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  1. Clustering textual contents is an important step in mining useful information on the web or other text-based resources. The common task in text clustering is to handle text in a multi-dimensional space, and to...

    Authors: Sun Kim and W John Wilbur
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 3):S6

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

  2. The concept of a mechanism has become a standard proposal for explanations in biology. It has been claimed that mechanistic explanations are appropriate for systems biology, because they occupy a middle ground...

    Authors: Johannes Röhl
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 2):S9

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

  3. Biomedical ontologies usually encode knowledge that applies always or at least most of the time, that is in normal circumstances. But for some applications like phenotype ontologies it is becoming increasingly...

    Authors: Niels Grewe
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 2):S8

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

  4. Despite the high coverage of biomedical ontologies, very few sound definitions of death can be found. Nevertheless, this concept has its relevance in epidemiology, such as for data integration within mortality...

    Authors: Filipe Santana, Fred Freitas, Roberta Fernandes, Zulma Medeiros and Daniel Schober
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 2):S7

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

  5. Ontologies are widely used in the biomedical community for annotation and integration of databases. Formal definitions can relate classes from different ontologies and thereby integrate data across different l...

    Authors: Georgios V Gkoutos and Robert Hoehndorf
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 2):S6

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

  6. Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. The Entity-Quality (EQ) formalism is a means to describe complex ph...

    Authors: Frank Loebe, Frank Stumpf, Robert Hoehndorf and Heinrich Herre
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 2):S5

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

  7. Although policy providers have outlined minimal metadata guidelines and naming conventions, ontologies of today still display inter- and intra-ontology heterogeneities in class labelling schemes and metadata c...

    Authors: Daniel Schober, Ilinca Tudose, Vojtech Svatek and Martin Boeker
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 2):S4

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

  8. We demonstrate a heterogeneity of representation types for breast cancer phenotypes and stress that the characterisation of a tumour phenotype often includes parameters that go beyond the representation of a c...

    Authors: Aleksandra Sojic and Oliver Kutz
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 2):S3

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

  9. Ontology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, ...

    Authors: Djamila Seddig-Raufie, Ludger Jansen, Daniel Schober, Martin Boeker, Niels Grewe and Stefan Schulz
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 2):S2

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

  10. Researchers use animal studies to better understand human diseases. In recent years, large-scale phenotype studies such as Phenoscape and EuroPhenome have been initiated to identify genetic causes of a species...

    Authors: Anika Oellrich, Georgios V Gkoutos, Robert Hoehndorf and Dietrich Rebholz-Schuhmann
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 2):S1

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

  11. With the development of high throughput methods of gene analyses, there is a growing need for mining tools to retrieve relevant articles in PubMed. As PubMed grows, literature searches become more complex and ...

    Authors: Charles Bettembourg, Christian Diot, Anita Burgun and Olivier Dameron
    Citation: Journal of Biomedical Semantics 2012 3:7
  12. Clinical phenotypes and disease-risk stratification are most often determined through the direct observations of clinicians in conjunction with published standards and guidelines, where the clinical expert is ...

    Authors: Soroush Samadian, Bruce McManus and Mark D Wilkinson
    Citation: Journal of Biomedical Semantics 2012 3:6
  13. Genome sequencing of many eukaryotic pathogens and the volume of data available on public resources have created a clear requirement for a consistent vocabulary to describe the range of developmental forms of ...

    Authors: Priti P Parikh, Jie Zheng, Flora Logan-Klumpler, Christian J Stoeckert Jr, Christos Louis, Pantelis Topalis, Anna V Protasio, Amit P Sheth, Mark Carrington, Matthew Berriman and Satya S Sahoo
    Citation: Journal of Biomedical Semantics 2012 3:5
  14. Transfusion and clinical laboratory services are high-volume activities involving complicated workflows across both ambulatory and inpatient environments. As a result, there are many opportunities for safety l...

    Authors: Julie M Whitehurst, John Schroder, Dave Leonard, Monica M Horvath, Heidi Cozart and Jeffrey Ferranti
    Citation: Journal of Biomedical Semantics 2012 3:4
  15. The OpenTox Framework, developed by the partners in the OpenTox project (http://​www.​opentox.​org), aims at providing a unified access to toxicity data, ...

    Authors: Olga Tcheremenskaia, Romualdo Benigni, Ivelina Nikolova, Nina Jeliazkova, Sylvia E Escher, Monika Batke, Thomas Baier, Vladimir Poroikov, Alexey Lagunin, Micha Rautenberg and Barry Hardy
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 1):S7

    This article is part of a Supplement: Volume 3 Supplement 1

  16. A variety of topic-focused wikis are used in the biomedical sciences to enable the mass-collaborative synthesis and distribution of diverse bodies of knowledge. To address complex problems such as defining the...

    Authors: Benjamin M Good, Erik L Clarke, Salvatore Loguercio and Andrew I Su
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 1):S6

    This article is part of a Supplement: Volume 3 Supplement 1

  17. The electronic surveillance for adverse drug events is largely based upon the analysis of coded data from reporting systems. Yet, the vast majority of electronic health data lies embedded within the free text ...

    Authors: Paea LePendu, Srinivasan V Iyer, Cédrick Fairon and Nigam H Shah
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 1):S5

    This article is part of a Supplement: Volume 3 Supplement 1

  18. Identifying relationships between hitherto unrelated entities in different ontologies is the key task of ontology alignment. An alignment is either manually created by domain experts or automatically by an ali...

    Authors: Elena Beisswanger and Udo Hahn
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 1):S4

    This article is part of a Supplement: Volume 3 Supplement 1

  19. Ontologies such as the Gene Ontology (GO) and their use in annotations make cross species comparisons of genes possible, along with a wide range of other analytical activities. The bio-ontologies community, in...

    Authors: Simon Jupp, Robert Stevens and Robert Hoehndorf
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 1):S3

    This article is part of a Supplement: Volume 3 Supplement 1

  20. The increasing number of scientific literature on the Web and the absence of efficient tools used for classifying and searching the documents are the two most important factors that influence the speed of the ...

    Authors: George Tsatsaronis, Natalia Macari, Sunna Torge, Heiko Dietze and Michael Schroeder
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 1):S2

    This article is part of a Supplement: Volume 3 Supplement 1

  21. Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more gene...

    Authors: Larisa N Soldatova, Susanna-Assunta Sansone, Michel Dumontier and Nigam H Shah
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 1):I1

    This article is part of a Supplement: Volume 3 Supplement 1

  22. 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
  23. 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
  24. 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
  25. 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
  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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
  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

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