Calculate ortholog relationships in Reactome

scripts/generate_reactome_orthologs.py

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+"""Generate orthologous relations between Reactome pathways."""
+
+import itertools as itt
+from collections import defaultdict
+from collections.abc import Iterable, Mapping
+
+import pyobo
+from curies import NamableReference
+from curies.vocabulary import structural_matching
+from sssom_pydantic import SemanticMapping
+from tqdm import tqdm
+
+from biomappings import append_predictions, get_script_url
+
+
+def iterate_orthologs() -> Iterable[SemanticMapping]:
+    """Iterate over Reactome orthologs based on identifier matching."""
+    get_script_url(__file__)
+    names = pyobo.get_id_name_mapping("reactome")
+    parent_identifier_to_species_identifier = _get_species_to_identifiers(names)
+    orthologous_to = NamableReference(
+        prefix="ro", identifier="HOM0000017", name="in orthology relationship with"
+    )
+    for identifiers in tqdm(parent_identifier_to_species_identifier.values()):
+        for source_id, target_id in itt.product(identifiers, repeat=2):
+            if source_id >= target_id:
+                continue
+            yield SemanticMapping(
+                subject=NamableReference(
+                    prefix="reactome", identifier=source_id, name=names[source_id]
+                ),
+                predicate=orthologous_to,
+                object=NamableReference(
+                    prefix="reactome", identifier=target_id, name=names[target_id]
+                ),
+                justification=structural_matching,
+            )
+
+
+def _get_species_to_identifiers(names: Mapping[str, str]) -> Mapping[str, list[str]]:
+    species_to_identifiers = defaultdict(list)
+    for identifier in names:
+        species_to_identifiers[identifier.split("-")[-1]].append(identifier)
+    return species_to_identifiers
+
+
+if __name__ == "__main__":
+    append_predictions(iterate_orthologs())