pyobo 0.10.11__py3-none-any.whl → 0.10.12__py3-none-any.whl

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