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PhD Publications

All my publications from 2005-2011 can be found here...
  1. GeneTUC: Natural Language Understanding in Medical Text
    (PhD Thesis, Norwegian University of Science and Technology, June 2006, ISBN 82-471-7865-6).
  2. GeneTUC, GENIA and Google: Natural Language Understanding in Molecular Biology Literature [pdf]
    (In Transactions on Computational Systems Biology V, pages 68-82, ISBN: 3-540-36048-4,
    Lecture Notes in Computer Science, ISSN: 0302-9743, August 2006).
  3. gProt: Annotating Protein Interactions using Google and Gene Ontology
    (KES Conference, September 2005). [pdf]
  4. Semantic Annotation of Biomedical Literature using Google
    (DMBIO Workshop, LNCS 3482, Singapore, May 2005).
    We used the Google API for (direct) semantic annotation of proteins in biomedical literature. The basic idea is: Search engines are the biggest information haystacks, and they probably contain (some) evidence of (most) ways of writing protein and gene names. This lead to a strategy of simply searching for " <name> is (an|a) " that was later quality checked by biologists.
    This work was extended into finding relationships (and GO terms) between proteins in the paper...
  5. ProtChew: Automatic Extraction of Protein Names from Biomedical Literature [pdf]
    (BMDE Workshop, ICDE, Tokyo, April 2005).

TUC Documents

  1. GeneTUC: Natural Language Understanding in Medical Text
    (PhD Thesis, Norwegian University of Science and Technology, June 2006, ISBN 82-471-7865-6).
  2. TUC: The Understanding Computer. (2006)
  3. GeneTUC - BioMolecular Information Retrieval, CSGSC Proeceedings. (2004)
  4. Natural Language Understanding (NLU), Automatic Information Extraction (IE) from Biomedical Texts, Masters Thesis. (2003)
  5. GeneTUC: A Biolinguistic Project, Report (2002)

Collection of relevant PDF files

Can be found here

Programs

  1. GProt and Bioogle