pyobo 0.12.12__py3-none-any.whl → 0.12.13__py3-none-any.whl

pyobo/sources/chebi.py

@@ -3,7 +3,7 @@
 from collections.abc import Mapping
 
 from ..api import get_filtered_properties_mapping, get_filtered_relations_df
-from ..struct import Reference, TypeDef
+from ..struct.typedef import has_role
 from ..utils.io import multisetdict
 
 __all__ = [
@@ -28,9 +28,6 @@ def get_chebi_smiles_id_mapping() -> Mapping[str, str]:
     return {v: k for k, v in get_chebi_id_smiles_mapping().items()}
 
 
-has_role = TypeDef(reference=Reference(prefix="chebi", identifier="has_role"))
-
-
 def get_chebi_role_to_children() -> Mapping[str, set[tuple[str, str]]]:
     """Get the ChEBI role to children mapping."""
     df = get_filtered_relations_df("chebi", relation=has_role)

pyobo/struct/struct_utils.py

@@ -1020,6 +1020,8 @@ def _format_obo_trailing_modifiers(
                     right = f'"{obo_escape_slim(value)}"'
                 else:
                     right = value
+            case _:
+                raise TypeError(f"invalid prop value: {type(prop.value)} - {prop.value}")
         modifiers.append((left, right))
     inner = ", ".join(f"{key}={value}" for key, value in modifiers)
     return " {" + inner + "}"

pyobo/struct/typedef.py

@@ -18,6 +18,7 @@ __all__ = [
     "contributes_to_condition",
     "default_typedefs",
     "derives_from_organism",
+    "directly_regulates_activity_of",
     "editor_note",
     "enables",
     "ends",
@@ -46,15 +47,20 @@ __all__ = [
     "has_successor",
     "has_taxonomy_rank",
     "is_a",
+    "is_agonist_of",
+    "is_antagonist_of",
+    "is_inverse_agonist_of",
     "located_in",
     "mapping_has_confidence",
     "mapping_has_justification",
     "match_typedefs",
     "member_of",
     "narrow_match",
+    "negatively_regulates",
     "orthologous",
     "part_of",
     "participates_in",
+    "positively_regulates",
     "related_match",
     "role_of",
     "see_also",
@@ -267,6 +273,19 @@ has_functional_parent = TypeDef(
     reference=Reference(prefix="ro", identifier="0018038", name="has functional parent"),
 )
 
+positively_regulates = TypeDef(
+    Reference(prefix="RO", identifier="0002213", name="positively regulates")
+)
+negatively_regulates = TypeDef(
+    Reference(prefix="RO", identifier="0002212", name="negatively regulates")
+)
+is_agonist_of = TypeDef.from_triple("RO", "0018027", "is agonist of")
+is_inverse_agonist_of = TypeDef.from_triple("RO", "0018028", "is inverse agonist of")
+is_antagonist_of = TypeDef.from_triple("RO", "0018029", "is antagonist of")
+directly_regulates_activity_of = TypeDef.from_triple(
+    "RO", "0002448", "directly regulates activity of"
+)
+
 is_mentioned_by = TypeDef(
     reference=v.is_mentioned_by,
     is_metadata_tag=True,

pyobo/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.12.12"
+VERSION = "0.12.13"
 
 
 def get_git_hash() -> str:

{pyobo-0.12.12.dist-info → pyobo-0.12.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.12
+Version: 0.12.13
 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-0.12.12.dist-info → pyobo-0.12.13.dist-info}/RECORD

@@ -59,7 +59,7 @@ pyobo/sources/bigg/bigg_reaction.py,sha256=45SIIae32GtDxzL_gpF7p1TKVfh6t3UgHpF4f
 pyobo/sources/biogrid.py,sha256=dYl6Pt3YpND2cvTl5LIAekWyJpclf7R1JvFJUT9XH9A,3297
 pyobo/sources/ccle.py,sha256=Fn1tY1YHHyZj6mlqg8ISMGUYG4o6W5MeeO7l_KlLmos,2924
 pyobo/sources/cgnc.py,sha256=XlwqqjJc7B97352-AgaRo8lazXnKf__JVV4ldfGJl1Q,2299
-pyobo/sources/chebi.py,sha256=-f_XyBLOHoC2uGqu8UzQ3HgAlbqAhm7-AUve0HK0TOA,1202
+pyobo/sources/chebi.py,sha256=1ESngeNgenO4DwMD0YFgRIQx6LLndqT0JS4lLhQTRCk,1119
 pyobo/sources/chembl/__init__.py,sha256=mfqYGDIjoUj66ooq2AUvzX2DLFheSdSsvwyKt9pLonY,414
 pyobo/sources/chembl/chembl_cell.py,sha256=q-O7wJyOT2bjtqN5-0d2gEkJr0R-ULKHvt6843j8gVA,2669
 pyobo/sources/chembl/chembl_compound.py,sha256=Ds9axuT1uO-9L3lQnEpr_8JdWo-mDNWJv9hTWG9WXsk,1888
@@ -192,8 +192,8 @@ pyobo/struct/obograph/reader.py,sha256=264yVeD8a3jGx9EaGUZVxFbSQ_pwQ_6ckVw9S8wiJ
 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=-JaApTZ7e50bRJ2dXPdAVuJ0ElIVJIJ-HHRsVdaiMxM,96291
-pyobo/struct/struct_utils.py,sha256=tqaUOYKfM3NAa9NfIrWUbaEFJuSOi05_fXPh1cNMY2w,40911
-pyobo/struct/typedef.py,sha256=9qO09bK641t_N37wGHuX9WpYRwUaApk1AhlS9hjLwek,13453
+pyobo/struct/struct_utils.py,sha256=VFC82fgphTs7sBSNGn53sv2WMl7Ho9srALFq92bRFQQ,41021
+pyobo/struct/typedef.py,sha256=LGDfJPAiTdp4PZPHUMgvhLsJrOZMIaGSBHA2oh8uCuU,14188
 pyobo/struct/utils.py,sha256=zkpOE42JQIfkN0rc5qNENK03VIKmkf_57tHojMJK71Y,906
 pyobo/struct/vocabulary.py,sha256=wY_wlV17NyoPQZMiCkf72GL4bIB9gwTHIoMlx7W8Cf4,5375
 pyobo/utils/__init__.py,sha256=CANSY8vGq_6v8rWhWRIdnk-Wo5LA2R9Wjg1nqbWqLOw,17
@@ -203,9 +203,9 @@ 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=snV58UHxHO6GI2QPPE46ssR4RWozaw83V59sS_I9BY8,4109
-pyobo/version.py,sha256=Eu_AwMBgCNMCmdFFfIt2yVQpL91vAj4m086WEmjvn6g,927
-pyobo-0.12.12.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
-pyobo-0.12.12.dist-info/WHEEL,sha256=UH59_qNuDUAa1VxQvC6fxmbl24EMw6DOIlT1yp8oeuU,78
-pyobo-0.12.12.dist-info/entry_points.txt,sha256=ANgzvuwF_9_1ipCoxJtbBM6A4i2Mkt39gMPzQO6hvGs,42
-pyobo-0.12.12.dist-info/METADATA,sha256=mC0mNzJrMLuFLelXKTY04R8Dm1nlU5rcXZsBA_M3YYI,22783
-pyobo-0.12.12.dist-info/RECORD,,
+pyobo/version.py,sha256=-3azDhk7QGSEF_6hXZvXJhIqE9utObgNlX9avQrhAtI,927
+pyobo-0.12.13.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
+pyobo-0.12.13.dist-info/WHEEL,sha256=YUH1mBqsx8Dh2cQG2rlcuRYUhJddG9iClegy4IgnHik,79
+pyobo-0.12.13.dist-info/entry_points.txt,sha256=ANgzvuwF_9_1ipCoxJtbBM6A4i2Mkt39gMPzQO6hvGs,42
+pyobo-0.12.13.dist-info/METADATA,sha256=RiVfL9jxKk1n8rRSTO4BdCbWMLDZOJF_Qb_ZJU94u_s,22783
+pyobo-0.12.13.dist-info/RECORD,,

{pyobo-0.12.12.dist-info → pyobo-0.12.13.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: uv 0.9.6
+Generator: uv 0.9.11
 Root-Is-Purelib: true
 Tag: py3-none-any