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...always be the best solution in terms of precision and recall. 3 Experimental Set-Up 3.1 Datasets The ontologies we use for the experiments are from the ontology alignment evaluation initiative (OAEI) =-=[5]-=-. We selected the conference and the large Biomed ontologies because these benchmarks are not artificially created (unlike, for instance, the benchmarks dataset), are not focused on a narrow alignment...

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...r 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. 2 Datasets 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): – Task 1: matching of the Human Phenotype Ontology (HPO) to the Mammalian Phenotype Ontology (MP). – Task 2: matching of the Human Disease Ontology (DOID) to the Orphanet and Rare Diseases Ontology (ORDO). The first task is important for translational science where HPO includes inherited diseases and MP originated from rodents as a model mammalian organism for many la...

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... reference alignments for the track based on the available BioPortal mappings [2]. Most of the BioPortal mappings are automatically generated by the LOOM system;10 therefore this BioPortal-based reference alignment will only be considered as a baseline since it is incomplete or may contain erroneous mappings. 3.2 OAEI Evaluation Process The evaluation of the Disease and Phenotype Track will be run with support of the SEALS infrastructure.11 Systems will be evaluated and ranked according to the following criteria: 4 The OAEI is an annual campaign for the evaluation of ontology matching systems [1]: http://oaei.ontologymatching.org/ 5 http://oaei.ontologymatching.org/2016/phenotype/index.html 6 http://bioportal.bioontology.org/ontologies/HP 7 http://bioportal.bioontology.org/ontologies/MP 8 http://bioportal.bioontology.org/ontologies/DOID 9 http://bioportal.bioontology.org/ontologies/ORDO 10 http://www.bioontology.org/wiki/index.php/BioPortal_Mappings 11 http://oaei.ontologymatching.org/2016/seals-eval.html – 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 using th...

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...zare la schedasHome.s9s─ Most of the participants in OAEI do not understand SKOS. Thus, thesauri needsto be sweeten into ontologies by means of a lossy and incorrect mapping [36]s─ As of 2014 results =-=[37]-=-, “the baselines with preferred labels are still very goodsand can only be beaten by one system”. Furthermore, the use of SKOSsannotations increases the performance of 7%sIt thus seems that the qualit...

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...ribed in Section 3. For the second use case we use Mouse anatomy (AMA) and a fragment of NCI human anatomy ontology (NCI-A) from the Anatomy track of the 2013 Ontology Alignment Evaluation Initiative =-=[3]-=-. The set of missing is-a relations for these two experiments were obtained using a logic-based approach presented in [7] which uses an alignment between these two ontologies to generate possible miss...