Pharmacogenomics datasets for Ontology Matching

Pharmacogenomics datasets for Ontology Matching

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.

Datasets

We provide different subsets of the alignments available in PGxLOD that have been created with the matching rules described in [3].

Task with 10 % of PGx relationships

Alignments: 942

relatedMatch alignments: 83

sameAs alignments: 315

closeMatch alignments: 46

broadMatch alignments: 332

narrowMatch alignments: 166

Entities to align in source: 2523

Triples in source: 211770

Entities to align in target: 2520

Triples in target: 208051

Task with 50 % of PGx relationships

Alignments: 23938

relatedMatch alignments: 1500

sameAs alignments: 8636

closeMatch alignments: 1128

broadMatch alignments: 8047

narrowMatch alignments: 4627

Entities to align in source: 12767

Triples in source: 459483

Entities to align in target: 12450

Triples in target: 450364

Task with 100 % of PGx relationships

Alignments: 88569

relatedMatch alignments: 5318

sameAs alignments: 34510

closeMatch alignments: 3978

broadMatch alignments: 24097

narrowMatch alignments: 20666

Entities to align in source: 25362

Triples in source: 691151

Entities to align in target: 25073

Triples in target: 687052

References

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]