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Referred Papers in Journals and Proceedings

  • A. Uciteli, C. Beger, S. Kropf and H. Herre 2019. Spreadsheet Model Generator (SMOG): A Lightweight Tool for Object-Spreadsheet Mapping Stud Health Technol Inform. Vol. 267, pp. 110-117. [BibTeX] [http://ebooks.iospress.nl/volumearticle/52754] BibTeX:
    @inproceedings{DBLP:conf/gmds/UciteliBKH19,
      author    = {Alexandr Uciteli and
                   Christoph Beger and
                   Stefan Kropf and
                   Heinrich Herre},
      editor    = {Rainer R{\"{o}}hrig and
                   Harald Binder and
                   Hans{-}Ulrich Prokosch and
                   Ulrich Sax and
                   Irene Schmidtmann and
                   Susanne Stolpe and
                   Antonia Zapf},
      title     = {Spreadsheet Model Generator {(SMOG):} {A} Lightweight Tool for Object-Spreadsheet
                   Mapping},
      booktitle = {German Medical Data Sciences: Shaping Change - Creative Solutions
                   for Innovative Medicine - Proceedings of the 64th Annual Meeting of
                   the German Association of Medical Informatics, Biometry and Epidemiology
                   (gmds e.V.) 2019 in Dortmund, Germany - {GMDS} 2019},
      series    = {Studies in Health Technology and Informatics},
      volume    = {267},
      pages     = {110--117},
      publisher = {{IOS} Press},
      year      = {2019},
      url       = {https://doi.org/10.3233/SHTI190814},
      doi       = {10.3233/SHTI190814},
      timestamp = {Fri, 08 Nov 2019 17:52:19 +0100},
      biburl    = {https://dblp.org/rec/conf/gmds/UciteliBKH19.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • A. Uciteli, C. Beger, T. Kirsten, F.A. Meineke,and H. Herre 2019. Ontological Modelling and Reasoning of Phenotypes Proceedings of the Joint Ontology Workshops (JOWO) 2019, Episode V: The Styrian Autumn of Ontology, Graz, Austria, 2019, CEUR Workshop Proceedings, Vol. 2518, 2019 CEUR Workshop Proceedings. Vol. 2518, [BibTeX] [http://ceur-ws.org/Vol-2518/paper-ODLS11.pdf] BibTeX:
    @inproceedings{DBLP:conf/jowo/UciteliBKMH19,
      author    = {Alexandr Uciteli and
                   Christoph Beger and
                   Toralf Kirsten and
                   Frank A. Meineke and
                   Heinrich Herre},
      editor    = {Adrien Barton and
                   Selja Sepp{\"{a}}l{\"{a}} and
                   Daniele Porello},
      title     = {Ontological Modelling and Reasoning of Phenotypes},
      booktitle = {Proceedings of the Joint Ontology Workshops 2019 Episode {V:} The
                   Styrian Autumn of Ontology, Graz, Austria, September 23-25, 2019},
      series    = {{CEUR} Workshop Proceedings},
      volume    = {2518},
      publisher = {CEUR-WS.org},
      year      = {2019},
      url       = {http://ceur-ws.org/Vol-2518/paper-ODLS11.pdf},
      timestamp = {Wed, 12 Feb 2020 16:44:53 +0100},
      biburl    = {https://dblp.org/rec/conf/jowo/UciteliBKMH19.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • A. Uciteli, S. Kropf, T. Weiland, S. Meese, K. Graef, S. Rohrer, M.O. Schurr, W. Bartussek, C. Goller, P. Blohm, R. Seidel, C. Bayer, M. Kernenbach, K. Pfeiffer, W. Lauer, J.-U. Meyer, M. Witte and H. Herre 2019. Ontology-based specification and generation of search queries for post-market surveillance Journal of Biomedical Semantics Vol. 10, (1) [BibTeX] [https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0203-7] BibTeX:
    @article{DBLP:journals/biomedsem/UciteliKWMGRSBG19,
      author    = {Alexandr Uciteli and
                   Stefan Kropf and
                   Timo Weiland and
                   Stefanie Meese and
                   Klaus Graef and
                   Sabrina Rohrer and
                   Marc O. Schurr and
                   Wolfram Bartussek and
                   Christoph Goller and
                   Philipp Blohm and
                   Robin Seidel and
                   Christian Bayer and
                   Manuel Kernenbach and
                   Kathrin Pfeiffer and
                   Wolfgang Lauer and
                   J{\"{o}}rg{-}Uwe Meyer and
                   Michael Witte and
                   Heinrich Herre},
      title     = {Ontology-based specification and generation of search queries for
                   post-market surveillance},
      journal   = {J. Biomedical Semantics},
      volume    = {10},
      number    = {1},
      pages     = {9:1--9:13},
      year      = {2019},
      url       = {https://doi.org/10.1186/s13326-019-0203-7},
      doi       = {10.1186/s13326-019-0203-7},
      timestamp = {Mon, 29 Jul 2019 15:59:32 +0200},
      biburl    = {https://dblp.org/rec/journals/biomedsem/UciteliKWMGRSBG19.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • F.A. Meineke, S. Stäubert, M. Löbe, A. Uciteli and M. Löffler 2019. Design and Concept of the SMITH Phenotyping Pipeline Stud Health Technol Inform. Vol. 267, pp. 164--172. [BibTeX] [http://ebooks.iospress.nl/publication/52761] BibTeX:
    @inproceedings{DBLP:conf/gmds/MeinekeSLUL19,
      author    = {Frank A. Meineke and
                   Sebastian St{\"{a}}ubert and
                   Matthias L{\"{o}}be and
                   Alexandr Uciteli and
                   Markus L{\"{o}}ffler},
      editor    = {Rainer R{\"{o}}hrig and
                   Harald Binder and
                   Hans{-}Ulrich Prokosch and
                   Ulrich Sax and
                   Irene Schmidtmann and
                   Susanne Stolpe and
                   Antonia Zapf},
      title     = {Design and Concept of the {SMITH} Phenotyping Pipeline},
      booktitle = {German Medical Data Sciences: Shaping Change - Creative Solutions
                   for Innovative Medicine - Proceedings of the 64th Annual Meeting of
                   the German Association of Medical Informatics, Biometry and Epidemiology
                   (gmds e.V.) 2019 in Dortmund, Germany - {GMDS} 2019},
      series    = {Studies in Health Technology and Informatics},
      volume    = {267},
      pages     = {164--172},
      publisher = {{IOS} Press},
      year      = {2019},
      url       = {https://doi.org/10.3233/SHTI190821},
      doi       = {10.3233/SHTI190821},
      timestamp = {Fri, 08 Nov 2019 17:52:19 +0100},
      biburl    = {https://dblp.org/rec/conf/gmds/MeinekeSLUL19.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • Hai Long, Yan Zhu, Lirong Jia, Bo Gao, Jing Liu, Lihong Liu and Heinrich Herre 2019. An ontological framework for the formalization, organization and usage of TCM-Knowledge BMC Medical Informatics and Decision Making Vol. 19-S, (2) pp. 79--89. [BibTeX] [https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-019-0760…] BibTeX:
    @article{DBLP:journals/midm/LongZJGLLH19,
      author    = {Hai Long and
                   Yan Zhu and
                   Lirong Jia and
                   Bo Gao and
                   Jing Liu and
                   Lihong Liu and
                   Heinrich Herre},
      title     = {An ontological framework for the formalization, organization and usage
                   of TCM-Knowledge},
      journal   = {{BMC} Med. Inf. {\&} Decision Making},
      volume    = {19-S},
      number    = {2},
      pages     = {79--89},
      year      = {2019},
      url       = {https://doi.org/10.1186/s12911-019-0760-9},
      doi       = {10.1186/s12911-019-0760-9},
      timestamp = {Sun, 02 Jun 2019 20:53:03 +0200},
      biburl    = {https://dblp.org/rec/journals/midm/LongZJGLLH19.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • Heinrich Herre 2019. Towards a New Foundational Ontology of Properties, Attributives and Data Ontology makes sense In: Ontology Makes Sense - Essays in honor of Nicola Guarino. Frontiers in Artificial Intelligence and Applications. Vol. 316, pp. 194--210. [BibTeX] [http://ebooks.iospress.nl/volume/ontology-makes-sense-essays-in-honor-of-nicola…] BibTeX:
    @inproceedings{DBLP:conf/birthday/Herre19,
      author    = {Heinrich Herre},
      editor    = {Stefano Borgo and
                   Roberta Ferrario and
                   Claudio Masolo and
                   Laure Vieu},
      title     = {Towards a New Foundational Ontology of Properties, Attributives and
                   Data},
      booktitle = {Ontology Makes Sense - Essays in honor of Nicola Guarino},
      series    = {Frontiers in Artificial Intelligence and Applications},
      volume    = {316},
      pages     = {194--210},
      publisher = {{IOS} Press},
      year      = {2019},
      url       = {https://doi.org/10.3233/978-1-61499-955-3-194},
      doi       = {10.3233/978-1-61499-955-3-194},
      timestamp = {Sun, 14 Apr 2019 14:33:54 +0200},
      biburl    = {https://dblp.org/rec/conf/birthday/Herre19.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • P. Burek, N. Scherf and H. Herre 2019. Foundations of the Cell Tracking Ontology Proceedings of the Joint Ontology Workshops (JOWO) 2019, Episode V: The Styrian Autumn of Ontology, Graz, Austria, 2019, CEUR Workshop Proceedings, Vol. 2518, 2019 CEUR Workshop Proceedings. Vol. 2518, [BibTeX] [http://ceur-ws.org/Vol-2518/paper-ODLS3.pdf] BibTeX:
    @inproceedings{DBLP:conf/jowo/BurekSH19,
      author    = {Patryk Burek and
                   Nico Scherf and
                   Heinrich Herre},
      editor    = {Adrien Barton and
                   Selja Sepp{\"{a}}l{\"{a}} and
                   Daniele Porello},
      title     = {Foundations of the Cell Tracking Ontology},
      booktitle = {Proceedings of the Joint Ontology Workshops 2019 Episode {V:} The
                   Styrian Autumn of Ontology, Graz, Austria, September 23-25, 2019},
      series    = {{CEUR} Workshop Proceedings},
      volume    = {2518},
      publisher = {CEUR-WS.org},
      year      = {2019},
      url       = {http://ceur-ws.org/Vol-2518/paper-ODLS3.pdf},
      timestamp = {Wed, 12 Feb 2020 16:44:53 +0100},
      biburl    = {https://dblp.org/rec/conf/jowo/BurekSH19.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • Patryk Burek, Nico Scherf and Heinrich Herre 2019. A pattern-based approach to a cell tracking ontology. Procedia Computer Science Procedia Computer Science. Vol. 159, pp. 784--793. [BibTeX] [https://www.sciencedirect.com/science/article/pii/S1877050919314243] BibTeX:
    @inproceedings{DBLP:conf/kes/BurekSH19,
      author    = {Patryk Burek and
                   Nico Scherf and
                   Heinrich Herre},
      editor    = {Imre J. Rudas and
                   J{\'{a}}nos Csirik and
                   Carlos Toro and
                   J{\'{a}}nos Botzheim and
                   Robert J. Howlett and
                   Lakhmi C. Jain},
      title     = {A pattern-based approach to a cell tracking ontology},
      booktitle = {Knowledge-Based and Intelligent Information {\&} Engineering Systems:
                   Proceedings of the 23rd International Conference KES-2019, Budapest,
                   Hungary, 4-6 September 2019},
      series    = {Procedia Computer Science},
      volume    = {159},
      pages     = {784--793},
      publisher = {Elsevier},
      year      = {2019},
      url       = {https://doi.org/10.1016/j.procs.2019.09.237},
      doi       = {10.1016/j.procs.2019.09.237},
      timestamp = {Tue, 05 Nov 2019 10:18:15 +0100},
      biburl    = {https://dblp.org/rec/conf/kes/BurekSH19.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • Patryk Burek, Nico Scherf and Heinrich Herre 2019. Ontology patterns for the representation of quality changes of cells in time Journal of Biomedical Semantics Vol. 10, (1) [BibTeX] [https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-019-0206-4] BibTeX:
    @article{DBLP:journals/biomedsem/BurekSH19,
      author    = {Patryk Burek and
                   Nico Scherf and
                   Heinrich Herre},
      title     = {Ontology patterns for the representation of quality changes of cells
                   in time},
      journal   = {J. Biomedical Semantics},
      volume    = {10},
      number    = {1},
      pages     = {16:1--16:18},
      year      = {2019},
      url       = {https://doi.org/10.1186/s13326-019-0206-4},
      doi       = {10.1186/s13326-019-0206-4},
      timestamp = {Tue, 12 Nov 2019 17:15:16 +0100},
      biburl    = {https://dblp.org/rec/journals/biomedsem/BurekSH19.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • Ralph Schäfermeier, Adrian Paschke and Heinrich Herre. 2019. Ontology Design Patterns for Representing Context in Ontologies Using Aspect Orientation Proceedings of the 10th Workshop on Ontology Design and Patterns (WOP 2019) CEUR Workshop Proceedings. Vol. 2459, pp. 32-46. [BibTeX] [http://ceur-ws.org/Vol-2459/paper3.pdf] BibTeX:
    inproceedings{DBLP:conf/semweb/SchafermeierPH19,
      author    = {Ralph Sch{\"{a}}fermeier and
                   Adrian Paschke and
                   Heinrich Herre},
      editor    = {Krzysztof Janowicz and
                   Adila Alfa Krisnadhi and
                   Mar{\'{\i}}a Poveda Villal{\'{o}}n and
                   Karl Hammar and
                   Cogan Shimizu},
      title     = {Ontology Design Patterns for Representing Context in Ontologies using
                   Aspect Orientation},
      booktitle = {Proceedings of the 10th Workshop on Ontology Design and Patterns {(WOP}
                   2019) co-located with 18th International Semantic Web Conference {(ISWC}
                   2019), Auckland, New Zealand, October 27, 2019},
      series    = {{CEUR} Workshop Proceedings},
      volume    = {2459},
      pages     = {32--46},
      publisher = {CEUR-WS.org},
      year      = {2019},
      url       = {http://ceur-ws.org/Vol-2459/paper3.pdf},
      timestamp = {Wed, 12 Feb 2020 16:44:49 +0100},
      biburl    = {https://dblp.org/rec/conf/semweb/SchafermeierPH19.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • Ringo Baumann, Frank Loebe and Heinrich Herre 2019. Properties Defined on the Basis of Coincidence in GFO-Space Proceedings of the Joint Ontology Workshops (JOWO) 2019, Episode V: The Styrian Autumn of Ontology, Graz, Austria, 2019, CEUR Workshop Proceedings, Vol. 2518, 2019 CEUR Workshop Proceedings. Vol. 2518, [BibTeX] [http://ceur-ws.org/Vol-2518/paper-FOUST3.pdf] BibTeX:
    @inproceedings{DBLP:conf/jowo/BaumannLH19,
      author    = {Ringo Baumann and
                   Frank Loebe and
                   Heinrich Herre},
      editor    = {Adrien Barton and
                   Selja Sepp{\"{a}}l{\"{a}} and
                   Daniele Porello},
      title     = {Properties Defined on the Basis of Coincidence in GFO-Space},
      booktitle = {Proceedings of the Joint Ontology Workshops 2019 Episode {V:} The
                   Styrian Autumn of Ontology, Graz, Austria, September 23-25, 2019},
      series    = {{CEUR} Workshop Proceedings},
      volume    = {2518},
      publisher = {CEUR-WS.org},
      year      = {2019},
      url       = {http://ceur-ws.org/Vol-2518/paper-FOUST3.pdf},
      timestamp = {Wed, 12 Feb 2020 16:44:53 +0100},
      biburl    = {https://dblp.org/rec/conf/jowo/BaumannLH19.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • Sebastian Siemoleit and Heinrich Herre 2019. An Axiomatic Reconstruction of the Basic Categories in Process Philosophy Axiomathes [BibTeX] [https://link.springer.com/article/10.1007/s10516-019-09450-1] BibTeX:
    @article{siemoleit2019axiomatic,
      title={An Axiomatic Reconstruction of the Basic Categories in Process Philosophy},
      author={Siemoleit, Sebastian and Herre, Heinrich},
      journal={Axiomathes},
      pages={1--41},
      year={2019},
      publisher={Springer}
    }
    
    
  • Bartussek, W.; Weiland, T.; Meese, S.; Schurr, M. O.; Leenen, M.; Uciteli, A.; Kropf, S.; Herre, H.; Goller, C.; Blohm, P.; Lauer, W.; and R. Seidel 2018. Ontology-based search for risk-relevant PMS data In: 3rd Biennial South African Biomedical Engineering Conference (SAIBMEC). pp. 1–4. [Abstract] [BibTeX] [Link] Abstract: We report on a small and medium-sized enterprise (SME) research project funded by the German Federal Ministry of Education and Research (Funding: 01IS15056D; project duration: Jan 2016–Dec 2017). The project focused on ontology based post market surveillance for risk analysis of medical devices. As a general result of the project, ontologies turned out to be a well-founded means for multiple purposes as e.g. searching, alerting, or to control crawling processes.
    BibTeX:
    @article{Bartussek2018OntologybasedSF,
      title={Ontology-based search for risk-relevant PMS data},
      author={Wolfram Bartussek and Timo Weiland and Stefanie Meese and Marc O. Schurr and Matthias Leenen and Alexandr Uciteli and Stefan Kropf and Heinrich Herre and Christoph Goller and Philipp Blohm and Wolfgang Lauer and Robin Seidel},
      journal={2018 3rd Biennial South African Biomedical Engineering Conference (SAIBMEC)},
      year={2018},
      pages={1-4}
    }
    
  • Kropf, S.; Uciteli, A.; Schierle, K.; Krücken, P.; Denecke, K.; Herre, H. 2018. Querying archetype-based EHRs by search ontology-based XPath engineering Journal of Biomedical Semantic Vol. 9, (1) pp. 16:1--16:14. [Abstract] [BibTeX] Abstract: Background
    Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of using free text searches, that lead to false positive results, the precision can be increased by constraining the search to certain parts of documents.

    Methods
    A search ontology-based specification of queries on XML documents defines search concepts and relates them to parts in the XML document structure. Such query specification method is practically introduced and evaluated by applying concrete research questions formulated in natural language on a data collection for information retrieval purposes. The search is performed by search ontology-based XPath engineering that reuses ontologies and XML-related W3C standards.

    Results
    The key result is that the specification of research questions can be supported by the usage of search ontology-based XPath engineering. A deeper recognition of entities and a semantic understanding of the content is necessary for a further improvement of precision and recall. Key limitation is that the application of the introduced process requires skills in ontology and software development. In future, the time consuming ontology development could be overcome by implementing a new clinical role: the clinical ontologist.

    Conclusion
    The introduced Search Ontology XML extension connects Search Terms to certain parts in XML documents and enables an ontology-based definition of queries. Search ontology-based XPath engineering can support research question answering by the specification of complex XPath expressions without deep syntax knowledge about XPaths.
    BibTeX:
    @article{DBLP:journals/biomedsem/KropfUSKDH18,
      author    = {Stefan Kropf and
                   Alexandr Uciteli and
                   Katrin Schierle and
                   Peter Kr{\"{u}}cken and
                   Kerstin Denecke and
                   Heinrich Herre},
      title     = {Querying archetype-based EHRs by search ontology-based XPath engineering},
      journal   = {J. Biomedical Semantics},
      volume    = {9},
      number    = {1},
      pages     = {16:1--16:14},
      year      = {2018},
      url       = {https://doi.org/10.1186/s13326-018-0180-2},
      doi       = {10.1186/s13326-018-0180-2},
      timestamp = {Wed, 25 Sep 2019 17:57:49 +0200},
      biburl    = {https://dblp.org/rec/journals/biomedsem/KropfUSKDH18.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • Tahar K, Uciteli A, Röppischer P, Herre H and Siemoleit S. 2018. Ontology-Guided Markerless Navigation and Situational Awareness for Endoscopic Surgery. Studies in Health Technology and Informatics Vol. 253, pp. 83 - 87. [BibTeX] [Link] BibTeX:
    @article{Tahar2018,
    author = {Tahar, Kais and Uciteli, Alexandr and R{\"{o}}ppischer, Philip and Herre, Heinrich},
    doi = {10.3233/978-1-61499-896-9-83},
    file = {:C$\backslash$:/Users/ktahar-org/Documents/pub/online Paper/Tahar{\_}BioPass{\_}GMDS2018.pdf:pdf},
    isbn = {9781614998969},
    keywords = {biomedical ontologies,endoscopic surgery,formal ontology,knowledge representation,situational awareness,surgical navigation},
    title = {{Ontology-Guided Markerless Navigation and Situational Awareness for Endoscopic Surgery}},
    volume = {0},
    year = {2018}
    }
    
    
  • Uciteli, A.; Beger, C.; Rillich, K.; Meineke, F. A.; Loeffler, M.; Herre, H. 2018. Ontology-Based Modelling of Web Content In: Hoppe, T.; Humm, B.; Reibold, A. (ed.) Semantic Applications. pp. 111-123. Springer Verlag. [Abstract] [BibTeX] [Link] Abstract: The realisation of a complex web portal, including the modelling of content, is a challenging process. The contents describe different interconnected entities that form a complex structure. The entities and their relations have to be systematically analysed, and the content has to be specified and integrated into a content management system (CMS). Ontologies provide a suitable solution for modelling and specifying complex entities and their relations. However, the functionality for automated import of ontologies is not available in current content management systems.

    In order to describe the content of a web portal, we developed an ontology. Based on this ontology, we implemented a pipeline that allows the specification of the portal’s content and its import into the CMS Drupal. Our method is generic. It enables the development of web portals with the focus on a suitable representation of structured knowledge (entities, their properties and relations). Furthermore, it makes it possible to represent existing ontologies in such a way that their content can be understood by users without knowledge of ontologies and their semantics.

    Our approach has successfully been applied in building the LHA (Leipzig Health Atlas) portal, which provides access to metadata, data, publications and methods from various research projects at the University of Leipzig.
    BibTeX:
    @incollection{DBLP:books/sp/18/UciteliBRMLH18,
      author    = {Alexandr Uciteli and
                   Christoph Beger and
                   Katja Rillich and
                   Frank A. Meineke and
                   Markus Loeffler and
                   Heinrich Herre},
      editor    = {Thomas Hoppe and
                   Bernhard Humm and
                   Anatol Reibold},
      title     = {Ontology-Based Modelling of Web Content: Example Leipzig Health Atlas},
      booktitle = {Semantic Applications, Methodology, Technology, Corporate Use},
      pages     = {111--123},
      publisher = {Springer},
      year      = {2018},
      url       = {https://doi.org/10.1007/978-3-662-55433-3\_9},
      doi       = {10.1007/978-3-662-55433-3\_9},
      timestamp = {Thu, 05 Mar 2020 08:25:28 +0100},
      biburl    = {https://dblp.org/rec/books/sp/18/UciteliBRMLH18.bib},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
    
  • Uciteli, A.; Siemoleit, S. ;Tahar, K .; Bieck, R.; Herre, H. 2018. Ontology-based Annotation of Endoscopic Images Proceedings of the 17th Annual Meeting of the German Society for Computer- and Robot-Assisted Surgery (CURAC) pp. 108–112. Leipzig: [Abstract] [Link] Abstract: The established optical surgical navigation systems require training and experience for the registration process and the overall optical marker setup. The use of these complex technologies is time-consuming and often errorprone.

    The BIOPASS project develops a novel localization approach for markerless navigation systems based on process and image databases of learned surgical procedures to intra-operatively identify anatomical landmarks and risk structures. In order to recognize anatomical structures visible in the endoscopic images, several classification algorithms were integrated into the system's architecture.

    We present the Annotation Configuration Ontology (ACO) and the software tool SWEConfigGen, which allow the annotation of endoscopic images using ontological concepts. Two external ontologies FMA and VCO were successfully integrated and used for annotating 30 video recordings of ENT procedures. This domain knowledge was utilized to train the system's classifiers developed in the BIOPASS project.
  • Beger, C.; Uciteli, A.; Herre, H. 2017. Light-Weighted Automatic Import of Standardized Ontologies into the Content Management System Drupal In: German Medical Data Sciences: Visions and Bridges. Studies in Health Technology and Informatics. Vol. 243, pp. 170-174. [BibTeX] [Link] BibTeX:
    incollection{beger-c-2017-a,
      author    = {Christoph Beger and
                   Alexandr Uciteli and
                   Heinrich Herre},
      title     = {Light-Weighted Automatic Import of Standardized Ontologies into the
                   Content Management System Drupal},
      booktitle = {German Medical Data Sciences: Visions and Bridges},
      series    = {Studies in Health Technology and Informatics},
      volume    = {243},
      pages     = {170--174},
      year      = {2017},
      doi       = {10.3233/978-1-61499-808-2-170},
      }
    
  • Burek, P.; Loebe, F.; Herre, H. 2017. Towards refactoring the Molecular Function Ontology with a UML profile for function modeling Journal of Biomedical Semantics Vol. 8, (N. 48) [BibTeX] [Link] BibTeX:
    @article{burek-p-2017-a,
      author    = {Patryk Burek and Frank Loebe and Heinrich Herre},
      title     = {Towards refactoring the Molecular Function Ontology
       with a UML profile for function modeling},
      journal   = {Journal of Biomedical Semantics},
      year      = {2017},
      volume    = {8},
      number    = {48},
      doi       = {10.1186/s13326-017-0152-y}
    }
    
  • Herre, H.; Benking, H. 2017. Formal Ontology and Principles and Prospects of Knowledge Organisation: An axiomatic Approach In: Babik, W.; Ohly, H.P.; Weber, K. (ed.) Theorie, Semantik und Organisation von Wissen. pp. 92-106. Ergon Verlag. [BibTeX] BibTeX:
    @inproceedings{herre-h-2017-a,
      author    = {Heinrich Herre and Heiner Benking},
      title     = {Formal Ontology and Principles and Prospects
       of Knowledge Organisation: An axiomatic Approach},
      booktitle = {Theorie, Semantik und Organisation von Wissen},
      editor    = {Wiesław  Babik and Heinz Peter Ohly and Karsten Weber},
      publisher = {Ergon Verlag},
      year      = {2017},
      pages     = {92-106}
    }
    
  • Kaeding, A.; Stucke, S.; Faulbrück-Röhr, S.; Neumuth, T.; Neumann, J.; Herre, H.; Uciteli, A.; Tahar, K.; Specht, M.; Saleh, K.; Portheine, F.; Besting, A.; Bürger, S. 2017. OntoMedRisk – Multiagentensystem für die Risikoüberwachung im Krankenhaus Forum Der Medizin_Dokumentation Und Medizin_Informatik Vol. 4, [BibTeX] BibTeX:
    @article{kaeding-a-2017-a,
      author    = {André Kaeding and Stephan Stucke 
      and Sebastian Faulbrück-Röhr and Thomas Neumuth and Juliane Neumann 
      and Heinrich Herre and Alexandr Uciteli and Kais Tahar and Martin Specht 
      and Kutaiba Saleh and Frank Portheine and Andreas Besting and Sebastian Bürger},
      title     = {OntoMedRisk – Multiagentensystem für die Risikoüberwachung im Krankenhaus},
      journal   = {Forum Der Medizin_Dokumentation Und Medizin_Informatik},
      year      = {2017},
      volume    = {4},
    }
    
  • Long, H.; Herre, H. 2017. Towards an Ontology of Dialectics In: Proceedings of -1th East Asian Confucianism Seminar and the inaugural conference of “The Belt and Road” Confucian Civilization Innovation Alliance. Vol. 2, pp. 535-556. Qufu, China: IEEE. [BibTeX] BibTeX:
    @inproceedings{long-h-2017-b,
      author    = {Hai Long and Heinrich Herre},
      title     = {Towards an Ontology of Dialectics},
      booktitle = {Proceedings of -1th East Asian Confucianism  Seminar 
      and the inaugural conference of 
      “The Belt and Road” Confucian Civilization Innovation Alliance},
      publisher = {IEEE},
      year      = {2017},
      note      = {25 -26 November},
      volume    = {2},
      pages     = {535 - 556},
      address   = {Qufu, China},
    }
    
  • Long, H.; Zhu, Y.; Jia, L.; Wang, J.; Herre, H. 2017. Outline of the Construction and Application of a GFO-based TCM Diagnoses Ontology for Syndrome Differentiation of Psoriasis Vulgaris In: 19th IEEE International Conference on e-Health Networking, Applications and Services. Dalian, China: IEEE. [BibTeX] BibTeX:
    @conference{long-h-2017-a,
      author    = {Hai Long and Yan Zhu and Lirong Jia and Junhui Wang and Heinrich Herre},
      title     = {Outline of the Construction and Application of a GFO-based 
      TCM Diagnoses Ontology for Syndrome Differentiation of Psoriasis Vulgaris},
      booktitle = {19th IEEE International Conference on e-Health Networking,
       Applications and Services},
      publisher = {IEEE},
      year      = {2017},
      isbn      = {978-1-5090-6704-6},
      month     = {Oktober}
      note      = {12 - 15 Oktober},
      address   = {Dalian, China},
    }
    
  • Saleh, K.; Stucke, S.; Uciteli, A.; Faubrück-Röhr, S.; Neumann, J.; Tahar, K.; Ammon, D.; Schmidt, T.; Neumuth, T.; Besting, A.; Portheine, F.; Herre, H.; Kaeding, A.; Specht, M 2017. Using Fast Healthcare Interoperability Resources (FHIR) for the Integration of Risk Minimization Systems in Hospitals 16th World Congress on Medical and Health Informatics (MedInfo2017) – Precision Healthcare in Health Informatics Hangzhou, China: [BibTeX] BibTeX:
    @article{saleh-k-2017-a,
      author    = {Kutaiba Saleh and Stephan Stucke and Alexandr Uciteli
       and Sebastian Faulbrück-Röhr and Juliane Neumann and Kais Tahar 
       and Danny Ammon and Tobias Schmidt and Thomas Neumuth and Andreas Besting
        and Frank Portheine and Heinrich Herre and André Kaeding and Martin Specht},
      title     = {Using Fast Healthcare Interoperability Resources (FHIR) for the 
      Integration of Risk Minimization Systems in Hospitals},
      journal   = {16th World Congress on Medical and Health Informatics (MedInfo2017)
       – Precision Healthcare in Health Informatics},
      year      = {2017},
      address   = {Hangzhou, China},
      note      = {21.-25. August}, 
    }
    
  • Siemoleit, S.; Uciteli, A.; Bieck, R.; Herre, H. 2017. Ontological Modelling of Situational Awareness in Surgical Interventions Proceedings of the Joint Ontology Workshops (JOWO) 2017, Episode 3: The Tyrolean Autumn of Ontology Bozen-Bolzano, Italy: CEUR Workshop Proceedings, Vol. 2050, Aachen, 2018. [BibTeX] BibTeX:
    @article{siemoleit-s-2017-a,
      author    = {Sebastian Siemoleit and Alexandr Uciteli 
      and Richard Bieck and Heinrich Herre},
      title     = {Ontological Modelling of Situational Awareness in Surgical Interventions},
      journal   = {Proceedings of the Joint Ontology Workshops (JOWO) 2017, Episode 3: The Tyrolean Autumn of Ontology},
      year      = {2017},
      address   = {Bolzano, Italy},
      publisher = {CEUR Workshop Proceedings, Vol. 2050, Aachen, 2018},
    }
    
  • Siemoleit, S.; Uciteli, A.; Bieck, R.; Herre, H. 2017. Processual Reasoning over Sequences of Situations in Endoscopic Surgery In: German Medical Data Sciences: Visions and Bridges. Studies in health technology and informatics. Vol. 243, pp. 222-226. [BibTeX] BibTeX:
    @incollection{siemoleit-s-2017-b,
      author    = {Sebastian Siemoleit and Alexandr Uciteli 
      and Richard Bieck and Heinrich Herre},
      title     = {Processual Reasoning over Sequences of Situations in Endoscopic Surgery},
      booktitle = {German Medical Data Sciences: Visions and Bridges},
      series    = {Studies in Health Technology and Informatics},
      pages     = {222--226},
      volume    = {243},
      year      = {2017},
      doi       = {10.3233/978-1-61499-808-2-222},
    }
    
  • Tahar, K.; Uciteli, A; Herre, H. 2017. Evaluation of an Ontology-based System for Risk Minimization in Hospitals In: 62. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS). Oldenburg, Germany: German Medical Science GMS Publishing House, Düsseldorf, 2017: p. DocAbstr. 142 [BibTeX] [Link] BibTeX:
    @conference{tahar-k-2017-a,
      author    = {Khais Tahar and Alexandr Uciteli and Heinrich Herre},
      title     = {Evaluation of an Ontology-based System for 
      Risk Minimization in Hospitals},
      booktitle = {GMDS 2017: 62. Jahrestagung der Deutschen Gesellschaft
       für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS)},
      year      = {2017},
      address   = {Oldenburg, Germany},
      note      = {German Medical Science GMS Publishing House, Düsseldorf, 2017: p. DocAbstr. 142},
      doi       = {10.3205/17gmds111},
    }
    
  • Tahar, K.; Xu, J.; Herre, H. 2017. Expert2OWL: A Methodology for Pattern-Based Ontology Development In: German Medical Data Sciences: Visions and Bridges. Studies in Health Technology and Informatics. Vol. 243, pp. 165-169. [BibTeX] [Link] BibTeX:
    @incollection{tahar-k-2017-b,
      author    = {Khais Tahar and Jie Xu and Heinrich Herre},
      title     = {A Methodology for Pattern-Based Ontology Development},
      series    = {Studies in Health Technology and Informatics},
      booktitle = {German Medical Data Sciences: Visions and Bridges},
      pages     = {165--169},
      year      = {2017},
      url       = {https://www.ncbi.nlm.nih.gov/pubmed/28883193},
      doi       = {10.3233/978-1-61499-808-2-165},
    }
    
  • Uciteli, A.; Neumann, J.; Tahar, K.; Saleh, K.; Stucke, S.; Faulbrück-Röhr, S.; Kaeding, A.; Specht, M. ; Schmidt, T.; Neumuth, T.; Besting, A.; Stegemann, D.; Portheine, F.; Herre, H. 2017. Ontology-based specification, identification and analysis of perioperative risks Journal of Biomedical Semantics. 8 (2017) 36 Vol. 8, (N. 36) [BibTeX] BibTeX:
    @article{uciteli-a-2017-b,
      author    = {Alexandr Uciteli and Juliane Neumann and Kais Tahar 
      and Kutaiba Saleh and Stephan Stucke and Sebastian Faulbrück-Röhr 
      and André Kaeding and Martin Specht and Tobias Schmidt and Thomas Neumuth 
      and Andreas Besting and Dominik Stegemann and Frank Portheine and Heinrich Herre},
      title     = {Ontology-based specification, identification 
      and analysis of perioperative risks},
      journal   = {Journal of Biomedical Semantics},
      volume    = {8},
      number    = {36},
      year      = {2017},
      doi       = {10.1186/s13326-017-0147-8},
    }
    
  • Uciteli, A.; Kropf, S. ; Weiland, T.; Meese, S.; Graef, K.; Rohrer, S.; Schurr, M.O.; Bartussek, W.; Goller, C.; Blohm, P.; Seidel, R.; Bayer, C.; Kernenbach M.; Lauer, W.; Meyer, J.-U.; Witte, M.; Herre, H. 2017. Search Ontology Generator (SONG): Ontology-based specification and generation of search queries Proceedings of the Joint Ontology Workshops (JOWO) 2017, Episode 3: The Tyrolean Autumn of Ontology Bozen-Bolzano, Italy: CEUR Workshop Proceedings, Vol. 2050, Aachen, 2018. [BibTeX] BibTeX:
    @article{uciteli-a-2017-a,
      author    = {Alexandr Uciteli and Stefan Kropf and Timo Weiland 
      and Stefanie Meese and Klaus Graef and Sabrina Rohrer and Marc O. Shurr 
      and Wolfram Bartussek and Christoph Goller and Philipp Blohm and Robin Seidl 
      and Christian Bayer and Manuel Kernenbach and Wolfgang Lauer and Jörg-Uwe Meyer 
      and Michael Witte and Heinrich Herre},
      title     = {Search Ontology Generator (SONG): Ontology-based specification
       and generation of search queries},
      journal   = {Proceedings of the Joint Ontology Workshops 
      (JOWO) 2017, Episode 3: The Tyrolean Autumn of Ontology},
      year      = {2017},
      address   = {Bolzano, Italy},
      publisher = {CEUR Workshop Proceedings, Vol. 2050, Aachen, 2018},
    }
    
  • Baumann, R.; Loebe, F.; Herre, H. 2016. Towards an Ontology of Space for GFO In: Formal Ontology and Information Systems. pp. 53-66. IOS Press. [BibTeX] BibTeX:
    @inproceedings{baumann-r-2016-a,
      author    = {Baumann, Ringo and Loebe, Frank and Herre, Heinrich},
      title     = {Towards an Ontology of Space for GFO},
      booktitle = {Formal Ontology and Information Systems},
      publisher = {IOS Press},
      year      = {2016},
      pages     = {53-66},
      isbn      = {978-1-61499-659-0}
    }
    
  • Burek, P.; Loebe, F.; Herre, H. 2016. FueL: Representing function structure and function dependencies with a UML profile for function modeling Vol. 11, (N. 2) pp. 155-203. IOS Press. [BibTeX] BibTeX:
    @article{burek-p-2016-a,
      author    = {Burek, Patryk and Loebe, Frank and Herre, Heinrich},
      title     = {FueL: Representing function structure and function dependencies with a UML profile for function modeling},
      journal   = {Journal of Applied Ontology},
      volume    = {11},
      number    = {2},
      publisher = {IOS Press},
      year      = {2016},
      pages     = {155-203},
      doi       = {10.3233/AO-160167},
    }
    
  • Herre, H. 2016. GFO-Data - Towards an ontological Foundation of integrated Data Semantics Festschrift zum 80. Geburtstag von Klaus Fuchs-Kittowski In: Lang, P. (ed.) Informatik und Gesellschaft. Internationaler Verlag der Wissenschaften. [BibTeX] [PDF] BibTeX:
    @article{herre-h-2016-a,
      author    = {Herre, Heinrich},
      title     = {GFO-Data: Towards an Ontological Foundation of an Integrated Data Semantics},
      booktitle = {Informatik und Gesellschaft},
      journal   = {Festschrift zum 80. Geburtstag von Klaus Fuchs-Kittowski},
      editor    = {Lang, Peter},
      publisher = {Internationaler Verlag der Wissenschaften},
      year      = {2016}
    }
    
  • Kaeding, A.; Stucke, S.; Faulbrück-Röhr, S.; Neumuth, T.; Neumann, J.; Herre, H.; Uciteli, A.; Tahar, K.; Specht, M.; Saleh, K.; Portheine, F.; Besting, A. 2016. OntoMedRisk – Ontologiebasierte Softwarelösung zur perioperativen Risikominimierung e-Health 2017: Informations- und Kommunikationstechnologien im Gesundheitswesen Duesberg, F (ed.) Solingen, Germany: Medical Future Verlag. [BibTeX] BibTeX:
    @inbook{kaeding-a-2016-a,
      author    = {André Kaeding and Stephan Stucke 
      and Sebastian Faulbrück-Röhr and Thomas Neumuth and Juliane Neumann 
      and Heinrich Herre and Alexandr Uciteli and Kais Tahar and Martin Specht 
      and Kutaiba Saleh and Frank Portheine and Andreas Besting},
      title     = {OntoMedRisk – Ontologiebasierte Softwarelösung
       zur perioperativen Risikominimierung},
      booktitle = {e-Health 2017: Informations- und 
      Kommunikationstechnologien im Gesundheitswesen},
      editor    = {Frank Duesberg},
      publisher = {Medical Future Verlag},
      year      = {2016},
      editor    = {Frank Duesberg},
      address   = {Solingen, Germany},
    }
    
  • Kropf, S.; Denecke, K.; Krücken, P.; Uciteli, A.; Herre, H. 2016. Querying standardized EHRs by a Search Ontology XML extension (SOX) In: Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences (ODLS), Organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML). Halle (Saale), Germany: CEUR Workshop Proceedings, Vol. 1692, Aachen, 2016. [BibTeX] BibTeX:
    @inproceedings{kropf-s-2016-a,
      author    = {Stefan Kropf and Kerstin Denecke and Peter Krücken and Alexandr Uciteli and Heinrich Herre},
      title     = {Querying standardized EHRs by a Search Ontology XML extension (SOX)},
      booktitle = {Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences (ODLS), Organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML)},
      publisher = {CEUR Workshop Proceedings, Vol. 1692, Aachen, 2016},
      year      = {2016},
      address   = {Halle(Saale), Germany},
    }
    
  • Siemoleit, S.; Herre, H. 2016. A Whiteheadian approach to data and knowledge In: Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences (ODLS), Organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML). Halle (Saale), Germany: CEUR Workshop Proceedings, Vol. 1692, Aachen, 2016. [BibTeX] BibTeX:
    @inproceedings{siemoleit-s-2016-a,
      author    = {Sebastian Siemoleit and Heinrich Herre},
      title     = {A Whiteheadian approach to data and knowledge},
      booktitle = {Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences (ODLS), Organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML)},
      publisher = {CEUR Workshop Proceedings, Vol. 1692, Aachen, 2016},
      year      = {2016},
      address   = {Halle(Saale), Germany},
    }
    
  • Uciteli, A.; Neumann, J.; Tahar, K.; Saleh, K.; Stucke, S.; Faulbrück-Röhr, S.; Kaeding, A.; Specht, M. ; Schmidt, T.; Neumuth, T.; Besting, A.; Stegemann, D.; Portheine, F.; Herre, H. 2016. Risk Identification Ontology (RIO): An ontology for specification and identification of perioperative risks Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences (ODLS), Organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML) Halle (Saale), Germany: CEUR Workshop Proceedings, Vol. 1692, Aachen, 2016. [BibTeX] BibTeX:
    @article{uciteli-a-2016-a,
      author    = {Alexandr Uciteli and Juliane Neumann and Kais Tahar 
      and Kutaiba Saleh and Stephan Stucke and Sebastian Faulbrück-Röhr 
      and André Kaeding and Martin Specht and Tobias Schmidt and Thomas Neumuth 
      and Andreas Besting and Dominik Stegemann and Frank Portheine and Heinrich Herre},
      title     = {Risk Identification Ontology (RIO): 
      An ontology for specification
       and identification of perioperative risks},
      journal   = {Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences (ODLS), Organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML)},
      year      = {2016},
      address   = {Halle (Saale), Germany},
      pulbisher = {CEUR Workshop Proceedings, Vol. 1692, Aachen, 2016},
    }
    
  • Burek, P.; Loebe, F.; Herre, H. 2015. A UML Profile for Functional Modeling applied to the molecular Function Ontology Proceedings ICBO pp. 12-16. [BibTeX] BibTeX:
    @inproceedings{burek-p-2015-a,
      author    = {P. Burek and F. Loebe and H. Herre},
      title     = {A UML Profile for Functional Modeling applied to the molecular Function Ontology},
      booktitle = {ICBO},
      year      = {2015},
      pages     = {12-16}
    }
    
  • Herre H.; Uciteli, A. 2015. Ontologien für klinische Studien - wie sich Top-Level-Ontologien und Domänen-Ontologien ergänzen Corporate Semantic Web In: Ege, B.; Humm, B.; Reibold, A. (ed.) Wie semantische Methoden in Unternehmen Nutzen stiften. pp. 307-318. Springer. [BibTeX] BibTeX:
    @incollection{herre-h-2015-a,
      author    = {Alexandr Uciteli and Heinrich Herre},
      title     = {Ontologien für klinische Studien: wie sich Top-Level-Ontologien und Domänen-Ontologien ergänzen},
      booktitle = {Wie semantische Methoden in Unternehmen Nutzen stiften},
      journal   = {Corporate Semantic Web},
      editor    = {B. Ege and B. Humm and A. Reibold},
      publisher = {Springer},
      year      = {2015},
      pages     = {307-318},
      isbn      = {978-3-642-54885-7}
    }
    
  • Herre, H. 2015. Formal Ontology - A new Discipline between Philosophy, Formal Logic and Artificial Intelligence Abhandlungen der Leibniz-Sozietät der Wissenschaften In: Fuchs-Kittowski, K.; Zimmermann, R.E. (ed.) Kybernetik, Logik, Semiotik, philosophische Sichtweisen. Vol. 40, pp. 375-389. trafo Wissenschaftsverlag. [BibTeX] [PDF] BibTeX:
    @incollection{herre-h-2015-b,
      author    = {Heinrich Herre},
      title     = {Formal Ontology - A new Discipline between Philosophy, Formal Logic and Artificial Intelligence},
      booktitle = {Kybernetik, Logik, Semiotik, philosophische Sichtweisen},
      journal   = {Abhandlungen der Leibniz-Sozietät der Wissenschaften},
      editor    = {K. Fuchs-Kittowski and R.E. Zimmermann},
      publisher = {trafo Wissenschaftsverlag},
      volume    = {40},
      year      = {2015},
      pages     = {375-389},
      isbn      = {978-3-86464-095-7}
    }
    
  • Herre, H. 2015. Persistence, Change, and the Integration of Objects and Processes in the Framework of the General Formal Ontology Essays in Process-Relational Ontology In: Petrov, V.; Scarfe, A.C. (ed.) Dynamic Being. pp. 337-354. Cambridge Scolar Publishing. [BibTeX] [PDF] BibTeX:
    @incollection{herre-h-2015-c,
      author    = {Heinrich Herre},
      title     = {Persistence, Change, and the Integration of Objects and Processes in the Framework of the General Formal Ontology},
      booktitle = {Dynamic Being},
      journal   = {Essays in Process-Relational Ontology},
      editor    = {Vesselin Petrov and Adam C. Scarfe},
      publisher = {Cambridge Scolar Publishing},
      year      = {2015},
      pages     = {337-354},
      isbn      = {978-1-4438-7695-7}
    }
    
  • Uciteli, A.; Herre H. 2015. OntoStudyEdit - A new Approach for ontology-based Representation and Management of Metadata in clinical and epidemiological Research Journal of Biomedical Semantics [BibTeX] [PDF] BibTeX:
    @article{uciteli-a-2015-a,
      author    = {Alexandr Uciteli and Heinrich Herre},
      title     = {OntoStudyEdit: A new Approach for ontology-based Representation and Management of Metadata in clinical and epidemiological Research},
      journal   = {Journal of Biomedical Semantics},
      year      = {2015},
      doi       = {10.1186-015-0042-0}
    }
    
  • Baumann R.; Loebe F.; Herre H. 2014. Axiomatic Theories of the Ontology of Time in GFO Applied Ontology Vol. 9, pp. 171-201. [BibTeX] [PDF] BibTeX:
    @article{baumann-r-2014-a,
      author    = {R. Baumann and F. Loebe and H. Herre},
      title     = {Axiomatic Theories of the Ontology of Time in GFO},
      journal   = {Applied Ontology},
      volume    = {9},
      year      = {2014},
      pages     = {171-201}
    }
    
  • Uciteli, A.; Herre H. et al. 2014. Semantic Search based on Search Ontology and Information Extraction Lecture Notes in Informatics Vol. 232, pp. 667-672. [BibTeX] BibTeX:
    @article{uciteli-a-2014-a,
      author    = {Alexandr Uciteli and Heinrich Herre and et al.},
      title     = {Semantic Search based on Search Ontology and Information Extraction},
      booktitle = {GI-Tagung},
      journal   = {Lecture Notes in Informatics},
      volume    = {40},
      year      = {2014},
      pages     = {667-672},
      isbn      = {978-3-88579-626-8}
    }
    
  • Burek, P.; Herre, H. 2013. A unifying Framework for the Representation, Realization and Ascription of Functions for material Entities In: Lecture Notes in Informatics (GI-Edition). pp. 1805-1820. Proceedings GI 2013. [BibTeX] BibTeX:
    @inproceedings{herre-h-2013-c,
      author    = {Patryk Burek and Heinrich Herre},
      title     = {A unifying Framework for the Representation, Realization and Ascription of Functions for material Entities},
      booktitle = {GI-Jahrestagung},
      year      = {2013},
      pages     = {1805-1820},
      crossref  = {DBLP:conf/gi/2013},
      bibsource = {DBLP, http://dblp.uni-trier.de}
    }
    
    @proceedings{DBLP:conf/gi/2013,
      editor    = {Matthias Horbach},
      title     = {Informatik 2013, 43. Jahrestagung der Gesellschaft f{\"u}r
                   Informatik e.V. (GI), Informatik angepasst an Mensch, Organisation
                   und Umwelt, 16.-20. September 2013, Koblenz},
      booktitle = {GI-Jahrestagung},
      publisher = {GI},
      series    = {LNI},
      volume    = {220},
      year      = {2013},
      isbn      = {978-3-88579-614-5},
      bibsource = {DBLP, http://dblp.uni-trier.de}
    }
    
  • Herre, H. 2013. Formal Ontology and the Foundation of Knowledge Organization Knowledge Organization Vol. 40, (5) pp. 332-339. [BibTeX] BibTeX:
    @article{herre-h-2013-d,
      author    = {Heinrich Herre},
      title     = {Formal Ontology and the Foundation of Knowledge Organization},
      journal   = {Knowledge Organization},
      volume    = {40/5},
      year      = {2013},
      pages     = {332-339}
    }
    
  • Herre, H. 2013. Persistence, Change, and the Integration of Objects and Processes in the Framework of the General Formal Ontology CoRR Vol. abs/1311.1632, [BibTeX] BibTeX:
    @article{DBLP:journals/corr/Herre13,
      author    = {Heinrich Herre},
      title     = {Persistence, Change, and the Integration of Objects and
                   Processes in the Framework of the General Formal Ontology},
      journal   = {CoRR},
      volume    = {abs/1311.1632},
      year      = {2013},
      ee        = {http://arxiv.org/abs/1311.1632},
      bibsource = {DBLP, http://dblp.uni-trier.de}
    }
    
  • Scherf, N.; Kunze, M.; Thierbach, K.; Zerjatke, T.; Burek, P.; Herre, H.; Glauche, I.; Roeder, I. 2013. Assisting the Machine Paradigms for Human-Machine Interaction in Single Cell Tracking In: Meinzer, H.; Deserno, T.M.; Handels, H.; Tolxdorff, T. (ed.) Bildverarbeitung für die Medizin. Informatik aktuell. Springer Berlin Heidelberg. [BibTeX] [PDF] BibTeX:
    @incollection{
      year={2013},
      isbn={978-3-642-36479-2},
      booktitle={Bildverarbeitung für die Medizin 2013},
      series={Informatik aktuell},
      editor={Meinzer, Hans-Peter and Deserno, Thomas Martin and Handels, Heinz and Tolxdorff, Thomas},
      doi={10.1007/978-3-642-36480-8_22},
      title={Assisting the Machine Paradigms for Human-Machine Interaction in Single Cell Tracking},
      url={http://dx.doi.org/10.1007/978-3-642-36480-8_22},
      publisher={Springer Berlin Heidelberg},
      author={Scherf, Nico and Kunze, Michael and Thierbach, Konstantin and Zerjatke, Thomas and Burek, Patryk and Herre, Heinrich and Glauche, Ingmar and Roeder, Ingo},
      pages={116-121},
      language={German}
    }
    
  • Baumann, R., Loebe, F., Herre, H. 2012. Ontology of Time in GFO Proceedings of the 7th International Conference on Formal Ontology in Information Systems, FOIS 2012, Graz, Austria. [BibTeX] [PDF] BibTeX:
    @inproceedings{herre-h-2012-a,
      author    = {Ringo Baumann and
                   Frank Loebe and
                   Heinrich Herre},
      title     = {Ontology of Time in GFO},
      booktitle = {FOIS},
      year      = {2012},
      pages     = {293-306},
      ee        = {http://dx.doi.org/10.3233/978-1-61499-084-0-293},
      crossref  = {DBLP:conf/fois/2012},
      bibsource = {DBLP, http://dblp.uni-trier.de}
    }
    @proceedings{DBLP:conf/fois/2012,
      editor    = {Maureen Donnelly and
                   Giancarlo Guizzardi},
      title     = {Formal Ontology in Information Systems - Proceedings of
                   the Seventh International Conference, FOIS 2012, Gray, Austra,
                   July 24-27, 2012},
      booktitle = {FOIS},
      publisher = {IOS Press},
      series    = {Frontiers in Artificial Intelligence and Applications},
      volume    = {239},
      year      = {2012},
      isbn      = {978-1-61499-083-3},
      ee        = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=31168},
      bibsource = {DBLP, http://dblp.uni-trier.de}
    }
    
  • Hoehndorf, R., Harris, M. A., Herre, H., Rustici, G., Gkoutos, G. V. 2012. Semantic Integration of physiology phenotypes with an application to the Cellular Phenotype Ontology Bioinformatics [BibTeX] [PDF] BibTeX:
    @article{Hoehndorf01072012,
      author = {Hoehndorf, Robert and Harris, Midori A. and Herre, Heinrich and Rustici, Gabriella and Gkoutos, Georgios V.},
      title = {Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology},
      volume = {28},
      number = {13},
      pages = {1783-1789},
      year = {2012},
      doi = {10.1093/bioinformatics/bts250},
      URL = {http://bioinformatics.oxfordjournals.org/content/28/13/1783.abstract},
      eprint = {http://bioinformatics.oxfordjournals.org/content/28/13/1783.full.pdf+html},
      journal = {Bioinformatics}
    }
    
  • Loebe, F., Stumpf, F., Hoehndorf, R., Herre, H. 2012. Towards improving phenotype representation in OWL BMC Biomedical Semantics [BibTeX] [PDF] BibTeX:
    @Article{herre-h-2012-c,
      AUTHOR = {Loebe, Frank and Stumpf, Frank and Hoehndorf, Robert and Herre, Heinrich},
      TITLE = {Towards improving phenotype representation in OWL},
      JOURNAL = {Journal of Biomedical Semantics},
      VOLUME = {3},
      YEAR = {2012},
      NUMBER = {Suppl 2},
      PAGES = {S5},
      URL = {http://www.jbiomedsem.com/content/3/S2/S5},
      DOI = {10.1186/2041-1480-3-S2-S5},
      PubMedID = {23046625},
      ISSN = {2041-1480},
    }
    
  • Herre, H., Hoehndorf, R., Kelso, J., Loebe, F. Schulz, S. 2011. OBML- Ontologies in Biomedicine and Life Sciences BMC Biomedical Semantics [BibTeX] [PDF] BibTeX:
    @Article{herre-h-2011-a,
      AUTHOR = {Herre, Heinrich and Hoehndorf, Robert and Kelso, Janet and Loebe, Frank and Schulz, Stefan},
      TITLE = {OBML - Ontologies in Biomedicine and Life Sciences},
      JOURNAL = {Journal of Biomedical Semantics},
      VOLUME = {2},
      YEAR = {2011},
      NUMBER = {Suppl 4},
      PAGES = {I1},
      URL = {http://www.jbiomedsem.com/content/2/S4/I1},
      DOI = {10.1186/2041-1480-2-S4-I1},
      PubMedID = {21996496},
      ISSN = {2041-1480},
    }
    
  • Neumuth, D., Loebe, F., Herre, H., Neumuth, T. 2011. Modeling surgical processes: A four-level translational approach Artificial Intelligence in Medicine Vol. 51, (3) [BibTeX] [PDF] BibTeX:
    @ARTICLE{neumuth-d-2011-a,
      author = {Neumuth, Dayana and Loebe, Frank and Herre, Heinrich and Neumuth, Thomas},
      title = {Modeling surgical processes: A four-level translational approach},
      journal = {Artificial Intelligence in Medicine},
      year = {2011},
     volume = {51}
    }
    
  • Uciteli, A., Gross, S., Herre, H. 2011. An Ontologically founded Architecture for Information Systems in Clinical and Epidemiological Research BMC Biomedical Semantics [BibTeX] [PDF] BibTeX:
    @ARTICLE{uciteli-a-2011-a,
      author = {Uciteli, Alexandr and Gross, Silvia and Herre, Heinrich},
      title = {An Ontologically founded Architecture for Information Systems in Clinical and Epidemiological Research},
      journal = {BMC Biomedical Semantics},
      year = {2011]}
    }
    
  • Hartung, M., Loebe, F., Herre, H., Rahm, E. 2010. Management of Evolving Semantic Grid Metadata Within a Collaborative Platform Information Sciences - Special Issue on Intelligent Distributed Information Systems Vol. 180, (10) pp. 1837-1849. Amsterdam: Elsevier. [BibTeX] BibTeX:
    @ARTICLE{hartung-m-2010-a,
      author = {Hartung, Michael and Loebe, Frank and Herre, Heinrich and Rahm, Erhard},
      title = {Management of Evolving Semantic Grid Metadata Within a Collaborative Platform},
      journal = {Information Sciences – Special Issue on "Intelligent Distributed Information Systems"},
      year = {2010}
    }
    
  • Herre, H. 2010. General Formal Ontology (GFO) : A Foundational Ontology for Conceptual Modelling In: Poli, R. & Obrst, L. (ed.) Theory and Applications of Ontology. Vol. 2, Berlin: Springer. [BibTeX] BibTeX:
    @INCOLLECTION{herre-h-2009-c,
      author = {Herre, Heinrich},
      title = {General Formal Ontology (GFO) : A Foundational Ontology for Conceptual Modelling},
      booktitle = {Theory and Applications of Ontology},
      publisher = {Springer},
      year = {2010},
      editor = {Poli, Roberto and Obrst, Leo},
      volume = {2},
      address = {Berlin}
    }
    
  • Herre, H. 2010. The Ontology of Medical Terminological Systems - Towards the Next Generation of Biomedical Ontologies In: Poli, R. & Obrst, L. (ed.) Theory and Applications of Ontology. Vol. 2, Berlin: Springer. [BibTeX] BibTeX:
    @INCOLLECTION{herre-h-2009-a,
      author = {Herre, Heinrich},
      title = {The Ontology of Medical Terminological Systems - Towards the Next Generation of Biomedical Ontologies},
      booktitle = {Theory and Applications of Ontology},
      publisher = {Springer},
      year = {2010},
      editor = {Poli, Roberto and Obrst, Leo},
      volume = {2},
      address = {Berlin}
    }
    
  • Herre, H. 2010. The Ontology of Mereological Systems: A Logical Approach In: Poli, R. & Obrst, L. (ed.) Theory and Applications of Ontology. Vol. 1, Berlin: Springer. [BibTeX] BibTeX:
    @INCOLLECTION{herre-h-2009-b,
      author = {Herre, Heinrich},
      title = {The Ontology of Mereological Systems: A Logical Approach,},
      booktitle = {Theory and Applications of Ontology},
      publisher = {Springer},
      year = {2010},
      editor = {Poli, Roberto and Obrst, Leo},
      volume = {1},
      address = {Berlin}
    }
    
  • Hoehndorf, R., Ngonga Ngomo, A.-C., Kelso, J. 2010. Applying the functional abnormality ontology pattern to anatomical functions Journal of Biomedical Semantics Vol. 1, (4) [BibTeX] [PDF] BibTeX:
    @ARTICLE{hoehndorf-r-2010-a,
      author = {Hoehndorf, Robert and Ngonga Ngomo, Axel-Cyrille and Kelso, Janet},
      title = {Applying the functional abnormality ontology pattern to anatomical functions},
      journal = {Journal of Biomedical Semantics},
      year = {2010},
     volume = {1}
    }
    
  • Hoehndorf, R., Oellrich, A., Dumontier, M., Kelso, J., Rebholz-Schuhmann, D., Herre, H. 2010. Relations as patterns: bridging the gap between OBO and the OWL BMC - Bioinformatics Vol. 11, (441) [BibTeX] [PDF] BibTeX:
    @ARTICLE{hoehndorf-r-2010-a,
      author = {Hoehndorf, Robert and Oellrich, Anika and Dumontier, Michel and Kelso, Janet and Rebholz-Schuhmann, Dietrich and Herre, Heinrich},
      title = {Relations as patterns: bridging the gap between OBO and the OWL},
      journal = {BMC- Bioinformatics},
      year = {2010},doi = {10.1186/1471-2105-11-441}
     volume = {11}
    }
    
  • Hoehndorf, R., Oellrich, A., Herre, H., Rebholz-Schuhmann, D. 2010. OWLDEF: using OWL reasoning to develop, maintain and enrich OBO ontologies
  • Hoehndorf, R., Prüfer, K. & Kelso, J. 2010. Biomedical Ontologies In: Poli, R. & Obrst, L. (ed.) Theory and Applications of Ontology. Vol. 2, Berlin: Springer. [BibTeX] BibTeX:
    @INCOLLECTION{hoehndorf-r-2009-a,
      author = {Hoehndorf, Robert and Prüfer, Kay and Kelso, Janet},
      title = {Biomedical Ontologies},
      booktitle = {Theory and Applications of Ontology},
      publisher = {Springer},
      year = {2010},
      editor = {Poli, Roberto and Obrst, Leo},
      volume = {2}
    }
    
  • Loebe, F. 2010. Organization and Management of Large Categorical Systems In: Poli, R. & Obrst, L. (ed.) Theory and Applications of Ontology. Vol. 2, Berlin: Springer. [BibTeX] BibTeX:
    @INCOLLECTION{loebe-f-2010-a,
      author = {Loebe, Frank},
      title = {Organization and Management of Large Categorical Systems},
      booktitle = {Theory and Applications of Ontology},
      publisher = {Springer},
      year = {2010},
      editor = {Poli, Roberto and Obrst, Leo},
      volume = {2},
      address = {Berlin}
    }
    
  • Burek, P., Herre, H., Loebe, F. 2009. Ontological Analysis of Functional Decompositions Proceedings of The 8th International Conference on Software Methodologies, Tools and Techniques (SOMET-2009) appear 2009 [BibTeX] BibTeX:
    @INPROCEEDINGS{burek-p-2009-a,
      author = {Burek, Patryk and Herre, Heinrich},
      title = {Ontological Analysis of Functional Decompositions},
      booktitle = {The 8th International Conference on Software Methodologies, Tools and Techniques (SOMET-2009)},
      year = {2009}
    }
    
  • Burek, P., Herre, H., Loebe, F. 2009. Ontological Analysis of Functional Decompositions Proceedings of The 8th International Conference on Software Methodologies, Tools and Techniques (SOMET-2009) to appear 2009. [BibTeX] BibTeX:
    @INPROCEEDINGS{burek-p-2009-a,
      author = {Burek, Patryk and Herre, Heinrich},
      title = {Ontological Analysis of Functional Decompositions},
      booktitle = {The 8th International Conference on Software Methodologies, Tools and Techniques (SOMET-2009)},
      year = {2009}
    }
    
  • Herre, H., Hummel, A. 2009. A Paraconsistent Semantics for Generalized Logic Programs In: Geske, U. & Wolf, A. (ed.) Proceedings of the 23rd Workshop on (Constraint) Logic Programming (WLP-2009). pp. 81-94. Universitätsverlag Potsdam. ISBN 978-3-86956-026-7 [BibTeX] BibTeX:
    @INPROCEEDINGS{herre-h-2009-d,
      author = {Herre, Heinrich and Hummel, Axel},
      title = {A Paraconsistent Semantics for Generalized Logic Programs},
      booktitle = {Proceedings of the 23rd Workshop on (Constraint) Logic Programming (WLP-2009)},
      publisher = {Universitätsverlag Potsdam},
      year = {2009},
      pages = {81-94},
      editor = {Geske, U. and Wolf, A},
      address ={Potsdam}
    }
    
  • Herre, H., Hummel, A. 2009. Stationary Generated Models of Generalized Logic Programs In: Geske, U. & Wolf, A. (ed.) Proceedings of the 23rd Workshop on (Constraint) Logic Programming (WLP-2009). pp. 95-108. Universitätsverlag Potsdam. ISBN 978-3-86956-026-7 [BibTeX] BibTeX:
    @INPROCEEDINGS{herre-h-2009-e,
      author = {Herre, Heinrich and Hummel, Axel},
      title = {Stationary Generated Models of Generalized Logic Programs},
      booktitle = {Proceedings of the 23rd Workshop on (Constraint) Logic Programming (WLP-2009)},
      publisher = {Universitätsverlag Potsdam},
      year = {2009},
      pages = {95-108},
      editor = {Geske, U. and Wolf, A},
      address ={Potsdam}
    }
    
  • Hoehndorf, R., Kelso, J., Herre, H. 2009. A Formal Ontology of Sequences Nature Precedings 10.1038/npre.2009.35372.2009. [PDF]
  • Hoehndorf, R., Kelso, J., Herre, H. 2009. The ontology of biological sequences BMC - Bioinformatics Vol. 10, (377) [BibTeX] [PDF] BibTeX:
    @INPROCEEDINGS{hoehndorf-r-2009-f,
               author = {Hoehndorf, Robert and Kelso, Janet and Herre, Heinrich},
               title = {The ontology of biological sequences},
               journal = {BMC Bioinformatics},
               year = {2009},
               volume = {10};
               doi = {10.3233/AO-2008-0055}
    }
    
  • Hoehndorf, R., Loebe, F., Bacher, J., Backhaus, M., Gregorio Jr., S., Prüfer, K., Visagie, J., Uciteli, A., Herre, H., Kelso, J. 2009. BOWIKI: an ontology-based wiki for annotation of data and integration of knowledge in biology BMC - Bioinformatics Vol. 10, (5) [BibTeX] BibTeX:
    @ARTICLE{hoehndorf-r-2009-b,
      author = {Hoehndorf, Robert and Loebe, Frank and Bacher, Joshua and Backhaus, Michael and Prüfer, Kay and Gregorio Jr., Sergio E. and Visagie, Johann and Uciteli, Alexandr and Herre, Heinrich and Kelso, Janet},
      title = {BOWIKI: an ontology-based wiki for annotation of data and integration of knowledge in biology},
      journal = {BMC- Bioinformatics},
      year = {2009},
      doi = {10.3233/AO-2008-0055}
     volume = {10}
    }
    
  • Hoehndorf, R., Ngonga Ngomo, A.-C., Herre, H. 2009. Developing Consistent and Modular Software Models with Ontologies Proceedings of The 8th International Conference on Software Methodologies, Tools and Techniques (SOMET-2009) to appear 2009 [BibTeX] [PDF] BibTeX:
    @INPROCEEDINGS{hoehndorf-r-2009-c,
      author = {Hoehndorf, Robert and Ngonga Ngomo, Axel-Cyrille and Herre, Heinrich},
      title = {Developing Consistent and Modular Software Models with Ontologies},
      booktitle = {The 8th International Conference on Software Methodologies, Tools and Techniques (SOMET-2009)},
      year = {2009}
    }
    
  • Mücke, R., Löbe, M., Knuth, M., Loebe, F. 2009. A Semantic Model for Representing Items in Clinical Trials Proceedings of The 22nd IEEE Symposium on Computer-Based Medical Systems, CBMS 2009, Albuquerque, New Mexico, USA, Aug 3-4, 2009 [BibTeX] BibTeX:
    @inproceedings{muecke-r-2009-a,
      author = {Mücke, Roland and Löbe, Matthias and Knuth, Magnus and Loebe, Frank},
      title = {A Semantic Model for Representing Items in Clinical Trials},
      booktitle = {Proceedings of the 22nd IEEE Symposium on Computer-Based Medical Systems (CBMS)},
      year = {2009}
    }
    
  • Stausberg, J., Löbe, M., Verplancke, P., Drepper, J., Herre, H., Löffler, M. 2009. Foundations of a Metadata Repository for Databases of Registers and Trials In: Adlassnig, K.-P. et al (ed.) Medical Informatics in a United and Healthy Europe (Proceedings of MIE 2009). Vol. 150 (Studies in Health Technology and Informatics), Amsterdam: IOS Press. [BibTeX] BibTeX:
    @INPROCEEDINGS{stausberg-j-2009-a,
      author = {Stausberg, Jürgen and Löbe, Matthias and Verplancke, Philippe and Drepper,Johannes and Herre, Heinrich and Löffler, Markus},
      title = {Foundations of a Metadata Repository for Databases of Registers and Trials},
      booktitle = {Medical Informatics in a United and Healthy Europe},
      publisher = {IOS Press},
      year = {2009},
      editor = {Adlassnig, Klaus-Peter et al},
      volume = {150},
      journal = {Studies in Health Technology and Informatics},
      address = {Amsterdam}
    }
    
  • Andreas, H. 2008. Ontological Aspects of Measurement Axiomathes Vol. 18, (3) pp. 379-394. Springer Netherlands. [BibTeX] [PDF] BibTeX:
    @article{andreas-h-2008-a,
      author = {Andreas, Holger},
      title = {Ontological Aspects of Measurement},
      publisher = {Springer Netherlands},
      journal = {Axiomathes},
      year = {2008},
      volume = {18},,
      number = {3},
      pages = {379-394},
      doi = {10.1007/s10516-008-9039-y}
    }
    
  • Hartung, M., Loebe, F., Herre, H. & Rahm, E. 2008. A Platform for Collaborative Management of Semantic Grid Metadata In: Badica, C., Mangioni, G., Carchiolo, V. & Burdescu, D.D. (ed.) Intelligent Distributed Computing, Systems and Applications: Proceedings of the 2nd International Symposium on Intelligent Distributed Computing, IDC 2008, Catania, Italy. Studies in Computational Intelligence. Vol. 162, pp. 115-125. Berlin: Springer. [BibTeX] [PDF] BibTeX:
    @inproceedings{hartung-m-2008-115-a,
      author = {Hartung, Michael and Loebe, Frank and Herre, Heinrich and Rahm, Erhard},
      title = {A Platform for Collaborative Management of Semantic Grid Metadata},
      booktitle = {Intelligent Distributed Computing, Systems and Applications: Proceedings of the 2nd International Symposium on Intelligent Distributed Computing, IDC 2008, Catania, Italy},
      publisher = {Springer},
      year = {2008},
      volume = {162},
      pages = {115--125},
      url = {http://dx.doi.org/10.1007/978-3-540-85257-5_12},
      doi = {http://dx.doi.org/10.1007/978-3-540-85257-5_12}
    }
    
  • Heußner, A. 2008. Conceptual Graphs with Relations and Roles — A GFO Coined View onto CG's Relations In: Eklund, P. & Haemmerle, O. (ed.) Supplementary Proceedings of the 16th International Conference on Conceptual Structures, ICCS-2008, Toulouse, France, Jul 7-11. pp. 25-32. Aachen, Germany: CEUR-WS.org. [BibTeX] BibTeX:
    @inproceedings{heussner-a-2008-20-a,
      author = {Heu{\ss}ner, Alexander},
      title = {Conceptual Graphs with Relations and Roles -- A GFO Coined View onto CG's Relations},
      booktitle = {Supplementary Proceedings of the 16th International Conference on Conceptual Structures, ICCS-2008, Toulouse, France, Jul 7-11},
      year = {2008},
      editor = {Eklund, Peter and Haemmerl{\'e}, Ollivier},
      volume = {354},
      series = {CEUR Workshop Proceedings},
      pages = {25--32},
      address = {Aachen, Germany},
      publisher = {CEUR-WS.org}
    }
    
  • Hoehndorf, R., Bacher, J., Backhaus, M., Gregorio, S.E.J., Loebe, F., Prüfer, K., Uciteli, A., Visagie, J., Herre, H. & Kelso, J. 2008. BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology In: Lord, P., Shah, N., Sansone, S. & Cockerill, M. (ed.) Proceedings of the 11th Annual Bio-Ontologies Meetings, Toronto, Canada, Jul 20. [BibTeX] [PDF] BibTeX:
    @inproceedings{hoehndorf-r-2008-b,
      author = {Hoehndorf, Robert and Bacher, Joshua and Backhaus, Michael and Gregorio, Serge E. Jr. and Loebe, Frank and Prüfer, Kay and Uciteli, Alexandr and Visagie, Johann and Herre, Heinrich and Kelso, Janet},
      title = {BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology},
      booktitle = {Proceedings of the 11th Annual Bio-Ontologies Meetings, Toronto, Canada, Jul 20},
      year = {2008}
    }
    
  • Hoehndorf, R., Loebe, F., Poli, R., Herre, H. & Kelso, J. 2008. GFO-Bio: A biological core ontology Applied Ontology Vol. 3, (4) pp. 219-227. [BibTeX] [PDF] BibTeX:
    @article{hoehndorf-r-2008-219-a,
      author = {Hoehndorf, Robert and Loebe, Frank and Poli, Roberto and Herre, Heinrich and Kelso, Janet},
      title = {GFO-Bio: A biological core ontology},
      journal = {Applied Ontology},
      year = {2008},
      volume = {3},,
      number = {4},
      pages = {219--227},
      doi = {10.3233/AO-2008-0055}
    }
    
  • Hoehndorf, R., Ngonga Ngomo, A. & Dannemann, M. 2008. Towards Ontological Interpretations for Improved Text Mining In: Salakoski, T., Rebholz-Schuhmann, D. & Pyysalo, S. (ed.) Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland. pp. 165-166. [BibTeX] [PDF] BibTeX:
    @inproceedings{hoehndorf-r-2008-165-a,
      author = {Robert Hoehndorf and Axel-Cyrille Ngonga Ngomo and Michael Dannemann},
      title = {Towards Ontological Interpretations for Improved Text Mining},
      booktitle = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland},
      editor = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
      year = {2008},
      pages = {165--166},
      publisher = {Turku Centre for Computer Science (TUCS)}
    }
    
  • Hoehndorf, R., Ngonga Ngomo, A., Dannemann, M. & Kelso, J. 2008. From Terms to Categories: Testing the Significance of Co-occurrences between Ontological Categories In: Salakoski, T., Rebholz-Schuhmann, D. & Pyysalo, S. (ed.) Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland. pp. 53-60. [BibTeX] [PDF] BibTeX:
    @inproceedings{hoehndorf-r-2008-53-a,
      author = {Robert Hoehndorf and Ngonga Ngomo, Axel-Cyrille and Michael Dannemann and Janet Kelso},
      title = {From Terms to Categories: Testing the Significance of Co-occurrences between Ontological Categories},
      booktitle = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland},
      editor = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
      year = {2008},
      pages = {53--60},
      publisher = {Turku Centre for Computer Science (TUCS)}
    }
    
  • Loebe, F. & Herre, H.</ 2008. Formal Semantics and Ontologies: Towards an Ontological Account of Formal Semantics In: Eschenbach, C. & Grüninger, M. (ed.) Formal Ontology in Information Systems: Proceedings of the 5th International Conference, FOIS 2008, Saarbr&uuml;cken, Germany, Oct 31-Nov 3. pp. 49-62. Amsterdam: IOS Press. [BibTeX] BibTeX:
    @inproceedings{loebe-f-2008-49-a,
      author = {Loebe, Frank and Herre, Heinrich},
      title = {Formal Semantics and Ontologies: Towards an Ontological Account of Formal Semantics},
      booktitle = {Formal Ontology in Information Systems: Proceedings of the 5th International Conference, FOIS 2008, Saarbr{\"u}cken, Germany, Oct 31-Nov 3},
      year = {2008},
      editor = {Eschenbach, Carola and Gr{\"u}ninger, Michael},
      volume = {183},
      series = {Frontiers in Artificial Intelligence},
      pages = {49--62},
      address = {Amsterdam},
      publisher = {IOS Press},
      doi = {10.3233/978-1-58603-923-3-49},
      isbn = {978-1-58603-923-3},
    }
    
  • Auer, Sö. & Herre, H. 2007. A Versioning and Evolution Framework for RDF Knowledge Base In: Voronkov, A. & Virbitskaite, I. (ed.) Perspectives of Systems Informatics: Revised Papers of the Sixth International Andrei Ershov Memorial Conference, PSI 2006, Novosibirsk, Russia, Jun 27-30. Lecture Notes in Computer Science. Vol. 4378, pp. 55-69. Berlin: Springer. [BibTeX] [PDF] BibTeX:
    @inproceedings{auer-s-2007-55-a,
      author = {Auer, S&ouml;ren and Herre, Heinrich},
      title = {A Versioning and Evolution Framework for RDF Knowledge Bases},
      booktitle = {Perspectives of Systems Informatics: Revised Papers of the Sixth International Andrei Ershov Memorial Conference, PSI 2006, Novosibirsk, Russia, Jun 27-30},
      publisher = {Springer},
      year = {2007},
      volume = {4378},
      pages = {55--69},
      doi = {http://dx.doi.org/10.1007/978-3-540-70881-0_8}
    }
    
  • Auer, Sö. & Herre, H. 2007. RapidOWL — an Agile Knowledge Engineering Methodology In: Voronkov, A. & Virbitskaite, I. (ed.) Perspectives of Systems Informatics: Revised Papers of the Sixth International Andrei Ershov Memorial Conference, PSI 2006, Novosibirsk, Russia, Jun 27-30. Lecture Notes in Computer Science. Vol. 4378, pp. 424-430. Berlin: Springer. [BibTeX] [PDF] BibTeX:
    @inproceedings{auer-s-2007-424-a,
      author = {Auer, S&ouml;ren and Herre, Heinrich},
      title = {RapidOWL -- an Agile Knowledge Engineering Methodology},
      booktitle = {Perspectives of Systems Informatics: Revised Papers of the Sixth International Andrei Ershov Memorial Conference, PSI 2006, Novosibirsk, Russia, Jun 27-30},
      publisher = {Springer},
      year = {2007},
      volume = {4378},
      pages = {424--430},
      doi = {http://dx.doi.org/10.1007/978-3-540-70881-0_36}
    }
    
  • Backhaus, M., Kelso, J., Bacher, J., Herre, H., Hoehndorf, R., Loebe, F. & Visagie, J. 2007. BOWiki — a collaborative annotation and ontology curation framework [demo description] In: Noy, N., Alani, H., Stumme, G., Mika, P., Sure, Y. & Vrandecic, D. (ed.) Proceedings of the Workshop on Social and Collaborative Construction of Structured Knowledge (CKC 2007) at the 16th International World Wide Web Conference (WWW2007), Banff, Canada, May 8. CEUR Workshop Proceedings. Vol. 273, Aachen, Germany: CEUR-WS.org. [PDF]
  • Hoehndorf, R., Loebe, F., Kelso, J. & Herre, H. 2007. Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies BMC Bioinformatics Vol. 8, pp. 377.1-377.12. [BibTeX] [PDF] BibTeX:
    @article{hoehndorf-r-2007-377-a,
      author = {Hoehndorf, Robert and Loebe, Frank and Kelso, Janet and Herre, Heinrich},
      title = {Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies},
      journal = {BMC Bioinformatics},
      year = {2007},
      volume = {8},
      pages = {377.1--377.12},
      url = {http://www.biomedcentral.com/1471-2105/8/377},
      doi = {http://dx.doi.org/10.1186/1471-2105-8-377}
    }
    
  • Loebe, F. 2007. Abstract vs. social roles — Towards a general theoretical account of roles. Applied Ontology Vol. 2, (2) pp. 127-158. [BibTeX] [PDF] BibTeX:
    @article{loebe-f-2007-127-a,
      author = {Loebe, Frank},
      title = {Abstract vs. social roles -- Towards a general theoretical account of roles},
      journal = {Applied Ontology},
      year = {2007},
      volume = {2},
      number = {2},
      pages = {127--158},
      url = {http://iospress.metapress.com/openurl.asp?genre=article&amp;issn=1570-5838&amp;volume=2&amp;issue=2&amp;spage=127}
    }
    
  • Herre, H. & Heller, B. 2006. Semantic Foundations of Medical Information Systems Based on Top-Level Ontologies Journal of Knowledge-Based Systems Vol. 19, (2) pp. 107-115. [BibTeX] BibTeX:
    @article{herre-h-2006-107-a,
      author = {Herre, Heinrich and Heller, Barbara},
      title = {Semantic Foundations of Medical Information Systems Based on Top-Level Ontologies},
      journal = {Journal of Knowledge-Based Systems},
      year = {2006},
      volume = {19},
      number = {2},
      pages = {107--115},
      doi = {http://dx.doi.org/10.1016/j.knosys.2005.10.002}
    }
    
  • Hoehndorf, R., Prüfer, K., Backhaus, M., Herre, H., Kelso, J., Loebe, F. & Visagie, J. 2006. A proposal for a gene functions wiki In: Meersman, R., Tari, Z. & Herrero, P. (ed.) On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops: Proceedings, Montpellier, France, Oct 29 - Nov 3, Part I [workshop title: Knowledge Systems in Bioinformatics, KSinBIT 2006]. Lecture Notes in Computer Science. Vol. 4277, pp. 669-678. Berlin: Springer. [BibTeX] [PDF] BibTeX:
    @inproceedings{hoehndorf-r-2006-669-a,
      author = {Robert Hoehndorf and Kay Pr&uuml;fer and Michael Backhaus and Heinrich Herre and Janet Kelso and Frank Loebe and Johann Visagie},
      title = {A proposal for a gene functions wiki},
      booktitle = {On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops: Proceedings, Montpellier, France, Oct 29 - Nov 3, Part I [workshop title: Knowledge Systems in Bioinformatics, KSinBIT 2006]},
      publisher = {Springer},
      year = {2006},
      volume = {4277},
      pages = {669--678},
      doi = {http://dx.doi.org/10.1007/11915034_91}
    }
    
  • Hoehndorf, R., Prüfer, K., Backhaus, M., Visagie, J. & Kelso, J. 2006. The design of a wiki-based curation system for the Ontology of Functions In: Stevens, R., Lord, P., McEntire, R., Butler, J.A., Shatkay, H., Hirschman, L., Blaschke, C. & Valencia, A. (ed.) Proceedings of the Joint BioLINK and 9th Bio-Ontologies Meeting (JBB 2006), Fortaleza, Brazil, Aug 5. [BibTeX] [PDF] BibTeX:
    @inproceedings{hoehndorf-r-2006-b,
      author = {Hoehndorf, Robert and Kay Pr&uuml;fer and Michael Backhaus and Johann Visagie and Janet Kelso},
      title = {The design of a wiki-based curation system for the Ontology of Functions},
      booktitle = {Proceedings of the Joint BioLINK and 9th Bio-Ontologies Meeting (JBB 2006), Fortaleza, Brazil, Aug 5},
      year = {2006},
      url = {http://onto.eva.mpg.de/publication/2006/HPBVK06}
    }
    
  • Loebe, F. 2006. Requirements for Logical Modules In: Haase, P., Honavar, V.G., Kutz, O., Sure, Y. & Tamilin, A. (ed.) Proceedings of the First Workshop on Modular Ontologies, Athens, Georgia, USA, Nov 5. [BibTeX] [PDF] BibTeX:
    @inproceedings{loebe-f-2006--a,
      author = {Loebe, Frank},
      title = {Requirements for Logical Modules},
      booktitle = {Proceedings of the First Workshop on Modular Ontologies, Athens, Georgia, USA, Nov 5},
      year = {2006}
    }
    
  • Mücke, R. & Löbe, M. 2006. Coupling Logfile Analysis and Content Management Systems for Improved Information Architecture In: Edmonds, A.K., Hawkey, K., Kellar, M. & Turnbull, D. (ed.) Proceedings of the Workshop on Logging Traces of Web Activity: The Mechanics of Data Collection, Edinburgh, Scotland, UK, May 23, 2006. [BibTeX] [PDF] BibTeX:
    @inproceedings{muecke-r-2006-a,
      author = {Roland Mücke and Matthias Löbe},
      title = {Coupling Logfile Analysis and Content Management Systems for Improved Information Architecture},
      booktitle = {Proceedings of the Workshop on Logging Traces of Web Activity: The Mechanics of Data Collection, Edinburgh, Scotland, UK, May 23, 2006},
      year = {2006}
    }
    
  • Burek, P. 2005. Essentialized Conceptual Structures in Ontology Modeling In: Khosla, R., Howlett, R.J. & Jain, L.C. (ed.) Knowledge-Based Intelligent Information and Engineering Systems: Proceedings of the 9th International Conference, KES 2005, Melbourne, Australia, Sep 14-16, Part II. Lecture Notes in Computer Science. Vol. 3682, pp. 880-886. Berlin: Springer. [BibTeX] BibTeX:
    @inproceedings{burek-p-2005-880-a,
      author = {Burek, Patryk},
      title = {Essentialized Conceptual Structures in Ontology Modeling},
      booktitle = {Knowledge-Based Intelligent Information and Engineering Systems: Proceedings of the 9th International Conference, KES 2005, Melbourne, Australia, Sep 14-16, Part II},
      publisher = {Springer},
      year = {2005},
      volume = {3682},
      pages = {880--886},
      doi = {http://dx.doi.org/10.1007/11552451_121}
    }
    
  • Burek, P. & Graboś, R. 2005. Dually Structured Concepts in the Semantic Web: Answer Set Programming Approach In: Gómez-Pérez, A. & Euzenat, Jé. (ed.) The Semantic Web: Research and Applications. Proceedings of the Second European Semantic Web Conference, ESWC 2005, Heraklion, Crete, Greece, May 29?Jun 1. Lecture Notes in Computer Science. Vol. 3532, pp. 377-391. Springer. [BibTeX] BibTeX:
    @inproceedings{burek-p-2005-377-a,
      author = {Burek, Patryk and Grabo&#347;, Rafal},
      title = {Dually Structured Concepts in the Semantic Web: Answer Set Programming Approach},
      booktitle = {The Semantic Web: Research and Applications. Proceedings of the Second European Semantic Web Conference, ESWC 2005, Heraklion, Crete, Greece, May 29?Jun 1},
      publisher = {Springer},
      year = {2005},
      volume = {3532},
      pages = {377--391}
    }
    
  • Dietzold, S. 2005. Generating RDF Models from LDAP Directories In: Auer, S., Bizer, C. & Miller, L. (ed.) Proceedings of the Workshop on Scripting for the Semantic Web, SFSW 2005, Hersonissos, Crete, Greece, May 30. CEUR Workshop Proceedings. Vol. 135, CEUR-WS. [Abstract] [BibTeX] Abstract: Lightweight Directory Access Protocol (LDAP) has gained importance as a database technology for the storage and retrieval of information on network and human resources. This paper describes a method to create RDF models from a directory information tree or an LDAP search query by mapping LDAP schema information into OWL ontologies and LDAP objects into RDF instance triples. Furthermore, it reports on an implementation of this method based on the RDF API for PHP. BibTeX:
    @inproceedings{dietzold-s-2005-d,
      author = {Sebastian Dietzold},
      title = {Generating RDF Models from LDAP Directories},
      booktitle = {Proceedings of the Workshop on Scripting for the Semantic Web, SFSW 2005, Hersonissos, Crete, Greece, May 30},
      publisher = {CEUR-WS},
      year = {2005},
      volume = {135}
    }
    
  • Heller, B., Kühn, K. & Löffler, M. 2005. Onto-Builder: Software-Werkzeug für den Aufbau von Data Dictionaries In: Steyer, G. & Tolxdorff, T. (ed.) bit for bit: Halbzeit auf dem Weg zur Telematikinfrastruktur. pp. 108-114. Berlin: Akademische V.-G. Aka. [Abstract] [BibTeX] Abstract: In vielen Fachgebieten sind präzise Begriffsdefinitionen äußerst wichtig, um eine eindeutige Kommunikation und Interoperabilität zu ermöglichen. Vor die-sem Hintergrund entstand die Idee des Onto-Builders, dessen Ziel zunächst dar-in besteht, die Definitionsalternativen von Begriffen zu sammeln und als Data Dictionary zur Verfügung zu stellen. Zusätzlich soll die Analyse der Definitionen in Bezug auf ihre Gemeinsamkeiten und Unterschiede sowie deren Harmonisierung unterstützt werden. Standardisierte Begriffsdefinitionen werden jedoch nicht erzwungen, da die Unterschiede in Definitionen inhaltlich gerechtfertigt sein können, z.B. aufgrund der Verwendung in unterschiedlichen Fachgebieten, durch studienspezifische Bedingungen oder verschiedene Expertensichten. BibTeX:
    @inproceedings{heller-b-2005-108-a,
      author = {Barbara Heller and Katrin Kühn and Markus Löffler},
      title = {Onto-Builder: Software-Werkzeug für den Aufbau von Data Dictionaries},
      booktitle = {bit for bit: Halbzeit auf dem Weg zur Telematikinfrastruktur},
      publisher = {Akademische V.-G. Aka},
      year = {2005},
      pages = {108--114}
    }
    
  • Herre, H. & Heller, B. 2005. Ontology of Time and Situoids in Medical Conceptual Modeling In: Miksch, S., Hunter, J. & Keravnou, E.T. (ed.) Proceedings of the 10th Conference on Artificial Intelligence in Medicine (AIME 05), Jul 23 - 27, Aberdeen, Scotland. Lecture Notes in Computer Science. Vol. 3581, pp. 266-275. Berlin: Springer. [BibTeX] BibTeX:
    @inproceedings{herre-h-2005-266-a,
      author = {Herre, Heinrich and Heller, Barbara},
      title = {Ontology of Time and Situoids in Medical Conceptual Modeling},
      booktitle = {Proceedings of the 10th Conference on Artificial Intelligence in Medicine (AIME 05), Jul 23 - 27, Aberdeen, Scotland},
      publisher = {Springer},
      year = {2005},
      volume = {3581},
      pages = {266--275}
      doi = {http://dx.doi.org/10.1007/11527770_39}
    }
    
  • Herre, H. & Loebe, F. 2005. A Meta-ontological Architecture for Foundational Ontologies In: Meersman, R. & Tari, Z. (ed.) On the Move to Meaningful Internet Systems 2005: CoopIS, DOA, and ODBASE: Proceedings of the OTM Confederated International Conferences, CoopIS, DOA, and ODBASE 2005, Agia Napa, Cyprus, Oct 31 - Nov 4, 2005 (Part II). Lecture Notes in Computer Science. Vol. 3761, pp. 1398-1415. Berlin: Springer. [BibTeX] [PDF] BibTeX:
    @inproceedings{herre-h-2005-1398-a,
      author = {Herre, Heinrich and Loebe, Frank},
      title = {A Meta-ontological Architecture for Foundational Ontologies},
      booktitle = {On the Move to Meaningful Internet Systems 2005: CoopIS, DOA, and ODBASE: Proceedings of the OTM Confederated International Conferences, CoopIS, DOA, and ODBASE 2005, Agia Napa, Cyprus, Oct 31 - Nov 4, 2005 (Part II)},
      publisher = {Springer},
      year = {2005},
      volume = {3761},
      pages = {1398--1415}
      doi = {http://dx.doi.org/10.1007/11575801}
    }
    
  • Löbe, M. 2005. SOP-Creator - A Tool for the Management of Standard Operating Procedures In: Jantke, K.P., Fähnrich, K. & Wittig, W.S. (ed.) Marktplatz Internet: von E-Learning bis E-Payment: 13. Leipziger Informatik-Tage (LIT 2005), Leipzig, Germany, Sep 21-23. Lecture Notes in Informatics. Vol. 72, pp. 313-319. Gesellschaft für Informatik (GI). [BibTeX] BibTeX:
    @inproceedings{loebe-m-2005-313-a,
      author = {Matthias L&ouml;be},
      title = {SOP-Creator - A Tool for the Management of Standard Operating Procedures},
      booktitle = {Marktplatz Internet: von E-Learning bis E-Payment: 13. Leipziger Informatik-Tage (LIT 2005), Leipzig, Germany, Sep 21-23},
      publisher = {Gesellschaft f&uuml;r Informatik (GI)},
      year = {2005},
      volume = {72},
      pages = {313--319}
    }
    
  • Loebe, F. 2005. Abstract vs. Social Roles: A Refined Top-level Ontological Analysis In: Boella, G., Odell, J., van der Torre, L. & Verhagen, H. (ed.) Proceedings of the 2005 AAAI Fall Symposium 'Roles, an Interdisciplinary Perspective: Ontologies, Languages, and Multiagent Systems', Arlington, Virginia, Nov 3-6. Fall Symposium Series Technical Reports. pp. 93-100. Menlo Park (California): AAAI Press. [BibTeX] BibTeX:
    @inproceedings{loebe-f-2005-93-a,
      author = {Loebe, Frank},
      title = {Abstract vs. Social Roles: A Refined Top-level Ontological Analysis},
      booktitle = {Proceedings of the 2005 AAAI Fall Symposium 'Roles, an Interdisciplinary Perspective: Ontologies, Languages, and Multiagent Systems', Arlington, Virginia, Nov 3-6},
      publisher = {AAAI Press},
      year = {2005},
      number = {FS-05-08},
      pages = {93--100}
    }
    
  • Michalek, H. 2005. A Causal Relation Based on Regularity and Manipulability In: Guizzardi, G. & Wagner, G. (ed.) Proceedings of the EDOC International Workshop on Vocabularies, Ontologies and Rules for the Enterprise (VORTE'05), Enschede, The Netherlands, Sep 20. CTIT Workshops Proceedings. pp. 1-7. Enschede (Netherlands): CTIT. [BibTeX] BibTeX:
    @inproceedings{michalek-h-2005-1-a,
      author = {Michalek, Hannes},
      title = {A Causal Relation Based on Regularity and Manipulability},
      booktitle = {Proceedings of the EDOC International Workshop on Vocabularies, Ontologies and Rules for the Enterprise (VORTE'05), Enschede, The Netherlands, Sep 20},
      publisher = {CTIT},
      year = {2005},
      pages = {1--7}
    }
    
  • Auer, Sö., Burek, P. & Grawe, T. 2004. Knowledge Engineering for IT-based Services In: Proceedings of the 4th International Conference on Knowledge Management (I-KNOW'04), Jun 30 - Jul 2, 2004, Graz, Austria. pp. 213-224. Graz: [BibTeX] [PDF] BibTeX:
    @inproceedings{auer-s-2004-213-a,
      author = {Auer, Sören and Burek, Patryk and Grawe, Tonio},
      title = {Knowledge Engineering for IT-based Services},
      booktitle = {Proceedings of the 4th International Conference on Knowledge Management (I-KNOW'04), Jun 30 - Jul 2, 2004, Graz, Austria},
      year = {2004},
      pages = {213--224}
    }
    
  • Burek, P. 2004. Adoption of the Classical Theory of Definition to Ontology Modeling In: Bussler, C. & Fensel, D. (ed.) Artificial Intelligence: Methodology, Systems, and Applications. Proceedings of the 11th International Conference, AIMSA 2004, Sep 2-4, Varna, Bulgaria. Lecture Notes in Computer Science. Vol. 3192, pp. 1-10. Berlin: Springer. [Abstract] [BibTeX] [PDF] Abstract: Ontology modeling requires modeling languages expressive enough to represent various definition types. A definition type which seems to be of particular significance is that provided by the Classical Theory of Definition. In this paper we investigate if and how far the Classical Theory of Definition is adopted by some of the ontology modeling formalisms, namely by UML, ORM and DL. Moreover, we provide a means for representing some crucial issues in the context of the Classical Theory of Definition which seem to have no representation in the formalisms discussed. Among them are the identification of essential, peculiar and incidental predications and the representation of subsumption in the manner of the genus-differentia definition. BibTeX:
    @inproceedings{burek-p-2004-1-a,
      author = {Burek, Patryk},
      title = {Adoption of the Classical Theory of Definition to Ontology Modeling},
      booktitle = {Artificial Intelligence: Methodology, Systems, and Applications. Proceedings of the 11th International Conference, AIMSA 2004, Sep 2-4, Varna, Bulgaria},
      publisher = {Springer},
      year = {2004},
      volume = {3192},
      pages = {1--10},
      url = {http://www.springerlink.com/openurl.asp?genre=article&amp;issn=0302-9743&amp;volume=3192&amp;spage=1},
      doi = {http://dx.doi.org/10.1007/b100218}
    }
    
  • Greiner, U., Müller, R., Rahm, E., Ramsch, J., Heller, B. & Löffler, M. 2004. AdaptFlow: Protocol Based Medical Treatment using Adaptive Workflows Journal of Methods of Information in Medicine [BibTeX] BibTeX:
    @article{greiner-u-2004-a,
      author = {Greiner, U. and Müller, R. and Rahm, E. and Ramsch, J. and Heller, B. and Löffler, M.},
      title = {AdaptFlow: Protocol Based Medical Treatment using Adaptive Workflows},
      journal = {Journal of Methods of Information in Medicine.},
      year = {2004},
      note = {in Druck}
    }
    
  • Greiner, U., Ramsch, J., Heller, B., Löffler, M., Rahm, E. & Müller, R. 2004. Adaptive Guideline-based Treatment Workflows with AdaptFlow In: Kaiser, K., Miksch, S. & Tu, S.W. (ed.) Computer-based Support for Clinical Guidelines and Protocols. Proceedings of the Symposium on Computerized Guidelines and Protocols (CGP 2004), 13.-14. April, Prag. Studies in Health Technology and Informatics. pp. 113-117. Amsterdam: IOS Press. [BibTeX] BibTeX:
    @inproceedings{greiner-u-2004-113-a,
      author = {Greiner, U. and Ramsch, J. and Heller, B. and Löffler, M. and Rahm, E. and Müller, R.},
      title = {Adaptive Guideline-based Treatment Workflows with AdaptFlow},
      booktitle = {Computer-based Support for Clinical Guidelines and Protocols. Proceedings of the Symposium on Computerized Guidelines and Protocols (CGP 2004), 13.-14. April, Prag},
      publisher = {IOS Press},
      year = {2004},
      pages = {113-117}
    }
    
  • Guizzardi, G., Wagner, G. & Herre, H. 2004. On the Foundations of UML as an Ontology Representation Language In: Motta, E., Shadbolt, N., Stutt, A. & Gibbins, N. (ed.) Engineering Knowledge in the Age of the Semantic Web: Proceedings of the 14th International Conference (EKAW 2004), Whittlebury Hall, UK, Oct 2004. Lecture Notes in Computer Science. Vol. 3257, pp. 47-62. Berlin: Springer. [Abstract] [BibTeX] Abstract: There is a growing interest in the use of UML class diagrams as a modeling language to represent domain ontologies. In a series of papers [1,2] we have been using the General Ontological Language (GOL) and its underly-ing foundational ontology, proposed in [3,4], to evaluate the ontological correctness of a conceptual UML class model and to develop guidelines for how the constructs of the UML should be used in conceptual modeling and ontology representation. This paper can be seen as a continuation of this work, in which we focus on analyzing the UML metaconcepts of classes, attributes, data types and associations from an ontological point of view. BibTeX:
    @inproceedings{guizzardi-g-2004-47-a,
      author = {Guizzardi, Giancarlo and Wagner, Gerd and Herre, Heinrich},
      title = {On the Foundations of UML as an Ontology Representation Language},
      booktitle = {Engineering Knowledge in the Age of the Semantic Web: Proceedings of the 14th International Conference (EKAW 2004), Whittlebury Hall, UK, Oct 2004},
      publisher = {Springer},
      year = {2004},
      volume = {3257},
      pages = {47--62},
      url = {http://www.springerlink.com/openurl.asp?genre=article&amp;issn=0302-9743&amp;volume=3257&amp;spage=47}
    }
    
  • Heller, B. & Herre, H. 2004. Ontological Categories in GOL Axiomathes Vol. 14, (1) pp. 57-76. [Abstract] [BibTeX] [PDF] Abstract: General Ontological Language (GOL) is a formal framework for representing and building ontologies. The purpose of GOL is to provide a system of top-level ontologies which can be used as a basis for building domain-specific ontologies. The present paper gives an overview about the basic categories of the GOL-ontology. GOL is part of the work of the research group Ontologies in Medicine (Onto-Med) at the University of Leipzig which is based on the collaborative work of the Institute of Medical Informatics (IMISE) and the Institute for Computer Science (IfI). It represents work in progress toward a proposal for an integrated family of top-level ontologies and will be applied to several fields of medicine, in particular to the field of Clinical Trials. BibTeX:
    @article{heller-b-2004-57-b,
      author = {Barbara Heller and Heinrich Herre},
      title = {Ontological Categories in GOL},
      journal = {Axiomathes},
      year = {2004},
      volume = {14},
      number = {1},
      pages = {57-76},
      doi = {doi:10.1023/B:AXIO.0000006788.44025.49}
    }
    
  • Heller, B. & Herre, H. 2004. Ontological Categories in GOL In: Seibt, J. (ed.) Process Theories: Crossdisciplinary Studies in Dynamic Categories. pp. 57-76. Dordrecht: Kluwer Academic Publishers. [Abstract] [BibTeX] [PDF] Abstract: General Ontological Language (GOL) is a formal framework for representing and building ontologies. The purpose of GOL is to provide a system of top-level ontologies which can be used as a basis for building domain-specific ontologies. The present paper gives an overview about the basic categories of the GOL-ontology. GOL is part of the work of the research group Ontologies in Medicine (Onto-Med) at the University of Leipzig which is based on the collaborative work of the Institute of Medical Informatics (IMISE) and the Institute for Computer Science (IfI). It represents work in progress toward a proposal for an integrated family of top-level ontologies and will be applied to several fields of medicine, in particular to the field of Clinical Trials. BibTeX:
    @incollection{heller-b-2004-57-a,
      author = {Heller, B. and Herre, H.},
      title = {Ontological Categories in GOL},
      booktitle = {Process Theories: Crossdisciplinary Studies in Dynamic Categories},
      publisher = {Kluwer Academic Publishers},
      year = {2004},
      pages = {57-76},
      note = {Nachgedruckt aus Axiomathes 14:1-2}
    }
    
  • Heller, B. & Herre, H. 2004. Ontological Foundations of Medical Information Systems In: Fujita, H. & Gruhn, V. (ed.) New Trends in Software Methodologies, Tools and Techniques: Proceedings of the Third SoMeT_W04. Frontiers in Artificial Intelligence and Applications. Vol. 111, pp. 3-17. Amsterdam: IOS Press. [Abstract] [BibTeX] [PDF] Abstract: The modeling of knowledge and implementing it in software systems is not sufficiently supported by proper guidelines and well-established principles. An interdisciplinary approach seems to be necessary because the development of guide-lines for ontologically sound knowledge modeling ? in particular in medicine ? re-quires knowledge and expertise from areas such as linguistics, informatics, medi-cine, cognitive science and philosophy. Moreover, the ever increasing amount of knowledge in the various fields of medicine and the increasing need for differing forms of presentation in very different electronic media including the Internet re-quire a harmonization of systems of concepts which transcends national borders. These challenges should be tackled by a research program which, in equal measure, takes account of the theoretical foundations, the medical application areas and the use of software in medicine. In the present paper we discuss important aspects of such an approach and outline some results of the work of the Onto-Med research group. In particular, we expound a methodology which supports the ontological foundation of medical information systems. This method is based on ontological mappings using reference top-level ontologies, and is inspired by rigorous logico-philosophical principles. BibTeX:
    @inproceedings{heller-b-2004-3-a,
      author = {Heller, Barbara and Herre, Heinrich},
      title = {Ontological Foundations of Medical Information Systems},
      booktitle = {New Trends in Software Methodologies, Tools and Techniques: Proceedings of the Third SoMeT_W04},
      publisher = {IOS Press},
      year = {2004},
      volume = {111},
      pages = {3--17}
    }
    
  • Heller, B., Herre, H. & Lippoldt, K. 2004. Domain-Specific Concepts and Ontological Reduction within a Data Dictionary Framework In: Rahm, E. (ed.) Data Integration in the Life Sciences (DILS 2004), 25.-26. März, Leipzig. Lecture Notes in Bioinformatics. pp. 47-62. Heidelberg: Springer. [Abstract] [PDF] Abstract: @inproceedings{heller-b-2004-47-a,
    author = {Heller, B. and Herre, H. and Lippoldt, K.},
    title = {Domain-Specific Concepts and Ontological Reduction within a Data Dictionary Framework},
    booktitle = {Data Integration in the Life Sciences (DILS 2004), 25.-26. März, Leipzig},
    publisher = {Springer},
    year = {2004},
    pages = {47-62}
    }
  • Heller, B., Herre, H. & Lippoldt, K. 2004. The Theory of Top-Level Ontological Mappings and its Application to Clinical Trial Protocols In: Motta, E., Shadbolt, N., Stutt, A. &amp; Gibbins, N. (ed.) Engineering Knowledge in the Age of the Semantic Web: Proceedings of the 14th International Conference (EKAW 2004), Whittlebury Hall, UK, Oct 2004. Lecture Notes in Computer Science. Vol. 3257, pp. 1-14. Berlin: Springer. [BibTeX] [PDF] BibTeX:
    @inproceedings{heller-b-2004-1-a,
      author = {Heller, Barbara and Herre, Heinrich and Lippoldt, Kristin},
      title = {The Theory of Top-Level Ontological Mappings and its Application to Clinical Trial Protocols},
      booktitle = {Engineering Knowledge in the Age of the Semantic Web: Proceedings of the 14th International Conference (EKAW 2004), Whittlebury Hall, UK, Oct 2004},
      publisher = {Springer},
      year = {2004},
      volume = {3257},
      pages = {1--14},
      url = {http://www.springerlink.com/openurl.asp?genre=article&amp;issn=0302-9743&amp;volume=3257&amp;spage=1}
    }
    
  • Heller, B., Herre, H., Lippoldt, K. & Loeffler, M. 2004. Standardized Terminology for Clinical Trial Protocols Based on Ontological Top-Level Categories In: Kaiser, K., Miksch, S. & Tu, S. (ed.) Computer-based Support for Clinical Guidelines and Protocols. Proceedings of the Symposium on Computerized Guidelines and Protocols. Studies in Health Technology and Informatics. Vol. 101, pp. 46-60. IOS Press. [Abstract] [BibTeX] [PDF] Abstract: This paper describes a new method for the ontologically based standardization of concepts with regard to the quality assurance of clinical trial protocols. We developed a data dictionary for medical and trial-specific terms in which concepts and relations are defined context-dependently. The data dictionary is provided to different medical research networks by means of the software tool Onto-Builder via the internet. The data dictionary is based on domain-specific ontologies and the toplevel ontology of GOL1. The concepts and relations described in the data dictionary are represented in natural language, semi formally or formally according to their use. BibTeX:
    @inproceedings{heller-b-2004-46-a,
      author = {Heller, B. and Herre, H. and Lippoldt, K. and Loeffler, M.},
      title = {Standardized Terminology for Clinical Trial Protocols Based on Ontological Top-Level Categories},
      booktitle = {Computer-based Support for Clinical Guidelines and Protocols. Proceedings of the Symposium on Computerized Guidelines and Protocols},
      publisher = {IOS Press},
      year = {2004},
      volume = {101},
      pages = {46-60}
    }
    
  • Löbe, M. 2004. Erfahrungen beim Einsatz von Content Management Systemen in verteilten Forschungsnetzwerken In: Fähnrich, K., Jantke, K.P. & Wittig, W.S. (ed.) Von e-Learning bis e-Payment 2004: Das Internet als sicherer Marktplatz. pp. 146-155. Berlin: Akademische Verlagsgesellschaft Aka GmbH. [BibTeX] BibTeX:
    @inproceedings{loebe-m-2004-146-a,
      author = {Matthias Löbe},
      title = {Erfahrungen beim Einsatz von Content Management Systemen in verteilten Forschungsnetzwerken},
      booktitle = {Von e-Learning bis e-Payment 2004: Das Internet als sicherer Marktplatz},
      publisher = {Akademische Verlagsgesellschaft Aka GmbH},
      year = {2004},
      pages = {146-155}
    }
    
  • Mücke, R. 2004. Untersuchung der Handhabung der Website Navigation in Content Management Systemen In: Jantke, K.P., Wittig, W. & Herrmann, J. (ed.) Von e-learning bis e-Payment — Das Internet als sicherer Marktplatz. pp. 135-145. Leipzig: Akademische Verlagsgesellschaft Aka. [BibTeX] BibTeX:
    @inproceedings{muecke-r-2004-135-a,
      author = {Mücke, R.},
      title = {Untersuchung der Handhabung der Website Navigation in Content Management Systemen},
      booktitle = {Von e-learning bis e-Payment -- Das Internet als sicherer Marktplatz},
      publisher = {Akademische Verlagsgesellschaft Aka},
      year = {2004},
      pages = {135-145}
    }
    
  • Burek, P. 2003. Conceptual Modeling based on Upper-Level Ontologies and Meta-Ontological Foundations In: Fähnrich, K. & Herre, H. (ed.) Content- und Wissensmanagement: Arbeiten aus dem Forschungsvorhaben PreBIS und Beiträge auf den Leipziger Informatik-Tagen 2003. Leipziger Beiträge zur Informatik. Vol. 1, pp. 153-157. Leipzig: Leipziger Informatik Verbund (LIV). [BibTeX] BibTeX:
    @inproceedings{burek-p-2003-153-a,
      author = {Burek, Patryk},
      title = {Conceptual Modeling based on Upper-Level Ontologies and Meta-Ontological Foundations},
      booktitle = {Content- und Wissensmanagement: Arbeiten aus dem Forschungsvorhaben PreBIS und Beiträge auf den Leipziger Informatik-Tagen 2003},
      publisher = {Leipziger Informatik Verbund (LIV)},
      year = {2003},
      volume = {1},
      pages = {153--157}
    }
    
  • Heller, B. & Herre, H. 2003. Formal Ontology and the Research Project GOL In: Fähnrich, K. & Herre, H. (ed.) Content and Knowledge Management: Beiträge auf den 11. Leipziger Informatik-Tagen (LIT 2003), 24.-26. Sept., Leipzig. pp. 106-116. [BibTeX] BibTeX:
    @inproceedings{heller-b-2003-106-a,
      author = {Heller, B. and Herre, H.},
      title = {Formal Ontology and the Research Project GOL},
      booktitle = {Content and Knowledge Management: Beiträge auf den 11. Leipziger Informatik-Tagen (LIT 2003), 24.-26. Sept., Leipzig},
      year = {2003},
      pages = {106-116}
    }
    
  • Guizzardi, G., Herre, H. & Wagner, G. 2002. On the General Ontological Foundation of Conceptual Modelling In: Spaccapietra, S., March, S. & Kambayashi, Y. (ed.) 21st International Conference on Conceptual Modelling (ER-2002),Tampere. Lectures Notes in Computer Science. pp. 97-112. Berlin: Springer. [BibTeX] [PDF] BibTeX:
    @inproceedings{guizzardi-g-2002-97-a,
      author = {Guizzardi, G. and Herre, H. and Wagner, G.},
      title = {On the General Ontological Foundation of Conceptual Modelling},
      booktitle = {21st International Conference on Conceptual Modelling (ER-2002),Tampere},
      publisher = {Springer},
      year = {2002},
      pages = {97-112}
    }
    
  • Guizzardi, G., Herre, H. & Wagner, G. 2002. Towards Ontological Foundations for UML Conceptual Models 1st International Conference on Ontologies, Databases and Applications of Semantics (ODBASE 2002), Irvine, California, USA Meersman, R. & Tari, Z. (ed.) Lectures Notes in Computer Science. Vol. 2519, pp. 1100-1117. Berlin: Springer. [BibTeX] [PDF] BibTeX:
    @inproceedings{guizzardi-g-2002-1100-a,
      author = {Guizzardi, G. and Herre, H. and Wagner, G.},
      title = {Towards Ontological Foundations for UML Conceptual Models},
      booktitle = {1st International Conference on Ontologies, Databases and Applications of Semantics (ODBASE 2002), Irvine, California, USA},
      publisher = {Springer},
      year = {2002},
      volume = {2519},
      pages = {1100-1117}
    }
    
  • Herre, H. 1995. Generalized compactness of nonmonotonic inference operations Journal of Applied Non-Classical Logics Vol. 5, (1) pp. 121-135. [BibTeX] BibTeX:
    @article{herre-h-1995-121-a,
      author = {Herre, Heinrich},
      title = {Generalized compactness of nonmonotonic inference operations},
      journal = {Journal of Applied Non-Classical Logics},
      year = {1995},
      volume = {5},
      number = {1},
      pages = {121--135},
      url = {http://jancl.e-revues.com/}
    }
    
  • Herre, H. 1993. Semantical Completeness of Model-Based Diagnosis In: Cardenosa, J. & Meseguer, P. (ed.) Proceedings of the European Symposium on the Validation and Verification of Knowledge Based Systems, EUROVAV '93, 24-26 March 1993, Universidad de las Islas Baleares, Palma de Mallorca, Spain. pp. 217-229. Universidad Politécnica de Madrid. [BibTeX] BibTeX:
    @inproceedings{herre-h-1993-217-a,
      author = {Heinrich Herre},
      title = {Semantical Completeness of Model-Based Diagnosis},
      booktitle = {Proceedings of the European Symposium on the Validation and Verification of Knowledge Based Systems, EUROVAV '93, 24-26 March 1993, Universidad de las Islas Baleares, Palma de Mallorca, Spain},
      publisher = {Universidad Polit&eacute;cnica de Madrid},
      year = {1993},
      pages = {217-229}
    }
    

Books / Proceedings

  • Fähnrich, K. & Herre, H. (ed.) 2003. Content- und Wissensmanagement: Beiträge auf der LIT '03. Leipzig: Universität Leipzig. [BibTeX] BibTeX:
    @book{faehnrich-k-2003-a,,
      editor = {Klaus-Peter Fähnrich and Heinrich Herre},
      title = {Content- und Wissensmanagement: Beiträge auf der LIT '03},
      publisher = {Universität Leipzig},
      year = {2003}
    }
    
  • Heller, B.; Löffler, M.; Musen, M. & Stefanelli, M. (ed.) 2001. Computer-Based Support for Clinical Guidelines and Protocols (EWGLP 2000). Studies in Health Care, Technology and Informatics Vol. 83. Amsterdam: IOS Press. [BibTeX] BibTeX:
    @book{heller-b-2001-a,,
      editor = {Barbara Heller and Markus Löffler and Mark Musen and Mario Stefanelli},
      title = {Computer-Based Support for Clinical Guidelines and Protocols (EWGLP 2000)},
      publisher = {IOS Press},
      year = {2001},
      volume = {83}
    }
    

Onto-Med-Reports

  • Herre, H., Heller, B., Burek, P., Hoehndorf, R., Loebe, F. & Michalek, H. 2006. General Formal Ontology (GFO): A Foundational Ontology Integrating Objects and Processes. Part I: Basic Principles (Version 1.0). Onto-Med Report, Nr. 8. Research Group Ontologies in Medicine (Onto-Med), University of Leipzig. [BibTeX] [PDF] BibTeX:
    @techreport{herre-h-2006-a,
      author = {Herre, Heinrich and Heller, Barbara and Burek, Patryk and Hoehndorf, Robert and Loebe, Frank and Michalek, Hannes},
      title = {General Formal Ontology (GFO): A Foundational Ontology Integrating Objects and Processes. Part I: Basic Principles (Version 1.0)},
      institution = {Research Group Ontologies in Medicine (Onto-Med), University of Leipzig},
      year = {2006},
      type = {Onto-Med Report},
      number = {8}
    }
    
  • Herre, H., Heller, B., Burek, P., Loebe, F. & Michalek, H. 2004. General Ontological Language: A Formal Framework for Building and Representing Ontologies (Version 1.0). Onto-Med Report, Nr. 7. Reseach Group Ontologies in Medicine, University of Leipzig. [BibTeX] BibTeX:
    @techreport{herre-h-2004-a,
      author = {Herre, Heinrich and Heller, Barbara and Burek, Patryk and Loebe, Frank and Michalek, Hannes},
      title = {General Ontological Language: A Formal Framework for Building and Representing Ontologies (Version 1.0)},
      institution = {Reseach Group Ontologies in Medicine, University of Leipzig},
      year = {2004},
      type = {Onto-Med Report},
      number = {7}
    }
    
  • Heller, B. & Herre, H. 2003. Formal Ontology and Principles of GOL. Onto-Med Report, Nr. 1/2003. Forschungsgruppe Ontologies in Medicine, Universität Leipzig. ISSN 1611-7352. [BibTeX] [PDF] BibTeX:
    @techreport{heller-b-2003-a,
      author = {Heller, B. and Herre, H.},
      title = {Formal Ontology and Principles of GOL},
      institution = {Forschungsgruppe Ontologies in Medicine, Universität Leipzig. ISSN 1611-7352},
      year = {2003},
      type = {Onto-Med Report Nr. 1/2003}
    }
    
  • Heller, B., Lippoldt, K. & Kuehn, K. 2003. Guideline for Creating Medical Terms. Onto-Med Report, Nr. 4/2003. Research Group Ontologies in Medicine, University of Leipzig. ISSN 1611-7352. [BibTeX] BibTeX:
    @techreport{heller-b-2003-c,
      author = {Heller, Barbara and Lippoldt, Kristin and Kuehn, Katrin},
      title = {Guideline for Creating Medical Terms},
      institution = {Research Group Ontologies in Medicine, University of Leipzig. ISSN 1611-7352},
      year = {2003},
      type = {Onto-Med Report},
      number = {4/2003}
    }
    
  • Heller, B., Lippoldt, K. & Kuehn, K. 2003. The Onto-Builder Handbook Version 1.1 Part I: The Construction of Medical Terms. Onto-Med Report, Nr. 5/2003. Research Group Ontologies in Medicine, University of Leipzig. ISSN 1611-7352. [BibTeX] [PDF] BibTeX:
    @techreport{heller-b-2003-b,
      author = {Heller, B. and Lippoldt, K. and Kuehn, K.},
      title = {The Onto-Builder Handbook Version 1.1 Part I: The Construction of Medical Terms},
      institution = {Research Group Ontologies in Medicine, University of Leipzig. ISSN 1611-7352},
      year = {2003},
      type = {Onto-Med Report},
      number = {5/2003}
    }
    
  • Loebe, F. 2003. An Analysis of Roles: Towards Ontology-Based Modelling. Onto-Med Report, Nr. 6. Onto-Med Research Group, University of Leipzig. [BibTeX] [PDF] BibTeX:
    @techreport{loebe-f-2003-a,
      author = {Loebe, Frank},
      title = {An Analysis of Roles: Towards Ontology-Based Modelling},
      institution = {Onto-Med Research Group, University of Leipzig},
      year = {2003},
      type = {Onto-Med Report},
      number = {6}
    }
    
  • Heller, B. & Löffler, M. 2002. Telematics and Computer-Based Quality Management in a Communication Network for Malignant Lymphoma. IMISE-Report, Nr. 1/2002. Universität Leipzig. ISSN 1610-7233. [BibTeX] BibTeX:
    @techreport{heller-b-2002-a,
      author = {Heller, B. and Löffler, M.},
      title = {Telematics and Computer-Based Quality Management in a Communication Network for Malignant Lymphoma},
      institution = {Universität Leipzig. ISSN 1610-7233},
      year = {2002},
      type = {IMISE-Report},
      number = {1/2002}
    }
    

Abstracts

  • Hoehndorf, R. 2007. Interoperability, non-monotonicity and core ontologies. In: Musen, M.A., Schröder, M. & Smith, B. (ed.) Towards Interoperability of Biomedical Ontologies: Proceedings of the Dagstuhl Seminar Nr. 07132, Schloss Dagstuhl, Germany, Mar 27-30. Wadern, Germany: [BibTeX] BibTeX:
    @inproceedings{hoehndorf-r-2007-b,
      author = {Hoehndorf, Robert},
      title = {Interoperability, non-monotonicity and core ontologies},
      booktitle = {Towards Interoperability of Biomedical Ontologies: Proceedings of the Dagstuhl Seminar Nr. 07132, Schloss Dagstuhl, Germany, Mar 27-30},
      year = {2007}
    }
    
  • Loebe, F. 2007. Towards a Definition of Roles for Software Engineering and Programming Languages. In: Boella, G., Goebel, S., Steimann, F., Zschaler, S. & Cebulla, M. (ed.) Roles'07: Proceedings of the 2nd Workshop on Roles and Relationships in Object Oriented Programming, Multiagent Systems, and Ontologies, Berlin, Germany, Jul 30-31. Forschungsberichte der Fakultät IV — Elektrotechnik und Informatik, pp. 47-49. Berlin, Germany: Technical University of Berlin. [BibTeX] BibTeX:
    @inproceedings{loebe-f-2007-47-a,
      author = {Loebe, Frank},
      title = {Towards a Definition of Roles for Software Engineering and Programming Languages},
      booktitle = {Roles'07: Proceedings of the 2nd Workshop on Roles and Relationships in Object Oriented Programming, Multiagent Systems, and Ontologies, Berlin, Germany, Jul 30-31},
      publisher = {Technical University of Berlin},
      year = {2007},
      number = {2007-9},
      pages = {47--49}
    }
    
  • Hoehndorf, R., Kelso, J. & Herre, H. 2006. GFO-Bio:A biomedical core ontology - Poster at the 2nd ISCB Student Council Symposiuml, Fortaleza, Brazil, Aug 6. [BibTeX] BibTeX:
    @misc{hoehndorf-r-2006-a,
      author = {Robert Hoehndorf and Janet Kelso and Heinrich Herre},
      title = {GFO-Bio:A biomedical core ontology},
      year = {2006},
      url = {http://onto.eva.mpg.de/publication/2006/HKH06/}
    }
    
  • Loebe, F. 2006. A Comparison of Roles in the General Formal Ontology and the HL7 Reference Information Model. In: Löffler, M. & Winter, A. (ed.) Klinische Forschung Vernetzen: Proceedings of the 51. Annual Conference of the Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS), Leipzig, Germany, Sep 10-14. pp. 131-132. University of Leipzig. [BibTeX] BibTeX:
    @inproceedings{loebe-f-2006-131-a,
      author = {Frank Loebe},
      title = {A Comparison of Roles in the General Formal Ontology and the HL7 Reference Information Model},
      booktitle = {Klinische Forschung Vernetzen: Proceedings of the 51. Annual Conference of the Deutsche Gesellschaft f&uuml;r Medizinische Informatik, Biometrie und Epidemiologie (GMDS), Leipzig, Germany, Sep 10–14},
      publisher = {University of Leipzig},
      year = {2006},
      pages = {131--132},
      note = {also published as open-access by: D&uuml;sseldorf (Germany): German Medical Science.},
      url = {http://www.egms.de/en/meetings/gmds2006/06gmds273.shtml}
    }
    
  • Löbe, M., Kühn, K. & Löffler, M. 2005. Unterstützung des Qualitätsmanagements klinischer Studien durch Integration eines semantisch fundierten Data Dictionary. In: Klar, Rü., Köpcke, W., Kuhn, K., Lax, H. & Zai, A. (ed.) Tagungsband der 50. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS), 12.-15. September 2005, und der 12. Jahrestagung der Deutschen Arbeitsgemeinschaft für Epidemiologie (DAE), 14.-15. September 2005. pp. 414-416. [BibTeX] [PDF] BibTeX:
    @inproceedings{loebe-m-2005-414-a,
      author = {L&ouml;be, Matthias and K&uuml;hn, Katrin and L&ouml;ffler, Markus},
      title = {Unterst&uuml;tzung des Qualit&auml;tsmanagements klinischer Studien durch Integration eines semantisch fundierten Data Dictionary},
      booktitle = {Tagungsband der 50. Jahrestagung der Deutschen Gesellschaft f&uuml;r Medizinische Informatik, Biometrie und Epidemiologie (GMDS), 12.-15. September 2005, und der 12. Jahrestagung der Deutschen Arbeitsgemeinschaft f&uuml;r Epidemiologie (DAE), 14.-15. September 2005},
      year = {2005},
      pages = {414--416},
      url = {http://www.egms.de/en/meetings/gmds2005/05gmds316.shtml}
    }
    
  • Greiner, U., Ramsch, J., Heller, B., Löffler, M. & Rahm, E. 2003. Flexible, protokollbasierte Therapie auf Basis adaptiver Workflows. In: 48. Jahrestagung der GMDS. Informatik, Biometrie und Epidemiologie in Medizin und Biologie, pp. 371. Münster: [BibTeX] BibTeX:
    @inproceedings{greiner-u-2003-371-a,
      author = {Greiner, U. and Ramsch, J. and Heller, B. and Löffler, M. and Rahm, E.},
      title = {Flexible, protokollbasierte Therapie auf Basis adaptiver Workflows},
      booktitle = {48. Jahrestagung der GMDS},
      year = {2003},
      pages = {371}
    }
    
  • Hatje, H., Speer, R., Hummel, M., Heller, B., Noack, F., Stein, H., Hogrefe, D. & Feller, A.C. 2003. Lymphknotenreferenzzentren: Aktuelle Online Studienpatienten- und Materialdatenbank. In: Telemedizinführer Deutschland: Ausgabe 2003. pp. 1-5. Deutsches Medizin Forum, Medizin Forum AG, Ober Mörlen. [BibTeX] BibTeX:
    @incollection{hatje-h-2003-a,
      author = {Hatje, Harald and Speer, Ronald and Hummel, Michael and Heller, Barbara and Noack, F. and Stein, H. and Hogrefe, D. and Feller, A. C.},
      title = {Lymphknotenreferenzzentren: Aktuelle Online Studienpatienten- und Materialdatenbank},
      booktitle = {Telemedizinführer Deutschland: Ausgabe 2003},
      publisher = {Deutsches Medizin Forum, Medizin Forum AG, Ober Mörlen},
      year = {2003},
      pages = {1-5}
    }
    
  • Meineke, F., Mishchenko, R., Mantovani, L., Löffler, M. & Heller, B. 2003. Onco-Workstation - ein Konsultations- und Planungswerkzeug zur Unterstützung der Auswahl und Durchführung von onkologischen Therapiestudien. In: 48. Jahrestagung der GMDS. Informatik, Biometrie und Epidemiologie in Medizin und Biologie, pp. 374. Münster: [BibTeX] BibTeX:
    @inproceedings{meineke-f-2003-374-a,
      author = {Meineke, F. and Mishchenko, R. and Mantovani, L. and Löffler, M. and Heller, B.},
      title = {Onco-Workstation - ein Konsultations- und Planungswerkzeug zur Unterstützung der Auswahl und Durchführung von onkologischen Therapiestudien},
      booktitle = {48. Jahrestagung der GMDS},
      year = {2003},
      pages = {374}
    }
    
  • Speer, R., Dolak, W., Heller, B., Meineke, F. & Ramsch, J. 2003. Sicherheitskonzepte in medizinischen Forschungsverbünden. In: Steyer, G., Löhr, K. & Tolxdorf, T. (ed.) Telemed. pp. 101-103. Berlin: [BibTeX] BibTeX:
    @inproceedings{speer-r-2003-a,
      author = {Speer, R. and Dolak, W. and Heller, B. and Meineke, F. and Ramsch, J.},
      title = {Sicherheitskonzepte in medizinischen Forschungsverbünden},
      booktitle = {Telemed},
      year = {2003},
      pages = {101-103}
    }
    
  • Speer, R., Kuchinke, W., Meisner, C., Schwabedissen, M., Troost, R. & Wittenberg, M. 2003. Systemvalidierung in Klinischen Studien-Erstellung eines Validierungspaketes für die KKS und andere Verbünde. In: 48. Jahrestagung der GMDS. In: Informatik, Biometrie und Epidemiologie in Medizin und Biologie, Vol. 34 (3), pp. 368. 14.18. Sept. 2002, Münster: [BibTeX] BibTeX:
    @inproceedings{speer-r-2003-368-a,
      author = {Speer, R. and Kuchinke, W. and Meisner, C. and Schwabedissen, M. and Troost, R. and Wittenberg, M.},
      title = {Systemvalidierung in Klinischen Studien-Erstellung eines Validierungspaketes für die KKS und andere Verbünde},
      booktitle = {48. Jahrestagung der GMDS},
      year = {2003},
      volume = {34 (3)},
      pages = {368}
    }
    
  • Dietzold, S., Heller, B. & Löbe, M 2002. Konzepte für ein modernes Informationsmanagement medizinischer Netzwerke. In: Abstracts der 46. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS). Informatik, Biometrie und Epidemiologie in Medizin und Biologie, Vol. 33, pp. 378. Berlin: Urban & Fischer. [BibTeX] [PDF] BibTeX:
    @inproceedings{dietzold-s-2002-378-a,
      author = {Sebastian Dietzold and Barbara Heller and Matthias Löbe},
      title = {Konzepte für ein modernes Informationsmanagement medizinischer Netzwerke},
      booktitle = {Abstracts der 46. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS)},
      publisher = {Urban & Fischer},
      year = {2002},
      volume = {33},
      number = {2-3},
      pages = {378}
    }
    
  • Heller, B., Hummel, M. & Speer, R. 2002. Aufbau einer standardisierten Terminologie für eine virtuelle medizinische Materialdatenbank. In: 47. Jahrestagung der GMDS. Informatik, Biometrie und Epidemiologie in Medizin und Biologie, pp. 379. Berlin: [BibTeX] [PDF] BibTeX:
    @inproceedings{heller-b-2002-379-a,
      author = {Heller, B. and Hummel, M. and Speer, R.},
      title = {Aufbau einer standardisierten Terminologie für eine virtuelle medizinische Materialdatenbank},
      booktitle = {47. Jahrestagung der GMDS},
      year = {2002},
      pages = {379}
    }
    
  • Heller, B., Krüger, M., Löffler, M., Mantovani, L., Meineke, F. & Mishchenko, R. 2002. OncoWorkstation - Ein adaptives Agentensystem für das Therapiemanagement klinischer Studien. In: 47. Jahrestagung der GMDS. Informatik, Biometrie und Epidemiologie in Medizin und Biologie, pp. 380. Berlin: [BibTeX] [PDF] BibTeX:
    @inproceedings{heller-b-2002-380-a,
      author = {Heller, B. and Krüger, M. and Löffler, M. and Mantovani, L. and Meineke, F. and Mishchenko, R.},
      title = {OncoWorkstation - Ein adaptives Agentensystem für das Therapiemanagement klinischer Studien},
      booktitle = {47. Jahrestagung der GMDS},
      year = {2002},
      pages = {380}
    }
    
  • Heller, B., Lippoldt, K., Kühn, K. & Löffler, M. 2002. Vorgehen beim Aufbau eines semantisch fundierten Data Dictionaries. In: 47. Jahrestagung der GMDS. Informatik, Biometrie und Epidemiologie in Medizin und Biologie, pp. 377. Berlin: [BibTeX] [PDF] BibTeX:
    @inproceedings{heller-b-2002-377-a,
      author = {Heller, B. and Lippoldt, K. and Kühn, K. and Löffler, M.},
      title = {Vorgehen beim Aufbau eines semantisch fundierten Data Dictionaries},
      booktitle = {47. Jahrestagung der GMDS},
      year = {2002},
      pages = {377}
    }
    
  • Dietzold, S. & Heller, B. 2001. Konzeption und Aufbau eines vertikalen Enterprise-Portals für ein medizinisches Kompetenznetzwerk. In: Abstracts der 46. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS). Biometrie und Epidemiologie in Medizin und Biologie, Vol. 32, pp. 134. Köln: Urban & Fischer. [BibTeX] [PDF] BibTeX:
    @inproceedings{dietzold-s-2001-134-a,
      author = {Sebastian Dietzold and Barbara Heller},
      title = {Konzeption und Aufbau eines vertikalen Enterprise-Portals für ein medizinisches Kompetenznetzwerk},
      booktitle = {Abstracts der 46. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS)},
      publisher = {Urban &amp; Fischer},
      year = {2001},
      volume = {32},
      number = {2-3},
      pages = {134}
    }
    
  • Heller, B., Lippoldt, K. & Löffler, M. 2001. Modell eines Data Dictionaries für Klinische Studien. In: 46. Jahrestagung der GMDS. Informatik Biometrie und Epidemiologie in Medizin und Biologie, pp. 170-171. Köln: [Abstract] [BibTeX] [PDF] Abstract: In der Planung, Durchführung und Auswertung von klinischer Studien sind verschiedene Institutionen beteiligt, welche eine Vielzahl unterschiedlicher Daten erheben, die größtenteils nicht einheitlich definiert und dokumentiert werden. Eine standardisierte semantisch fundierte Aufbereitung verwendeter Konzepte (z.B. Begriffe, Relationen, Prozesse) in Form eines Data Dictionaries für den klinischen Studienkontext ist jedoch unbedingt erfolderlich, um eine: - Wiederverwendbarkeit von Konzepten (z.B. bei Neudefinition von Studien) - Harmonisierung von Konzepten (z.B. Metamodell für Studiendatenbanken) - Qualitätssicherung in der Studiendurchfürhung - studienübergreifende Vergleichbarkeit von Ergebnissen - einheitliche Konzeptionsbasis für studienübergreifende Applikationen zu ermöglichen. Das Modell eines solchen Data Dictionaries soll über die herkömmliche statistische Beschreibung von Begriffen (deklarative Sicht) hinausgehen und den Fokus auf die prozeduralen Aspekte hinsichtlich des Verwendungszwecks von Begriffen (dynamische Sicht) beispielsweise in unterschiedlichen Anwendungen setzen. Hierbei besteht das Data Dictionary Modell u.a. aus funktionalen, inhaltlichen und Granularitäsaspekten unter welchen die Konzepte zu betrachten sind. Im Gegensatz zu den früheren traditionellen Begriffssystemen in der Medizin (z.B. SNOMED; UMLS) soll der Aufbau eines flexibel handhabbaren Data Dictionaries einen statischen Aufbau hierarchischer Konzeptbeziehungen, die Vermengung verschiedenener Sichten (z.B. nach Ursache, nach Krankheitsverlauf, nach Organmanifestation), unterschiedliche Partitionierungskriterien und Polyhierarchien vermeiden. Insbesondere die Verwendung unterschiedlicher Granularitäten auf einer Ebene sowie die Vermengung verschiedener Relationen (z.B. is-a, part-of) innerhalb einer Taxonomie führen zu einer starren Struktur welche nicht widerspruchsfrei und in anderen Kontexten nicht wiederverwebar ist. Ziel dieses Papiers ist die Beschreibung eines neuartigen Ansatzes zum Aufbau eines Data Dictionaries, welcher eine Lösung zur Überwindung der Beschränkungen traditioneller Begriffssysteme aufzeigt. BibTeX:
    @inproceedings{heller-b-2001-170-a,
      author = {Heller, B. and Lippoldt, K. and Löffler, M.},
      title = {Modell eines Data Dictionaries für Klinische Studien},
      booktitle = {46. Jahrestagung der GMDS},
      year = {2001},
      pages = {170-171}
    }
    
  • Krüger, M., Heller, B., Mishchenko, R. & Mantovani, L. 2001. Onco-Workstation: Ein wissensbasiertes Agentensystem zur Unterstützung der Therapie und Dokumentation in der Onkologie. In: 46. Jahrestag der GMDS. Informatik Biometrie und Epidemiologie in Medizin und Biologie, pp. 201-202. Köln: [Abstract] [BibTeX] Abstract: Mit der Onco-Workstation wird ein modulares, wissensbasiertes Agentensystem zur Unterst&uuml;tzung von Klinikern und niedergelassenen Fachonkologen bei der Therapie von malignen Tumoren und Dokumentation des Therapieablaufs von Studienpatienten vorgestellt. Der Funktionsumfang der Onco-Workstation beinhaltet die Studienprotokoll-Eingabe, die Studienprotokoll-Auswahl, die Therapieplanung und die Verwaltung der Studienpatientendaten sowie die standardisierte Aufbereitung von Studienprotokollen. Die modulare Architektur der Onco-Workstation erm&ouml;glicht eine genaue Anpassung der Funktionalit&auml;ten an die speziellen Anforderungen der einzelnen Nutzergruppen. Die L&ouml;sung der Aufgaben und die Bereitstellung der einzelnen Funktionen werden von einzelnen Agenten (Applikationsagenten) &uuml;bernommen, die &uuml;ber XML-basierte Protokolle untereinander und mit untergeordneten Agenten (Serviceagenten) kommunizieren. Die Eingabe der Studienprotokolle wird mit Hilfe des hierf&uuml;r zust&auml;ndigen Applikationsagenten unter Verwendung dynamischer Formulare und individueller Autorisierung der Protokolle durch den Anwender (z.B. Studienleiter) vorgenommen. Zur Identifizierung potentiell geeigneter Studienprotokolle verwendet ein weiterer Applikationsagent fallbasierte Strategien. F&uuml;r die Identifikation werden Patientendaten und die Diagnose herangezogen. Die Planung von der Therapien und die Erstellung individueller Therapiepl&auml;ne wird von einem regelbasierten Planungsagenten &uuml;bernommen. Das von den einzelnen Applikationsagenten ben&ouml;tigte Wissen wird durch Serviceagenten bereitgestellt. Die Serviceagenten operieren auf einer gemeinsamen XML-basierten Wissensbasis, welche strategisches Wissen &uuml;ber den Verwendungszweck des Applikationswissens bereitstellt. Die modulare, agentenbasierte Architektur erm&ouml;glicht ein verteiltes Arbeiten (Client/Server), so dass mehrere Anwender in einer Klinik oder Praxis auf den gleichen Daten- bzw. Wissenbest&auml;nden arbeiten k&ouml;nnen. Ziel dieser Arbeit ist die Pr&auml;sentation der Ergebnisse aus der Entwicklung eines modularen agentenbasierten Ansatz f&uuml;r eine flexible Handhabung bei der rechnerbasierten Unterst&uuml;tzung des Therapieablaufs und der Dokumentation. Insbesondere wird auf die M&ouml;glichkeiten und Vorteile bei der Verwendung von XML zum Aufbau von Wissensbasen und f&uuml;r die Kommunikation der Agenten im Bereich multizentrischer klinischer Studien eingegangen. BibTeX:
    @inproceedings{heller-b-2001-201-a,
      author = {Krüger, M. and Heller, B. and Mishchenko, R. and Mantovani, L.},
      title = {Onco-Workstation: Ein wissensbasiertes Agentensystem zur Unterstützung der Therapie und Dokumentation in der Onkologie},
      booktitle = {46. Jahrestag der GMDS},
      year = {2001},
      pages = {201-202}
    }
    
  • Speer, R. & Heller, B. 1999. Object-oriented modular data dictionaries of reusable components based on registration and analysis of data in clinical trials. In: 44. Jahrestagung der GMDS. Medical informatics, biostatistics and epidemiology for efficient health care and medical research, pp. 429. Heidelberg: [BibTeX] [PDF] BibTeX:
    @inproceedings{speer-r-1999-429-a,
      author = {Speer, R. and Heller, B.},
      title = {Object-oriented modular data dictionaries of reusable components based on registration and analysis of data in clinical trials},
      booktitle = {44. Jahrestagung der GMDS},
      year = {1999},
      pages = {429}
    }
    
  • Müller, R., Heller, B., Löffler, M., Rahm, E., Winter, A., Speer, R., Berger, H., Klöss, M., Mantovani, L., Brümmer, F., Jödecke, E., Neubert, U. & Fiebig, F. 1998. HematoWork: A Knowledge-based Workflow System for Cancer Therapy. In: Greiser, E. & Wischnewsky, M. (ed.) Methoden der Medizinischen Informatik, Biometrie und Epidemiologie in der modernen Informationsgesellschaft: Proceedings of the 43th Annual Conference of GMDS, Bremen, Sep 14-16.. pp. 63-66. Munich: Medien & Medizin Verlag. [BibTeX] [PDF] BibTeX:
    @incollection{mueller-r-1998-63-a,
      author = {Müller, R. and Heller, B. and Löffler, M. and Rahm, E. and Winter, A. and Speer, R. and Berger, H. and Klöss, M. and Mantovani, L. and Brümmer, F. and Jödecke, E. and Neubert, U. and Fiebig, F.},
      title = {HematoWork: A Knowledge-based Workflow System for Cancer Therapy},
      booktitle = {Methoden der Medizinischen Informatik, Biometrie und Epidemiologie in der modernen Informationsgesellschaft: Proceedings of the 43th Annual Conference of GMDS, Bremen, Sep 14-16},
      publisher = {Medien & Medizin Verlag},
      year = {1998},
      pages = {63--66}
    }
    
  • Speer, R. & Heller, B. 1998. Einsatz moderner Kommunikationstechniken bei der Durchführung multizentrischer klinischer Studien. In: Greiser, E. & Wischnewsky, M. (ed.) Methoden der Medizinischen Informatik, Biometrie und Epidemiologie in der modernen Informationsgesellschaft. 43. Jahrestagung der GMDS, 14.-16. Sept., Bremen. pp. 125-129. München: Medien & Medizin Verlag. [BibTeX] [PDF] BibTeX:
    inproceedings{speer-r-1998-125-a,
      author = {Speer, R. and Heller, B.},
      title = {Einsatz moderner Kommunikationstechniken bei der Durchführung multizentrischer klinischer Studien},
      booktitle = {Methoden der Medizinischen Informatik, Biometrie und Epidemiologie in der modernen Informationsgesellschaft. 43. Jahrestagung der GMDS, 14.-16. Sept., Bremen},
      publisher = {Medien & Medizin Verlag},
      year = {1998},
      pages = {125-129}
    }
    

Theses

  • Loebe, F. 2015. Ontological Semantic. An Attempt at Foundation of Ontology Representation. (PhD Thesis) Faculty of Mathematics and Informatics, University of Leipzig, Leipzig. [BibTeX] BibTeX:
    @PHDTHESIS(loebe-f-2015-a,
        author = {Loebe, Frank},
        title = {Ontological Semantic. An Attempt at Foundation of Ontology Representation},
        school = {Universität Leipzig},
        year = {2015}
      }
    
  • Baumann, R. 2009. The Mereotopological Structure of the Brentanoraum B(3) and Material Entities. Department of Mathematics, University of Leipzig, Leipzig. [BibTeX] [PDF] BibTeX:
    @MASTERSTHESIS{baumann-r-2009--a,
      author = {Baumann, Ringo},
      title = {The Mereotopological Structure of the Brentanoraum B(3) and Material Entities},
      school = {Department of Mathematics, Universität Leipzig},
      address = {Leipzig, Germany},
      year = {2009}
    }
    
  • Hoehndorf, R. 2009. Basic considerations for improving interoperability between ontology-based biological information systems. (PhD Thesis) Faculty of Mathematics and Informatics, University of Leipzig, Leipzig. [BibTeX] [PDF] BibTeX:
    @PHDTHESIS{hoehndorf-r-2009-a,
      author = {Hoehndorf, Robert},
      title = {Basic considerations for improving interoperability between ontology-based biological information systems},
      school = {Universität Leipzig},
      year = {2009}
    }
    
  • Hummel, A. 2009. Untersuchungen von Ontologiesprachen mit modelltheoretischer Semantik. Department of Computer Science, University of Leipzig, Leipzig. [BibTeX] BibTeX:
    @MASTERSTHESIS{hummel-a-2009-a,
      author = {Hummel, Axel},
      title = {Untersuchungen von Ontologiesprachen mit modelltheoretischer Semantik},
      school = {Universität Leipzig},
      year = {2009}
    }
    
  • Michalek, H. 2009. A formal ontological Approach to Causality embedded in the Top-level Ontology of GFO (General Formal Ontology). (PhD Thesis) Faculty of Mathematics and Informatics, University of Leipzig, Leipzig. [BibTeX] [PDF] BibTeX:
    @PHDTHESIS{michalek-h-2009-a,
        author = {Michalek, Hannes},
        title = {A formal ontological Approach to Causality embedded
        in the Top-level Ontology of GFO (General Formal Ontology)},
        school = {Universität Leipzig},
        year = {2009}
      }
    
  • Uciteli, A. 2008. Ontologien und kollaborative Taggingsysteme. Department of Computer Science, University of Leipzig, Leipzig. [BibTeX] BibTeX:
    @MASTERSTHESIS{uciteli-a-2008-a,
      author = {Uciteli, Alexandr},
      title = {Ontologien und kollaborative Taggingsysteme},
      school = {Universität Leipzig},
      year = {2008}
    }
    
  • Backhaus, M. 2007. BOWIKI- A collaborative ontology annotation and curation framework. Department of Computer Science, University of Leipzig, Leipzig. [BibTeX] BibTeX:
    @MASTERSTHESIS{backhaus-m-2007-a,
      author = {Backhaus, Michael},
      title = {BOWIKI- A collaborative ontology annotation and curation framework},
      school = {Universität Leipzig},
      year = {2007}
    }
    
  • Burek, P. 2007. Ontology of Functions: A Domain-Independent Framework for Modeling Functions. (PhD Thesis) Faculty of Mathematics and Informatics, University of Leipzig, Leipzig. [BibTeX] [PDF] BibTeX:
    @phdthesis{burek-p-2007-a,
      author = {Burek, Patryk},
      title = {Ontology of Functions: A Domain-Independent Framework for Modeling Functions},
      school = {Faculty of Mathematics and Informatics, University of Leipzig},
      year = {2007}
    }
    
  • Hartmann, K.-G. 2007. Vergleiche von Top-Level-Ontologien am Beispiel GPT und SUMO. Department of Computer Science, University of Leipzig, Leipzig. [BibTeX] BibTeX:
    @MASTERSTHESIS{hartmann-kg-2007-a,
      author = {Hartmann, Karl-Georg},
      title = {Vergleiche von Top-Level-Ontologien am Beispiel GPT und SUMO},
      school = {Universität Leipzig},
      year = {2007}
    }
    
  • Heußner, A. 2007. Semantic Foundation of Diagrammatic Modelling Languages: Applying the Pictorial Turn to Conceptual Modelling. Department of Computer Science, University of Leipzig, Leipzig. [BibTeX] [PDF] BibTeX:
    @masterthesis{heussner-a-2007-a,
      author = {Heu{\ss}ner, Alexander},
      title = {Semantic Foundation of Diagrammatic Modelling Languages: Applying the Pictorial Turn to Conceptual Modelling},
      school = {Department of Computer Science, University of Leipzig},
      year = {2007}
    }
    
  • Knuth, M. 2007. Konzeption und Implementierung eines Editors für prädikatenlogische Theorien mit Unterstützung verschiedener Notationen. Department of Computer Science, University of Leipzig, Leipzig. [BibTeX] BibTeX:
    @mastersthesis{knuth-m-2007-a,
      author = {Knuth, Magnus},
      title = {Konzeption und Implementierung eines Editors für prädikatenlogische Theorien mit Unterstützung verschiedener Notationen},
      school = {Department of Computer Science, University of Leipzig},
      year = {2007}
    }
    
  • Dietzold, S. 2005. GOL Web - Konzept eines Frameworks für eine axiombasierte Entwicklung von Semantic Web Ontologien auf Basis der Web Ontology Language (OWL). IMISE, University of Leipzig, [BibTeX] BibTeX:
    @mastersthesis{dietzold-s-2005-a,
      author = {Sebastian Dietzold},
      title = {GOL Web - Konzept eines Frameworks für eine axiombasierte Entwicklung von Semantic Web Ontologien auf Basis der Web Ontology Language (OWL)},
      school = {IMISE, University of Leipzig},
      year = {2005}
    }
    
  • Hoehndorf, R. 2005. Situoid theory: An ontological approach to situation theory. Department of Computer Science, University of Leipzig, [BibTeX] [PDF] BibTeX:
    @mastersthesis{hoehndorf-r-2005-a,
      author = {Hoehndorf, Robert},
      title = {Situoid theory: An ontological approach to situation theory},
      school = {Department of Computer Science, University of Leipzig},
      year = {2005}
    }
    
  • Kühn, K. 2004. A Model for a Data Dictionary Supporting Multiple Definitions, Views and Contexts. (Modell eines Data Dictionary mit Unterstützung für alternative Definitionen, Sichten und Kontexte.). Universität Leipzig, [BibTeX] [PDF] BibTeX:
    @mastersthesis{kuehn-k-2004-a,
      author = {Kühn, Katrin},
      title = {A Model for a Data Dictionary Supporting Multiple Definitions, Views and Contexts. (Modell eines Data Dictionary mit Unterstützung für alternative Definitionen, Sichten und Kontexte.)},
      school = {Universität Leipzig},
      year = {2004}
    }
    
  • Loebe, F. 2003. An Analysis of Roles: Towards Ontology-Based Modelling. Institute of Computer Science, University of Leipzig, [BibTeX] BibTeX:
    @mastersthesis{loebe-f-2003-b,
      author = {Loebe, Frank},
      title = {An Analysis of Roles: Towards Ontology-Based Modelling},
      school = {Institute of Computer Science, University of Leipzig},
      year = {2003}
    }
    
  • Löbe, M. 2001. Hochverfügbare Middlewareplattform für ein mobiles Patientenbetreuungssystem. Universität Leipzig, [BibTeX] [PDF] BibTeX:
    @mastersthesis{loebe-m-2001-a,
      author = {Löbe, Matthias},
      title = {Hochverfügbare Middlewareplattform für ein mobiles Patientenbetreuungssystem},
      school = {Universität Leipzig},
      year = {2001}
    }
    
  • Duc, H. 2000. Resource-bounded Reasoning about Knowledge. (PhD Thesis) Universität Leipzig, [BibTeX] BibTeX:
    @PHDTHESIS{duc-h-2000-a,
      author = {Ho Ngoc Duc},
      title = {Resource-bounded Reasoning about Knowledge},
      school = {University of Leipzig},
      year = {2000}
    }
    
  • Lippoldt, K. 2000. Festlegung von zielgerichteten differentiellen Dokumentationsprozessen am Beispiel der Integration der Referenzzentren für Pathologie innerhalb des Kompetenznetzwerkes Maligne Lymphome. Universität Leipzig, [BibTeX] [PDF] BibTeX:
    @mastersthesis{lippoldt-k-2000-a,
      author = {Lippoldt, K.},
      title = {Festlegung von zielgerichteten differentiellen Dokumentationsprozessen am Beispiel der Integration der Referenzzentren für Pathologie innerhalb des Kompetenznetzwerkes Maligne Lymphome},
      school = {Universität Leipzig},
      year = {2000}
    }
    
  • Krüger, M. 1999. Konzeption und Realisierung eines wissensbasierten Protokollauswahlmodul für die Hämatoonkologie. Universität Leipzig, [BibTeX] BibTeX:
    @mastersthesis{krueger-m-1999-a,
      author = {Krüger, M.},
      title = {Konzeption und Realisierung eines wissensbasierten Protokollauswahlmodul für die Hämatoonkologie},
      school = {Universität Leipzig},
      year = {1999}
    }
    
  • Than Hai, N. 1999. Erkenntnistheoretische und begriffliche Grundlagen der objektorientierten Datenmodellierung. University of Leipzig, [BibTeX] BibTeX:
    @MASTERSTHESIS{than-hai-1999-a,
      author = {Than Hai, Nguyen},
      title = {Erkenntnistheoretische und begriffliche Grundlagen der objektorientierten Datenmodellierung},
      school = {Universität Leipzig},
      year = {1999}
    }
    
  • Berger, H. 1997. Konzeption und Implementierung eines Konsultationssystems zur Therapieplanung in der Erwachsenenonkologie. Universität Leipzig, [BibTeX] BibTeX:
        @mastersthesis{berger-h-1997-a,
          author = {Berger, H.},
          title = {Konzeption und Implementierung eines Konsultationssystems zur Therapieplanung in der Erwachsenenonkologie},
          school = {Universität Leipzig},
          year = {1997}
        }