Proceedings of the 2nd OWL Reasoner Evaluation Workshop (ORE 2013)

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OWL is a logic-based ontology language standard designed to promote interoperability, particularly in the context of the (Semantic) Web. The standard has encouraged the development of numerous OWL reasoning systems, and such systems are already key components of many applications.

The goal of this workshop is to bring together both developers and users of reasoners for (subsets of) OWL, including systems focusing on both intensional (ontology) and extensional (data) query answering.

This volume contains the papers presented at ORE 2013: The 2nd International Workshop on OWL Reasoner Evaluation, held in Ulm, Germany, on July 22, 2013. ORE 2013 was collocated with the 26th edition of the DL workshop. The workshop received a 18 submissions (14 system papers and 4 ontology/benchmark papers) each of which was reviewed by at least three members of the program committee or additional reviewers. Since there was not any o -topic submission, we accepted all submission, following the inclusive tradition of DL, for oral presentation at the workshop.

In addition to workshop paper submissions, ORE 2013 also included a competition in which OWL reasoners were faced with di erent reasoning task, such as ontology classi cation, consistency checking, and satis ability checking of concepts. The tasks were performed on several large corpora of real-life OWL ontologies obtained from the web, as well as user-submitted ontologies which were found to be challenging for reasoners. The proceedings also contains a short report summarizing the main results of the competition.

Fourteen OWL reasoners participated in the ORE 2013 competition: ii

BaseVISor http://vistology.com/basevisor/basevisor.html TrOWL http://trowl.eu/ Konclude http://www.derivo.de/en/produkte/konclude/ ELepHant https://code.google.com/p/elephant-reasoner/ TReasoner https://code.google.com/p/treasoner/ HermiT http://www.hermit-reasoner.com/ MORe http://code.google.com/p/more-reasoner/ ELK http://code.google.com/p/elk-reasoner/ jcel http://jcel.sourceforge.net/ SnoRocket http://research.ict.csiro.au/software/snorocket FaCT++ http://code.google.com/p/factplusplus/ Jfact http://sourceforge.net/projects/jfact/ Chainsaw http://sourceforge.net/projects/chainsaw/

WSClassi er https://code.google.com/p/wsclassifier/

Acknowledgements

We thank all members of the program committee, competition organisers, additional reviewers, authors of the submitted papers, developers of the submitted reasoners and ontologies, and local organizers for their invaluable e ort.

We also thank Konstantin Korovin (supported by the Royal Society grant RG080491) at the University of Manchester who kindly provided us with the PC cluster for the competition.

We also gratefully acknowledge the support of our sponsors. In particular, we thank the main workshop sponsor: B2i Healthcare (https://www.b2international.com/).

We would also like to acknowledge that the work of the ORE organisers was greatly simpli ed by using the EasyChair conference management system (http://www.easychair.org) and the CEUR Workshop Proceedings publication service (http://ceur-ws.org/).

Organisers, PC Chairs

Samantha Bail

Ernesto Jimenez-Ruiz

University of Manchester University of Oxford

Competition Organisers

Rafael Goncalves Nicolas Matentzoglu Bijan Parsia

Local Organisers

Birte Glimm Yevgeny Kazakov

Program

Committee

Ana Armas

Franz Baader Christine Golbreich Janna Hastings Pavel Klinov Despoina Magka Francisco Martin-Recuerda Christian Meilicke Julian Mendez Maria Del Mar Roldan Garc a Stefan Schlobach Kavitha Srinivas Dmitry Tsarkov

Zhe Wang

Additional Reviewers

Andrew Bate

David Carral Maria Copeland Jared Leo Jose Mora Weihong Song Yujiao Zhou iv

University of Manchester University of Manchester University of Manchester

University of Ulm University of Ulm

University of Oxford

TU Dresden LIRMM, CNRS, Montpellier & Univ. Versailles Saint-Quentin European Bioinformatics Institute University of Ulm University of Oxford Universidad Politecnica de Madrid University of Mannheim TU Dresden Universidad de Malaga Vrije Universiteit Amsterdam IBM Research University of Manchester Gri th University

University of Oxford

Wright State University University of Manchester University of Manchester Universidad Politecnica de Madrid University of New Brunswick

University of Oxford Ontology and benchmark papers Genomic CDS: an example of a complex ontology for pharmacogenetics and clinical decision support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

Matthias Samwald

References

OBDA with Ontop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Mariano Rodriguez-Muro , Roman Kontchakov and Michael Zakharyaschev

Reasoning the FMA Ontologies with TrOWL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 Je Z. Pan , Yuan Ren, Nophadol Jekjantuk and Jhonatan Garcia

KB Bio 101 : A Challenge for OWL Reasoners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114 Michael Wessel , Vinay Chaudhri and Stijn Heymans

Evaluating OWL 2 Reasoners in the context of Clinical Decision Support in Lung

Cancer Treatment Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121 Berkan Sesen , Ernesto Jimenez-Ruiz, Rene Banares-Alcantara and Michael Brady

A large-scale gene-centric semantic web knowledge base for molecular biology . . . . . . . . . . . . . 134 Jose Cruz-Toledo, Alison Callahan and Michel Dumontier