pyobo 0.10.6__py3-none-any.whl → 0.10.7__py3-none-any.whl

pyobo/identifier_utils.py

@@ -119,7 +119,7 @@ def wrap_norm_prefix(f):
 
 def standardize_ec(ec: str) -> str:
     """Standardize an EC code identifier by removing all trailing dashes and dots."""
-    ec = ec.strip()
+    ec = ec.strip().replace(" ", "")
     for _ in range(4):
         ec = ec.rstrip("-").rstrip(".")
     return ec

pyobo/obographs.py

@@ -19,7 +19,7 @@ from bioontologies.obograph import (
 from bioontologies.robot import ParseResults
 
 from pyobo.struct import Obo, Reference, Term
-from pyobo.struct.typedef import is_a
+from pyobo.struct.typedef import definition_source, is_a
 
 __all__ = [
     "graph_from_obo",
@@ -61,12 +61,12 @@ def _rewire(r: Reference) -> curies.Reference:
 
 
 def _get_class_node(term: Term) -> Node:
-    if not term.definition:
-        definition = None
-    else:
+    if term.definition or term.provenance:
         definition = Definition.from_parsed(
             value=term.definition, references=[_rewire(p) for p in term.provenance]
         )
+    else:
+        definition = None
 
     if term.xrefs:
         if not term.xref_types:
@@ -126,3 +126,11 @@ def _iter_edges(term: Term) -> Iterable[Edge]:
                 _rewire(typedef.reference),
                 _rewire(target),
             )
+
+    for provenance_reference in term.provenance:
+        yield Edge.from_parsed(
+            _rewire(term.reference),
+            _rewire(definition_source.reference),
+            _rewire(provenance_reference),
+        )
+    # TODO also look through xrefs and seealso to get provenance xrefs?

pyobo/reader.py

@@ -444,20 +444,23 @@ def _extract_synonym(
             break
 
     stype: Optional[SynonymTypeDef] = None
-    if specificity is not None:  # go fishing for a synonym type definition
-        for _stype in synonym_typedefs.values():
-            # Since there aren't a lot of carefully defined synonym definitions, it
-            # can appear as a string or curie. Therefore, we might see temporary prefixes
-            # get added, so we should check against full curies as well as local unique
-            # identifiers
-            if rest.startswith(_stype.curie):
-                rest = rest[len(_stype.curie) :].strip()
-                stype = _stype
-                break
-            elif rest.startswith(_stype.identifier):
-                rest = rest[len(_stype.identifier) :].strip()
-                stype = _stype
-                break
+    for _stype in synonym_typedefs.values():
+        # Since there aren't a lot of carefully defined synonym definitions, it
+        # can appear as a string or curie. Therefore, we might see temporary prefixes
+        # get added, so we should check against full curies as well as local unique
+        # identifiers
+        if rest.startswith(_stype.curie):
+            rest = rest[len(_stype.curie) :].strip()
+            stype = _stype
+            break
+        elif rest.startswith(_stype.preferred_curie):
+            rest = rest[len(_stype.preferred_curie) :].strip()
+            stype = _stype
+            break
+        elif rest.startswith(_stype.identifier):
+            rest = rest[len(_stype.identifier) :].strip()
+            stype = _stype
+            break
 
     if not rest.startswith("[") or not rest.endswith("]"):
         logger.warning("[%s:%s] problem with synonym: %s", prefix, identifier, s)

pyobo/sources/complexportal.py

@@ -82,6 +82,17 @@ def _parse_xrefs(s) -> List[Tuple[Reference, str]]:
             logger.warning("xref missing (: %s", xref)
             continue
         note = note.rstrip(")")
+        note.replace("rhea:rhea ", "rhea:")
+        note.replace("rhea:Rhea ", "rhea:")
+        note.replace("eccode::", "eccode:")
+        note.replace("eccode:EC:", "eccode:")
+        note.replace("eccode:RHEA:", "rhea:")
+        if note.lower().startswith("rhea "):
+            note = note[len("Rhea ") :]
+            if note.lower().startswith("rhea:rhea "):
+                note = note[len("rhea:rhea ") :]
+        if note.lower().startswith("EC:"):
+            note = note[len("EC:") :]
         try:
             reference = Reference.from_curie(xref_curie)
         except ValueError:

pyobo/sources/geonames.py

@@ -38,7 +38,9 @@ def get_terms(*, force: bool = False) -> Collection[Term]:
     """Get terms."""
     code_to_country = get_code_to_country(force=force)
     code_to_admin1 = get_code_to_admin1(code_to_country, force=force)
-    code_to_admin2 = get_code_to_admin2(code_to_admin1, force=force)
+    code_to_admin2 = get_code_to_admin2(
+        code_to_country=code_to_country, code_to_admin1=code_to_admin1, force=force
+    )
     id_to_term = get_cities(
         code_to_country=code_to_country,
         code_to_admin1=code_to_admin1,
@@ -113,7 +115,7 @@ def get_code_to_admin1(
 
 
 def get_code_to_admin2(
-    code_to_admin1: Mapping[str, Term], *, force: bool = False
+    *, code_to_country: Mapping[str, Term], code_to_admin1: Mapping[str, Term], force: bool = False
 ) -> Mapping[str, Term]:
     """Get a mapping from admin2 code to term."""
     admin2_df = ensure_df(
@@ -134,8 +136,13 @@ def get_code_to_admin2(
         term.append_property("code", code)
         code_to_admin2[code] = term
         admin1_code = code.rsplit(".", 1)[0]
-        admin1_term = code_to_admin1[admin1_code]
-        term.append_relationship(part_of, admin1_term)
+        admin1_term = code_to_admin1.get(admin1_code)
+        if admin1_term:
+            term.append_relationship(part_of, admin1_term)
+        else:
+            country_code = admin1_code.split(".", 1)[0]
+            country_term = code_to_country[country_code]
+            term.append_relationship(part_of, country_term)
     return code_to_admin2
 
 
@@ -197,7 +204,10 @@ def get_cities(
                     term.append_synonym(synonym)
 
         if pd.isna(admin1):
-            tqdm.write(f"[geonames:{identifier}] missing admin 1 code for {name} ({country})")
+            # TODO try to annotate these directly onto countries
+            tqdm.write(
+                f"[geonames:{identifier}] {name}, a city in {country}, is missing admin 1 code"
+            )
             continue
 
         admin1_full = f"{country}.{admin1}"

pyobo/sources/npass.py

@@ -72,7 +72,9 @@ def iter_terms(version: str, force: bool = False) -> Iterable[Term]:
 
         # TODO check that the first is always the parent compound?
         if pd.notna(pubchem_compound_ids):
-            pubchem_compound_ids = pubchem_compound_ids.split(";")
+            pubchem_compound_ids = [
+                yy.strip() for xx in pubchem_compound_ids.split(";") for yy in xx.strip().split(",")
+            ]
             if len(pubchem_compound_ids) > 1:
                 logger.debug("multiple cids for %s: %s", identifier, pubchem_compound_ids)
             for pubchem_compound_id in pubchem_compound_ids:

pyobo/sources/uniprot/uniprot.py

@@ -30,7 +30,7 @@ class UniProtGetter(Obo):
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
-        yield from iter_terms(force=force, version=self._version_or_raise)
+        yield from iter_terms(version=self._version_or_raise)
 
 
 def get_obo(force: bool = False) -> Obo:
@@ -38,9 +38,9 @@ def get_obo(force: bool = False) -> Obo:
     return UniProtGetter(force=force)
 
 
-def iter_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Term]:
+def iter_terms(version: Optional[str] = None) -> Iterable[Term]:
     """Iterate over UniProt Terms."""
-    with open_reader(ensure(version=version, force=force)) as reader:
+    with open_reader(ensure(version=version)) as reader:
         _ = next(reader)  # header
         for uniprot_id, name, taxonomy_id, _synonyms, ecs, pubmeds, pdbs in tqdm(
             reader, desc="Mapping UniProt", unit_scale=True
@@ -63,11 +63,11 @@ def iter_terms(version: Optional[str] = None, force: bool = False) -> Iterable[T
             yield term
 
 
-def ensure(version: Optional[str] = None, force: bool = False) -> Path:
+def ensure(version: Optional[str] = None) -> Path:
     """Ensure the reviewed uniprot names are available."""
     if version is None:
         version = bioversions.get_version("uniprot")
-    return RAW_MODULE.ensure(PREFIX, version, name="reviewed.tsv.gz", url=REVIEWED_URL, force=force)
+    return RAW_MODULE.ensure(PREFIX, version, name="reviewed.tsv.gz", url=REVIEWED_URL)
 
 
 if __name__ == "__main__":

pyobo/struct/reference.py

@@ -31,11 +31,15 @@ class Reference(curies.Reference):
             raise ExpansionError(f"Unknown prefix: {v}")
         return norm_prefix
 
+    @property
+    def preferred_prefix(self) -> str:
+        """Get the preferred curie for this reference."""
+        return bioregistry.get_preferred_prefix(self.prefix) or self.prefix
+
     @property
     def preferred_curie(self) -> str:
         """Get the preferred curie for this reference."""
-        pp = bioregistry.get_preferred_prefix(self.prefix) or self.prefix
-        return f"{pp}:{self.identifier}"
+        return f"{self.preferred_prefix}:{self.identifier}"
 
     @root_validator(pre=True)
     def validate_identifier(cls, values):  # noqa
@@ -125,7 +129,7 @@ class Reference(curies.Reference):
         if identifier_lower.startswith(f"{self.prefix.lower()}:"):
             rv = identifier_lower
         else:
-            rv = f"{self.prefix}:{self._escaped_identifier}"
+            rv = f"{self.preferred_prefix}:{self._escaped_identifier}"
         if self.name:
             rv = f"{rv} ! {self.name}"
         return rv

pyobo/struct/struct.py

@@ -384,9 +384,9 @@ class Term(Referenced):
     ) -> None:
         """Append a property."""
         if isinstance(prop, (Reference, Referenced)):
-            prop = prop.curie
+            prop = prop.preferred_curie
         if isinstance(value, (Reference, Referenced)):
-            value = value.curie
+            value = value.preferred_curie
         self.properties[prop].append(value)
 
     def _definition_fp(self) -> str:
@@ -423,11 +423,11 @@ class Term(Referenced):
             yield f"def: {self._definition_fp()}"
 
         for xref in sorted(self.xrefs, key=attrgetter("prefix", "identifier")):
-            yield f"xref: {xref.preferred_curie}"
+            yield f"xref: {xref}"  # __str__ bakes in the ! name
 
         parent_tag = "is_a" if self.type == "Term" else "instance_of"
         for parent in sorted(self.parents, key=attrgetter("prefix", "identifier")):
-            yield f"{parent_tag}: {parent.preferred_curie}"
+            yield f"{parent_tag}: {parent}"  # __str__ bakes in the ! name
 
         for typedef, references in sorted(self.relationships.items(), key=_sort_relations):
             if (not typedefs or typedef not in typedefs) and (

pyobo/struct/typedef.py

@@ -50,7 +50,10 @@ __all__ = [
 
 @dataclass
 class TypeDef(Referenced):
-    """A type definition in OBO."""
+    """A type definition in OBO.
+
+    See the subsection of https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html#S.2.2.
+    """
 
     reference: Reference
     comment: Optional[str] = None
@@ -108,6 +111,8 @@ class TypeDef(Referenced):
             _chain = " ".join(link.preferred_curie for link in self.holds_over_chain)
             _names = " / ".join(link.name or "_" for link in self.holds_over_chain)
             yield f"holds_over_chain: {_chain} ! {_names}"
+        if self.inverse:
+            yield f"inverse_of: {self.inverse}"
 
     @classmethod
     def from_triple(cls, prefix: str, identifier: str, name: Optional[str] = None) -> "TypeDef":
@@ -276,6 +281,9 @@ alternative_term = TypeDef.from_triple(
 has_ontology_root_term = TypeDef.from_triple(
     prefix=IAO_PREFIX, identifier="0000700", name="has ontology root term"
 )
+definition_source = TypeDef.from_triple(
+    prefix=IAO_PREFIX, identifier="0000119", name="definition source"
+)
 has_dbxref = TypeDef.from_curie("oboInOwl:hasDbXref", name="has database cross-reference")
 
 editor_note = TypeDef.from_triple(prefix=IAO_PREFIX, identifier="0000116", name="editor note")

pyobo/version.py

@@ -14,7 +14,7 @@ __all__ = [
     "get_git_hash",
 ]
 
-VERSION = "0.10.6"
+VERSION = "0.10.7"
 
 
 def get_git_hash() -> str:

{pyobo-0.10.6.dist-info → pyobo-0.10.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyobo
-Version: 0.10.6
+Version: 0.10.7
 Summary: Handling and writing OBO
 Home-page: https://github.com/pyobo/pyobo
 Download-URL: https://github.com/pyobo/pyobo/releases

{pyobo-0.10.6.dist-info → pyobo-0.10.7.dist-info}/RECORD

@@ -4,14 +4,14 @@ pyobo/aws.py,sha256=EUXsN_sQEOWOV2oZXrVrkO8R6Zo_JJHGeGzzWWgpvzo,5948
 pyobo/constants.py,sha256=gj8xSUmCO0rU-eGXHOW7Vix3SAHl50cLAM3HXuoAFt4,2200
 pyobo/getters.py,sha256=PFKV03izOK8wIU9CpZVRKgu5x-Mqnl39Kzo_bVPs8cs,15528
 pyobo/gilda_utils.py,sha256=XNgtk41hp1gMJjlmthMp9SQ0gLrVrjWZ4AUC9-lR4bU,6850
-pyobo/identifier_utils.py,sha256=4I5Na4B8BYh3l1MfbePbolT0aCYpR8hJ-q-yJZlUqzk,3642
+pyobo/identifier_utils.py,sha256=y4eFbJJQGoGe0HKRqQoUc_3tani22W_K4z7OZFL6Z0E,3659
 pyobo/mocks.py,sha256=R-4W3Rm5NarIHfNjxurbvBYsLHXt6jmDb6THMUt6K1w,2432
 pyobo/normalizer.py,sha256=OHME2CDQSZYSbqmP-L_-4nxete9W9mtAjUzXVs1hnjU,8293
-pyobo/obographs.py,sha256=CyEBuEa89QaC1AHwzwyjxW7-mYgXZ6OfMioQnz_BgrM,3430
+pyobo/obographs.py,sha256=JKE0a7e-gmxqdJoeX2zb_xQ6Tv5PAe60YhnIpAvrrYg,3758
 pyobo/plugins.py,sha256=dXWGoFuQktNeQUWSJlPz2a7FeLysggc9ry6auEZdw98,1227
-pyobo/reader.py,sha256=92mEpYWY8qcjSobMxass4x7M0hs_rkPI4jTtSgDjfsk,21237
+pyobo/reader.py,sha256=3VTWQMmA-AHi3RdA2jb48d2deXO-lYKqXbcMa9Qhi_4,21271
 pyobo/resource_utils.py,sha256=JBcJRihZhNwp78-qWZPrzSCGoYfyOjzBwMkfmOkO_no,4289
-pyobo/version.py,sha256=C0_iNdG0JbjCFHPA_ffkTmeLuJBsJMvAnU-ir8lk2XM,977
+pyobo/version.py,sha256=4zWbRnfTzmpe4izKe0mVCjyI8gxa0fCIboUcmzf12Tg,977
 pyobo/api/__init__.py,sha256=Hq8p5uPW8fFYG2KfLqUsHhtLkTPqE4TqItGkedZzvXM,1326
 pyobo/api/alts.py,sha256=xmAb-gGQCJ9MbaFvoNK6E-V0B3TV9hxulkfbkHIvOso,2617
 pyobo/api/hierarchy.py,sha256=TBZs6SqG1wBP3026D7_bsznH-PAXeM2t1Onwb6_10R4,9010
@@ -60,7 +60,7 @@ pyobo/sources/ccle.py,sha256=KqqVokOq0HYE980plNa3987O1ixLkpcC0j9rYoQIM70,2963
 pyobo/sources/cgnc.py,sha256=5epG5LK9RWMAUp2pL7rvd-5A-QPloqCNjw1MxHn6x-c,2308
 pyobo/sources/chebi.py,sha256=YSxLIV90P-AhQCq9q0AKzWwBgr_BgnxScUW-5AjY2DA,1198
 pyobo/sources/chembl.py,sha256=MG_bTilUwhhkeuTA3owLn1gro1QicMyGGfcd-48NGgE,2296
-pyobo/sources/complexportal.py,sha256=cEFXVJFK7iZUSv6pcIwEUR9A3PL9YhcFuNdfXTGtcdk,5529
+pyobo/sources/complexportal.py,sha256=nhEaUzw4riuN31OLiwpGffj66YMCeLigekblTWGk3nk,6022
 pyobo/sources/conso.py,sha256=ZLQ_T5EgrcuX9q6kCBKCwfGzAEVxgN6xADl-LKzJtbk,2460
 pyobo/sources/cpt.py,sha256=x8P15D9UX5Fwf6bmeVsU1DAFJvZ22rxVPy5ur-GUk_Q,1482
 pyobo/sources/cvx.py,sha256=Jo9b2S7lGfY8YyVIyoBLbOBn47LiUA3IcMFOD4L2j_k,2195
@@ -72,7 +72,7 @@ pyobo/sources/drugcentral.py,sha256=05mGolBIyKCxAYzpH9LY_ZQrTVnizup2JUiWi2wW9OI,
 pyobo/sources/expasy.py,sha256=h8RcFtRd4wHBDVHC7tK8C1dT2M0dCknhfoWao7DLOx4,9507
 pyobo/sources/famplex.py,sha256=O5-pUBsT-GMedAAoTkZDnpNdWDFIf4NnZwXSv7qXWaA,5784
 pyobo/sources/flybase.py,sha256=0-BCNsp-L-CgGPN9VdJec6-8e4-fJuzaZAZiNra3ZUQ,5768
-pyobo/sources/geonames.py,sha256=oUUKnvTRdSFgtgaF9JfSF4WBZO53RBvPEoFQe2LXwe4,7507
+pyobo/sources/geonames.py,sha256=XpSc-_6653MrjunVJhqbHHLtkT8kmbJZzfRuF6DoWU8,7929
 pyobo/sources/gmt_utils.py,sha256=NAWyUZ1p1HcO8RPL9mEEcL9KoaBDPuU-tbyG2QLb98k,1401
 pyobo/sources/go.py,sha256=IJul9eAXxKifZiWKJL1Dl9PFDFdoPMQ0ZVydzhnRtX0,1275
 pyobo/sources/gwascentral_phenotype.py,sha256=dCzyw_jbmhol69Li0g2ocMQJRqjoV2fZM_pno6i7xyA,1889
@@ -92,7 +92,7 @@ pyobo/sources/mirbase_family.py,sha256=Yj3oXaeBWDxcmBKnvOl0q_7nzlye5EXhSJPWlV3Yp
 pyobo/sources/mirbase_mature.py,sha256=nvWcQVDMBucPu6v5DLFb_W_9fz_J_Id7HZrilkUhaFI,1504
 pyobo/sources/msigdb.py,sha256=YKgFyPgYKdYQtu22P69IVyLeBsLfgNyaNOl7q0Sy8IU,5019
 pyobo/sources/ncbigene.py,sha256=FXGwSrnPSQREiF2k3qtZvRBEiung3bbVb-NAJv33uHU,4890
-pyobo/sources/npass.py,sha256=T_ehde-DOXFLizgm52fWN9CU-ANNBhJo_bNkIt8d-h4,2720
+pyobo/sources/npass.py,sha256=t8TDdxpfvvXYo8VczT4ngoSspPAdPJuLKigvHZ9OHrE,2805
 pyobo/sources/pathbank.py,sha256=yhdS4BCbGxQf0o3HCGzL2cYRY7zyvHvDzzSBkkezoog,4989
 pyobo/sources/pfam.py,sha256=aHXdXmoG6xyNkScHft_xYe4J2DzRr22EinyfjpmwEj4,1846
 pyobo/sources/pfam_clan.py,sha256=hjJ0UUEcrNoaQVWbXZ_EaTWFo4iB9VG9Sp6pcO90gxY,1340
@@ -124,7 +124,7 @@ pyobo/sources/umls/get_synonym_types.py,sha256=5u1ZEl8gp_StuQxrasvHK4S0DyVWdgp_r
 pyobo/sources/umls/synonym_types.tsv,sha256=z--ngeAqA_Kk8ft2YD8qOU_XUxhnTxF0OhL8jRd5xqo,8551
 pyobo/sources/umls/umls.py,sha256=nCeUPTJyKKs7K5Yft2ZSgVXaC6sCau0387AVzDXzXk0,3730
 pyobo/sources/uniprot/__init__.py,sha256=dsL0BvfMn3O_swtNhzQpjJUlP56NUBCcjSYdFvRlwmI,225
-pyobo/sources/uniprot/uniprot.py,sha256=cN1vZ3uhlSt70-PigADEA667z6Y36b3GfuG4F-C_Slg,2638
+pyobo/sources/uniprot/uniprot.py,sha256=tJqSubCTMBfFkIRQxXqzVGlS7PTCrA9c_0mofjAFmj8,2557
 pyobo/sources/uniprot/uniprot_ptm.py,sha256=ze1cf0_kkqslhS-lXa7EdfasV4reUDp6niJat6yymT8,3551
 pyobo/ssg/__init__.py,sha256=Q5vYmk1LZwriShmA3TcYZ1Z1yiyjTWItcGxep5Fi2pw,5390
 pyobo/ssg/base.html,sha256=_vldUCa-gL2YTNY6GgAuxNT3TgaED585vF_q7TrrjYs,2844
@@ -132,9 +132,9 @@ pyobo/ssg/index.html,sha256=zDGkwIQBtbpnhCYALXQ0vr7qsVmAqDtbwOyPqU3hZ8s,3993
 pyobo/ssg/term.html,sha256=QU6piGOq4dq8zlNhJvLFxqFjhVQyWlkiG31I0Sg5frg,3559
 pyobo/ssg/typedef.html,sha256=KrdqzB6xjt689bG33D26AL-11JrvNuEkoxNNI-EG-Tg,2038
 pyobo/struct/__init__.py,sha256=imJ-ffEGBI8f_kSbmDC-VQMCZksLxoHh7OjwvF4chwM,653
-pyobo/struct/reference.py,sha256=p6DDe7O73zaOvoc5spyHBBId8eRjRYIyy37PzRy0mBM,5569
-pyobo/struct/struct.py,sha256=zWoMfP3KlgRvxX57Uck0KPOArZacs3F1AprwcDmWx8M,54035
-pyobo/struct/typedef.py,sha256=hJKfGawq8BnQqzO0yrlFDSmr1kAwNzIlyVpD1U_wCIU,11978
+pyobo/struct/reference.py,sha256=U2qHIANj_0XhSxh7UBaXUiOXWtVjtyIBeDQ03heWuxA,5712
+pyobo/struct/struct.py,sha256=_azCiXAQwRObLpZMPrX0BJWm3Xscx-WKrEvUOOJQyxA,54085
+pyobo/struct/typedef.py,sha256=pkowFqTdJrrg61Du86i2JGERnMHerFoQSx690HO2DS4,12268
 pyobo/struct/utils.py,sha256=-XHuCETp7jPNhjHCW72gikaKoaiTPTNhDK5BZYyJsVw,815
 pyobo/utils/__init__.py,sha256=wXtcjcasWRBtJdTSMCC3jT8yFG8ZkQC-Xdh9lLiQDAo,42
 pyobo/utils/cache.py,sha256=bmuEE0DyppY6szNEzkS1tLLKfsLIrHQFhp0P-q94KFs,2677
@@ -159,9 +159,9 @@ pyobo/xrefdb/sources/intact.py,sha256=F0z6WrOwI79aZSuM5MsvQwzqoyzh9J0UuB4Mseoj9X
 pyobo/xrefdb/sources/ncit.py,sha256=unoIKJqdcfitTc6pU9P1SxJ1w8ax0iDjvEOlqe64nCY,3745
 pyobo/xrefdb/sources/pubchem.py,sha256=GaqgqtSV-T_P-900nL3alPx_ZB36MlmnEepOnZMONA4,780
 pyobo/xrefdb/sources/wikidata.py,sha256=ODi87EMsE3pJKkZTmaOgjbxsHFgqROGsZ6r0w2gbHC8,3351
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