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  1. The wide variety of morphological variants of domain-specific technical terms contributes to the complexity of performing natural language processing of the scientific literature related to molecular biology. ...

    Authors: Haibin Liu, Tom Christiansen, William A Baumgartner Jr and Karin Verspoor
    Citation: Journal of Biomedical Semantics 2012 3:3
  2. Rapid identification of subject experts for medical topics helps in improving the implementation of discoveries by speeding the time to market drugs and aiding in clinical trial recruitment, etc. Identifying s...

    Authors: Siddhartha Jonnalagadda, Ryan Peeler and Philip Topham
    Citation: Journal of Biomedical Semantics 2012 3:2
  3. The International Classification of Functioning, Disability and Health (ICF) is a classification of health and health-related issues, aimed at describing and measuring health and disability at both individual ...

    Authors: Vincenzo Della Mea and Andrea Simoncello
    Citation: Journal of Biomedical Semantics 2012 3:1
  4. The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past dec...

    Authors: Mark D Wilkinson, Benjamin Vandervalk and Luke McCarthy
    Citation: Journal of Biomedical Semantics 2011 2:8
  5. 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...

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

    This article is part of a Supplement: Volume 2 Supplement 5

  6. 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...

    Authors: Nigel Collier, Nguyen Truong Son and Ngoc Mai Nguyen
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 5):S9

    This article is part of a Supplement: Volume 2 Supplement 5

  7. 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...

    Authors: Veronika Vincze, György Szarvas, György Móra, Tomoko Ohta and Richárd Farkas
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 5):S8

    This article is part of a Supplement: Volume 2 Supplement 5

  8. This paper presents a novel approach to the problem of hedge detection, which involves identifying so-called hedge cues for labeling sentences as certain or uncertain. This is the classification problem for Task ...

    Authors: Erik Velldal
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 5):S7

    This article is part of a Supplement: Volume 2 Supplement 5

  9. 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...

    Authors: Katsumasa Yoshikawa, Sebastian Riedel, Tsutomu Hirao, Masayuki Asahara and Yuji Matsumoto
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 5):S6

    This article is part of a Supplement: Volume 2 Supplement 5

  10. 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...

    Authors: Sampo Pyysalo, Tomoko Ohta and Jun’ichi Tsujii
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 5):S5

    This article is part of a Supplement: Volume 2 Supplement 5

  11. Information extraction is a complex task which is necessary to develop high-precision information retrieval tools. In this paper, we present the platform MeTAE (Medical Texts Annotation and Exploration). MeTAE...

    Authors: Asma Ben Abacha and Pierre Zweigenbaum
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 5):S4

    This article is part of a Supplement: Volume 2 Supplement 5

  12. The extraction of complex events from biomedical text is a challenging task and requires in-depth semantic analysis. Previous approaches associate lexical and syntactic resources with ontologies for the semant...

    Authors: Jung-jae Kim and Dietrich Rebholz-Schuhmann
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 5):S3

    This article is part of a Supplement: Volume 2 Supplement 5

  13. 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...

    Authors: Tomoko Ohta, Sampo Pyysalo, Makoto Miwa and Jun’ichi Tsujii
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 5):S2

    This article is part of a Supplement: Volume 2 Supplement 5

  14. 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...

    Authors: Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich and Dietrich Rebholz-Schuhmann
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 5):S1

    This article is part of a Supplement: Volume 2 Supplement 5

  15. Ontologies are increasingly used to structure and semantically describe entities of domains, such as genes and proteins in life sciences. Their increasing size and the high frequency of updates resulting in a ...

    Authors: Toralf Kirsten, Anika Gross, Michael Hartung and Erhard Rahm
    Citation: Journal of Biomedical Semantics 2011 2:6
  16. Dispositions and tendencies feature significantly in the biomedical domain and therefore in representations of knowledge of that domain. They are not only important for specific applications like an infectious...

    Authors: Johannes Röhl and Ludger Jansen
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 4):S4

    This article is part of a Supplement: Volume 2 Supplement 4

  17. To evaluate how well current anatomical ontologies fit the way real-world users apply anatomy terms in their data annotations.

    Authors: Ravensara S Travillian, Tomasz Adamusiak, Tony Burdett, Michael Gruenberger, John Hancock, Ann-Marie Mallon, James Malone, Paul Schofield and Helen Parkinson
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 4):S3

    This article is part of a Supplement: Volume 2 Supplement 4

  18. In biomedical ontologies, mereological relations have always been subject to special interest due to their high relevance in structural descriptions of anatomical entities, cells, and biomolecules. This paper ...

    Authors: Ludger Jansen and Stefan Schulz
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 4):S2

    This article is part of a Supplement: Volume 2 Supplement 4

  19. This paper presents an ontologically founded basic architecture for information systems, which are intended to capture, represent, and maintain metadata for various domains of clinical and epidemiological rese...

    Authors: Alexandr Uciteli, Silvia Groß, Sergej Kireyev and Heinrich Herre
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 4):S1

    This article is part of a Supplement: Volume 2 Supplement 4

  20. The OBML 2010 workshop, held at the University of Mannheim on September 9-10, 2010, is the 2 nd in a series of meetings organized by the Working Group “Ontologies in Biomedicine...

    Authors: Heinrich Herre, Robert Hoehndorf, Janet Kelso, Frank Loebe and Stefan Schulz
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 4):I1

    This article is part of a Supplement: Volume 2 Supplement 4

  21. The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively ...

    Authors: Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano, Jan Aerts, Kiyoko F Aoki-Kinoshita, Kazuharu Arakawa, Bruno Aranda, Raoul JP Bonnal, José M Fernández…
    Citation: Journal of Biomedical Semantics 2011 2:4
  22. The HL7 Clinical Document Architecture (CDA) constrains the HL7 Reference Information model (RIM) to specify the format of HL7-compliant clinical documents, dubbed CDA documents. The use of clinical terminologies...

    Authors: Stijn Heymans, Matthew McKennirey and Joshua Phillips
    Citation: Journal of Biomedical Semantics 2011 2:2
  23. In this paper we present a detailed scheme for annotating medical web pages designed for health care consumers. The annotation is along two axes: first, by reliability (the extent to which the medical informat...

    Authors: Melanie J Martin
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 3):S5

    This article is part of a Supplement: Volume 2 Supplement 3

  24. Test collections for information retrieval are scarce. Domain specific test collections even more so, and medical test collections in the Swedish language non-existent prior to the making of the MedEval test c...

    Authors: Karin Friberg Heppin
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 3):S4

    This article is part of a Supplement: Volume 2 Supplement 3

  25. Most methods for negation detection in clinical text have been developed for English text, and there is a need for evaluating the feasibility of adapting these methods to other languages. A Swedish adaption of...

    Authors: Maria Skeppstedt
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 3):S3

    This article is part of a Supplement: Volume 2 Supplement 3

  26. Extracting medication information from clinical records has many potential applications, and recently published research, systems, and competitions reflect an interest therein. Much of the early extraction wor...

    Authors: Scott Russell Halgrim, Fei Xia, Imre Solti, Eithon Cadag and Özlem Uzuner
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 3):S2

    This article is part of a Supplement: Volume 2 Supplement 3

  27. Free text is helpful for entering information into electronic health records, but reusing it is a challenge. The need for language technology for processing Finnish and Swedish healthcare text is therefore evi...

    Authors: Helen Allvin, Elin Carlsson, Hercules Dalianis, Riitta Danielsson-Ojala, Vidas Daudaravičius, Martin Hassel, Dimitrios Kokkinakis, Heljä Lundgrén-Laine, Gunnar H Nilsson, Øystein Nytrø, Sanna Salanterä, Maria Skeppstedt, Hanna Suominen and Sumithra Velupillai
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 3):S1

    This article is part of a Supplement: Volume 2 Supplement 3

  28. The papers presented in this supplement focus and reflect on computer use in every-day clinical work in hospitals and clinics such as electronic health record systems, pre-processing for computer aided summari...

    Authors: Hercules Dalianis, Martin Hassel and Sumithra Velupillai
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 3):I1

    This article is part of a Supplement: Volume 2 Supplement 3

  29. Advances in Natural Language Processing (NLP) techniques enable the extraction of fine-grained relationships mentioned in biomedical text. The variability and the complexity of natural language in expressing s...

    Authors: Adrien Coulet, Yael Garten, Michel Dumontier, Russ B Altman, Mark A Musen and Nigam H Shah
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 2):S10

    This article is part of a Supplement: Volume 2 Supplement 2

  30. Hypotheses are now being automatically produced on an industrial scale by computers in biology, e.g. the annotation of a genome is essentially a large set of hypotheses generated by sequence similarity programs; ...

    Authors: Larisa N Soldatova and Andrey Rzhetsky
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 2):S9

    This article is part of a Supplement: Volume 2 Supplement 2

  31. Interferon-gamma (IFN-γ) is vital in vaccine-induced immune defense against bacterial and viral infections and tumor. Our recent study demonstrated the power of a literature-based discovery method in extractio...

    Authors: Arzucan Özgür, Zuoshuang Xiang, Dragomir R Radev and Yongqun He
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 2):S8

    This article is part of a Supplement: Volume 2 Supplement 2

  32. Chronic renal disease is a global health problem. The identification of suitable biomarkers could facilitate early detection and diagnosis and allow better understanding of the underlying pathology. One of the...

    Authors: Simon Jupp, Julie Klein, Joost Schanstra and Robert Stevens
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 2):S7

    This article is part of a Supplement: Volume 2 Supplement 2

  33. The realm of pathological entities can be subdivided into pathological dispositions, pathological processes, and pathological structures. The latter are the bearer of dispositions, which can then be realized b...

    Authors: Stefan Schulz, Kent Spackman, Andrew James, Cristian Cocos and Martin Boeker
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 2):S6

    This article is part of a Supplement: Volume 2 Supplement 2

  34. Text definitions for entities within bio-ontologies are a cornerstone of the effort to gain a consensus in understanding and usage of those ontologies. Writing these definitions is, however, a considerable eff...

    Authors: Robert Stevens, James Malone, Sandra Williams, Richard Power and Allan Third
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 2):S5

    This article is part of a Supplement: Volume 2 Supplement 2

  35. There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific research...

    Authors: Paolo Ciccarese, Marco Ocana, Leyla Jael Garcia Castro, Sudeshna Das and Tim Clark
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 2):S4

    This article is part of a Supplement: Volume 2 Supplement 2

  36. Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integr...

    Authors: Alison Callahan, Michel Dumontier and Nigam H Shah
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 2):S3

    This article is part of a Supplement: Volume 2 Supplement 2

  37. Ontologies in biomedicine facilitate information integration, data exchange, search and query of biomedical data, and other critical knowledge-intensive tasks. The OBO Foundry is a collaborative effort to esta...

    Authors: Amir Ghazvinian, Natalya F Noy and Mark A Musen
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 2):S2

    This article is part of a Supplement: Volume 2 Supplement 2

  38. Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medici...

    Authors: Joanne S Luciano, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christine K Denney, Christopher Domarew, Thomas Gambet, Lee Harland, Anja Jentzsch, Vipul Kashyap, Peter Kos, Julia Kozlovsky, Timothy Lebo, Scott M Marshall, Jamie P McCusker…
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 2):S1

    This article is part of a Supplement: Volume 2 Supplement 2

  39. Over the years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organisation, presentation ...

    Authors: Larisa N Soldatova, Susanna-Assunta Sansone, Susie M Stephens and Nigam H Shah
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 2):I1

    This article is part of a Supplement: Volume 2 Supplement 2

  40. More than in other domains the heterogeneous services world in bioinformatics demands for a methodology to classify and relate resources in a both human and machine accessible manner. The Semantic Web, which i...

    Authors: Anna-Lena Lamprecht, Stefan Naujokat, Tiziana Margaria and Bernhard Steffen
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 1):S5

    This article is part of a Supplement: Volume 2 Supplement 1

  41. Ontologies are commonly used in biomedicine to organize concepts to describe domains such as anatomies, environments, experiment, taxonomies etc. NCBO BioPortal currently hosts about 180 different biomedical o...

    Authors: Syed Hamid Tirmizi, Stuart Aitken, Dilvan A Moreira, Chris Mungall, Juan Sequeda, Nigam H Shah and Daniel P Miranker
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 1):S3

    This article is part of a Supplement: Volume 2 Supplement 1

  42. The UMLS Metathesaurus (UMLS-Meta) is currently the most comprehensive effort for integrating independently-developed medical thesauri and ontologies. UMLS-Meta is being used in many applications, including PubMe...

    Authors: Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau, Ian Horrocks and Rafael Berlanga
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 1):S2

    This article is part of a Supplement: Volume 2 Supplement 1

  43. The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development and application of analytical tools to address problems in data-intens...

    Authors: Andrea Splendiani, Albert Burger, Adrian Paschke, Paolo Romano and M Scott Marshall
    Citation: Journal of Biomedical Semantics 2011 2(Suppl 1):S1

    This article is part of a Supplement: Volume 2 Supplement 1

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