Volume 2 Supplement 5

Proceedings of the Fourth International Symposium on Semantic Mining in Biomedicine (SMBM)

Research

Edited by Nigel Collier, Udo Hahn, Sampo Pyysalo, Dietrich Rebholz-Schuhmann and Fabio Rinaldi

Fourth International Symposium on Semantic Mining in Biomedicine (SMBM).

Hinxton, UK

25-26 October 2010

  1. Research

    Ontology design patterns to disambiguate relations between genes and gene products in GENIA

    Annotated reference corpora play an important role in biomedical information extraction. A semantic annotation of the natural language texts in these reference corpora using formal ontologies is challenging du...

    Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich and Dietrich Rebholz-Schuhmann

    Journal of Biomedical Semantics 2011 2(Suppl 5):S1

    Published on: 6 October 2011

  2. Research

    Event extraction for DNA methylation

    We consider the task of automatically extracting DNA methylation events from the biomedical domain literature. DNA methylation is a key mechanism of epigenetic control of gene expression and implicated in many...

    Tomoko Ohta, Sampo Pyysalo, Makoto Miwa and Jun’ichi Tsujii

    Journal of Biomedical Semantics 2011 2(Suppl 5):S2

    Published on: 6 October 2011

  3. Research

    An analysis of gene/protein associations at PubMed scale

    Event extraction following the GENIA Event corpus and BioNLP shared task models has been a considerable focus of recent work in biomedical information extraction. This work includes efforts applying event extr...

    Sampo Pyysalo, Tomoko Ohta and Jun’ichi Tsujii

    Journal of Biomedical Semantics 2011 2(Suppl 5):S5

    Published on: 6 October 2011

  4. Research

    Coreference based event-argument relation extraction on biomedical text

    This paper presents a new approach to exploit coreference information for extracting event-argument (E-A) relations from biomedical documents. This approach has two advantages: (1) it can extract a large numbe...

    Katsumasa Yoshikawa, Sebastian Riedel, Tsutomu Hirao, Masayuki Asahara and Yuji Matsumoto

    Journal of Biomedical Semantics 2011 2(Suppl 5):S6

    Published on: 6 October 2011

  5. Research

    Linguistic scope-based and biological event-based speculation and negation annotations in the BioScope and Genia Event corpora

    The treatment of negation and hedging in natural language processing has received much interest recently, especially in the biomedical domain. However, open access corpora annotated for negation and/or specula...

    Veronika Vincze, György Szarvas, György Móra, Tomoko Ohta and Richárd Farkas

    Journal of Biomedical Semantics 2011 2(Suppl 5):S8

    Published on: 6 October 2011

  6. Research

    OMG U got flu? Analysis of shared health messages for bio-surveillance

    Micro-blogging services such as Twitter offer the potential to crowdsource epidemics in real-time. However, Twitter posts (‘tweets’) are often ambiguous and reactive to media trends. In order to ground user me...

    Nigel Collier, Nguyen Truong Son and Ngoc Mai Nguyen

    Journal of Biomedical Semantics 2011 2(Suppl 5):S9

    Published on: 6 October 2011

  7. Research

    Towards cross-lingual alerting for bursty epidemic events

    Online news reports are increasingly becoming a source for event-based early warning systems that detect natural disasters. Harnessing the massive volume of information available from multilingual newswire pre...

    Nigel Collier

    Journal of Biomedical Semantics 2011 2(Suppl 5):S10

    Published on: 6 October 2011

  8. Research

    Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

    Competitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is time-consumin...

    Dietrich Rebholz-Schuhmann, Antonio Jimeno Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, René Witte, Jonas B Laurila, Christopher JO Baker, Cheng-Ju Kuo…

    Journal of Biomedical Semantics 2011 2(Suppl 5):S11

    Published on: 6 October 2011

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