Publications

Refereed Papers in Journals and Proceedings
Books / Proceedings
Onto-Med-Reports
Abstracts
Theses

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Refereed Papers in Journals and Proceedings

Herre, H., Hoehndorf, R., Kelso, J., Loebe, F. Schulz, S. 2011. OBML- Ontologies in Biomedicine and Life Sciences. BMC Biomedical Semantics

Uciteli, A., Gross, S., Herre, H. 2011. An Ontologically founded Architecture for Information Systems in Clinical and Epidemiological Research. BMC Biomedical Semantics. [BibTeX] 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]}
}

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}
}

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., Herre, H., Rebholz-Schuhmann, D. 2010. OWLDEF: using OWL reasoning to develop, maintain and enrich OBO ontologies. [BibTeX] BibTeX:

@ARTICLE{hoehndorf-r-2010-b,
  author = {Hoehndorf, Robert and Oellrich, Anika and Herre, Heinrich and Rebholz-Schuhmann, Dietrich},
  title = {OWLDEF: using OWL reasoning to develop, maintain and enrich OBO ontologies},
  year = {2010}
}

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}
}

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}
}

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}
}

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}
}

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}
}
}

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}
}

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}
}

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}
}

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}
}

Hoehndorf, R., Kelso, J., Herre, H. 2009. A Formal Ontology of Sequences. Nature Precedings 10.1038/npre.2009.35372.2009[PDF]

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}
}

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), S5. [BibTeX] [PDF] 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}
}

@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}
}

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}
}

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}
}

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}
}

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, Saarbrücken, 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},
}

Heußner, A. 2008. Conceptual Graphs with Relations and Roles — A GFO Coined View onto CG's Relations. In: Eklund, P. & Haemmerlé, 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., 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)}
}

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)}
}

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}
}

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}
}

Auer, Sö. & Herre, H. 2007. A Versioning and Evolution Framework for RDF Knowledge Bases. 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, Sören 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}
}

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&issn=1570-5838&volume=2&issue=2&spage=127}
}

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}
}

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. [BibTeX] [PDF] BibTeX:

@inproceedings{backhaus-m-2007-a,
  author = {Backhaus, Michael and Kelso, Janet and Bacher, Joshua and Herre, Heinrich and Hoehndorf, Robert and Loebe, Frank and Visagie, Johann},
  title = {BOWiki -- a collaborative annotation and ontology curation framework [demo description]},
  booktitle = {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},
  publisher = {CEUR-WS.org},
  year = {2007},
  volume = {273}
}

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, Sören 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}
}

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 Prüfer 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}
}

Burek, P., Hoehndorf, R., Loebe, F., Visagie, J., Herre, H. & Kelso, J. 2006. A top-level ontology of functions and its application in the Open Biomedical Ontologies. Bioinformatics Vol. 22(14), pp. e66-e73. [BibTeX] [PDF] BibTeX:

@article{burek-p-2006-e66-a,
  author = {Patryk Burek and Robert Hoehndorf and Frank Loebe and Johann Visagie and Heinrich Herre and Janet Kelso},
  title = {A top-level ontology of functions and its application in the Open Biomedical Ontologies},
  journal = {Bioinformatics},
  year = {2006},
  volume = {22},
  number = {14},
  pages = {e66--e73},
  url = {http://onto.eva.mpg.de/publication/2006/BHLVKH06/},
  doi = {http://dx.doi.org/10.1093/bioinformatics/btl266}
}

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}
}

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}
}

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., 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 Prüfer 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}
}

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}
}

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}
}

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}
}

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 Graboś, 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}
}

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}
}

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}
}
```

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}
}

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 Löbe},
  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 für Informatik (GI)},
  year = {2005},
  volume = {72},
  pages = {313--319}
}

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}
}
```

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}
}

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&issn=0302-9743&volume=3192&spage=1},
  doi = {http://dx.doi.org/10.1007/b100218}
}
```

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. [BibTeX] [PDF] BibTeX:

@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}
}

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}
}

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&issn=0302-9743&volume=3257&spage=47}
}
```
Heller, B. & Herre, H.; Seibt, J. (ed.) 2004. Ontological Categories in GOL. In Process Theories: Crossdisciplinary Studies in Dynamic Categories. Dordrecht. Kluwer Academic Publishers. 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:
```
@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. & 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: 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}
}
```

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. & 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&issn=0302-9743&volume=3257&spage=1}
}

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}
}

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}
}

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}
}
```

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. In: Meersman, R. & Tari, Z. (ed.) 1st International Conference on Ontologies, Databases and Applications of Semantics (ODBASE 2002), Irvine, California, USA. 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 Politécnica 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}
}

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. & 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}
}

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}
}
```

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 für Medizinische Informatik, Biometrie und Epidemiologie (GMDS), Leipzig, Germany, Sep 1014},
  publisher = {University of Leipzig},
  year = {2006},
  pages = {131--132},
  note = {also published as open-access by: Düsseldorf (Germany): German Medical Science.},
  url = {http://www.egms.de/en/meetings/gmds2006/06gmds273.shtml}
}

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/}
}

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 = {Löbe, Matthias and Kühn, Katrin and Löffler, Markus},
  title = {Unterstützung des Qualitätsmanagements klinischer Studien durch Integration eines semantisch fundierten Data Dictionary},
  booktitle = {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},
  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. Deutsches Medizin Forum, Medizin Forum AG, Ober Mörlen. pp. 1-5. [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}
}

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}
}

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., 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). Informatik, 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 & 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 Unterstützung 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 ermöglicht eine genaue Anpassung der Funktionalitäten an die speziellen Anforderungen der einzelnen Nutzergruppen. Die Lösung der Aufgaben und die Bereitstellung der einzelnen Funktionen werden von einzelnen Agenten (Applikationsagenten) übernommen, die über XML-basierte Protokolle untereinander und mit untergeordneten Agenten (Serviceagenten) kommunizieren. Die Eingabe der Studienprotokolle wird mit Hilfe des hierfür zuständigen 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. Für die Identifikation werden Patientendaten und die Diagnose herangezogen. Die Planung von der Therapien und die Erstellung individueller Therapiepläne wird von einem regelbasierten Planungsagenten übernommen. Das von den einzelnen Applikationsagenten benötigte Wissen wird durch Serviceagenten bereitgestellt. Die Serviceagenten operieren auf einer gemeinsamen XML-basierten Wissensbasis, welche strategisches Wissen über den Verwendungszweck des Applikationswissens bereitstellt. Die modulare, agentenbasierte Architektur ermöglicht ein verteiltes Arbeiten (Client/Server), so dass mehrere Anwender in einer Klinik oder Praxis auf den gleichen Daten- bzw. Wissenbeständen arbeiten können. Ziel dieser Arbeit ist die Präsentation der Ergebnisse aus der Entwicklung eines modularen agentenbasierten Ansatz für eine flexible Handhabung bei der rechnerbasierten Unterstützung des Therapieablaufs und der Dokumentation. Insbesondere wird auf die Möglichkeiten und Vorteile bei der Verwendung von XML zum Aufbau von Wissensbasen und für 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}
}
```

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}
}

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.; Greiser, E. & Wischnewsky, M. (ed.) 1998. HematoWork: A Knowledge-based Workflow System for Cancer Therapy. In Methoden der Medizinischen Informatik, Biometrie und Epidemiologie in der modernen Informationsgesellschaft: Proceedings of the 43th Annual Conference of GMDS, Bremen, Sep 14-16. Munich. Medien & Medizin Verlag. pp. 63-66. [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}
}

Theses

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 = {UniversitÃ¤t 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 = {UniversitÃ¤t Leipzig},
  year = {2009}
}

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, UniversitÃ¤t Leipzig},
  address = {Leipzig, Germany},
  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 = {UniversitÃ¤t 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 = {UniversitÃ¤t 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}
}

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 = {UniversitÃ¤t 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}
}

Höhndorf, R. 2005. Situoid theory: An ontological approach to situation theory. Department of Computer Science, University of Leipzig. [BibTeX] [PS] BibTeX:

@mastersthesis{hoehndorf-r-2005-a,
  author = {Höhndorf, 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] [PDF, report version] 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}
}

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 = {UniversitÃ¤t Leipzig},
  year = {1999}
}

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}
}

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}
}

Ontologies in Medicine and Life Sciences Foundations, Development and Applications