pyobo 0.10.5__py3-none-any.whl → 0.10.7__py3-none-any.whl

pyobo/struct/struct.py

@@ -47,6 +47,7 @@ from .typedef import (
     exact_match,
     from_species,
     get_reference_tuple,
+    has_ontology_root_term,
     has_part,
     is_a,
     orthologous,
@@ -108,7 +109,7 @@ class Synonym:
     def _fp(self) -> str:
         x = f'"{self._escape(self.name)}" {self.specificity}'
         if self.type and self.type.pair != DEFAULT_SYNONYM_TYPE.pair:
-            x = f"{x} {self.type.curie}"
+            x = f"{x} {self.type.preferred_curie}"
         return f"{x} [{comma_separate(self.provenance)}]"
 
     @staticmethod
@@ -125,7 +126,7 @@ class SynonymTypeDef(Referenced):
 
     def to_obo(self) -> str:
         """Serialize to OBO."""
-        rv = f'synonymtypedef: {self.curie} "{self.name}"'
+        rv = f'synonymtypedef: {self.preferred_curie} "{self.name}"'
         if self.specificity:
             rv = f"{rv} {self.specificity}"
         return rv
@@ -157,6 +158,11 @@ class SynonymTypeDef(Referenced):
 DEFAULT_SYNONYM_TYPE = SynonymTypeDef(
     reference=Reference(prefix="oboInOwl", identifier="SynonymType", name="Synonym"),
 )
+abbreviation = SynonymTypeDef(
+    reference=Reference(prefix="OMO", identifier="0003000", name="abbreviation")
+)
+acronym = SynonymTypeDef(reference=Reference(prefix="omo", identifier="0003012", name="acronym"))
+
 
 ReferenceHint = Union[Reference, "Term", Tuple[str, str], str]
 
@@ -216,6 +222,8 @@ class Term(Referenced):
     #: An annotation for obsolescence. By default, is None, but this means that it is not obsolete.
     is_obsolete: Optional[bool] = None
 
+    type: Literal["Term", "Instance"] = "Term"
+
     def __hash__(self):  # noqa: D105
         return hash((self.__class__, self.prefix, self.identifier))
 
@@ -226,11 +234,13 @@ class Term(Referenced):
         identifier: str,
         name: Optional[str] = None,
         definition: Optional[str] = None,
+        **kwargs,
     ) -> "Term":
         """Create a term from a reference."""
         return cls(
             reference=Reference(prefix=prefix, identifier=identifier, name=name),
             definition=definition,
+            **kwargs,
         )
 
     @classmethod
@@ -260,11 +270,17 @@ class Term(Referenced):
         self.provenance.append(_ensure_ref(reference))
 
     def append_synonym(
-        self, synonym: Union[str, Synonym], type: Optional[SynonymTypeDef] = None
+        self,
+        synonym: Union[str, Synonym],
+        *,
+        type: Optional[SynonymTypeDef] = None,
+        specificity: Optional[SynonymSpecificity] = None,
     ) -> None:
         """Add a synonym."""
         if isinstance(synonym, str):
-            synonym = Synonym(synonym, type=type or DEFAULT_SYNONYM_TYPE)
+            synonym = Synonym(
+                synonym, type=type or DEFAULT_SYNONYM_TYPE, specificity=specificity or "EXACT"
+            )
         self.synonyms.append(synonym)
 
     def append_alt(self, alt: Union[str, Reference]) -> None:
@@ -322,7 +338,7 @@ class Term(Referenced):
         """Get relationships from the given type."""
         return self.relationships[typedef]
 
-    def append_exact_match(self, reference):
+    def append_exact_match(self, reference: ReferenceHint):
         """Append an exact match, also adding an xref."""
         reference = _ensure_ref(reference)
         self.append_relationship(exact_match, reference)
@@ -363,12 +379,14 @@ class Term(Referenced):
             raise ValueError("can not extend a collection that includes a null reference")
         self.relationships[typedef].extend(references)
 
-    def append_property(self, prop: Union[str, TypeDef], value: Union[str, Reference]) -> None:
+    def append_property(
+        self, prop: Union[str, Reference, Referenced], value: Union[str, Reference, Referenced]
+    ) -> None:
         """Append a property."""
-        if isinstance(prop, TypeDef):
-            prop = prop.curie
-        if isinstance(value, Reference):
-            value = value.curie
+        if isinstance(prop, (Reference, Referenced)):
+            prop = prop.preferred_curie
+        if isinstance(value, (Reference, Referenced)):
+            value = value.preferred_curie
         self.properties[prop].append(value)
 
     def _definition_fp(self) -> str:
@@ -387,10 +405,12 @@ class Term(Referenced):
             for value in values:
                 yield prop, value
 
-    def iterate_obo_lines(self) -> Iterable[str]:
+    def iterate_obo_lines(self, *, ontology, typedefs) -> Iterable[str]:
         """Iterate over the lines to write in an OBO file."""
-        yield "\n[Term]"
-        yield f"id: {self.curie}"
+        yield f"\n[{self.type}]"
+        yield f"id: {self.preferred_curie}"
+        if self.is_obsolete:
+            yield "is_obsolete: true"
         if self.name:
             yield f"name: {obo_escape_slim(self.name)}"
         if self.namespace and self.namespace != "?":
@@ -403,14 +423,23 @@ class Term(Referenced):
             yield f"def: {self._definition_fp()}"
 
         for xref in sorted(self.xrefs, key=attrgetter("prefix", "identifier")):
-            yield f"xref: {xref}"
+            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"is_a: {parent}"
+            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 (
+                ontology,
+                typedef.curie,
+            ) not in _TYPEDEF_WARNINGS:
+                logger.warning(f"[{ontology}] typedef not defined in OBO: {typedef.curie}")
+                _TYPEDEF_WARNINGS.add((ontology, typedef.curie))
+
+            typedef_preferred_curie = typedef.preferred_curie
             for reference in sorted(references, key=attrgetter("prefix", "identifier")):
-                s = f"relationship: {typedef.curie} {reference.curie}"
+                s = f"relationship: {typedef_preferred_curie} {reference.preferred_curie}"
                 if typedef.name or reference.name:
                     s += " !"
                 if typedef.name:
@@ -420,6 +449,7 @@ class Term(Referenced):
                 yield s
 
         for prop, value in sorted(self.iterate_properties(), key=_sort_properties):
+            # TODO deal with typedefs for properties
             yield f'property_value: {prop} "{value}" xsd:string'  # TODO deal with types later
 
         for synonym in sorted(self.synonyms, key=attrgetter("name")):
@@ -430,6 +460,10 @@ class Term(Referenced):
         return s.replace("\n", "\\n").replace('"', '\\"')
 
 
+#: A set of warnings, used to make sure we don't show the same one over and over
+_TYPEDEF_WARNINGS: Set[Tuple[str, str]] = set()
+
+
 def _sort_relations(r):
     typedef, _references = r
     return typedef.reference.name or typedef.reference.identifier
@@ -632,6 +666,8 @@ class Obo:
             yield f"idspace: {prefix} {url}"
 
         for synonym_typedef in sorted((self.synonym_typedefs or []), key=attrgetter("curie")):
+            if synonym_typedef.curie == DEFAULT_SYNONYM_TYPE.curie:
+                continue
             yield synonym_typedef.to_obo()
 
         yield f"ontology: {self.ontology}"
@@ -639,15 +675,23 @@ class Obo:
         if self.name is None:
             raise ValueError("ontology is missing name")
         yield f'property_value: http://purl.org/dc/elements/1.1/title "{self.name}" xsd:string'
+        license_spdx_id = bioregistry.get_license(self.ontology)
+        if license_spdx_id:
+            # TODO add SPDX to idspaces and use as a CURIE?
+            yield f'property_value: http://purl.org/dc/terms/license "{license_spdx_id}" xsd:string'
+        description = bioregistry.get_description(self.ontology)
+        if description:
+            description = obo_escape_slim(description.strip())
+            yield f'property_value: http://purl.org/dc/elements/1.1/description "{description}" xsd:string'
 
         for root_term in self.root_terms or []:
-            yield f"property_value: IAO:0000700 {root_term.curie}"
+            yield f"property_value: {has_ontology_root_term.preferred_curie} {root_term.preferred_curie}"
 
         for typedef in sorted(self.typedefs or [], key=attrgetter("curie")):
             yield from typedef.iterate_obo_lines()
 
         for term in self:
-            yield from term.iterate_obo_lines()
+            yield from term.iterate_obo_lines(ontology=self.ontology, typedefs=self.typedefs)
 
     def write_obo(
         self, file: Union[None, str, TextIO, Path] = None, use_tqdm: bool = False
@@ -992,6 +1036,16 @@ class Obo:
         """Get a mapping from identifiers to definitions."""
         return dict(self.iterate_id_definition(use_tqdm=use_tqdm))
 
+    def get_obsolete(self, *, use_tqdm: bool = False) -> Set[str]:
+        """Get the set of obsolete identifiers."""
+        return {
+            term.identifier
+            for term in self._iter_terms(
+                use_tqdm=use_tqdm, desc=f"[{self.ontology}] getting obsolete"
+            )
+            if term.identifier and term.is_obsolete
+        }
+
     ############
     # TYPEDEFS #
     ############
@@ -1416,4 +1470,4 @@ def _convert_synonym_typedefs(synonym_typedefs: Optional[Iterable[SynonymTypeDef
 
 
 def _convert_synonym_typedef(synonym_typedef: SynonymTypeDef) -> str:
-    return f'{synonym_typedef.curie} "{synonym_typedef.name}"'
+    return f'{synonym_typedef.preferred_curie} "{synonym_typedef.name}"'

pyobo/struct/typedef.py

@@ -40,6 +40,9 @@ __all__ = [
     "enables",
     "participates_in",
     "has_participant",
+    "exact_match",
+    "has_dbxref",
+    # Properties
     "has_inchi",
     "has_smiles",
 ]
@@ -47,7 +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
@@ -75,7 +81,7 @@ class TypeDef(Referenced):
     def iterate_obo_lines(self) -> Iterable[str]:
         """Iterate over the lines to write in an OBO file."""
         yield "\n[Typedef]"
-        yield f"id: {self.reference.curie}"
+        yield f"id: {self.reference.preferred_curie}"
         if self.name:
             yield f"name: {self.reference.name}"
         if self.definition:
@@ -94,7 +100,7 @@ class TypeDef(Referenced):
             yield f"comment: {self.comment}"
 
         for xref in self.xrefs:
-            yield f"xref: {xref}"
+            yield f"xref: {xref.preferred_curie}"
 
         if self.is_transitive is not None:
             yield f'is_transitive: {"true" if self.is_transitive else "false"}'
@@ -102,9 +108,11 @@ class TypeDef(Referenced):
         if self.is_symmetric is not None:
             yield f'is_symmetric: {"true" if self.is_symmetric else "false"}'
         if self.holds_over_chain:
-            _chain = " ".join(link.curie for link in self.holds_over_chain)
+            _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":
@@ -261,9 +269,24 @@ has_salt = TypeDef(
     reference=Reference(prefix="debio", identifier="0000006", name="has salt"),
 )
 
-example_of_usage = Reference(prefix=IAO_PREFIX, identifier="0000112", name="example of usage")
-alternative_term = Reference(prefix=IAO_PREFIX, identifier="0000118", name="alternative term")
-editor_note = Reference(prefix=IAO_PREFIX, identifier="0000116", name="editor note")
+term_replaced_by = TypeDef.from_triple(
+    prefix=IAO_PREFIX, identifier="0100001", name="term replaced by"
+)
+example_of_usage = TypeDef.from_triple(
+    prefix=IAO_PREFIX, identifier="0000112", name="example of usage"
+)
+alternative_term = TypeDef.from_triple(
+    prefix=IAO_PREFIX, identifier="0000118", name="alternative term"
+)
+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")
 
 is_immediately_transformed_from = TypeDef.from_triple(
     prefix=SIO_PREFIX, identifier="000658", name="is immediately transformed from"

pyobo/version.py

@@ -14,7 +14,7 @@ __all__ = [
     "get_git_hash",
 ]
 
-VERSION = "0.10.5"
+VERSION = "0.10.7"
 
 
 def get_git_hash() -> str:

{pyobo-0.10.5.dist-info → pyobo-0.10.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyobo
-Version: 0.10.5
+Version: 0.10.7
 Summary: Handling and writing OBO
 Home-page: https://github.com/pyobo/pyobo
 Download-URL: https://github.com/pyobo/pyobo/releases
@@ -49,7 +49,7 @@ Requires-Dist: class-resolver
 Requires-Dist: psycopg2-binary
 Requires-Dist: drugbank-downloader
 Requires-Dist: chembl-downloader
-Requires-Dist: umls-downloader
+Requires-Dist: umls-downloader >=0.1.2
 Requires-Dist: typing-extensions
 Provides-Extra: agrovoc
 Requires-Dist: rdflib ; extra == 'agrovoc'

{pyobo-0.10.5.dist-info → pyobo-0.10.7.dist-info}/RECORD

@@ -1,22 +1,22 @@
-pyobo/__init__.py,sha256=qnXvit-N0GItG8tZQ5qkjGI4IXARMSQGzuuTjy08Ozc,1844
+pyobo/__init__.py,sha256=mZ96iZ-5ucxe2eLBi0xuSKaa2ZfeInaSR5Ajc_NkvUo,1862
 pyobo/__main__.py,sha256=cQjBabQ2wlFKcv54PFdt0SgPXNeb3oWneuOHaBgHx1Q,108
 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=MOBoNT_BXbi6lzaNd7z2Noubvo86RVlJqU4KJa7t2AE,7034
-pyobo/identifier_utils.py,sha256=4I5Na4B8BYh3l1MfbePbolT0aCYpR8hJ-q-yJZlUqzk,3642
+pyobo/gilda_utils.py,sha256=XNgtk41hp1gMJjlmthMp9SQ0gLrVrjWZ4AUC9-lR4bU,6850
+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=Yio6dpeUaGKZmDQ6P1SfSxKUWP7bmDDT8U5HqOkntnw,977
-pyobo/api/__init__.py,sha256=7kDkA26zvk8xQYQ95wXwnmaHxeUGqVSNS2UDD2o_gEU,1308
+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
 pyobo/api/metadata.py,sha256=62E7j0ZW3vYK2Rh-R7NCMKnChbYjZwPjVDoaE1AsCOc,1070
-pyobo/api/names.py,sha256=rQkLOndJEQ0QI_cjod8OqqlPJwKWyl6z3TzzdV9UIFU,6955
+pyobo/api/names.py,sha256=A5HprOfdt7twF2LfjdQQaIj3FNj4_GD7MZ7CrKllY5M,7559
 pyobo/api/properties.py,sha256=PTCYsYmma3cym-dYY44p2NVGD7Z1dKZdC1otcfUflqg,7342
 pyobo/api/relations.py,sha256=VEQCQjPamehyGaL-wFzUYH9OeVq9pVzj70sl9K3ttKw,5996
 pyobo/api/species.py,sha256=xRPRoD6n1wcDaqlC_tHLw3rKMWa4razWsSPNa228g_4,2181
@@ -52,31 +52,32 @@ pyobo/resources/ncbitaxon.py,sha256=kyJDMGm8qIpIpckN6NSGovCBDacG1qGYTIpvJ--HXhM,
 pyobo/resources/ncbitaxon.tsv.gz,sha256=43zHjnVt62TA4_lV58X-FCPdMDfLg1B1PvZSr_Xy9hY,22981954
 pyobo/resources/ro.py,sha256=_CYD90vftMZvu8Rj6H9kOiw6wRBbs1LWmCl-HToxMIg,1484
 pyobo/resources/ro.tsv,sha256=YvlBLPAKy2w4IheYzO9ox1Yg6WkHdMVzMQTikIlECog,26586
-pyobo/sources/__init__.py,sha256=4OCytk4FwLNv2NehCNqOwfyuSQoNXpdiPP4dgn48Ybc,3563
+pyobo/sources/__init__.py,sha256=vWzTP4kraQulrA4h2NTAhsjouehsEj0hQBwpqLypXSs,3666
 pyobo/sources/agrovoc.py,sha256=J425AyyOVAeqeyN5MhmAR9OtJom41GDvKArfyz1iIU8,795
 pyobo/sources/antibodyregistry.py,sha256=5i2qRhGgyi11Ke9xrHU1NRFxD3xMCnHQWWKh9fQCXDs,3178
 pyobo/sources/biogrid.py,sha256=Rr5gSLmOK95YPm2cYcFbGLDm3LWNckLvlarmbSIP-5M,3290
 pyobo/sources/ccle.py,sha256=KqqVokOq0HYE980plNa3987O1ixLkpcC0j9rYoQIM70,2963
-pyobo/sources/cgnc.py,sha256=HsER4HihwjEeFaLobK0FW1izLflpzKA7k_7Vuppnt6k,2250
+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=vwRVUxtv9e7T3fJGn2P54ozK3_8OUSqVhpR2mtQeahQ,2254
-pyobo/sources/complexportal.py,sha256=cEFXVJFK7iZUSv6pcIwEUR9A3PL9YhcFuNdfXTGtcdk,5529
+pyobo/sources/chembl.py,sha256=MG_bTilUwhhkeuTA3owLn1gro1QicMyGGfcd-48NGgE,2296
+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
-pyobo/sources/depmap.py,sha256=Row0hZxjDUf4WhIILNFlkEog0vvGKD-czG4YpXm4xJk,3582
+pyobo/sources/depmap.py,sha256=VuZduDgCduiAHPLwPDXgWpxhMSOZCC4UsxFdj7hNkYQ,3656
 pyobo/sources/dictybase_gene.py,sha256=EgWBwUZ83ev7x5Lp_nUkgSq2zumkDjJ7_13m3f6kJz0,2564
 pyobo/sources/drugbank.py,sha256=pb2IdVQF4FqDvefwRdqlDV5j6pR9R1b3rGxHC-GSWb4,11028
 pyobo/sources/drugbank_salt.py,sha256=hx16G41mP2KXT4fsAQRCRkJMGn-z5cafs-bwm4wMtwo,1783
-pyobo/sources/drugcentral.py,sha256=FUBVTnF9m-YlWUDwNTa9sB3hhEJ6-KUHTj-TROv2T-Q,3545
+pyobo/sources/drugcentral.py,sha256=05mGolBIyKCxAYzpH9LY_ZQrTVnizup2JUiWi2wW9OI,3587
 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=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
 pyobo/sources/gwascentral_study.py,sha256=_YH9TRWsCOHjOrJ2pAqQ7fi_HmF1WbMmTUj5iqWDUwY,2812
-pyobo/sources/hgnc.py,sha256=_6Do7ZwRzAeWESiTepic0DTpNSACOg7MdFaePe85rsw,14949
+pyobo/sources/hgnc.py,sha256=kVxVIv4LIy_H_rvVQbwvj3Jn6KmLwpk-XRn5jkpnjN4,15951
 pyobo/sources/hgncgenefamily.py,sha256=o7gCI5raXkCMr8ONfAZpRW7PtsZ8lkRC4T1kEjTxBn4,3645
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 pyobo/sources/icd11.py,sha256=04nLt-Lr64hAroOLH4OP-iNbuIjBk-mYcg-Ib34zgMM,2834
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 pyobo/sources/mirbase_mature.py,sha256=nvWcQVDMBucPu6v5DLFb_W_9fz_J_Id7HZrilkUhaFI,1504
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 pyobo/sources/rhea.py,sha256=YZBFB6JLzHv6_bnCH5XZruJpwUaFaiH206oxE0THr0M,4109
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 pyobo/sources/kegg/genes.py,sha256=i0OOtso4bU1bz9UVckvsMGQ8DvJnQDhOSoHqv1wmqPc,3705
@@ -118,10 +120,11 @@ pyobo/sources/selventa/sdis.py,sha256=5LRPNHJonDZ2aojg6juTsBNbGKv55k8dtFex9LHYDd
 pyobo/sources/selventa/sfam.py,sha256=F9HzH_OZucofsAkOkvinyoiUmnw3_0pBMB7pgU9fSZg,1620
 pyobo/sources/umls/__init__.py,sha256=L49nPxoXFtFHwzP327cEOTr1oJrKAz7_nS2tahajpnY,104
 pyobo/sources/umls/__main__.py,sha256=mz2UqO02rnA68XM3420Nev4yocBn20QFSqU3E0oqNx8,133
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+pyobo/sources/umls/get_synonym_types.py,sha256=5u1ZEl8gp_StuQxrasvHK4S0DyVWdgp_rLzo3aFOALI,1111
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 pyobo/sources/uniprot/__init__.py,sha256=dsL0BvfMn3O_swtNhzQpjJUlP56NUBCcjSYdFvRlwmI,225
-pyobo/sources/uniprot/uniprot.py,sha256=cN1vZ3uhlSt70-PigADEA667z6Y36b3GfuG4F-C_Slg,2638
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 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
@@ -129,9 +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
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 pyobo/struct/utils.py,sha256=-XHuCETp7jPNhjHCW72gikaKoaiTPTNhDK5BZYyJsVw,815
 pyobo/utils/__init__.py,sha256=wXtcjcasWRBtJdTSMCC3jT8yFG8ZkQC-Xdh9lLiQDAo,42
 pyobo/utils/cache.py,sha256=bmuEE0DyppY6szNEzkS1tLLKfsLIrHQFhp0P-q94KFs,2677
@@ -156,9 +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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-pyobo-0.10.5.dist-info/RECORD,,
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+pyobo-0.10.7.dist-info/RECORD,,

{pyobo-0.10.5.dist-info → pyobo-0.10.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
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+Generator: bdist_wheel (0.41.3)
 Root-Is-Purelib: true
 Tag: py3-none-any