Introducing the Disease and Phenotype OAEI Track

Abstract

The Pistoia Alliance Ontologies Mapping project1 was set up to find or create better tools and services for mapping between ontologies (including controlled vocabularies) in the same domain and to establish best practices for ontology management in the Life Sciences. The project has developed a formal process to define and submit a request for information (RFI) from existing ontologies mapping tool providers to enable their evaluation.2 A critical component of any Ontologies Mapping tool is the embedded ontology matching algorithm, therefore the project is supporting their development and evaluation through sponsorship and organisation of the new Disease and Phenotype track for the OAEI campaign3 [1] which is described in this paper.

1 Introduction

The Disease and Phenotype track4 comprises two tasks that will involve the pairwise alignment of the HPO, MP, DOID and ORDO ontologies (Table 1 shows the metrics of these ontologies): 2 3

Evaluation process

The evaluation of the Disease and Phenotype Track will be run with support of the SEALS infrastructure.5 Systems will be evaluated and ranked according to the following criteria: – Precision and Recall with respect to a voted reference alignment that will be built automatically to generate consensus voting for the outputs of the participating systems. – Recall with respect to manually generated mappings for three areas (carbohydrate, obesity and breast cancer). – Manual assessment of a subset of the generated mappings, specially the ones that are not suggested by other systems. – Performance in other tracks will also be taken into account, especially the OAEI interactive track [ 3 ] where the Disease and Phenotype dataset is also used.6 Additionally, systems able to discover complex logic relations in mappings beyond equivalence and subsumption will also be considered. The evaluation of these mappings will be in parallel to the evaluation of standard equivalence and subsumption mappings. Complex mappings should be provided in OWL 2 format.

Acknowledgements References

This work was partially funded by the Pistoia Alliance Ontology Mappings project, the EU project Optique (FP7-ICT-318338), and the EPSRC projects ED3 and DBOnto.

References

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2. Fridman Noy , N. , Shah , N.H. , Whetzel , P.L. , Dai , B. , Dorf , M. , Griffith , N. , Jonquet , C. , Rubin , D.L. , Storey , M.A.D. , Chute , C.G. , Musen , M.A. : BioPortal: ontologies and integrated data resources at the click of a mouse . Nucleic Acids Research 37 ( Web-Server-Issue) ( 2009 )

3. Dragisic , Z. , Ivanova , V. , Lambrix , P. , Faria , D. , Jimenez-Ruiz , E. , Pesquita , C. : User validation in ontology alignment . In: International Semantic Web Conference. ( 2016 )