From feb07c3aabbb3c3208d2a397d3ba4ff02b4070f7 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Mon, 28 Apr 2025 12:31:09 +0200
Subject: [PATCH] Add cross-species rules

---
 src/semra/rules.py | 28 ++++++++++++++++++++++++++--
 1 file changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/semra/rules.py b/src/semra/rules.py
index fc91122e..417be58e 100644
--- a/src/semra/rules.py
+++ b/src/semra/rules.py
@@ -22,6 +22,9 @@ def _f(r: curies.NamedReference) -> Reference:
 DB_XREF = _f(v.has_dbxref)
 EQUIVALENT_TO = Reference(prefix="owl", identifier="equivalentTo")
 REPLACED_BY = _f(v.term_replaced_by)
+CROSS_SPECIES_EXACT = Reference.from_curie("semapv:crossSpeciesExactMatch")
+CROSS_SPECIES_NARROW = Reference.from_curie("semapv:crossSpeciesNarrowMatch")
+CROSS_SPECIES_BROAD = Reference.from_curie("semapv:crossSpeciesBroadMatch")
 
 RELATIONS: list[Reference] = [
     EXACT_MATCH,
@@ -31,6 +34,9 @@ def _f(r: curies.NamedReference) -> Reference:
     CLOSE_MATCH,
     EQUIVALENT_TO,
     REPLACED_BY,
+    CROSS_SPECIES_EXACT,
+    CROSS_SPECIES_NARROW,
+    CROSS_SPECIES_BROAD,
 ]
 
 IMPRECISE: set[Reference] = {DB_XREF, CLOSE_MATCH}
@@ -41,11 +47,29 @@ def _f(r: curies.NamedReference) -> Reference:
     CLOSE_MATCH: CLOSE_MATCH,
     DB_XREF: DB_XREF,
     EQUIVALENT_TO: EQUIVALENT_TO,
+    CROSS_SPECIES_EXACT: CROSS_SPECIES_EXACT,
+    CROSS_SPECIES_BROAD: CROSS_SPECIES_NARROW,
+    CROSS_SPECIES_NARROW: CROSS_SPECIES_BROAD,
 }
+
+# TODO transitivity and two-step with cross-species relations?
+
 #: Which predicates are transitive? This excludes the imprecise onces
-TRANSITIVE: set[Reference] = {BROAD_MATCH, NARROW_MATCH, EXACT_MATCH, EQUIVALENT_TO}
+TRANSITIVE: set[Reference] = {
+    BROAD_MATCH,
+    NARROW_MATCH,
+    EXACT_MATCH,
+    EQUIVALENT_TO,
+    CROSS_SPECIES_EXACT,
+}
 #: Which predicates are directionless
-DIRECTIONLESS: set[Reference] = {EXACT_MATCH, CLOSE_MATCH, DB_XREF, EQUIVALENT_TO}
+DIRECTIONLESS: set[Reference] = {
+    EXACT_MATCH,
+    CLOSE_MATCH,
+    DB_XREF,
+    EQUIVALENT_TO,
+    CROSS_SPECIES_EXACT,
+}
 
 #: Two step chain inference rules
 TWO_STEP: dict[tuple[Reference, Reference], Reference] = {