Dr. Andreas Doms

Publications

  • GoPubMed: Exploring PubMed with Ontological Background Knowledge.
    Heiko Dietze, Dimitra Alexopoulou, Michael R.Alvers, Liliana Barrio-Alvers, Bill Andreopoulos, Andreas Doms, Jörg Hakenberg, Jan Mönnich, Conrad Plake, Andreas Reischuck, Loic Royer, Thomas Wächter, Matthias Zschunke, and Michael Schroeder.
    In Bioinformatics for Systems Biology. The Human Press, 2008.
  • Agents in bioinformatics, computational and systems biology.
    Emanuela Merelli, Giuliano Armano, Nicola Cannata, Flavio Corradini, Mark d'Inverno, Andrea Doms, Phil Lord, Andrew Martin, Luciano Milanesi, Steffen Moeller, Michael Schroeder, and Michael Luck.
    Briefings in Bioinformatics, 8(1):45--59, 2006
  • SCOWLP: A web-based database for detailed characterization and visualization of protein interfaces. Joan Teyra, Andreas Doms, Michael Schroeder, and M. Teresa Pisabarro.
    BMC Bioinformatics, 7(1):104, 2006
  • GoPubMed: Exploring PubMed with the GeneOntology. Andreas Doms and Michael Schroeder. [Full Text]
    Nucleic Acid Research, 33(Web Server Issue):W783--W786, 2005, Impact factor 7.552
  • How to query the GeneOntology.
    Andreas Doms, Tim Furche, Albert Burger, and Michael Schroeder.
    In Catherine Bounsaythip, editor, Proc. of KRBIO'05: Symposium on Knowledge Representation in Bioinformatics, 2005.
  • GoPubMed: ontology-based literature search applied to Gene Ontology and PubMed
    Ralph Delfs, Andreas Doms, Alexander Kozlenkov, and Michael Schroeder.
    In proceedings of German Conference on Bioinformatics, 2004.
  • GoPubMed: Answering biomedical questions
    Andreas Doms.
    In EMBnet.news, Vol. 14, 2008.
  • Facts from text
    Rainer Winnenburg, Thomas Wächter, Conrad Plake, Andreas Doms, and Michael Schroeder.
    Briefings in Bioinformatics, accepted
  • Literature Search with Ontologies
    Andreas Doms, Heiko Dietze, Thomas Wächter and Michael Schroeder.
    In proceedings of Web4WeB Workshop, 2008
  • Biomedical word sense disambiguation with ontologies and meta-data automation meets accuracy
    Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder and Thomas Wächter.
    BMC Bioinformatics , submitted, 2008.

Book Chapters

  • Ontologies and Text Mining as a Basis for a Semantic Web for the Life Sciences.
    Andreas Doms, Vaida Jakonien, Patrick Lambrix, Michael Schroeder, and Thomas Wächter.
    In REWERSE Summerschool 2006, LNCS 4126. Springer, 2006.
  • GoPubMed: Exploring PubMed with Ontological Background Knowledge
    Heiko Dietze, Dimitra Alexopoulou, Michael R. Alvers, Liliana Barrio-Alvers, Bill Andreopoulos, Andreas Doms, Jörg Hakenberg, Jan Mönnich, Conrad Plake, Andreas Reischuck, Loic Royer, Thomas Wächter, Matthias Zschunke, and Michael Schroeder.
    In: Bioinformatics for Systems Biology, Humana Press, 2008.

Technical Reports

  • Usage of Bioinformatics Tools and Identifcation of Information Sources
    Rolf Backofen, Li viu Badea, Pedro Barahona, Albert Burger, Gihan Dawelbait, Andreas Doms, Franois Fages, Anca Hotaran, Vaida Jakonien, Ludwig Krippahl, Patrick Lambrix, Kenneth McLeod, Steffen Möller, Werner Nutt, Bjorn Olsson, Michael Schroeder, Sylvain Soliman.
    Reasoning on the Web with Rules and Semantics, 2004.
  • Requirements and specification of bioinformatics use cases
    Rolf Backofen, Liviu Badea, Pedro Barahona, Mikael Berndtsson, Albert Burger, Gihan Dawelbait, Andreas Doms, Franois Fages, Anca Hotaran, Vaida Jakonien, Ludwig Krippahl, Patrick Lambrix, Kenneth McLeod, Werner Nutt, Bjorn Olsson, Michael Schroeder, Anna Schroi , Loic Royer, Sylvain Soliman, He Tan, Doina Tilivea, Sebastian Will.
    Reasoning on the Web with Rules and Semantics, 2005.
  • Bioinformatics Demonstrators
    Gihan Dawelbait, Andreas Doms, Patrick Lambrix, Loic Royer, Michael Schroeder.
    Reasoning on the Web with Rules and Semantics, 2006.
  • GoPubMed: ontology-based literature search for the life sciences
    Dimitra A lexopoulou, Michael R. Alvers, Bill Andreopoulos, Liliana Barrio-Alvers, Gihan Dawelbait, Heiko Dietze, Andreas Doms, Cecilia Eyre, Jörg Hakenb erg, Jan Mönnich, Laura Pickersgill, Conrad Plake, Andreas Reischuck, Loic Royer, Michael Schroeder, Thomas Wächter, Matthias Zschunke.
    Reasoning on the Web with Rules and Semantics, 2007.

Posters

  • www.GoPubMed.org Ontology-based literature search German Conference on Bioinformatics, 2004.
  • Wet Spots in Protein Interfaces European Conferences on Computational Biology, 2005.
  • GoPubMed: exploring PubMed with the Gene Ontology
    European Life Scientist Organization Conference, 2005.

Presentations / Talks

  • GoPubMed: Searching is now sorted
    Biotec TU Dresden PhD Seminar, March, 2008.
  • Searching is now sorted
    Embrace Workshop, Bari, Italy, 2007.
  • Reasoning over GoPubMed's RDF data
    International RuleML Symposium on Rule Interchange and Applications, Orlando, Florida 2007, Video-Conference.
  • AdaBoost: adaptive Boosting
    Biotec TU Dresden Bioinformatics Journal Club, July, 2006.
  • Ontology-based literature mining with GoPubMed
    Bioinformatics-Seminar, Humboldt-Universität Berlin, 2006.
  • Imitating Manual Curation of Text-Minded Facts in Biomedicine
    Biotec TU Dresden Bioinformatics Journal Club, December, 2006.
  • Ontology-based literature mining with GoPubMed
    Biotec TU Dresden PhD Seminar, December, 2005.
  • GATE, A General Architecture for Text Engineering
    Biotec TU Dresden Bioinformatics Journal Club, August 2005.
  • Knowledge-based literature mining for the Life Sciences
    REWERSE A2 Workgroup Meeting, Edinburgh 2005.
  • How to query the GeneOntology?
    Symposium: KRBIO'05 - Symposium on Knowledge Representation in Bioinformatics, Helsinki, Finland, 2005.
  • Extending the mutual inforamtion measures to rank inferred literature relationships
    Biotec TU Dresden Bioinformatics Journal Club, October, 2004.
  • RelEx: Relation extraction using dependency parse trees
    Biotec TU Dresden Bioinformatics Journal Club, January, 2008.

Events

  • Reasoning Web Summer School, Dresden, 2007
  • Sealife Kickoff Meeting, 2006
  • Semantics, Vienna, 2006
  • Reasoning Web Summer School, Malta, 2005
  • Semantic Web Days, Munich, 2005
  • Knowledge Management Europe, Amsterdam, 2004

Peer Reviewing

Conferences

  • Pacific Symposium on Biocomputing (2006)

Workshops

  • Data Integration in The Life Sciences (2006)

Teaching

  • Question answering with GoPubMed Bioinformatics III, WS 2007.
  • Ontology-based literature search for the life sciences Integrated Logic Systems, SS 2007.
  • GoPubMed - Ontologie-basierte Literaturrecherche für die Lebenswissenschaften
    Ringvorlesung: Softwareentwicklung in der industriellen Praxis, SS 2007.
  • The Semantic Web and Ontology term extraction from research articles Integrated Logic Systems, SS 2005.

Other Tasks

(e.g. project deliverables, grant writing, long night of science, collaborations, organization of events, ...):

  • REWERSE deputy co-ordinator 2004-2008
  • Deputy co-ordinator REWERSE Summer School 2007

Interests