pyobo 0.10.11__py3-none-any.whl → 0.11.0__py3-none-any.whl

pyobo-0.11.0.dist-info/RECORD

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+pyobo/xrefdb/sources/cbms2019.py,sha256=U1nP-LpMu4M0KnRka1RW66LeYXRk0dqoowpjlIY9Ctg,2818
+pyobo/xrefdb/sources/chembl.py,sha256=RhWupYbItd5FF4VeLrPOjc8yPSmeA1A0iKV2Acge8sw,2610
+pyobo/xrefdb/sources/compath.py,sha256=xkS4vXctgOCBp08JR10CEUR5UxgnhmYdDZg2AiShwuw,2318
+pyobo/xrefdb/sources/famplex.py,sha256=d2adWCl7NlqGCU-NKdllxRcDzuv41tM3yaMMzmcabbc,1808
+pyobo/xrefdb/sources/gilda.py,sha256=zENDa49IvJA3HuyTfjjUVd34g4vGbDDtWcVwa6RF9pI,1045
+pyobo/xrefdb/sources/intact.py,sha256=l2gqxm9OLPpQqhNqAIT_jk7AHx61itsUCz-5dowwMbo,2952
+pyobo/xrefdb/sources/ncit.py,sha256=QTo9BSGuurvy9M54viS6_v6dF36O8DbUGU6iiyqKsPI,3729
+pyobo/xrefdb/sources/pubchem.py,sha256=VK_yPCaoa-CKQNkq9iAF0Zh0D_zxqa92YG4OBbvnA9c,771
+pyobo/xrefdb/sources/wikidata.py,sha256=JSrl3YWMQA_gxw7IXJRnxWWetcAV82aM5-5J3IHFzoQ,3562
+pyobo-0.11.0.dist-info/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
+pyobo-0.11.0.dist-info/METADATA,sha256=ydZIch8oh6smWoaZ7SATHqOxIgqWrsRyeDVZaGTAW3U,25208
+pyobo-0.11.0.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+pyobo-0.11.0.dist-info/entry_points.txt,sha256=YfZYzQyXBZ5dGiy4GsOUCOKKlNRNDcmR4vnlpD50q08,41
+pyobo-0.11.0.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
+pyobo-0.11.0.dist-info/RECORD,,

{pyobo-0.10.11.dist-info → pyobo-0.11.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (75.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pyobo-0.11.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+pyobo = pyobo.cli:main

pyobo/xrefdb/bengo.py

@@ -1,44 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""Pipeline for building a large ontology graph."""
-
-import logging
-
-import bioregistry
-import networkx as nx
-from tqdm.auto import tqdm
-
-from pyobo import get_hierarchy
-from pyobo.getters import SKIP
-from pyobo.resource_utils import ensure_inspector_javert_df
-
-logger = logging.getLogger(__name__)
-
-
-def bens_magical_ontology(use_tqdm: bool = True) -> nx.DiGraph:
-    """Make a super graph containing is_a, part_of, and xref relationships."""
-    rv = nx.DiGraph()
-
-    df = ensure_inspector_javert_df()
-    for source_ns, source_id, target_ns, target_id, provenance in df.values:
-        rv.add_edge(
-            f"{source_ns}:{source_id}",
-            f"{target_ns}:{target_id}",
-            relation="xref",
-            provenance=provenance,
-        )
-
-    logger.info("getting hierarchies")
-    it = tqdm(sorted(bioregistry.read_registry()), desc="Entries", disable=not use_tqdm)
-    for prefix in it:
-        if bioregistry.is_deprecated(prefix) or prefix in SKIP:
-            continue
-        if use_tqdm:
-            it.set_postfix({"prefix": prefix})
-
-        hierarchy = get_hierarchy(prefix, include_has_member=True, include_part_of=True)
-        rv.add_edges_from(hierarchy.edges(data=True))
-
-    # TODO include translates_to, transcribes_to, and has_variant
-
-    return rv