pyobo 0.12.13__py3-none-any.whl → 0.12.14__py3-none-any.whl

pyobo/constants.py

@@ -267,7 +267,7 @@ def _get_json_download(prefix: str) -> str | None:
 def _get_rdf_download(prefix: str) -> str | None:
     import bioregistry
 
-    return bioregistry.get_rdf_download(prefix)
+    return bioregistry.get_rdf_download(prefix, get_format=False)
 
 
 #: Functions that get ontology files. Order matters in this list,

pyobo/sources/hgnc/hgnc.py

@@ -210,6 +210,7 @@ class HGNCGetter(Obo):
         for so_id in sorted(set(LOCUS_TYPE_TO_SO.values()))
         if so_id
     ]
+    skip_maintainers = True
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
@@ -342,6 +343,8 @@ def get_terms(version: str | None = None, force: bool = False) -> Iterable[Term]
                 term.append_exact_match(
                     Reference(prefix="iuphar.ligand", identifier=iuphar[len("ligandId:") :])
                 )
+            elif iuphar.startswith("HGNC:"):
+                pass
             else:
                 tqdm.write(f"[hgnc:{identifier}] unhandled IUPHAR: {iuphar}")
 

pyobo/sources/mesh.py

@@ -131,7 +131,14 @@ def get_terms(version: str, *, force: bool = False) -> Iterable[Term]:
             for term in concept["terms"]:
                 synonyms.add(term["name"])
             for xref_prefix, xref_identifier in concept.get("xrefs", []):
-                xrefs.append(Reference(prefix=xref_prefix, identifier=xref_identifier))
+                try:
+                    xref = Reference(prefix=xref_prefix, identifier=xref_identifier)
+                except ValueError:
+                    tqdm.write(
+                        f"[mesh:{identifier}] has invalid xref {xref_prefix}:{xref_identifier}"
+                    )
+                else:
+                    xrefs.append(xref)
 
         mesh_id_to_term[identifier] = Term(
             definition=definition,

pyobo/sources/ror.py

@@ -2,15 +2,18 @@
 
 from __future__ import annotations
 
+import datetime
 import json
 import logging
 import zipfile
 from collections.abc import Iterable
-from typing import Any
+from functools import lru_cache
+from pathlib import Path
+from typing import Any, Literal, NamedTuple, TypeAlias
 
 import bioregistry
 import zenodo_client
-from pydantic import ValidationError
+from pydantic import BaseModel, ValidationError
 from tqdm.auto import tqdm
 
 from pyobo.struct import Obo, Reference, Term
@@ -25,21 +28,29 @@ from pyobo.struct.typedef import (
     see_also,
 )
 
+__all__ = [
+    "OrganizationType",
+    "RORStatus",
+    "get_ror_records",
+    "get_ror_status",
+    "get_ror_to_country_geonames",
+]
+
 logger = logging.getLogger(__name__)
 PREFIX = "ror"
-ROR_ZENODO_RECORD_ID = "10086202"
+ROR_ZENODO_RECORD_ID = "17953395"
 
 # Constants
 ORG_CLASS = Reference(prefix="OBI", identifier="0000245", name="organization")
 CITY_CLASS = Reference(prefix="ENVO", identifier="00000856", name="city")
 
 RMAP = {
-    "Related": see_also,
-    "Child": has_part,
-    "Parent": part_of,
-    "Predecessor": has_predecessor,
-    "Successor": has_successor,
-    "Located in": located_in,
+    "related": see_also,
+    "child": has_part,
+    "parent": part_of,
+    "predecessor": has_predecessor,
+    "successor": has_successor,
+    "located in": located_in,
 }
 NAME_REMAPPING = {
     "'s-Hertogenbosch": "Den Bosch",  # SMH Netherlands, why u gotta be like this
@@ -59,7 +70,7 @@ class RORGetter(Obo):
     root_terms = [CITY_CLASS, ORG_CLASS]
 
     def __post_init__(self):
-        self.data_version, _url, _path = _get_info()
+        self.data_version, _url, _path = get_ror_status()
         super().__post_init__()
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
@@ -72,14 +83,27 @@ class RORGetter(Obo):
         yield from iterate_ror_terms(force=force)
 
 
-ROR_ORGANIZATION_TYPE_TO_OBI: dict[str, Term] = {
-    "Education": Term.default(PREFIX, "education", "educational organization"),
-    "Facility": Term.default(PREFIX, "facility", "facility"),
-    "Company": Term.default(PREFIX, "company", "company"),
-    "Government": Term.default(PREFIX, "government", "government organization"),
-    "Healthcare": Term.default(PREFIX, "healthcare", "healthcare organization"),
-    "Archive": Term.default(PREFIX, "archive", "archival organization"),
-    "Nonprofit": Term.default(PREFIX, "healthcare", "nonprofit organization")
+OrganizationType: TypeAlias = Literal[
+    "education",
+    "facility",
+    "funder",
+    "company",
+    "government",
+    "healthcare",
+    "archive",
+    "nonprofit",
+    "other",
+]
+
+ROR_ORGANIZATION_TYPE_TO_OBI: dict[OrganizationType, Term] = {
+    "education": Term.default(PREFIX, "education", "educational organization"),
+    "facility": Term.default(PREFIX, "facility", "facility"),
+    "funder": Term.default(PREFIX, "funder", "funder"),
+    "company": Term.default(PREFIX, "company", "company"),
+    "government": Term.default(PREFIX, "government", "government organization"),
+    "healthcare": Term.default(PREFIX, "healthcare", "healthcare organization"),
+    "archive": Term.default(PREFIX, "archive", "archival organization"),
+    "nonprofit": Term.default(PREFIX, "healthcare", "nonprofit organization")
     .append_xref(Reference(prefix="ICO", identifier="0000048"))
     .append_xref(Reference(prefix="GSSO", identifier="004615")),
 }
@@ -91,93 +115,214 @@ for _k, v in ROR_ORGANIZATION_TYPE_TO_OBI.items():
 _MISSED_ORG_TYPES: set[str] = set()
 
 
+class LocationDetails(BaseModel):
+    """The location details slot in the ROR schema."""
+
+    continent_code: str
+    continent_name: str
+    country_code: str
+    country_name: str
+    country_subdivision_code: str | None = None
+    country_subdivision_name: str | None = None
+    lat: float
+    lng: float
+    name: str
+
+
+class Location(BaseModel):
+    """The lcoation slot in the ROR schema."""
+
+    geonames_id: int
+    geonames_details: LocationDetails
+
+
+class ExternalID(BaseModel):
+    """The external ID slot in the ROR schema."""
+
+    type: str
+    all: list[str]
+    preferred: str | None = None
+
+
+class Link(BaseModel):
+    """The link slot in the ROR schema."""
+
+    type: str
+    value: str
+
+
+class Name(BaseModel):
+    """The name slot in the ROR schema."""
+
+    value: str
+    types: list[str]
+    lang: str | None = None
+
+
+class Relationship(BaseModel):
+    """The relationship slot in the ROR schema."""
+
+    type: str
+    label: str
+    id: str
+
+
+class DateAnnotated(BaseModel):
+    """The annotated date slot in the ROR schema."""
+
+    date: datetime.date
+    schema_version: str
+
+
+class Admin(BaseModel):
+    """The admin slot in the ROR schema."""
+
+    created: DateAnnotated
+    last_modified: DateAnnotated
+
+
+Status: TypeAlias = Literal["active", "inactive", "withdrawn"]
+
+
+class Record(BaseModel):
+    """A ROR record."""
+
+    locations: list[Location]
+    established: int | None = None
+    external_ids: list[ExternalID]
+    id: str
+    domains: list[str]
+    links: list[Link]
+    names: list[Name]
+    relationships: list[Relationship]
+    status: Status
+    types: list[OrganizationType]
+    admin: Admin
+
+    def get_preferred_label(self) -> str | None:
+        """Get the preferred label."""
+        primary_name: str | None = None
+        for name in self.names:
+            if "ror_display" in name.types:
+                primary_name = name.value
+        if primary_name is None:
+            return None
+        primary_name = NAME_REMAPPING.get(primary_name, primary_name)
+        return primary_name
+
+
+_description_prefix = {
+    "education": "an educational organization",
+    "facility": "a facility",
+    "funder": "a funder",
+    "company": "a company",
+    "government": "a governmental organization",
+    "healthcare": "a healthcare organization",
+    "archive": "an archive",
+    "nonprofit": "a nonprofit organization",
+    "other": "an organization",
+}
+
+
+def _get_description(record: Record) -> str | None:
+    description = (
+        f"{_description_prefix[record.types[0]]} in {record.locations[0].geonames_details.name}"
+    )
+    if record.established:
+        description += f" established in {record.established}"
+    return description
+
+
 def iterate_ror_terms(*, force: bool = False) -> Iterable[Term]:
     """Iterate over terms in ROR."""
-    _version, _source_uri, records = get_latest(force=force)
+    status, records = get_ror_records(force=force)
     unhandled_xref_prefixes: set[str] = set()
 
     seen_geonames_references = set()
-    for record in tqdm(records, unit_scale=True, unit="record", desc=f"{PREFIX} v{_version}"):
-        identifier = record["id"].removeprefix("https://ror.org/")
-        name = record["name"]
-        name = NAME_REMAPPING.get(name, name)
+    for record in tqdm(records, unit_scale=True, unit="record", desc=f"{PREFIX} v{status.version}"):
+        identifier = record.id.removeprefix("https://ror.org/")
 
-        organization_types = record.get("types", [])
-        description = f"{organization_types[0]} in {record['country']['country_name']}"
-        if established := record["established"]:
-            description += f" established in {established}"
+        primary_name = record.get_preferred_label()
+        if primary_name is None:
+            raise ValueError("should have got a primary name...")
 
         term = Term(
-            reference=Reference(prefix=PREFIX, identifier=identifier, name=name),
+            reference=Reference(prefix=PREFIX, identifier=identifier, name=primary_name),
             type="Instance",
-            definition=description,
+            definition=_get_description(record),
         )
-        for organization_type in organization_types:
-            if organization_type == "Other":
-                term.append_parent(ORG_CLASS)
-            else:
+        for organization_type in record.types:
+            if organization_type in ROR_ORGANIZATION_TYPE_TO_OBI:
                 term.append_parent(ROR_ORGANIZATION_TYPE_TO_OBI[organization_type])
+            else:
+                term.append_parent(ORG_CLASS)
 
-        for link in record.get("links", []):
-            term.annotate_uri(has_homepage, link)
+        for link in record.links:
+            term.annotate_uri(has_homepage, link.value)
 
-        if name.startswith("The "):
-            term.append_synonym(name.removeprefix("The "))
+        if primary_name.startswith("The "):
+            term.append_synonym(primary_name.removeprefix("The "))
 
-        for relationship in record.get("relationships", []):
-            target_id = relationship["id"].removeprefix("https://ror.org/")
+        for relationship in record.relationships:
+            target_id = relationship.id.removeprefix("https://ror.org/")
             term.append_relationship(
-                RMAP[relationship["type"]], Reference(prefix=PREFIX, identifier=target_id)
+                RMAP[relationship.type], Reference(prefix=PREFIX, identifier=target_id)
             )
 
-        if record.get("status") != "active":
+        if record.status != "active":
             term.is_obsolete = True
 
-        for address in record.get("addresses", []):
-            city = address.get("geonames_city")
-            if not city:
-                continue
+        for location in record.locations:
             geonames_reference = Reference(
-                prefix="geonames", identifier=str(city["id"]), name=city["city"]
+                prefix="geonames",
+                identifier=str(location.geonames_id),
+                name=location.geonames_details.name,
             )
             seen_geonames_references.add(geonames_reference)
-            term.append_relationship(RMAP["Located in"], geonames_reference)
-
-        for label_dict in record.get("labels", []):
-            label = label_dict["label"]
-            label = label.strip().replace("\n", " ")
-            language = label_dict["iso639"]
-            term.append_synonym(label, language=language)
-            if label.startswith("The "):
-                term.append_synonym(label.removeprefix("The "), language=language)
-
-        for synonym in record.get("aliases", []):
-            synonym = synonym.strip().replace("\n", " ")
-            term.append_synonym(synonym)
-            if synonym.startswith("The "):
-                term.append_synonym(synonym.removeprefix("The "))
-
-        for acronym_synonym in record.get("acronyms", []):
-            term.append_synonym(acronym_synonym, type=acronym)
-
-        for prefix, xref_data in record.get("external_ids", {}).items():
-            if prefix == "OrgRef":
+            term.append_relationship(RMAP["located in"], geonames_reference)
+
+        for name in record.names:
+            if "ror_display" in name.types:
+                continue
+            elif name.types == ["acronym"]:
+                term.append_synonym(name.value, type=acronym)
+            elif name.types == ["alias"]:
+                synonym = name.value.strip().replace("\n", " ")
+                term.append_synonym(synonym)
+                if synonym.startswith("The "):
+                    term.append_synonym(synonym.removeprefix("The "), language=name.lang)
+            elif name.types == ["label"]:
+                label = name.value.strip().replace("\n", " ")
+                term.append_synonym(label, language=name.lang)
+                if label.startswith("The "):
+                    term.append_synonym(label.removeprefix("The "), language=name.lang)
+            else:
+                tqdm.write(
+                    f"[ror:{identifier}] unhandled name types: {name.types} for {name.value}"
+                )
+                continue
+
+        for external_id in record.external_ids:
+            if external_id.type.lower() == "orgref":
                 # OrgRef refers to wikipedia page id, see
                 # https://stackoverflow.com/questions/6168020/what-is-wikipedia-pageid-how-to-change-it-into-real-page-url
                 continue
-            norm_prefix = bioregistry.normalize_prefix(prefix)
+            norm_prefix = bioregistry.normalize_prefix(external_id.type)
+            xref_ids = external_id.all
+
             if norm_prefix is None:
-                if prefix not in unhandled_xref_prefixes:
-                    tqdm.write(f"Unhandled prefix: {prefix} in {name} ({term.curie}). Values:")
-                    for xref_id in xref_data["all"]:
+                if external_id.type not in unhandled_xref_prefixes:
+                    tqdm.write(
+                        f"Unhandled prefix: {external_id.type} in {primary_name} ({term.curie}). Values:"
+                    )
+                    for xref_id in xref_ids:
                         tqdm.write(f"- {xref_id}")
-                    unhandled_xref_prefixes.add(prefix)
+                    unhandled_xref_prefixes.add(external_id.type)
                 continue
 
-            identifiers = xref_data["all"]
-            if isinstance(identifiers, str):
-                identifiers = [identifiers]
-            for xref_id in identifiers:
+            if isinstance(xref_ids, str):
+                xref_ids = [xref_ids]
+            for xref_id in xref_ids:
                 xref_id = xref_id.replace(" ", "")
                 try:
                     xref = Reference(prefix=norm_prefix, identifier=xref_id)
@@ -194,27 +339,60 @@ def iterate_ror_terms(*, force: bool = False) -> Iterable[Term]:
         yield geonames_term
 
 
-def _get_info(*, force: bool = False):
+class RORStatus(NamedTuple):
+    """A version information tuple."""
+
+    version: str
+    url: str
+    path: Path
+
+
+def get_ror_status(*, force: bool = False, authenticate_zenodo: bool = True) -> RORStatus:
+    """Ensure the latest ROR record, metadata, and filepath.
+
+    :param force: Should the record be downloaded again? This almost
+        never needs to be true, since the data doesn't change for
+        a given version
+    :param authenticate_zenodo: Should Zenodo be authenticated?
+        This isn't required, but can help avoid rate limits
+    :return: A version information tuple
+
+    .. note::
+
+        this goes into the ``~/.data/zenodo/6347574`` folder,
+        because 6347574 is the super-record ID, which groups all
+        versions together. this is different from the value
+        for :data:`ROR_ZENODO_RECORD_ID`
+    """
     client = zenodo_client.Zenodo()
-    latest_record_id = client.get_latest_record(ROR_ZENODO_RECORD_ID)
-    response = client.get_record(latest_record_id)
+    latest_record_id = client.get_latest_record(
+        ROR_ZENODO_RECORD_ID, authenticate=authenticate_zenodo
+    )
+    response = client.get_record(latest_record_id, authenticate=authenticate_zenodo)
     response_json = response.json()
     version = response_json["metadata"]["version"].lstrip("v")
     file_record = response_json["files"][0]
     name = file_record["key"]
     url = file_record["links"]["self"]
     path = client.download(latest_record_id, name=name, force=force)
-    return version, url, path
+    return RORStatus(version=version, url=url, path=path)
 
 
-def get_latest(*, force: bool = False):
+@lru_cache
+def get_ror_records(
+    *, force: bool = False, authenticate_zenodo: bool = True
+) -> tuple[RORStatus, list[Record]]:
     """Get the latest ROR metadata and records."""
-    version, url, path = _get_info(force=force)
-    with zipfile.ZipFile(path) as zf:
+    status = get_ror_status(force=force, authenticate_zenodo=authenticate_zenodo)
+    with zipfile.ZipFile(status.path) as zf:
         for zip_info in zf.filelist:
             if zip_info.filename.endswith(".json"):
                 with zf.open(zip_info) as file:
-                    return version, url, json.load(file)
+                    records = [
+                        Record.model_validate(record)
+                        for record in tqdm(json.load(file), unit_scale=True)
+                    ]
+                    return status, records
     raise FileNotFoundError
 
 

pyobo/struct/struct.py

@@ -611,6 +611,11 @@ class Obo:
 
     ontology_version_iri: ClassVar[str | None] = None
 
+    #: Allow skipping adding maintainers annotations, in case
+    #: the resource maintainers don't want their names associated
+    #: with the OWL exports that e.g. end up on EBI OLS
+    skip_maintainers: ClassVar[bool] = False
+
     def __post_init__(self):
         """Run post-init checks."""
         if self.ontology is None:
@@ -978,19 +983,22 @@ class Obo:
                 yield Annotation(v.has_logo, OBOLiteral.uri(logo))
             if mailing_list := resource.get_mailing_list():
                 yield Annotation(v.has_mailing_list, OBOLiteral.string(mailing_list))
-            if (maintainer := resource.get_contact()) and maintainer.orcid:
-                yield Annotation(
-                    v.has_maintainer,
-                    Reference(prefix="orcid", identifier=maintainer.orcid, name=maintainer.name),
-                )
-            for maintainer in resource.contact_extras or []:
-                if maintainer.orcid:
+            if not self.skip_maintainers:
+                if (maintainer := resource.get_contact()) and maintainer.orcid:
                     yield Annotation(
                         v.has_maintainer,
                         Reference(
                             prefix="orcid", identifier=maintainer.orcid, name=maintainer.name
                         ),
                     )
+                for maintainer in resource.contact_extras or []:
+                    if maintainer.orcid:
+                        yield Annotation(
+                            v.has_maintainer,
+                            Reference(
+                                prefix="orcid", identifier=maintainer.orcid, name=maintainer.name
+                            ),
+                        )
 
         # Root terms
         for root_term in self.root_terms or []:

pyobo/struct/typedef.py

@@ -20,6 +20,7 @@ __all__ = [
     "derives_from_organism",
     "directly_regulates_activity_of",
     "editor_note",
+    "editor_preferred_term",
     "enables",
     "ends",
     "exact_match",
@@ -28,6 +29,7 @@ __all__ = [
     "gene_product_member_of",
     "has_contributor",
     "has_creator",
+    "has_curation_status",
     "has_dbxref",
     "has_depiction",
     "has_end_date",
@@ -43,17 +45,20 @@ __all__ = [
     "has_role",
     "has_salt",
     "has_smiles",
+    "has_source",
     "has_start_date",
     "has_successor",
     "has_taxonomy_rank",
     "is_a",
     "is_agonist_of",
     "is_antagonist_of",
+    "is_defined_by",
     "is_inverse_agonist_of",
     "located_in",
     "mapping_has_confidence",
     "mapping_has_justification",
     "match_typedefs",
+    "may_be_identical_to",
     "member_of",
     "narrow_match",
     "negatively_regulates",
@@ -151,6 +156,10 @@ subproperty_of = TypeDef(reference=v.subproperty_of)
 see_also = TypeDef(reference=v.see_also, is_metadata_tag=True)
 comment = TypeDef(reference=v.comment, is_metadata_tag=True)
 label = TypeDef(reference=v.label, is_metadata_tag=True)
+is_defined_by = TypeDef(
+    reference=Reference(prefix="rdfs", identifier="isDefinedBy", name="is defined by"),
+    is_metadata_tag=True,
+)
 has_member = TypeDef(
     reference=Reference(prefix=RO_PREFIX, identifier="0002351", name="has member"),
 )
@@ -227,6 +236,17 @@ definition_source = TypeDef(
     reference=Reference(prefix=IAO_PREFIX, identifier="0000119", name="definition source"),
     is_metadata_tag=True,
 )
+may_be_identical_to = TypeDef(
+    reference=Reference(prefix=IAO_PREFIX, identifier="0006011", name="may be identical to")
+)
+# todo this is also useful for SSSLM
+editor_preferred_term = TypeDef(
+    reference=Reference(prefix=IAO_PREFIX, identifier="0000111", name="editor preferred term")
+)
+has_curation_status = TypeDef(
+    reference=Reference(prefix=IAO_PREFIX, identifier="0000114", name="has curation status")
+)
+
 has_dbxref = TypeDef(reference=v.has_dbxref, is_metadata_tag=True)
 
 editor_note = TypeDef(

pyobo/utils/misc.py

@@ -48,6 +48,12 @@ VERSION_PREFIXES = [
     "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
+    "http://publications.europa.eu/ontology/euvoc#",
+    "http://purls.helmholtz-metadaten.de/cdos/cdco/",  # http://purls.helmholtz-metadaten.de/cdos/cdco/1.0.0
+    "https://endlessforms.info/gdo/releases/gdoa-",
+    "https://openenergyplatform.org/ontology/oeo/releases/",
 ]
 VERSION_PREFIX_SPLITS = [
     "http://www.ebi.ac.uk/efo/releases/v",
@@ -56,10 +62,13 @@ VERSION_PREFIX_SPLITS = [
     "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
+    "https://spec.industrialontologies.org/ontology/",  # as in https://spec.industrialontologies.org/ontology/202401/core/Core
 ]
 BAD = {
     "http://purl.obolibrary.org/obo",
     "http://www.bioassayontology.org/bao/bao_complete",
+    "https://vocabularies.wikipathways.org",
 }
 
 

pyobo/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.12.13"
+VERSION = "0.12.14"
 
 
 def get_git_hash() -> str:

{pyobo-0.12.13.dist-info → pyobo-0.12.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.13
+Version: 0.12.14
 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
@@ -40,11 +40,11 @@ Requires-Dist: bioversions>=0.8.101
 Requires-Dist: bioregistry>=0.12.30
 Requires-Dist: bioontologies>=0.7.2
 Requires-Dist: ssslm>=0.0.13
-Requires-Dist: zenodo-client>=0.3.6
+Requires-Dist: zenodo-client>=0.4.0
 Requires-Dist: class-resolver>=0.6.0
 Requires-Dist: pydantic>=2.0
 Requires-Dist: curies>=0.10.17
-Requires-Dist: curies-processing>=0.1.2
+Requires-Dist: curies-processing>=0.1.6
 Requires-Dist: python-dateutil
 Requires-Dist: networkx>=3.4
 Requires-Dist: drugbank-downloader

{pyobo-0.12.13.dist-info → pyobo-0.12.14.dist-info}/RECORD

@@ -21,7 +21,7 @@ pyobo/cli/database.py,sha256=iq4-eJ_8Kgim0MMnSqf1wu2hvHDZk9BWNMVuwykz2Ko,13407
 pyobo/cli/database_utils.py,sha256=jQ7qSg-oZk-Q-RC121NkUbqXeNg0K8fV96igXaK3ra4,5540
 pyobo/cli/lookup.py,sha256=-Tz6E3OP6HBPipVqSrMn7LyzrezbT0pngeDExF5uyn4,9467
 pyobo/cli/utils.py,sha256=SfW9JC8olzp4AcAsDodMPdgHfteeXq0Ngd8yQ2kzOMA,1812
-pyobo/constants.py,sha256=K3d8gjfty6zVc3nUBX32oVQX7tzFxnEkGCO1THlC5Qw,7564
+pyobo/constants.py,sha256=_Y4IACPsRu5jHntoc8nEHKLGDl1Bl7YrdS0gG4qxmqw,7582
 pyobo/getters.py,sha256=exZNjlseRoWhshQYArWwN2KLvkk4NmCQnHM88YUYf-w,18340
 pyobo/gilda_utils.py,sha256=uThAArALSNzJi-hrR9lUvtQci5VIw4Cqq2L6mtkp0Ko,1990
 pyobo/identifier_utils/__init__.py,sha256=iSHAZhOwqWZmYpOfpXNLuKouSYj7ZSViaX7BF5uT8so,793
@@ -95,7 +95,7 @@ pyobo/sources/gwascentral/__init__.py,sha256=VdHIgBVR-36B7gLuhR4XV5UXn_EgNZ0-i1g
 pyobo/sources/gwascentral/gwascentral_phenotype.py,sha256=SvMCF3sYqc3F5nNXCf76AzIhNT698ZHHnTpO0IGft8o,1788
 pyobo/sources/gwascentral/gwascentral_study.py,sha256=fzDiRuWU84085gclzuWNLbxDEsIdVysqXScMU0BdXnM,2672
 pyobo/sources/hgnc/__init__.py,sha256=1QhM7GdP6_AxCMzaBz2k3SRLkDTOkS2hUhPMLETSGWM,157
-pyobo/sources/hgnc/hgnc.py,sha256=jaCEZZR2YzjrrZNFtvEbfhrVu9HTLX7_sWkshgi022M,20332
+pyobo/sources/hgnc/hgnc.py,sha256=vGpohqlDIZAvF372EDmhqik22z5yuCOAAMZ1TtNnSwo,20426
 pyobo/sources/hgnc/hgncgenefamily.py,sha256=NGkQXlyac0283WHeYXr3_o__Ak-hpbNnB0NIr2J0QGo,3912
 pyobo/sources/iana_media_type.py,sha256=X20G2a1ozF-JPaqNs3tUrNoeSb7jv_YsClKSTPH-8io,5024
 pyobo/sources/icd/__init__.py,sha256=DrZVl76P8essJ4tlZPcauFVrXVkIIZB6sJ0c6Km6SWI,142
@@ -111,7 +111,7 @@ pyobo/sources/kegg/api.py,sha256=szu25gS3ED5vUcKHqh6XI6g5EZz52VDS_UFIaIvU5Jw,419
 pyobo/sources/kegg/genes.py,sha256=x0oVbRYS5xUPUHhYuoAojsIPyfjAi8t7Rfr3Faptdw0,3558
 pyobo/sources/kegg/genome.py,sha256=Mq7bZitjfJbIHk2g2gnSJEqZljABRlqhpXIDXlOGzHo,4161
 pyobo/sources/kegg/pathway.py,sha256=gjM97-nWmgpJO2k2gRLWHZIhldMz0IHtNnmzVb-yNa8,5892
-pyobo/sources/mesh.py,sha256=LqN8M01tuM2ow4To3xEB24rruOQfniqg4HkawdR53sg,15573
+pyobo/sources/mesh.py,sha256=7BXsrBCSnpHlJ_zb5udo9YvTC6S3Wkc-eaHt5O5grgE,15837
 pyobo/sources/mgi.py,sha256=fUD4bUuwe8k-H4tF54VvDyUxT-xeBMZUj_flYRsfpc8,5541
 pyobo/sources/mirbase/__init__.py,sha256=8_YENjSy55_CKkGdGTA7Ujuv8dt-Yfh90V-ht3jwplk,252
 pyobo/sources/mirbase/mirbase.py,sha256=9huL0PWAVcEDk-4unZw-GInyEE1C_FXwRxN65HG3xxc,6387
@@ -146,7 +146,7 @@ pyobo/sources/pubchem.py,sha256=lTsc0dgrSJ5kxlcaUcUXJydi-xsMf2fI2EcWsbW8xTU,5153
 pyobo/sources/reactome.py,sha256=yzeCCy19Hxr7KFUrg1tePjN40eZLN9G4dm4q0A7izbI,5842
 pyobo/sources/rgd.py,sha256=I6HC7_GZqFPXlRIuuroOgZM7wG85jcE3Po-sry8a1XU,5194
 pyobo/sources/rhea.py,sha256=dbhyVJ1yoAQoxoWp47OKegLAmMh6qoe-7_DafJDeWrk,8164
-pyobo/sources/ror.py,sha256=IS_KUtMeKgAndrbLjhcoK8ilp-jOeiDwzGTy5R9cIwk,8882
+pyobo/sources/ror.py,sha256=pFKV5qzTSU2XxvZhMOB-WyMLQ6u2dsAqadACswCqyNk,13387
 pyobo/sources/selventa/__init__.py,sha256=cIIDlWL9znL2r0aZIJ2r1FN3NM9io74w-He2egzJwX8,254
 pyobo/sources/selventa/schem.py,sha256=vqN_a_NLeshj-2dRuZelfOLJQ5dyU3ZghfSRIq9EFVA,1162
 pyobo/sources/selventa/scomp.py,sha256=nshskLQeXuzf5t79STJsVKJg3R80CX3DuJBUrEhwSbc,1531
@@ -191,21 +191,21 @@ 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=-JaApTZ7e50bRJ2dXPdAVuJ0ElIVJIJ-HHRsVdaiMxM,96291
+pyobo/struct/struct.py,sha256=FaNyYUSFgM700xE74i8zSVQQiR4g91jbmAMOqPyJ9NQ,96669
 pyobo/struct/struct_utils.py,sha256=VFC82fgphTs7sBSNGn53sv2WMl7Ho9srALFq92bRFQQ,41021
-pyobo/struct/typedef.py,sha256=LGDfJPAiTdp4PZPHUMgvhLsJrOZMIaGSBHA2oh8uCuU,14188
+pyobo/struct/typedef.py,sha256=jvETRmNc4g09X7waSjcvEkw7g0kNteLaDOt3mjKbmDc,14871
 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
 pyobo/utils/cache.py,sha256=x7Dnw8vHYsoslXWiV9L9ZdTu5ZueIR1ki5Ncdpb7H10,3136
 pyobo/utils/io.py,sha256=QTvGjNDkaIf78Tca23B5RW_aVweKiSsxmgwSKXcMSNo,3921
 pyobo/utils/iter.py,sha256=rYRbbaFJHxMaE0yU-rQZoCagYIrtev09uY0mxFkf5zY,1524
-pyobo/utils/misc.py,sha256=499pencyDqW9_xm0H0Cq0FhOw0MoNoq-9IVQTKh-eaE,7992
+pyobo/utils/misc.py,sha256=DVLxPynunSubp2xSVKFF_E57BPS3p5wU4Z4A38PI17M,8717
 pyobo/utils/ndex_utils.py,sha256=EokCWS00Wrk_4y8ldeQuUyaaC6yNzBg3DagUl-J2czY,2326
 pyobo/utils/path.py,sha256=snV58UHxHO6GI2QPPE46ssR4RWozaw83V59sS_I9BY8,4109
-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/version.py,sha256=-RjPuUzkByyIQ26Vfaw4q_Cb--M-vMCnMRNP78aBv58,927
+pyobo-0.12.14.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
+pyobo-0.12.14.dist-info/WHEEL,sha256=eycQt0QpYmJMLKpE3X9iDk8R04v2ZF0x82ogq-zP6bQ,79
+pyobo-0.12.14.dist-info/entry_points.txt,sha256=ANgzvuwF_9_1ipCoxJtbBM6A4i2Mkt39gMPzQO6hvGs,42
+pyobo-0.12.14.dist-info/METADATA,sha256=3bCbmYuRjLGPhWqwRm337UrFL0Nb7iU1--Ici26iZnc,22783
+pyobo-0.12.14.dist-info/RECORD,,

{pyobo-0.12.13.dist-info → pyobo-0.12.14.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: uv 0.9.11
+Generator: uv 0.9.24
 Root-Is-Purelib: true
 Tag: py3-none-any