Volume 9 Supplement 3

Proceedings of the Second International Symposium on Languages in Biology and Medicine (LBM) 2007


Edited by Christopher JO Baker and Su Jian

The Second International Symposium on Languages in Biology and Medicine (LBM) 2007. Go to conference site.


6-7 December 2007

  1. Proceedings

    Normalizing biomedical terms by minimizing ambiguity and variability

    One of the difficulties in mapping biomedical named entities, e.g. genes, proteins, chemicals and diseases, to their concept identifiers stems from the potential variability of the terms. Soft string matching ...

    Yoshimasa Tsuruoka, John McNaught and Sophia Ananiadou

    BMC Bioinformatics 2008 9(Suppl 3):S2

    Published on: 11 April 2008

  2. Proceedings

    Assessment of disease named entity recognition on a corpus of annotated sentences

    In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other sema...

    Antonio Jimeno, Ernesto Jimenez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga and Dietrich Rebholz-Schuhmann

    BMC Bioinformatics 2008 9(Suppl 3):S3

    Published on: 11 April 2008

  3. Proceedings

    New challenges for text mining: mapping between text and manually curated pathways

    Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or...

    Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Daisuke Okanohara, Takuya Matsuzaki, Yuka Tateisi and Jun'ichi Tsujii

    BMC Bioinformatics 2008 9(Suppl 3):S5

    Published on: 11 April 2008

  4. Proceedings

    Comparative analysis of five protein-protein interaction corpora

    Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction (PPI) extraction. Howe...

    Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter and Tapio Salakoski

    BMC Bioinformatics 2008 9(Suppl 3):S6

    Published on: 11 April 2008

  5. Proceedings

    Structuring an event ontology for disease outbreak detection

    This paper describes the design of an event ontology being developed for application in the machine understanding of infectious disease-related events reported in natural language text. This event ontology is ...

    Ai Kawazoe, Hutchatai Chanlekha, Mika Shigematsu and Nigel Collier

    BMC Bioinformatics 2008 9(Suppl 3):S8

    Published on: 11 April 2008

  6. Proceedings

    Automatic construction of rule-based ICD-9-CM coding systems

    In this paper we focus on the problem of automatically constructing ICD-9-CM coding systems for radiology reports. ICD-9-CM codes are used for billing purposes by health institutes and are assigned to clinical...

    Richárd Farkas and György Szarvas

    BMC Bioinformatics 2008 9(Suppl 3):S10

    Published on: 11 April 2008