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  1. Content type: Research

    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

    Published on:

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

  2. Content type: Research

    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

    Published on:

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

  3. Content type: Research

    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

    Published on:

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

  4. Content type: Research

    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

    Published on:

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

  5. Content type: Research

    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

    Published on:

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

  6. Content type: Research

    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

    Published on:

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

  7. Content type: Research

    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

    Published on:

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

  8. Content type: Research

    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

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  9. Content type: Proceedings

    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

    Published on:

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

  10. Content type: Proceedings

    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

    Published on:

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

  11. Content type: Proceedings

    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

    Published on:

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

  12. Content type: Proceedings

    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

    Published on:

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

  13. Content type: Introduction

    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

    Published on:

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

  14. Content type: Review

    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

    Published on:

  15. Content type: Research

    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

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  16. Content type: Proceedings

    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

    Published on:

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

  17. Content type: Proceedings

    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

    Published on:

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

  18. Content type: Proceedings

    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

    Published on:

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

  19. Content type: Proceedings

    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

    Published on:

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

  20. Content type: Proceedings

    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

    Published on:

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

  21. Content type: Introduction

    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

    Published on:

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

  22. Content type: Proceedings

    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

    Published on:

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

  23. Content type: Proceedings

    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

    Published on:

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

  24. Content type: Proceedings

    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

    Published on:

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

  25. Content type: Proceedings

    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

    Published on:

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

  26. Content type: Proceedings

    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

    Published on:

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

  27. Content type: Proceedings

    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

    Published on:

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

  28. Content type: Proceedings

    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

    Published on:

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

  29. Content type: Proceedings

    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

    Published on:

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

  30. Content type: Proceedings

    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

    Published on:

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

  31. Content type: Proceedings

    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, James P McCusker…

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

    Published on:

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

  32. Content type: Introduction

    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

    Published on:

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

  33. Content type: Research

    Semantic web technologies are finding their way into the life sciences. Ontologies and semantic markup have already been used for more than a decade in molecular sciences, but have not found widespread use yet...

    Authors: Egon L Willighagen, Jonathan Alvarsson, Annsofie Andersson, Martin Eklund, Samuel Lampa, Maris Lapins, Ola Spjuth and Jarl ES Wikberg

    Citation: Journal of Biomedical Semantics 2011 2(Suppl 1):S6

    Published on:

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

  34. Content type: Research

    There have been a number of recent efforts (e.g. BioCatalogue, BioMoby) to systematically catalogue bioinformatics tools, services and datasets. These efforts rely on manual curation, making it difficult to co...

    Authors: Hammad Afzal, James Eales, Robert Stevens and Goran Nenadic

    Citation: Journal of Biomedical Semantics 2011 2(Suppl 1):S4

    Published on:

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

  35. Content type: Research

    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

    Published on:

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

  36. Content type: Research

    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

    Published on:

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

  37. Content type: Research

    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

    Published on:

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

  38. Content type: Research

    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

    Published on:

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

  39. Content type: Research

    While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontolo...

    Authors: Werner Ceusters and Barry Smith

    Citation: Journal of Biomedical Semantics 2010 1:10

    Published on:

  40. Content type: Review

    Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems ...

    Authors: Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Lord Hendrix Barboza, Raoul JP Bonnal, Richard Bruskiewich, Jan C Bryne, José M Fernández…

    Citation: Journal of Biomedical Semantics 2010 1:8

    Published on:

  41. Content type: Proceedings

    Researchers in biomedical informatics use ontologies and terminologies to annotate their data in order to facilitate data integration and translational discoveries. As the use of ontologies for annotation of b...

    Authors: Clement Jonquet, Mark A Musen and Nigam H Shah

    Citation: Journal of Biomedical Semantics 2010 1(Suppl 1):S1

    Published on:

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

  42. Content type: Proceedings

    Understanding the distinction between function and role is vexing and difficult. While it appears to be useful, in practice this distinction is hard to apply, particularly within biology.

    Authors: Phillip Lord

    Citation: Journal of Biomedical Semantics 2010 1(Suppl 1):S4

    Published on:

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

  43. Content type: Proceedings

    Increasingly sophisticated knowledge about RNA structure and function requires an inclusive knowledge representation that facilitates the integration of independently –generated information arising from such e...

    Authors: Jose Cruz-Toledo, Michel Dumontier, Marc Parisien and François Major

    Citation: Journal of Biomedical Semantics 2010 1(Suppl 1):S2

    Published on:

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

  44. Content type: Proceedings

    Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data e...

    Authors: Ryan R Brinkman, Mélanie Courtot, Dirk Derom, Jennifer M Fostel, Yongqun He, Phillip Lord, James Malone, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Larisa N Soldatova, Christian J Stoeckert Jr., Jessica A Turner and Jie Zheng

    Citation: Journal of Biomedical Semantics 2010 1(Suppl 1):S7

    Published on:

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

  45. Content type: Proceedings

    Information technology has the potential to increase the pace of scientific progress by helping researchers in formulating, publishing and finding information. There are numerous projects that employ ontologie...

    Authors: Matthias Samwald and Holger Stenzhorn

    Citation: Journal of Biomedical Semantics 2010 1(Suppl 1):S5

    Published on:

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

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