ODLS 2016 ONTOLOGIES AND DATA IN LIFE SCIENCES Proceedings of the 7th Workshop of the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML) Halle (Saale), Germany September 29-30, 2016 edited by Frank Loebe, Martin Boeker, Heinrich Herre, Ludger Jansen and Daniel Schober Imprint Publishers and Editors: Frank Loebe1, Martin Boeker2, Heinrich Herre3, Ludger Jansen4, 5, Daniel Schober6 1 University of Leipzig, Computer Science Institute, Leipzig, Germany 2 University Medical Center Freiburg, Institute for Medical Biometry and Statistics (IMBI), Freiburg im Breisgau, Germany 3 University of Leipzig, Institute for Medical Informatics, Statistics and Epidemiology (IMISE), Leipzig, Germany 4 Ruhr University Bochum, Faculty of Catholic Theology, Bochum, Germany 5 University of Rostock, Institute of Philosophy, Rostock, Germany 6 Leibniz Institute of Plant Biochemistry (IPB), Department of Stress and Developmental Biology, Halle (Saale), Germany Contact: Frank Loebe University of Leipzig Computer Science Institute Postal Address: P.O.Box 100920, 04009 Leipzig, Germany Street Address: Augustusplatz 10, 04109 Leipzig, Germany Phone: +49 341 97 32236 Fax: +49 341 97 32299 Email: frank.loebe@informatik.uni-leipzig.de Published for: Ontologien in der Biomedizin und den Lebenswissenschaften (OBML), Fachgruppe im Fachbereich Informatik in den Lebenswissenschaften der Gesellschaft für Informatik e.V. (GI), Bonn Speaker: Prof. Dr. Heinrich Herre, University of Leipzig, Germany Deputy Speaker: Dr. Martin Boeker, University Medical Center Freiburg, Germany Workgroup website: https://wiki.imise.uni-leipzig.de/Gruppen/OBML Online publication: CEUR Workshop Proceedings (CEUR-WS.org), ISSN 1613-0073 http://ceur-ws.org Preferred citation: Frank Loebe, Martin Boeker, Heinrich Herre, Ludger Jansen, Daniel Schober (eds.): ODLS 2016 – Onto- logies and Data in Life Sciences. Proceedings of the 7th Workshop of the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML), Halle (Saale), Germany, September 29-30, 2016. CEUR-WS.org. It is recommended to include further the CEUR-WS.org volume number and the URL to that volume. Editorial deadline: September 25, 2016 Copyright  2016 for the individual papers by the papers’ authors. Copying permitted for private and academic purposes. This volume is published and copyrighted by its editors. ii Organizers Martin Boeker University Medical Center Freiburg Heinrich Herre University of Leipzig Ludger Jansen Ruhr University Bochum & University of Rostock Frank Loebe (main contact) University of Leipzig Daniel Schober Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) Local Organizers Daniel Schober (main local contact) Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) Steffen Neumann Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) Stefan Brass Martin-Luther-University of Halle-Wittenberg Keynote Speakers Johannes Hübner Martin-Luther-University of Halle-Wittenberg Robert Stevens University of Manchester, UK Program Committee Adrien Barton Sherbrooke University, Canada Martin Boeker University Medical Center Freiburg Jesualdo Tomás Fernández-Breis University of Murcia, Spain Georgios V. Gkoutos University of Birmingham, UK Anika Groß University of Leipzig Heinrich Herre University of Leipzig Robert Hoehndorf King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia Ludger Jansen Ruhr University Bochum & University of Rostock Toralf Kirsten University of Leipzig Frank Loebe University of Leipzig Wolfgang Müller Heidelberg Institute for Theoretical Studies (HITS) gGmbH Fabian Neuhaus Otto von Guericke University Magdeburg Axel Ngonga-Ngomo University of Leipzig Anika Oellrich King’s College London, UK Oscar Pastor Polytechnical University of Valencia, Spain Dietrich Rebholz-Schuhmann Insight Centre for Data Analytics, Galway, Ireland Luc Schneider Saarland University, Saarbrücken Daniel Schober Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) Falk Schreiber Monash University, Melbourne, Australia Stefan Schulz Medical University of Graz, Austria Aleksandra Sojic Institute of Industrial Technologies and Automation, National Research Council (ITIA-CNR), Milan, Italy Holger Stenzhorn Saarland University Medical Center, Homburg George Tsatsaronis Technical University of Dresden Dagmar Waltemath University of Rostock iii Authors Mercedes Argüello Casteleiro University of Manchester, UK Adrien Barton Sherbrooke University, Canada Andreas Besting SurgiTAIX AG, Herzogenrath Aisha Blfgeh Newcastle University, UK & King Abdulaziz University, Jeddah, Saudia Arabia Vasa Curcin King’s College London, UK Brendan C. Delaney Imperial College London, UK George Demetriou University of Manchester, UK Kerstin Denecke Bern University of Applied Sciences, Switzerland Richard J. B. Dobson King’s College London & University College London, UK Jean-François Ethier Centre de Recherche des Cordeliers (CRC), Paris, France Sebastian Faulbrück-Röhr GMC Systems mbH, Ilmenau Maria Jesus Fernandez Prieto University of Salford, UK Fred Freitas Federal University of Pernambuco (UFPE), Recife, Brazil Carole A. Goble University of Manchester, UK Martin Golebiewski Heidelberg Institute for Theoretical Studies (HITS) gGmbH Heinrich Herre University of Leipzig Catharien M. U. Hilkens Newcastle University, UK Tim J. P. Hubbard King’s College London, UK Ludger Jansen Ruhr University Bochum & University of Rostock André Kaeding GMC Systems mbH, Ilmenau John A. Keane University of Manchester, UK Julie Klein National Institute of Health and Medical Research (INSERM) & Paul Sabatier University / Toulouse III, Toulouse, France Matthias König Humboldt University Berlin Olga Krebs Heidelberg Institute for Theoretical Studies (HITS) gGmbH Stefan Kropf University of Leipzig Peter Krücken University of Leipzig Rostyk Kuzyakiv University of Zurich, Switzerland Shao Fen Liang King’s College London, UK Phillip Lord Newcastle University, UK Catalina Martínez-Costa Medical University of Graz, Austria Diego Maseda-Fernandez Mid Cheshire Hospitals NHS Foundation Trust, UK José Antonio Miñarro-Giménez Medical University of Graz, Austria Norman Morrison University of Manchester, UK Wolfgang Müller Heidelberg Institute for Theoretical Studies (HITS) gGmbH Goran Nenadic University of Manchester, UK Juliane Neumann University of Leipzig Steffen Neumann Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) Thomas Neumuth University of Leipzig Quyen Nguyen Heidelberg Institute for Theoretical Studies (HITS) gGmbH Andreas Niekler University of Leipzig Anika Oellrich King’s College London, UK Stuart Owen University of Manchester, UK Talya Porat King’s College London, UK Frank Portheine SurgiTAIX AG, Herzogenrath Warren J. Read University of Manchester, UK Kutaiba Saleh Jena University Hospital Reza M. Salek European Bioinformatics Institute (EBI), Hinxton, UK Filipe Santana da Silva Federal University of Pernambuco (UFPE), Recife, Brazil iv Daniel Schober Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) Tobias Schmidt Jena University Hospital Stefan Schulz Medical University of Graz, Austria Sebastian Siemoleit University of Leipzig Jacky L. Snoep University of Manchester, UK Martin Specht Jena University Hospital Natalie J. Stanford University of Manchester, UK Robert Stevens University of Manchester, UK Stephan Stucke GMC Systems mbH, Ilmenau Kais Tahar University of Leipzig Archana Tapuria King’s College London, UK Alexandr Uciteli University of Leipzig Dagmar Waltemath University of Rostock Jennifer D. Warrender Newcastle University, UK Olaf Wolkenhauer University of Rostock Katy Wolstencroft Leiden Institute of Advanced Computer Science, The Netherlands Statistics and History Each submission to ODLS 2016 has been assessed by three reviewers, where 18 of the 24 PC members provided two reviews, the remaining six only one. Contributions could be submitted either as paper or as extended abstract. Eight paper submissions were received, seven of which were accepted as papers. The authors of one paper were invited to resubmit an extended abstract on the topic of the initial submission. In addition to the paper submissions, six extended abstracts were received and five among them have been selected for inclusion in the present proceedings. Concerning former editions of this workshop series, it started with a workshop on Ontologies in Bio- medicine and Life Sciences (OBML) in 2009. In 2013, integration with the formerly independent workshop on Data in Life Sciences led to the renaming to Ontologies and Data in Life Sciences (ODLS). Accordingly, ODLS 2016 follows up on ODLS 2014 (Oct 7-8, Freiburg im Breisgau), ODLS 2013 (Sep 6-7, held as a workshop of INFORMATIK 2013 in Koblenz), OBML 2012 (Sep 27-28, Dresden), OBML 2011 (Oct 6-7, Berlin), OBML 2010 (Sep 9-10, Mannheim) and OBML 2009 (Nov 25-26, Leipzig). Further information on those is available via https://wiki.imise.uni-leipzig.de/Gruppen/OBML/Workshops/ . Acknowledgements and Sponsorship The organizers thank everyone involved in making ODLS 2016 happen: the keynote speakers, the authors of contributions, the Program Committee members, those who contribute to the organization behind the scenes, as well as those participating in the sessions, with or without their own presentation. Moreover, we appreciate the acknowledgement of the workshop by the International Association for Ontology and its Applications (IAOA) as an IAOA Supported Event and we are grateful for the free services provided by EasyChair as well as CEUR-WS.org. Last but not least, we acknowledge the generous sponsorship of ODLS 2016 by OntoChem IT Solutions, Halle (Saale), Germany. http://www.ontochem.de v Keynote Abstracts Dispositions, capacities, abilities. Towards a classification of the powers of living beings Johannes Hübner In my talk I want to investigate the active and passive powers of living beings. Usually, abilities are classified as dispositions to voluntary action. I want to argue, first, that a broader concept of abilities is necessary both in the case of human beings and in the case of other animals. Second, abilities are not a species of dispositions. The pragmatics and formality of authoring ontologies Robert Stevens In this talk I will explore ideas of pragmatics and formality in our approaches to authoring biomedical ontologies. Formality can come from the philosophical approach to ontology development, from the area of knowledge representation, ontological analysis used and the rigor of the method applied in the ontology development. I will advocate a moderately pragmatic approach for one’s philosophical rigor and being much more formal, but not always so, on the representational side. I will illustrate both my pragmatics and formality with some recent work on normalising the Molecular Function sub-ontology of the Gene Ontology. This shows that the “functions” of gene products are very few; that upper ontologies can be of practical use and avoiding ‘distinctions that make no difference’. Fully normalising the GO’s molecular function ontology shows some reasonable insights in the biology and again demonstrates how a formal KR language can help. Even here, to make it work sensibly, pragmatics also come into play. The formality of using a language with strict semantics can be demonstrated, aided by some ontological rigor, but with some representational compromises or pragmatics to make the reasoning with the ontology sensible. At the end of the talk I will give a set of guidelines that I use that help me decide whether or not to be pragmatic or formal when authoring an ontology. vi ODLS 2016 Program as of September 25, 2016 THURSDAY Sep 29, 2016 (13:00 – 13:45) (Getting together / Registration / COFFEE) 13:45 – 14:00 Organizers Welcome remarks Session 1 – Methods and software for terminologies | Applied ontologies 14:00 – 14:20 S. Schulz Qualitative assessment of annotations using SNOMED CT 14:20 – 14:40 S.F. Liang MeTMapS – Medical Terminology Mapping System 14:40 – 15:00 D. Schober Towards standardized evidence descriptors for metabolite annotations 15:00 – 15:20 J. Neumann Risk Identification Ontology (RIO): An ontology for specification and identification of perioperative risks 15:20 – 15:50 COFFEE 15:50 – 16:40 J. Hübner KEYNOTE: Dispositions, capacities, abilities. Towards a classification of the powers of living beings 16:40 – 17:00 COFFEE Session 2 – Ontological analysis and interpretation 17:00 – 17:20 L. Jansen A modelling pattern for multi-track dispositions for life-science ontologies 17:20 – 17:40 S. Siemoleit A Whiteheadian approach to data and knowledge 17:40 – 18:00 S. Schulz Ontological interpretation of biomedical database annotations starting 19:30 DINNER FRIDAY Sep 30, 2016 Session 3 – Publication and text mining 09:00 – 09:20 M. Argüello Deep Learning meets Semantic Web: A feasibility study with the Casteleiro Cardiovascular Disease Ontology and PubMed citations 09:20 – 09:40 A. Niekler Extracting process graphs from medical text data 09:40 – 10:00 COFFEE 10:00 – 10:50 R. Stevens KEYNOTE: The pragmatics and formality of authoring ontologies 10:50 – 11:10 COFFEE Session 4 – Ontology building and use | Methods regarding systems biology 11:10 – 11:30 A. Blfgeh A document-centric approach for developing the tolAPC Ontology 11:30 – 11:50 S. Kropf Querying standardized EHRs by a Search Ontology XML extension (SOX) 11:50 – 12:10 D. Waltemath Challenges and opportunities for system biology standards and tools in medical research 12:10 – 12:30 O. Krebs FAIRDOM approach for semantic interoperability of systems biology data and models 12:30 – 13:45 LUNCH 13:45 – 15:00 Open discussion & OBML session vii Table of Contents (within categories in alphabetic order according to last names of first authors) ID Nr. of Letter Pages Papers Deep Learning meets Semantic Web: A feasibility study with the Cardiovascular Disease A 6 Ontology and PubMed citations Mercedes Argüello Casteleiro, George Demetriou, Warren J. Read, Maria Jesus Fernandez Prieto, Diego Maseda-Fernandez, Goran Nenadic, Julie Klein, John A. Keane, Robert Stevens A document-centric approach for developing the tolAPC Ontology B 6 Aisha Blfgeh, Jennifer D. Warrender, Catharien M. U. Hilkens, Phillip Lord Challenges and opportunities for system biology standards and tools in medical research C 6 Matthias König, Anika Oellrich, Dagmar Waltemath, Richard J. B. Dobson, Tim J. P. Hubbard, Olaf Wolkenhauer Querying standardized EHRs by a Search Ontology XML extension (SOX) D 5 Stefan Kropf, Alexandr Uciteli, Peter Krücken, Kerstin Denecke, Heinrich Herre Towards standardized evidence descriptors for metabolite annotations E 5 Daniel Schober, Reza M. Salek, Steffen Neumann A Whiteheadian approach to data and knowledge F 6 Sebastian Siemoleit, Heinrich Herre Risk Identification Ontology (RIO): An ontology for specification and identification of G 7 perioperative risks Alexandr Uciteli, Juliane Neumann, Kais Tahar, Kutaiba Saleh, Stephan Stucke, Sebastian Faulbrück-Röhr, André Kaeding, Martin Specht, Tobias Schmidt, Thomas Neumuth, Andreas Besting, Frank Portheine, Heinrich Herre Extended Abstracts A modelling pattern for multi-track dispositions for life-science ontologies H 2 Adrien Barton, Ludger Jansen FAIRDOM approach for semantic interoperability of systems biology data and models I 2 Olga Krebs, Katy Wolstencroft, Natalie J. Stanford, Norman Morrison, Martin Golebiewski, Rostyk Kuzyakiv, Stuart Owen, Quyen Nguyen, Jacky L. Snoep, Wolfgang Müller, Carole A. Goble MeTMapS – Medical Terminology Mapping System J 2 Shao Fen Liang, Jean-François Ethier, Talya Porat, Archana Tapuria, Brendan C. Delaney, Vasa Curcin Qualitative assessment of annotations using SNOMED CT K 2 José Antonio Miñarro-Giménez, Catalina Martínez-Costa, Stefan Schulz Extracting process graphs from medical text data L 2 Andreas Niekler Ontological interpretation of biomedical database annotations M 2 Filipe Santana da Silva, Ludger Jansen, Fred Freitas, Stefan Schulz viii