Service

2014

• Röhl J, Jansen L: "Why functions are not special dispositions: An improved classification of realizables for top-level ontologies", Journal of Biomedical Semantics, forthcoming.

2013

• Boeker M, Vach W, Motschall E: "Google Scholar as replacement for systematic literature searches: good relative recall and precision are not enough". BMC Med Res Methodol, 2013; 13 (1) (online): 131-131. 

• Boeker M, Vach W, Motschall E: "Time-dependent migration of citations through PubMed and OvidSP subsets: a study on a series of simultaneous PubMed and OvidSP searches" [Poster 791]. Studies in Health Technology and Informatics, 2013; 192: 1196 (MEDINFO 2013 Copenhagen), Lehmann CU, Ammenwerth E, Nøhr C (eds.). 

• Braun M, Metzger J, Boeker M, Vach W, Gramsch K, Kirschner J: "Entwicklung einer mobilen Applikation zur Information von Patienten, Angehörigen und Personen aus Gesundheitsberufen über die Muskeldystrophie Duchenne", GMS German Medical Science, 2013 (online) (58. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS), Lübeck 1.-5.9.2013), ed. by Handels H, Ingenerf J.

• Schulz S, Bernhardt-Melischnig J, Kreuzthaler M, Daumke P, Boeker M: "Machine vs. Human Translation of SNOMED CT Terms", Stud Health Technol Inform, 2013; 192: 581-584 (MEDINFO 2013 Copenhagen). 

• Seltmann S, Stachelscheid H, Damaschun A, Jansen L, Lekschas F, Fontaine J-F, Nguyen-Dobinsky T N, Leser U, Kurtz A, "CELDA – an ontology for the comprehensive representation of cells in complex systems", BMC Bioinformatics 14:228 (2013), DOI: 0.1186/10.1186/1471-2105-14-228.

• Boeker M, Jansen L, Grewe N, Röhl J, Schober D, Seddig-Raufie D, Schulz S, "Effects of Guideline-Based Training on the Quality of Formal Ontologies: A Randomized Controlled Trial", in: PLoS ONE (7 May 2013).

• Schulz S, Jansen L, "Formal ontologies in biomedical knowledge representation",in: Yearbook of Medical Informatics 8 (2013) 132-146.

• Kless D, Jansen L, "How fit is OWL to represent realist ontologies? The semantics of representational units in realist ontologies and the Web Ontology Language", in: M. Horbach (Hg.), Informatik 2013. Informatik angepasst an Mensch, Organisation und Umwelt, Bonn: Gesellschaft für Informatik,1851-1865.

• Boeker M, Grewe N, Röhl J, Schober D, Schulz S, Seddig-Raufie D, Jansen L, "Measuring the Effect of a Guideline-based Training on Ontology Design with a Competency Questions based Evaluation Approach", in: M. Horbach (ed.), Informatik 2013. Informatik angepasst an Mensch, Organisation und Umwelt, Bonn: Gesellschaft für Informatik, 1783-1795.

• Fuellen G, Jansen L, Leser U, Kurtz A, "Using ontologies to study cell transitions", in: Journal of Biomedical Semantics 4:25 (8 October 2013), DOI: 10.1186/2041-1480-4-25.

• Georg Fuellen, Melanie Boerries, Hauke Busch, Aubrey D.N.J. de Grey, Udo Hahn, Thomas Hiller, Andreas Hoeflich, Ludger Jansen, Georges E. Janssens, Christoph Kaleta, Anne C. Meinema, Sascha Schäuble, Paul N. Schofield, Barry Smith, Jürgen Sühnel, Julio Vera, Wolfgang Wagner, Eva C. Wönne, Daniel Wuttke, Andreas Simm, "In-Silico-Approaches and the Role of Ontologies in Aging Research", in: Rejuvenation Journal 16:6 (December 2013), 540-546, DOI: 10.1089/rej.2013.1517.

• Johannes Röhl: "Ontological categories for fields and waves", in Horbach, M. (ed.): INFORMATIK 2013. Informatik angepasst an Organisation, Mensch und Umwelt. 16.-20. September 2013 Koblenz. Gesellschaft für Informatik, Bonn 2013, 1866-1874.

• Johannes Röhl: "Dispositions, Causation and Mathematical Physics", in Hoeltje, M.; Spitzley, Th.; Spohn, W. (eds.): Was dürfen wir glauben? Was sollen wir tun? Sektionsbeiträge des achten internationalen Kongresses der Gesellschaft für Analytische Philosophie, Universität Duisburg-Essen (DuEPublico) 2013, urn:nbn:de:hbz:464-20130612-081113-3, 162-171.

2012

• Niels Grewe, Daniel Schober, Martin Boeker: "Comparing closely related, semantically rich ontologies: The GoodOD Similarity Evaluator", Proceedings of the 4th Workshop of Ontologies in Biomedicine and Life Sciences (OBML 2012), Dresden, 27.-28.09. 2012) www.onto-med.de/obml/ws2012/obml2012report.pdf

• Ludger Jansen, Georg Fuellen, Ulf Leser, Andreas Kurtz: "Using Ontologies to Study Cell Transitions", OBML 2012, http://www.onto-med.de/obml/ws2012/obml2012report.pdf#page=27

• Daniel Kless, Ludger Jansen, Jutta Lindenthal, Jens Wiebensohn: "A method for re-engineering a thesaurus into an ontology" Formal Ontology in Information Systems. Proceedings of the Seventh International Conference (FOIS 2012), ed. by Maureen Donnelly, Giancarlo Guizzardi (= Frontiers in Artificial Intelligence and Applications 239) Amsterdam: IOS 2012: 133-146.

• Johannes Röhl, Ludger Jansen: "Functions, roles and dispositions revisited. A new classification of realizables", OBML 2012, http://www.onto-med.de/obml/ws2012/obml2012report.pdf#page=47

• Daniel Schober, Niels Grewe, Johannes Röhl, Martin Boeker:  "ZooAnimals.owl: A Didactically Sound Example‐Ontology for Teaching Description Logics in OWL 2", OBML 2012, http://www.onto-med.de/obml/ws2012/obml2012report.pdf#page=73

• Daniel Schober, Vojtech Svatek, Martin Boeker: "Checking Class Labels against Naming Conventions: First experiences with the OntoCheck Protégé plugin", Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), KR-MED Series, Graz, Austria, July 21-25, 2012, ed. by Ronald Cornet and Robert Stevens. http://ceur-ws.org/Vol-897/

• Martin Boeker, Daniel Schober, Djamila Raufie, Niels Grewe, Johannes Röhl, Ludger Jansen, Stefan Schulz: "Teaching Good Biomedical Ontology Design", Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), KR-MED Series, Graz, Austria, July 21-25, 2012, ed. by Ronald Cornet and Robert Stevens.

• Daniel Schober, Ilinca Tudose, Vojtech Svatek, Martin Boeker:“OntoCheck: Verifying Ontology Naming Conventions and Metadata Completeness in Protégé 4", Journal of Biomedical Semantics 2012, 3(Suppl 2):S2 (21 September 2012),http://www.jbiomedsem.com/content/3/S2/S4/abstract 

• Djamila Seddig-Raufie, Stefan Schulz, Daniel Schober, Ludger Jansen, Martin Boeker, Niels Grewe:"Proposed Actions are no Actions: Re-Modeling an Ontology Design Pattern with a Realist Top-Level Ontology",Journal of Biomedical Semantics 2012, 3(Suppl 2):S2 (21 September 2012), http://www.jbiomedsem.com/content/3/S2/S2/

• Niels Grewe: "Continuation-like semantics for modeling structural process anomalies", Journal of Biomedical Semantics 2012, (Suppl 2):S8 (21 September 2012)

• Johannes Röhl:"Mechanisms in biomedical ontology",  Journal of Biomedical Semantics 2012, 3(Suppl 2):S9 (21 September 2012)

• Johannes Röhl: "Was ist ein Mechanismus? Ontologische Anmerkungen zu einem zentralen Begriff der Philosophie der Biologie", Crossing Borders - Grenzen (über)denken - Thinking (across) Boundaries. Beiträge zum 9. Kongress der Österreichischen Gesellschaft für Philosophie, 725-735. http://phaidra.univie.ac.at/o:128384

2011

• Ludger Jansen, Stefan Schulz: "Grains, components and mixtures in biomedical ontologies", Journal of Biomedical Semantics 2011, 2 (Suppl 4):S2 (9 August 2011) http://www.jbiomedsem.com/content/2/S4/S2
• Johannes Röhl, Ludger Jansen: "Representing dispositions", Journal of Biomedical Semantics/ 2011, 2(Suppl 4):S4 (9 August 2011) <http://www.jbiomedsem.com/content/2/S4/S4>
• Niels Grewe. Relating Processes and Events for Granularity-neutral Modeling. In:Proceedings of the 14th Annual Bio-Ontologies Meeting, pp. 62?67, 2011. URL: http://bio-ontologies.knowledgeblog.org/174
• Janna Hastings, Ludger Jansen, Christoph Steinbeck, Stefan Schulz:"Modelling Threshold Phenomena in OWL: Metabolite Concentrations as Evidence For Disorders", Proc. of 8th International Workshop on OWL: Experiences and Directions (OWLED2011), San Francisco, USA, June 5-6, 2011, CEUR-WS.org, ISSN 1613-0073, online CEUR-WS.org/Vol-796/xxx.pdf
  
• Martin Boeker, Janna Hastings, Daniel Schober, Stefan Schulz: "A T-Box Generator for Testing Scalability of OWL Mereotopological Patterns", OWLED 2011
  
  
• Johannes Röhl: "The ontology of biological mechanisms", Proceedings of the 3rd Workshop of Ontologies in Biomedicine and Life Sciences (OBML), Berlin, 06.-07.10. 2011), http://www.onto-med.de/obml/ws2011/obml2011report.pdf#page=25
• Niels Grewe: "Continuation-like Semantics for Modeling Structural Event Anomalies", OBML 2011, http://www.onto-med.de/obml/ws2011/obml2011report.pdf#page=35
• Ludger Jansen, Stefan Schulz: "The Ten Commandments of Ontological Engineering", Proceedings of the 3rd Workshop of Ontologies in Biomedicine and Life Sciences (OBML), Berlin, 06.-07.10. 2011), www.onto-med.de/obml/ws2011/obml2011report.pdf
• Djamila Raufie, Stefan Schulz, Daniel Schober, Ludger Jansen, Martin Boeker: "Redesigning an Ontology Design Pattern for Realist Ontologies", OBML 2011, www.onto-med.de/obml/ws2011/obml2011report.pdf
• Daniel Schober, Ilinca Tudose, Vojtech Svatek, Martin Boeker: "OntoCheck: Verifying ontology Naming Conventions in Protégé 4", OBML 2011, www.onto-med.de/obml/ws2011/obml2011report.pdf

2010

• Janna Hastings, Christoph Steinbeck, Colin Batchelor, Stefan Schulz: "What are chemical structures and their relations?" Frontiers in Artificial Intelligence and Applications, 2010; 209: 257-270 (Sixth International Conference (FOIS 2010), Toronto), Galton A, Mizoguchi R (Hrsg): http://dx.doi.org/10.3233/978-1-60750-535-8-257
• Janna Hastings, Christoph Steinbeck, Ludger Jansen, Stefan Schulz: "Substance concentrations as conditions for the realization of dispositions", 2010 (The 13th Annual Bio-Ontologies Meeting, Boston MA): http://linkshrink.de/17716/
• Stefan Schulz, Daniel Schober, Christel Daniel, Marie-Christine Jaulent: "Bridging the semantics gap between terminologies, ontologies, and information models", Stud Health Technol Inform, 2010; 160 (Pt 2): 1000-1004: http://booksonline.iospress.nl/Content/View.aspx?piid=17524
• Stefan Schulz, Daniel Schober, Ilinca Tudose, Holger Stenzhorn: "The Pitfalls of Thesaurus Ontologization ? the Case of the NCI Thesaurus", 2010, AMIA Annu Symp Proc, 2010: 727-731 (AMIA 2010 Annual Symposium, Washington D.C. USA, November 2010): http://proceedings.amia.org/127gtf/1
• Stefan Schulz, Djamila Raufie, Martin Boeker: "Scalable representations of diseases in biomedical ontologies", 2010 (The 13th Annual Bio-Ontologies Meeting, Boston MA): http://linkshrink.de/17716/
• Niels Grewe: "A generic reification strategy for n-ary relations in DL", (2nd Workshop of Ontologies in Biomedicine and Life Sciences (OBML), Mannheim, 9.-10.9. 2010): http://www.bioontology.org/node/628
• Ludger Jansen, StefanSchulz: "Grains, Components and Mixtures in Biomedical Ontologies", (2nd Workshop of Ontologies in Biomedicine and Life Sciences (OBML), Mannheim, 9.-10.9. 2010): http://www.bioontology.org/node/628
• Johannes Röhl, Ludger Jansen: "Representing Dispositions", (2nd Workshop of Ontologies in Biomedicine and Life Sciences (OBML), Mannheim, 9.-10.9. 2010): http://www.bioontology.org/node/628
• Daniel Schober, Martin Boeker: "Ontology Simplification: new buzzword or real need?": (2nd Workshop of Ontologies in Biomedicine and Life Sciences (OBML), Mannheim, 9.-10.9. 2010): http://www.bioontology.org/node/628
• Stefan Schulz, Daniel Schober, Djamila Raufie, Martin Boeker: "Pre- and Postcoordination in Biomedical Ontologies": (2nd Workshop of Ontologies in Biomedicine and Life Sciences (OBML), Mannheim, 9.-10.9. 2010): http://www.bioontology.org/node/628
• Stefan Schulz, Daniel Schober, Djamila Raufie, Martin Boeker: "Pre- and Postcoordination in Biomedical Ontologies", European Conference on Artificial Intelligence (ECAI 2010), Lisbon, Portugal, August 16-20, 2010. http://www.onto-med.de/obml/ws2010/obml2010report.pdf#page=65
• Ludger Jansen: "What is a Formal Ontology? Some Meta-Ontological Remarks", in: Klaus Mainzer (Hg.), ECAP10. VIII European Conference on Computing and Philosophy, München: Hut 2010, 256-260.
• Ludger Jansen, Stefan Schulz: ?GoodOD: Ontology, empirically tested, 2010-2012? (mit Stefan Schulz), in: The Reasoner 4/4 (April 2010) 58-59.
• Daniel Schober et al. :" Survey-based naming conventions for use in OBO foundry ontology development", BMC Bioinformatics 2009, 10:125 http://www.biomedcentral.com/1471-2105/10/125

Complete personal lists of publications are available for Ludger Jansen and Stefan Schulz.

Textbook for Biomedical Ontology

Ludger Jansen und Barry Smith (Hrsg.), Biomedizinische Ontologie. Wissen strukturieren für den Informatik-Einsatz, Zürich: vdf 2008, 252 Seiten, zahlreiche Abbildungen, ISBN 978-3-7281-3183-6

• Look inside" (amazon.de)