Publishers and Editors: 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 – 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. 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.
Johannes Hübner Robert Stevens
(main contact)
University Medical Center Freiburg University of Leipzig Ruhr University Bochum & University of Rostock University of Leipzig Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale)
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 Martin-Luther-University of Halle-Wittenberg
University of Manchester, UK 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 Mercedes Argüello Casteleiro Adrien Barton Andreas Besting Aisha Blfgeh Vasa Curcin Brendan C. Delaney George Demetriou Kerstin Denecke Richard J. B. Dobson Jean-François Ethier Sebastian Faulbrück-Röhr Maria Jesus Fernandez Prieto Fred Freitas Carole A. Goble Martin Golebiewski Heinrich Herre Catharien M. U. Hilkens Tim J. P. Hubbard Ludger Jansen André Kaeding John A. Keane Julie Klein Matthias König Olga Krebs Stefan Kropf Peter Krücken Rostyk Kuzyakiv Shao Fen Liang Phillip Lord Catalina Martínez-Costa Diego Maseda-Fernandez José Antonio Miñarro-Giménez Norman Morrison Wolfgang Müller Goran Nenadic Juliane Neumann Steffen Neumann Thomas Neumuth Quyen Nguyen Andreas Niekler Anika Oellrich Stuart Owen Talya Porat Frank Portheine Warren J. Read Kutaiba Saleh Reza M. Salek Filipe Santana da Silva
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 Biomedicine 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
Dispositions, capacities, abilities. Towards a classification of the powers of living beings
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.
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.
COFFEE 15:50 – 16:40 J. Hübner 16:40 – 17:00
COFFEE starting 19:30
DINNER FRIDAY
Sep 30, 2016 09:40 – 10:00
COFFEE 10:50 – 11:10
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 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 10:00 – 10:50 R. Stevens
KEYNOTE: The pragmatics and formality of authoring ontologies 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 KEYNOTE: Dispositions, capacities, abilities. Towards a classification of the
powers of living beings 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 13:45 – 15:00
LUNCH
Open discussion & OBML session (within categories in alphabetic order according to last names of first authors)
Deep Learning meets Semantic Web: A feasibility study with the Cardiovascular Disease 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
Aisha Blfgeh, Jennifer D. Warrender, Catharien M. U. Hilkens, Phillip Lord Challenges and opportunities for system biology standards and tools in medical research 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)
Stefan Kropf, Alexandr Uciteli, Peter Krücken, Kerstin Denecke, Heinrich Herre Towards standardized evidence descriptors for metabolite annotations
Daniel Schober, Reza M. Salek, Steffen Neumann A Whiteheadian approach to data and knowledge
Sebastian Siemoleit, Heinrich Herre Risk Identification Ontology (RIO): An ontology for specification and identification of perioperative risks
A modelling pattern for multi-track dispositions for life-science ontologies
Adrien Barton, Ludger Jansen FAIRDOM approach for semantic interoperability of systems biology data and models 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
Shao Fen Liang, Jean-François Ethier, Talya Porat, Archana Tapuria, Brendan C. Delaney, Vasa Curcin Qualitative assessment of annotations using SNOMED CT
José Antonio Miñarro-Giménez, Catalina Martínez-Costa, Stefan Schulz Extracting process graphs from medical text data
Andreas Niekler Ontological interpretation of biomedical database annotations
Filipe Santana da Silva, Ludger Jansen, Fred Freitas, Stefan Schulz
Nr. of
Pages A B C D E F G H I J K L M 6 6 6 5 5 6 7 2 2 2 2 2 2