Pharmacogenomics datasets for Ontology Matching

<strong>Pharmacogenomics datasets for Ontology Matching</strong> Pharmacogenomics (or PGx for short) involves n-ary tuples representing so-called "pharmacogenomic relationships" and their components of three distinct types: drugs, genetic factors, and phenotypes. Tuples are reified as instances of the class ``pgxo:PharmacogenomicRelationship``. The goal of the matching task is to match these tuples (instance matching). Motivation: Pharmacogenomic tuples involve drugs, genetic factors, and phenotypes, and state that patients being treated by the specified drugs while having the specified genetic factors may experience the given phenotypes. Knowledge in pharmacogenomics is scattered across several resources, e.g., reference databases (PharmGKB) or the biomedical literature. Hence, there is a need to build a consolidated view of the knowledge of this domain by aligning tuples from different sources. See [1] for a detailed motivation and [2] for a detailed task description. <strong>Datasets</strong> We provide different subsets of the alignments available in PGxLOD that have been created with the matching rules described in [3]. <em>Task with 10 % of PGx relationships</em> Alignments: 1092 relatedMatch alignments: 66 sameAs alignments: 498 closeMatch alignments: 53 broadMatch alignments: 333 narrowMatch alignments: 142 Entities to align in source: 2525 Triples in source: 816604 Entities to align in target: 2518 Triples in target: 816859 <em>Task with 50 % of PGx relationships</em> Alignments: 23630 relatedMatch alignments: 1245 sameAs alignments: 9219 closeMatch alignments: 1175 broadMatch alignments: 7183 narrowMatch alignments: 4808 Entities to align in source: 12816 Triples in source: 894723 Entities to align in target: 12401 Triples in target: 889735 <em>Task with 100 % of PGx relationships</em> Alignments: 89926 relatedMatch alignments: 4979 sameAs alignments: 35499 closeMatch alignments: 4603 broadMatch alignments: 26135 narrowMatch alignments: 18710 Entities to align in source: 25406 Triples in source: 982548 Entities to align in target: 25029 Triples in target: 980543 <strong>References</strong> Pierre Monnin, Joël Legrand, Graziella Husson, Patrice Ringot, Andon Tchechmedjiev, Clément Jonquet, Amedeo Napoli, Adrien Coulet: PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison. BMC Bioinformatics 20-S(4): 139:1-139:16 (2019) [pdf] Pierre Monnin, Adrien Coulet: Matching pharmacogenomic knowledge: particularities, results, and perspectives. OM@ISWC 2022: 79-83 [pdf] Pierre Monnin, Miguel Couceiro, Amedeo Napoli, Adrien Coulet: Knowledge-Based Matching of n-ary Tuples. ICCS 2020: 48-56 [pdf]