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Remove Aragorn rules that use the invalid affects_response_to predicate - #197
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- biolink:affects_response_to is no longer a valid Biolink predicate (fixes #157) - Swap it for biolink:affects_sensitivity_to in the 22 AMIE rules that used it (1 treats rule, 21 affects/activity rules), in both the query templates and the human-readable Rule strings - affects_sensitivity_to is the direct successor: Biolink lists CTD:affects_response_to as its exact mapping, and it is the parent of increases_/decreases_sensitivity_to, so queries pick up those edges too - Chose swap over removal because the merged translator_kg (1.0.2) carries ~17.5k CTD edges in this family, mostly gene -> chemical as the rules expect; associated_with_response_to has no edges, so it was not a usable replacement - Rule confidence stats were mined on the old graph and were not re-mined - Update the matching predicate in the test message helper
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Probably a good idea to run the acceptance tests against this change as well. |
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Acceptance tests have been run and with these new predicates we swamp two TopAnswer tests and fail one more Acceptable test. So overall just slightly worse with this new predicate over these rules just being thrown out. |
- Testing showed results are better without these rules than with the affects_sensitivity_to swap, so drop all 22 of them - Removed 1 treats rule and 21 affects activity/abundance rules; the contraindicated_for rules were never affected - Deleted the rule blocks in place rather than re-serializing the JSON, so the file's existing formatting is preserved and the diff is deletions only - Kept affects_sensitivity_to in tests/helpers/generate_messages.py: that fixture is a generic callback response unrelated to the rules, and it should still use a valid Biolink predicate
cbizon
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Ok, now taken out. |
The treats rule that used affects_sensitivity_to was dropped, so a pinned treats lookup now expands to ten templates plus the direct lookup (11). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01S2yuRCTqohAzMDKNwK31zv
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- #198: the stored response starts with an empty knowledge graph and results when the query has none. Ported to 1.6's add_query, whose stored response is the whole query (no 2.0 prepare_stored_response); test_stored_response.py (2.0's stored form) stays deleted. - #197: the 22 rules that used affects_response_to are removed from the 1.x rules file, matched by their Rule text; every category now holds the same rules as devel's, in the same order, and nothing else changed. - #196: catrax-pathfinder 3.1.0, already on this branch (v1.3.3). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TtsBikU9y9AFQ5uu9tcioz
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Fixes #157
biolink:affects_response_tois no longer a valid Biolink predicatetreatsrule and 21affectsactivity/abundance rules (thecontraindicated_forrules never used it)biolink:affects_sensitivity_to, its closest current equivalenttests/helpers/generate_messages.pytoaffects_sensitivity_to; that fixture is a generic callback response unrelated to the rules, but it should use a valid predicateRules remaining per rule set:
treatscontraindicated_foraffectsactivity increasedaffectsactivity decreasedaffectsactivity_or_abundance increasedaffectsactivity_or_abundance decreasedNote: the branch history shows the predicate swap followed by the removal; squash-merging gives a single clean commit.