebase object for usage with :mod:`scispacy`.
+    """Get a lexical index for usage with :mod:`scispacy`.
 
-    :param prefix :
-        The ontology's prefix, such as ``go` for Gene Ontology, ``doid`` for the Disease
-        Ontology, or more.
-
-    :param kwargs :
-        keyword arguments to pass to :func:`pyobo.get_ontology`, such as ``version``.
+    :param prefix: The ontology's prefix, such as ``go` for Gene Ontology, ``doid`` for
+        the Disease Ontology, or more.
+    :param kwargs: keyword arguments to pass to :func:`pyobo.get_ontology`, such as
+        ``version``.
 
     :returns: An object that represents a lexical index over name, synonym, and
         definition strings from the ontology.
@@ -219,12 +215,10 @@ def get_scispacy_knowledgebase(prefix: str, **kwargs: Unpack[GetOntologyKwargs])
 def get_scispacy_entities(prefix: str, **kwargs: Unpack[GetOntologyKwargs]) -> Iterable[Entity]:
     """Iterate over entities in a given ontology via :mod:`pyobo`.
 
-    :param prefix :
-        The ontology's prefix, such as ``go` for Gene Ontology, ``doid`` for the Disease
-        Ontology, or more.
-
-    :param kwargs :
-        keyword arguments to pass to :func:`pyobo.get_ontology`, such as ``version``.
+    :param prefix: The ontology's prefix, such as ``go` for Gene Ontology, ``doid`` for
+        the Disease Ontology, or more.
+    :param kwargs: keyword arguments to pass to :func:`pyobo.get_ontology`, such as
+        ``version``.
 
     :yields: Entity objects for all terms in the ontology
     """

pyobo/struct/struct.py

@@ -1903,6 +1903,46 @@ class Obo:
         """Get a mapping from identifiers to a list of sorted synonym strings."""
         return multidict(self.iterate_synonym_rows(use_tqdm=use_tqdm))
 
+    def get_grounder(self) -> ssslm.Grounder:
+        """Get a grounder from this ontology.
+
+        :returns: An object that can be used for named entity recognition and named
+            entity normalization
+
+        Here's example usage for a built-in ontology:
+
+        .. code-block:: python
+
+            import pyobo
+            import ssslm
+
+            ontology = pyobo.get_ontology("taxrank")
+            grounder: ssslm.Grounder = ontology.get_grounder()
+            matches: list[ssslm.Match] = grounder.ground("species")
+
+        Here's example usage for a custom ontology:
+
+        .. code-block:: python
+
+            import pyobo
+            import ssslm
+            from urllib.request import urlretrieve
+
+            url = "http://purl.obolibrary.org/obo/taxrank.obo"
+            path = "taxrank.obo"
+            urlretrieve(url, path)
+
+            ontology = pyobo.from_obo_path(path, prefix="taxrank")
+            grounder: ssslm.Grounder = ontology.get_grounder()
+            matches: list[ssslm.Match] = grounder.get_matches("species")
+
+        .. warning::
+
+            It's required to tell PyOBO the prefix for a custom ontology when using
+            :func:`pyobo.from_obo_path`, and it must be registered in the Bioregistry
+        """
+        return ssslm.make_grounder(self.get_literal_mappings())
+
     def get_literal_mappings(self) -> Iterable[ssslm.LiteralMapping]:
         """Get literal mappings in a standard data model."""
         stanzas: Iterable[Stanza] = itt.chain(self, self.typedefs or [])

pyobo/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.12.9"
+VERSION = "0.12.10"
 
 
 def get_git_hash() -> str:

{pyobo-0.12.9.dist-info → pyobo-0.12.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.9
+Version: 0.12.10
 Summary: A python package for handling and generating OBO
 Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
 Author: Charles Tapley Hoyt

{pyobo-0.12.9.dist-info → pyobo-0.12.10.dist-info}/RECORD

@@ -36,7 +36,7 @@ pyobo/mocks.py,sha256=j545K9P_DPsDBuYHDrhyTLjmlPoNlRdEtcRlLhXlbXI,2440
 pyobo/ner/__init__.py,sha256=7Os84d8_gZktUxyUW9Tn2dW33rYFWSO8cviJJef-ZeE,373
 pyobo/ner/api.py,sha256=s0MJgz6sj13qiB1TEyO_aC8103fgnYBwZroRgygpZNw,2167
 pyobo/ner/normalizer.py,sha256=pdvwFG9elriK83FKqjQfT2s-ZuC-QZZuMPudjfay21w,954
-pyobo/ner/scispacy_utils.py,sha256=trEwCeLzMJdD_b7SmSrbZrw1DgGlMDI39iH6RyNOLjs,8201
+pyobo/ner/scispacy_utils.py,sha256=4NRGJ1JJB-OmlVthHhyms1iPMwJYrkVMQP1jgZfJ18U,8170
 pyobo/plugins.py,sha256=wEr-NpyZ7Z6uEr0uGDNOeXLOGZokGbFmo3e-z2PNKJM,1232
 pyobo/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyobo/resource_utils.py,sha256=bloSKbHfMLz0hB8AkhMkfLOGqw6FyO8CEU6LNg0PVMk,4406
@@ -190,7 +190,7 @@ pyobo/struct/obograph/export.py,sha256=yk3MHulDM_SMohfwiFdeB62-XGJ2ZNgRUZGjGjiyo
 pyobo/struct/obograph/reader.py,sha256=264yVeD8a3jGx9EaGUZVxFbSQ_pwQ_6ckVw9S8wiJfM,8525
 pyobo/struct/obograph/utils.py,sha256=je0kSkC24MU9pWRHq1_K-J5jWhjWESY6NI3TpZqvZ_Q,1516
 pyobo/struct/reference.py,sha256=qgwTa-0VIoDklQ7LjlYH-mf2WG0_uO7KlHt0PSBail4,11744
-pyobo/struct/struct.py,sha256=_1rJa5vmVNyjtE2wdnGUkWtyHd2l5AQJnr4TZ3206YM,93789
+pyobo/struct/struct.py,sha256=0is3zpmLQoH8XNVKPDAOqYlQ7IIL7Xr7onx6auLjYJA,95115
 pyobo/struct/struct_utils.py,sha256=_D689bNlGg1_r-4vQQ-imVEOxzq95XBqBFxqFMV077U,40346
 pyobo/struct/typedef.py,sha256=iLm8-DVY0v_dK_RwoNKCeOF7nI6XlaieS2CaCHePSlI,13088
 pyobo/struct/utils.py,sha256=zkpOE42JQIfkN0rc5qNENK03VIKmkf_57tHojMJK71Y,906
@@ -202,9 +202,9 @@ pyobo/utils/iter.py,sha256=rYRbbaFJHxMaE0yU-rQZoCagYIrtev09uY0mxFkf5zY,1524
 pyobo/utils/misc.py,sha256=499pencyDqW9_xm0H0Cq0FhOw0MoNoq-9IVQTKh-eaE,7992
 pyobo/utils/ndex_utils.py,sha256=EokCWS00Wrk_4y8ldeQuUyaaC6yNzBg3DagUl-J2czY,2326
 pyobo/utils/path.py,sha256=Ep8lTRWgFU9_XF5vqJV5B3G4PcUBglIitMkaUNxjzvo,4091
-pyobo/version.py,sha256=J-kjTBsp13Gn9z_AZZpwjfHq3kBfqfmvaT-s9SxrWLQ,926
-pyobo-0.12.9.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
-pyobo-0.12.9.dist-info/WHEEL,sha256=Pi5uDq5Fdo_Rr-HD5h9BiPn9Et29Y9Sh8NhcJNnFU1c,79
-pyobo-0.12.9.dist-info/entry_points.txt,sha256=ANgzvuwF_9_1ipCoxJtbBM6A4i2Mkt39gMPzQO6hvGs,42
-pyobo-0.12.9.dist-info/METADATA,sha256=WoRJx_9HRg8cs2EDXmteoZObNFc-ZLK7QdjxusVpiXI,22095
-pyobo-0.12.9.dist-info/RECORD,,
+pyobo/version.py,sha256=r3VLmEhyOat5T5vXiDW6v0isg_jC5J9BzcsOTJg1OxY,927
+pyobo-0.12.10.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
+pyobo-0.12.10.dist-info/WHEEL,sha256=Pi5uDq5Fdo_Rr-HD5h9BiPn9Et29Y9Sh8NhcJNnFU1c,79
+pyobo-0.12.10.dist-info/entry_points.txt,sha256=ANgzvuwF_9_1ipCoxJtbBM6A4i2Mkt39gMPzQO6hvGs,42
+pyobo-0.12.10.dist-info/METADATA,sha256=PdeYdweM7uV4yHveuaDqAyD_sS7Xh3PIT9kUwZ8Kycw,22096
+pyobo-0.12.10.dist-info/RECORD,,