pyobo 0.8.11__py3-none-any.whl → 0.8.13__py3-none-any.whl

pyobo/api/relations.py

@@ -69,10 +69,12 @@ def get_filtered_relations_df(
     *,
     use_tqdm: bool = False,
     force: bool = False,
+    version: Optional[str] = None,
 ) -> pd.DataFrame:
     """Get all of the given relation."""
     relation_prefix, relation_identifier = relation = get_reference_tuple(relation)
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     path = prefix_cache_join(
         prefix,
         "relations",

pyobo/gilda_utils.py

@@ -118,6 +118,7 @@ def get_grounder(
     unnamed: Optional[Iterable[str]] = None,
     grounder_cls: Optional[Type[Grounder]] = None,
     versions: Union[None, str, Iterable[Union[str, None]]] = None,
+    strict: bool = True,
 ) -> Grounder:
     """Get a Gilda grounder for the given prefix(es)."""
     unnamed = set() if unnamed is None else set(unnamed)
@@ -138,7 +139,9 @@ def get_grounder(
     for prefix, version in zip(prefixes, versions):
         try:
             p_terms = list(
-                get_gilda_terms(prefix, identifiers_are_names=prefix in unnamed, version=version)
+                get_gilda_terms(
+                    prefix, identifiers_are_names=prefix in unnamed, version=version, strict=strict
+                )
             )
         except NoBuild:
             continue
@@ -156,10 +159,11 @@ def get_gilda_terms(
     prefix: str,
     identifiers_are_names: bool = False,
     version: Optional[str] = None,
+    strict: bool = True,
 ) -> Iterable[gilda.term.Term]:
     """Get gilda terms for the given namespace."""
-    id_to_name = get_id_name_mapping(prefix, version=version)
-    id_to_species = get_id_species_mapping(prefix, version=version)
+    id_to_name = get_id_name_mapping(prefix, version=version, strict=strict)
+    id_to_species = get_id_species_mapping(prefix, version=version, strict=strict)
 
     it = tqdm(id_to_name.items(), desc=f"[{prefix}] mapping", unit_scale=True, unit="name")
     for identifier, name in it:

pyobo/reader.py

@@ -123,7 +123,7 @@ def from_obonet(graph: nx.MultiDiGraph, *, strict: bool = True) -> "Obo":  # noq
             # if name isn't available, it means its external to this ontology
             name=data.get("name"),
         )
-        for prefix, identifier, data in _iter_obo_graph(graph=graph)
+        for prefix, identifier, data in _iter_obo_graph(graph=graph, strict=strict)
     }
 
     #: CURIEs to typedefs
@@ -140,7 +140,7 @@ def from_obonet(graph: nx.MultiDiGraph, *, strict: bool = True) -> "Obo":  # noq
     missing_typedefs = set()
     terms = []
     n_alt_ids, n_parents, n_synonyms, n_relations, n_properties, n_xrefs = 0, 0, 0, 0, 0, 0
-    for prefix, identifier, data in _iter_obo_graph(graph=graph):
+    for prefix, identifier, data in _iter_obo_graph(graph=graph, strict=strict):
         if prefix != ontology or not data:
             continue
 

pyobo/sources/expasy.py

@@ -44,6 +44,20 @@ class ExpasyGetter(Obo):
 
     bioversions_key = ontology = PREFIX
     typedefs = [has_member, enables]
+    root_terms = [
+        Reference("eccode", "1"),
+        Reference("eccode", "2"),
+        Reference("eccode", "3"),
+        Reference("eccode", "4"),
+        Reference("eccode", "5"),
+        Reference("eccode", "6"),
+        Reference("eccode", "7"),
+    ]
+    idspaces = {
+        "uniprot": "https://bioregistry.io/uniprot:",
+        "eccode": "https://bioregistry.io/eccode:",
+        "go": "http://purl.obolibrary.org/obo/GO_",
+    }
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""

pyobo/sources/hgnc.py

@@ -2,6 +2,7 @@
 
 """Converter for HGNC."""
 
+import itertools as itt
 import json
 import logging
 import typing
@@ -145,7 +146,7 @@ LOCUS_TYPE_TO_SO = {
 
 IDSPACES = {
     prefix: f"https://bioregistry.io/{prefix}:"
-    for prefix in [
+    for prefix in {
         "rgd",
         "mgi",
         "eccode",
@@ -154,17 +155,34 @@ IDSPACES = {
         "uniprot",
         "mirbase",
         "snornabase",
+        "hgnc",
         "hgnc.genegroup",
-    ]
+        "debio",
+        "ensembl",
+        "NCBIGene",
+        "vega",
+        "ucsc",
+        "ena",
+        "ccds",
+        "omim",
+        "cosmic",
+        "merops",
+        "orphanet",
+        "pseudogene",
+        "lncipedia",
+        "refseq",
+    }
 }
-IDSPACES["NCBITaxon"] = "http://purl.obolibrary.org/obo/NCBITaxon_"
+IDSPACES.update(
+    NCBITaxon="http://purl.obolibrary.org/obo/NCBITaxon_",
+    SO="http://purl.obolibrary.org/obo/SO_",
+)
 
 
 class HGNCGetter(Obo):
     """An ontology representation of HGNC's gene nomenclature."""
 
     bioversions_key = ontology = PREFIX
-    dynamic_version = True
     typedefs = [
         from_species,
         has_gene_product,
@@ -180,6 +198,7 @@ class HGNCGetter(Obo):
         alias_name_type,
         alias_symbol_type,
     ]
+    root_terms = [Reference("SO", so_id) for so_id in sorted(set(LOCUS_TYPE_TO_SO.values()))]
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
@@ -207,6 +226,7 @@ def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Te
     with open(path) as file:
         entries = json.load(file)["response"]["docs"]
 
+    yield Term.from_triple("NCBITaxon", "9606", "Homo sapiens")
     yield from sorted(
         {
             Term(reference=Reference.auto("SO", so_id))
@@ -242,14 +262,14 @@ def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Te
         for uniprot_id in entry.pop("uniprot_ids", []):
             term.append_relationship(
                 has_gene_product,
-                Reference.auto("uniprot", uniprot_id),
+                Reference("uniprot", uniprot_id),
             )
         for ec_code in entry.pop("enzyme_id", []):
             if "-" in ec_code:
                 continue  # only add concrete annotations
             term.append_relationship(
                 gene_product_member_of,
-                Reference.auto("eccode", ec_code),
+                Reference("eccode", ec_code),
             )
         for rna_central_ids in entry.pop("rna_central_id", []):
             for rna_central_id in rna_central_ids.split(","):
@@ -261,7 +281,7 @@ def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Te
         if mirbase_id:
             term.append_relationship(
                 transcribes_to,
-                Reference.auto(
+                Reference(
                     "mirbase",
                     mirbase_id,
                 ),
@@ -279,7 +299,7 @@ def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Te
             rgd_id = rgd_curie[len("RGD:") :]
             term.append_relationship(
                 orthologous,
-                Reference.auto(prefix="rgd", identifier=rgd_id),
+                Reference(prefix="rgd", identifier=rgd_id),
             )
         for mgi_curie in entry.pop("mgd_id", []):
             if not mgi_curie.startswith("MGI:"):
@@ -290,7 +310,7 @@ def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Te
                 continue
             term.append_relationship(
                 orthologous,
-                Reference.auto(prefix="mgi", identifier=mgi_id),
+                Reference(prefix="mgi", identifier=mgi_id),
             )
 
         for xref_prefix, key in gene_xrefs:
@@ -321,7 +341,9 @@ def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Te
             term.append_synonym(Synonym(name=alias_symbol, type=alias_symbol_type))
         for alias_name in entry.pop("alias_name", []):
             term.append_synonym(Synonym(name=alias_name, type=alias_name_type))
-        for previous_symbol in entry.pop("previous_symbol", []):
+        for previous_symbol in itt.chain(
+            entry.pop("previous_symbol", []), entry.pop("prev_symbol", [])
+        ):
             term.append_synonym(Synonym(name=previous_symbol, type=previous_symbol_type))
         for previous_name in entry.pop("prev_name", []):
             term.append_synonym(Synonym(name=previous_name, type=previous_name_type))

pyobo/sources/kegg/pathway.py

@@ -63,9 +63,7 @@ def iter_terms(version: str, skip_missing: bool = True) -> Iterable[Term]:
     # since old kegg versions go away forever, do NOT add a force option
     yield from _iter_map_terms(version=version)
     it = iter_kegg_pathway_paths(version=version, skip_missing=skip_missing)
-    for row in tqdm(
-        it, unit_scale=True, unit="genome", desc="Parsing genomes"
-    ):
+    for row in tqdm(it, unit_scale=True, unit="genome", desc="Parsing genomes"):
         if not row:
             continue
         kegg_genome, list_pathway_path, link_pathway_path = row

pyobo/sources/mgi.py

@@ -150,7 +150,7 @@ def get_terms(force: bool = False) -> Iterable[Term]:
                 mgi_to_ensemble_protein_ids[mgi_id].append(ensemble_protein_id)
 
     for mgi_curie, name, definition in tqdm(
-        df[COLUMNS].values, total=len(df.index), desc=f"Mapping {PREFIX}"
+        df[COLUMNS].values, total=len(df.index), desc=f"Mapping {PREFIX}", unit_scale=True
     ):
         identifier = mgi_curie[len("MGI:") :]
         term = Term(

pyobo/sources/mirbase_mature.py

@@ -4,6 +4,7 @@
 
 from typing import Iterable
 
+import pandas as pd
 from tqdm.auto import tqdm
 
 from .mirbase_constants import get_mature_df
@@ -35,9 +36,13 @@ def get_obo(force: bool = False) -> Obo:
 def iter_terms(version: str, force: bool = False) -> Iterable[Term]:
     """Get miRBase mature terms."""
     df = get_mature_df(version, force=force)
-    for _, name, previous_name, mirbase_mature_id in tqdm(df.values, total=len(df.index)):
+    for _, name, previous_name, mirbase_mature_id in tqdm(
+        df.values, total=len(df.index), unit_scale=True
+    ):
         yield Term(
-            reference=Reference(prefix=PREFIX, identifier=mirbase_mature_id, name=name),
+            reference=Reference(
+                prefix=PREFIX, identifier=mirbase_mature_id, name=name if pd.notna(name) else None
+            ),
             synonyms=[
                 Synonym(name=previous_name),
             ],

pyobo/sources/msigdb.py

@@ -52,7 +52,7 @@ KEGG_URL_PREFIX = "http://www.genome.jp/kegg/pathway/hsa/"
 
 def iter_terms(version: str, force: bool = False) -> Iterable[Term]:
     """Get MSigDb terms."""
-    xml_url = f"{BASE_URL}/{version}/msigdb_v{version}.xml"
+    xml_url = f"{BASE_URL}/{version}.Hs/msigdb_v{version}.Hs.xml"
     path = ensure_path(prefix=PREFIX, url=xml_url, version=version, force=force)
     tree = ElementTree.parse(path)
 

pyobo/sources/npass.py

@@ -58,39 +58,34 @@ def iter_terms(version: str, force: bool = False) -> Iterable[Term]:
     """Iterate NPASS terms."""
     df = get_df(version=version, force=force)
     it = tqdm(df.values, total=len(df.index), desc=f"mapping {PREFIX}")
-    for identifier, name, iupac, chembl_id, pubchem_compound_ids, zinc_id in it:
-        xrefs = [
-            Reference(prefix=xref_prefix, identifier=xref_id)
-            for xref_prefix, xref_id in [
-                ("chembl", chembl_id),
-                ("zinc", zinc_id),
-            ]
-            if pd.notna(xref_id)
-        ]
+    for identifier, name, iupac, chembl_id, pubchem_compound_ids, _, _, _, _ in it:
+        term = Term.from_triple(
+            PREFIX, identifier=identifier, name=name if pd.notna(name) else identifier
+        )
+
+        for xref_prefix, xref_id in [
+            ("chembl", chembl_id),
+            # ("zinc", zinc_id),
+        ]:
+            if pd.notna(xref_id):
+                term.append_xref(Reference(prefix=xref_prefix, identifier=xref_id))
 
         # TODO check that the first is always the parent compound?
         if pd.notna(pubchem_compound_ids):
             pubchem_compound_ids = pubchem_compound_ids.split(";")
             if len(pubchem_compound_ids) > 1:
-                logger.warning("multiple cids for %s: %s", identifier, pubchem_compound_ids)
-            pubchem_compound_id = pubchem_compound_ids[0]
-            xrefs.append(Reference(prefix="pubchem.compound", identifier=pubchem_compound_id))
-
-        yield Term(
-            # TODO look up name from pubchem?
-            reference=Reference(
-                PREFIX, identifier=identifier, name=name if pd.notna(name) else identifier
-            ),
-            xrefs=xrefs,
-            synonyms=[
-                Synonym(name=name)
-                for name in [
-                    iupac,
-                ]
-                if pd.notna(name)
-            ],
-        )
+                logger.debug("multiple cids for %s: %s", identifier, pubchem_compound_ids)
+            for pubchem_compound_id in pubchem_compound_ids:
+                term.append_xref(
+                    Reference(prefix="pubchem.compound", identifier=pubchem_compound_id)
+                )
+
+        for synonym in [iupac]:
+            if pd.notna(synonym):
+                term.append_synonym(Synonym(name=synonym))
+
+        yield term
 
 
 if __name__ == "__main__":
-    get_obo().write_default()
+    NPASSGetter.cli()

pyobo/sources/pombase.py

@@ -11,7 +11,7 @@ from tqdm.auto import tqdm
 
 import pyobo
 from pyobo import Reference
-from pyobo.struct import Obo, Synonym, Term, from_species, has_gene_product, orthologous
+from pyobo.struct import Obo, Term, from_species, has_gene_product, orthologous
 from pyobo.utils.path import ensure_df
 
 __all__ = [
@@ -43,6 +43,8 @@ def get_obo(force: bool = False) -> Obo:
 
 #: A mapping from PomBase gene type to sequence ontology terms
 POMBASE_TO_SO = {
+    # None: "0000704",  # gene,
+    "gene_type": "0000704",  # unannotated
     "protein coding gene": "0001217",
     "pseudogene": "0000336",
     "tRNA gene": "0001272",
@@ -74,6 +76,8 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
     for _, reference in sorted(so.items()):
         yield Term(reference=reference)
     for identifier, _, symbol, chromosome, name, uniprot_id, gtype, synonyms in tqdm(df.values):
+        if pd.isna(identifier):
+            continue
         term = Term.from_triple(
             prefix=PREFIX,
             identifier=identifier,
@@ -84,12 +88,12 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
         term.append_parent(so[gtype])
         term.set_species(identifier="4896", name="Schizosaccharomyces pombe")
         for hgnc_id in identifier_to_hgnc_ids.get(identifier, []):
-            term.append_relationship(orthologous, Reference.auto("hgnc", hgnc_id))
+            term.append_relationship(orthologous, Reference("hgnc", hgnc_id))
         if uniprot_id and pd.notna(uniprot_id):
-            term.append_relationship(has_gene_product, Reference.auto("uniprot", uniprot_id))
+            term.append_relationship(has_gene_product, Reference("uniprot", uniprot_id))
         if synonyms and pd.notna(synonyms):
             for synonym in synonyms.split(","):
-                term.append_synonym(Synonym(synonym))
+                term.append_synonym(synonym.strip())
         yield term
 
 

pyobo/struct/struct.py

@@ -453,7 +453,7 @@ class Obo:
     #: For super-sized datasets that shouldn't be read into memory
     iter_only: ClassVar[bool] = False
 
-    #: Set to true for resources that are unversioned/very dynamic, like HGNC
+    #: Set to true for resources that are unversioned/very dynamic, like MGI
     dynamic_version: ClassVar[bool] = False
 
     #: Set to a static version for the resource (i.e., the resource is not itself versioned)
@@ -461,6 +461,9 @@ class Obo:
 
     bioversions_key: ClassVar[Optional[str]] = None
 
+    #: Root terms to use for the ontology
+    root_terms: ClassVar[Optional[List[Reference]]] = None
+
     #: The date the ontology was generated
     date: Optional[datetime] = field(default_factory=datetime.today)
 

pyobo/utils/misc.py

@@ -79,6 +79,6 @@ def cleanup_version(data_version: str, prefix: str) -> Optional[str]:
         else:
             return v
     if (prefix, data_version) not in BIZARRE_LOGGED:
-        logger.warning("[%s] bizarre version: %s", prefix, data_version)
+        logger.debug("[%s] bizarre version: %s", prefix, data_version)
         BIZARRE_LOGGED.add((prefix, data_version))
     return data_version

pyobo/version.py

@@ -14,7 +14,7 @@ __all__ = [
     "get_git_hash",
 ]
 
-VERSION = "0.8.11"
+VERSION = "0.8.13"
 
 
 def get_git_hash() -> str:

{pyobo-0.8.11.dist-info → pyobo-0.8.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyobo
-Version: 0.8.11
+Version: 0.8.13
 Summary: Handling and writing OBO
 Home-page: https://github.com/pyobo/pyobo
 Download-URL: https://github.com/pyobo/pyobo/releases
@@ -41,7 +41,7 @@ Requires-Dist: humanize
 Requires-Dist: tabulate
 Requires-Dist: cachier
 Requires-Dist: pystow (>=0.2.7)
-Requires-Dist: bioversions (>=0.5.82)
+Requires-Dist: bioversions (>=0.5.83)
 Requires-Dist: bioregistry (>=0.4.29)
 Requires-Dist: zenodo-client (>=0.0.5)
 Requires-Dist: class-resolver

{pyobo-0.8.11.dist-info → pyobo-0.8.13.dist-info}/RECORD

@@ -10,7 +10,7 @@ pyobo/config.py,sha256=HSvXW75czWoS2D7grudn9fh3bWMrVooF8USkVE-qPAE,937
 pyobo/constants.py,sha256=gj8xSUmCO0rU-eGXHOW7Vix3SAHl50cLAM3HXuoAFt4,2200
 pyobo/extract.py,sha256=SvI9gy4E6BgAFa99RmLS6WkC1zdl-Uy1Dz_XkXrgb_0,22815
 pyobo/getters.py,sha256=5L0HhIo5dig-CraK7bJONplPugP7EK_sr4jG0IWJ6hg,14962
-pyobo/gilda_utils.py,sha256=mS9MwcTUEshGwXgEPOz8VbXJZ-AtVwOMfY08JbwxQLA,6847
+pyobo/gilda_utils.py,sha256=s2_-jzsd0d7wyrfq5ut8P_jDC2cbSnnAqy4WAtNNNLY,6980
 pyobo/identifier_utils.py,sha256=gSqc35l9patTxk-H-lCjtPffk3ksXO7hJRE_yhSzFT4,3399
 pyobo/io_utils.py,sha256=XlGpfcosANwVW5awnRWwnyifnzncrnUCvh5IgIpP2D4,3518
 pyobo/iter_utils.py,sha256=w8zSiopOEapJsFG_ZBvaof60M3BOP_YkCM4DnRZeyuk,1420
@@ -19,9 +19,9 @@ pyobo/ndex_utils.py,sha256=l-fQ74tOW74oi29_r3DCs0RSh138uqweW_fPfjxESq4,2207
 pyobo/normalizer.py,sha256=OHME2CDQSZYSbqmP-L_-4nxete9W9mtAjUzXVs1hnjU,8293
 pyobo/path_utils.py,sha256=MzihlFwW2ia7DIppCxudQVdGsmn-CpneTtRzXVCCnzE,4386
 pyobo/plugins.py,sha256=dXWGoFuQktNeQUWSJlPz2a7FeLysggc9ry6auEZdw98,1227
-pyobo/reader.py,sha256=hDbgRqLDl5Sx9qlhwWO6Nd9y19PMlUVakEUQ4dFaM0s,19839
+pyobo/reader.py,sha256=Cm3JLpRuCS8AE-pQzf71HirZtUrBY1ax1BHndKnfFsU,19869
 pyobo/resource_utils.py,sha256=JBcJRihZhNwp78-qWZPrzSCGoYfyOjzBwMkfmOkO_no,4289
-pyobo/version.py,sha256=-06YBpRTcBwmXA6i2aFSEEGX6asahx5V3zaxigWT7KQ,977
+pyobo/version.py,sha256=V_9kVhK0qY8rydoswR_GsGePBi7MZU3qzIJiHBKMpC8,977
 pyobo/zenodo_client.py,sha256=Ei4L3OeqzMITI8AwhmzSWAFYbpD2zlesCihy8dqksLI,5170
 pyobo/api/__init__.py,sha256=PFgalyQ32ZvJmeHvapdngH10gSlaAkCdLY2E30tHHxc,1236
 pyobo/api/alts.py,sha256=xmAb-gGQCJ9MbaFvoNK6E-V0B3TV9hxulkfbkHIvOso,2617
@@ -29,7 +29,7 @@ pyobo/api/hierarchy.py,sha256=dZIR2mp1Zh1V9WzTwF6EoCQOEa1MRB7WY31nd2_wTbc,8336
 pyobo/api/metadata.py,sha256=62E7j0ZW3vYK2Rh-R7NCMKnChbYjZwPjVDoaE1AsCOc,1070
 pyobo/api/names.py,sha256=VSrFS2VQZGBRE2ixn016eRC7xRXQQFuJ6ldzbERg0nY,6178
 pyobo/api/properties.py,sha256=PTCYsYmma3cym-dYY44p2NVGD7Z1dKZdC1otcfUflqg,7342
-pyobo/api/relations.py,sha256=SeMaZoNRWJykR-K0zuSVU-MSna10GwJadx2LLmeJM2Y,5316
+pyobo/api/relations.py,sha256=3O1iM-dWyxphrccUoIYaSRtKLKDzmmGIM4wXOC6voVc,5379
 pyobo/api/species.py,sha256=xRPRoD6n1wcDaqlC_tHLw3rKMWa4razWsSPNa228g_4,2181
 pyobo/api/typedefs.py,sha256=TqNZ8_5ntw6PXwvqIlHtMHqD7l2jWwHn48vccUPbJiI,1061
 pyobo/api/utils.py,sha256=QAROqQPzr51VJb2uS5R8gZqIe4vclfUL0MbmirnGgc0,937
@@ -110,14 +110,14 @@ pyobo/sources/dictybase_gene.py,sha256=EgWBwUZ83ev7x5Lp_nUkgSq2zumkDjJ7_13m3f6kJ
 pyobo/sources/drugbank.py,sha256=R-N5I52tCo8EjlJY61iUvFlyoiGZB_a3bALl6C8pI3s,10750
 pyobo/sources/drugbank_salt.py,sha256=hx16G41mP2KXT4fsAQRCRkJMGn-z5cafs-bwm4wMtwo,1783
 pyobo/sources/drugcentral.py,sha256=aiL51iN8xC6Jsq7PnSAhwCdRJin5cdkteuYQFCarynE,3317
-pyobo/sources/expasy.py,sha256=QUZWcBH-d2AQg7OYPE8aYBdYwx30hI4SxYRsWbk550o,8885
+pyobo/sources/expasy.py,sha256=Vjq3QHqmrpH60I9Gb15s66vzTBx4GcBvfI3BpMMUZXc,9329
 pyobo/sources/famplex.py,sha256=SpxRaAROie5a4ig-Zza0vfgQbbO82arZ-d9sgjJsIKs,5643
 pyobo/sources/flybase.py,sha256=0-BCNsp-L-CgGPN9VdJec6-8e4-fJuzaZAZiNra3ZUQ,5768
 pyobo/sources/gmt_utils.py,sha256=3lHrN5zYJy9AECTMeeEjr8LqsI9GLlP2xo2ZWpCT0uw,1297
 pyobo/sources/go.py,sha256=IJul9eAXxKifZiWKJL1Dl9PFDFdoPMQ0ZVydzhnRtX0,1275
 pyobo/sources/gwascentral_phenotype.py,sha256=jNai819u9NWvfsUkafjcROIwc-oZ6z7ISKyq2S_SZus,1866
 pyobo/sources/gwascentral_study.py,sha256=h7dfOhS77yc09O9Lv4L6ZFPH50evIaov6LYhwGiHgdU,2782
-pyobo/sources/hgnc.py,sha256=YGyGGOZB2S2g7JONZiX4C_TxhdNYu7KyZjT6-7lOJsQ,13304
+pyobo/sources/hgnc.py,sha256=9URsvvPTZWBN-UWmK10p41N8exuzbHwysnxLoLp3U2A,13820
 pyobo/sources/hgncgenefamily.py,sha256=F6ZJvOokfAHwXYJqireyyy43F8688nHYnrNrUzuGpGA,3722
 pyobo/sources/icd10.py,sha256=KhenR1U8LvZQF97mRZIoSEE_daKcJ2hTJ41BQU7SNuM,2286
 pyobo/sources/icd11.py,sha256=04nLt-Lr64hAroOLH4OP-iNbuIjBk-mYcg-Ib34zgMM,2834
@@ -125,20 +125,20 @@ pyobo/sources/icd_utils.py,sha256=i52zlxKU-QjGAgaPZcwKbqAdjYi091pYXmrTRv2Kt08,29
 pyobo/sources/interpro.py,sha256=IRI7IUDAlvdyYJHS6y_eppc32fXoZIqHlJXNP57inus,4941
 pyobo/sources/itis.py,sha256=LXS4MTL7OMmdfo-ypoF75UJkePw7VnHDrgq10RF_VUk,2967
 pyobo/sources/mesh.py,sha256=bpKVgzAULZ0biUEk4orRlmZsAEImt6rIgdsyq9wT-SA,9398
-pyobo/sources/mgi.py,sha256=f2kRe66wN6CRtaSOqbjWasCrUebR6riaJVcmAxYmpAY,5653
+pyobo/sources/mgi.py,sha256=3L4qmnEO_MjFAt6YCu37-cRaB4a0SGclSDc91tzV_mg,5670
 pyobo/sources/mirbase.py,sha256=N6_GfJ76OxnXMBbdoxnvTBCIqiGYoZoG3EAlyn7LlCM,6072
 pyobo/sources/mirbase_constants.py,sha256=d23A5hCWjEW4CQMdLqxOmBaon95MiGEIEQnQaG1S8ds,1948
 pyobo/sources/mirbase_family.py,sha256=0hsbmSxLh9YOK7_W0cacw6cQAiVs7gBTwvsRQ5LXhP0,2038
-pyobo/sources/mirbase_mature.py,sha256=yOpyMMrXYG-FPZaPkD-tI-C8eXn01hpV5w-EBFOv3bU,1265
+pyobo/sources/mirbase_mature.py,sha256=ND4OtAd8hxkDbszyFyFvfJbsUUozyeh-1xt15VbeFO0,1374
 pyobo/sources/msig.py,sha256=m46F7Q4zEqagiRaRI-5sq09MyQwxnA7u-aZ9mJ-A9qE,1727
-pyobo/sources/msigdb.py,sha256=gKqGLd13F9aVKjNpPUrxan0Pjfoe9tEccRqXjLq4juE,4882
+pyobo/sources/msigdb.py,sha256=_7wI10CCaUisJhR56WsEpXGXhurs2ycwgl9UqVUwLC4,4888
 pyobo/sources/ncbigene.py,sha256=AFxaRHMmxvemTMWmN2zge1Ex2HjhpY3K-o1MsPN0Ao0,4507
-pyobo/sources/npass.py,sha256=rhFZo3xePCpaalyxtRbzvQKP1Euqi43UVRnmD3Krt80,2834
+pyobo/sources/npass.py,sha256=7h5GYfSXPYQCdQ9ykEHPk8yHVvSvc_pT1pSl_snqeWg,2712
 pyobo/sources/pathbank.py,sha256=yhdS4BCbGxQf0o3HCGzL2cYRY7zyvHvDzzSBkkezoog,4989
 pyobo/sources/pfam.py,sha256=4GT-NN3fbCgS1bbfBdGI9iTpc1o3NxzLBsW4zvSeDxw,1898
 pyobo/sources/pfam_clan.py,sha256=YdjxdUn5155uj9KJcyTeMiZY4XrpIfi-Cf91z-QEc4I,1333
 pyobo/sources/pid.py,sha256=bICTkOaWl6iFS0mTUoPB3UrhiIsOvqGaXhXW_1j6d_s,4512
-pyobo/sources/pombase.py,sha256=OrVYPyA0h4mOTI34NG7q5YjoIi7ncfggcl3yzeUJEx0,3323
+pyobo/sources/pombase.py,sha256=1w_YuVbZVL6r4t_xDkjNg8yP28_PaNqmr0HuQxSYdhY,3431
 pyobo/sources/pubchem.py,sha256=JcvrKTH3NklBvO25Ur5WWzxBk1f_SV-Uj2egP-1xZUQ,5218
 pyobo/sources/reactome.py,sha256=V9YahRefhTmV1CMNRSR80FnaqJw8ztOd6HO-INhtdpY,5004
 pyobo/sources/rgd.py,sha256=RzIhwtQNca6RWfOO0mOg4LC_LuNqtsq4BSA80Th8zGM,5421
@@ -152,7 +152,7 @@ pyobo/sources/kegg/__init__.py,sha256=g0Ui2giVNV_y8LYWJEz-1TIcp_NY8YWDuwHORw4RmK
 pyobo/sources/kegg/api.py,sha256=CBTO72PIfLh6ZczDrPBDtnxEkuXN9_DCgXqQo6CNwQQ,4721
 pyobo/sources/kegg/genes.py,sha256=CkhjAoShKJepmLilvW7ATbK5ru0sbCX3PonIjm96zo4,3687
 pyobo/sources/kegg/genome.py,sha256=F0ymTvwAS55lWCuvUcn67uUwGad7_z-9JOeavRDjB1c,3984
-pyobo/sources/kegg/pathway.py,sha256=HTiHubaXko2sVMPCKnFVAX7qN4uBOe46tbh8YUenRNM,6201
+pyobo/sources/kegg/pathway.py,sha256=QXypKRrG2dcX9nFhGzSi0YgJeflNhfZd4MHHpUBGy1M,6187
 pyobo/sources/selventa/__init__.py,sha256=RHKjcBvyovcyJVRhfSU7oCyNY9j79Qos7GCfdmh_riM,279
 pyobo/sources/selventa/schem.py,sha256=XvTMhX4QLPAAOfN9mGwM_aEdVfemv2lqO-PqbI4_YUo,1329
 pyobo/sources/selventa/scomp.py,sha256=N30DQ3ElGLODcbHhRvRnq6t8b4Yl7lAqNJFM3Nrqc1E,1704
@@ -173,7 +173,7 @@ 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=ukUcTqVpdcEDyBfIjFn4wuZpqUtPunC-zPr8JgMx0t4,4746
 pyobo/struct/registry.py,sha256=oTip6K-dN12bwKaraCv2kfugGrOB9uV77yi3b8xxj7E,840
-pyobo/struct/struct.py,sha256=hU9D2_zTQoWddamSsS2FhOJHqphuTWzr7m87eHgxtqE,49149
+pyobo/struct/struct.py,sha256=4lhoy_hCslMCcJ5FtRviO8RNH3VKKuAyXHntZ-fh9xo,49250
 pyobo/struct/typedef.py,sha256=pTij8QerL5mYqgMjQppa_f1CXytNZLRsljTYAZLjTyM,10817
 pyobo/struct/utils.py,sha256=-XHuCETp7jPNhjHCW72gikaKoaiTPTNhDK5BZYyJsVw,815
 pyobo/utils/__init__.py,sha256=wXtcjcasWRBtJdTSMCC3jT8yFG8ZkQC-Xdh9lLiQDAo,42
@@ -181,7 +181,7 @@ pyobo/utils/cache.py,sha256=bmuEE0DyppY6szNEzkS1tLLKfsLIrHQFhp0P-q94KFs,2677
 pyobo/utils/citation.py,sha256=R7PqtWoQh8lqedg542Q3anWev1B_iQeIHB3xSN-FMaw,904
 pyobo/utils/io.py,sha256=9kiqHVSjnlsiG6cjrQ67bPcXE6K0HWZMNdaU_22Xvqw,4716
 pyobo/utils/iter.py,sha256=VyISqr04Pg2xLSLJhypUuZnh7WzxVmpp3MsASCuL8Tk,1475
-pyobo/utils/misc.py,sha256=tRzerTmnAvC-xoGzhmQPbXI_48bBS4Nw31BUY4_R5QI,3237
+pyobo/utils/misc.py,sha256=iJuog7Koluf_qF1Q5AMYdlzOQIiKnEebMxsD5ZcmqjE,3235
 pyobo/utils/ndex_utils.py,sha256=gxmGfR_O-ZMOsBil_YFSn99x_Fvatg7O8s9iZp4Iy10,2351
 pyobo/utils/path.py,sha256=B6hmWbrEXoIox6rBzHggfc6GmxzSmMHxcuiUGvRjZ9o,3319
 pyobo/xrefdb/__init__.py,sha256=0W6AuvghFHQ1zY-Dq26z8V_MRC9xL39aWqLb-JbU8T8,74
@@ -203,9 +203,9 @@ 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
-pyobo-0.8.11.dist-info/LICENSE,sha256=GRbxxtZEWtZiFGDENk1gntCQK4HEJYYbylEJEwpSLao,1076
-pyobo-0.8.11.dist-info/METADATA,sha256=cxlgI-TRzPBr5rRTgvatITcEJOzS88eazqZZgAn25a0,19895
-pyobo-0.8.11.dist-info/WHEEL,sha256=G16H4A3IeoQmnOrYV4ueZGKSjhipXx8zc8nu9FGlvMA,92
-pyobo-0.8.11.dist-info/entry_points.txt,sha256=Du5V6qw_T917Z5ZoMhLTTJoolK7kkVuUWkdE7aJWea0,669
-pyobo-0.8.11.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
-pyobo-0.8.11.dist-info/RECORD,,
+pyobo-0.8.13.dist-info/LICENSE,sha256=GRbxxtZEWtZiFGDENk1gntCQK4HEJYYbylEJEwpSLao,1076
+pyobo-0.8.13.dist-info/METADATA,sha256=WFrBL_Y_KmMYOuboeFPShJio1t9dU5b2Z4jGC8dVyQ4,19895
+pyobo-0.8.13.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+pyobo-0.8.13.dist-info/entry_points.txt,sha256=Du5V6qw_T917Z5ZoMhLTTJoolK7kkVuUWkdE7aJWea0,669
+pyobo-0.8.13.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
+pyobo-0.8.13.dist-info/RECORD,,

{pyobo-0.8.11.dist-info → pyobo-0.8.13.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.37.1)
+Generator: bdist_wheel (0.38.4)
 Root-Is-Purelib: true
 Tag: py3-none-any