From 90f73cdfcfcd85d5c4cc27adb3816a6efc3c2de1 Mon Sep 17 00:00:00 2001 From: Leonardo macOS Date: Thu, 20 Jun 2024 13:41:34 +0200 Subject: [PATCH] add get_adapter in docstring --- src/malco/post_process/mondo_score_utils.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/malco/post_process/mondo_score_utils.py b/src/malco/post_process/mondo_score_utils.py index 7a702c477..756a1a8c8 100644 --- a/src/malco/post_process/mondo_score_utils.py +++ b/src/malco/post_process/mondo_score_utils.py @@ -17,7 +17,7 @@ def omim_mappings(term: str, adapter) -> List[str]: Example: - >>> omim_mappings("MONDO:0007566", mondo_adapter()) + >>> omim_mappings("MONDO:0007566", get_adapter("sqlite:obo:mondo")) ['OMIM:132800'] Args: @@ -41,13 +41,13 @@ def score_grounded_result(prediction: str, ground_truth: str, mondo) -> float: Exact match: - >>> score_grounded_result("OMIM:132800", "OMIM:132800", mondo_adapter()) + >>> score_grounded_result("OMIM:132800", "OMIM:132800", get_adapter("sqlite:obo:mondo")) 1.0 The predicted Mondo is equivalent to the ground truth OMIM (via skos:exactMatches in Mondo): - >>> score_grounded_result("MONDO:0007566", "OMIM:132800", mondo_adapter()) + >>> score_grounded_result("MONDO:0007566", "OMIM:132800", get_adapter("sqlite:obo:mondo")) 1.0 The predicted Mondo is a disease entity that groups multiple