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Add cross-species rules #55

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28 changes: 26 additions & 2 deletions src/semra/rules.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand All @@ -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}
Expand All @@ -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] = {
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