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  1. 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

    Content type: Proceedings

    Published on:

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

  2. 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

    Content type: Proceedings

    Published on:

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

  3. 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

    Content type: Proceedings

    Published on:

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

  4. 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

    Content type: Proceedings

    Published on:

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

  5. 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

    Content type: Proceedings

    Published on:

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

  6. 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

    Content type: Proceedings

    Published on:

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

  7. 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

    Content type: Proceedings

    Published on:

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

  8. 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

    Content type: Proceedings

    Published on:

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

  9. 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

    Content type: Proceedings

    Published on:

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

  10. 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

    Content type: Research

    Published on:

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

  11. 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

    Content type: Research

    Published on:

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

  12. 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

    Content type: Research

    Published on:

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

  13. 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

    Content type: Research

    Published on:

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

  14. 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

    Content type: Research

    Published on:

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

  15. 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

    Content type: Research

    Published on:

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

  16. 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

    Content type: Research

    Published on:

  17. 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

    Content type: Review

    Published on:

  18. 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

    Content type: Proceedings

    Published on:

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

  19. CiTO, the Citation Typing Ontology, is an ontology for describing the nature of reference citations in scientific research articles and other scholarly works, both to other such publications and also to Web in...

    Authors: David Shotton

    Citation: Journal of Biomedical Semantics 2010 1(Suppl 1):S6

    Content type: Proceedings

    Published on:

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

  20. 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

    Content type: Proceedings

    Published on:

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

  21. 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

    Content type: Proceedings

    Published on:

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

  22. The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small ...

    Authors: Allyson L Lister, Phillip Lord, Matthew Pocock and Anil Wipat

    Citation: Journal of Biomedical Semantics 2010 1(Suppl 1):S3

    Content type: Proceedings

    Published on:

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

  23. 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

    Content type: Proceedings

    Published on:

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

  24. 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

    Content type: Proceedings

    Published on:

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

  25. In order to satisfy different needs, medical terminology systems must have richer structures. This study examines whether a Swedish primary health care version of the mono-hierarchical ICD-10 (KSH97-P) may obt...

    Authors: Mikael Nyström, Anna Vikström, Gunnar H Nilsson, Hans Åhlfeldt and Håkan Örman

    Citation: Journal of Biomedical Semantics 2010 1:7

    Content type: Research

    Published on:

  26. In order to perform research on the information contained in Electronic Patient Records (EPRs), access to the data itself is needed. This is often very difficult due to confidentiality regulations. The data se...

    Authors: Hercules Dalianis and Sumithra Velupillai

    Citation: Journal of Biomedical Semantics 2010 1:6

    Content type: Research

    Published on:

  27. Identification of terms is essential for biomedical text mining.. We concentrate here on the use of vocabularies for term identification, specifically the Unified Medical Language System (UMLS). To make the UM...

    Authors: Kristina M Hettne, Erik M van Mulligen, Martijn J Schuemie, Bob JA Schijvenaars and Jan A Kors

    Citation: Journal of Biomedical Semantics 2010 1:5

    Content type: Research

    Published on:

  28. Previous studies have suggested that epidemiological reasoning needs a fine-grained modelling of events, especially their spatial and temporal attributes. While the temporal analysis of events has been intensi...

    Authors: Hutchatai Chanlekha and Nigel Collier

    Citation: Journal of Biomedical Semantics 2010 1:3

    Content type: Research

    Published on:

  29. Accurate and timely detection of public health events of international concern is necessary to help support risk assessment and response and save lives. Novel event-based methods that use the World Wide Web as...

    Authors: Nigel Collier

    Citation: Journal of Biomedical Semantics 2010 1:2

    Content type: Research

    Published on:

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