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  1. Content type: Database

    We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representati...

    Authors: Mark Jensen, Alexander P Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William Duncan, Patrick Ray, Bianca Weinstock-Guttman, Barry Smith, Alan Ruttenberg, Kinga Szigeti and Alexander D Diehl

    Citation: Journal of Biomedical Semantics 2013 4:42

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  2. Content type: Research

    In prior work, we presented the Ontology of Physics for Biology (OPB) as a computational ontology for use in the annotation and representations of biophysical knowledge encoded in repositories of physics-based...

    Authors: Daniel L Cook, Maxwell L Neal, Fred L Bookstein and John H Gennari

    Citation: Journal of Biomedical Semantics 2013 4:41

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  3. Content type: Research

    Licensed human vaccines can induce various adverse events (AE) in vaccinated patients. Due to the involvement of the whole immune system and complex immunological reactions after vaccination, it is difficult t...

    Authors: Erica Marcos, Bin Zhao and Yongqun He

    Citation: Journal of Biomedical Semantics 2013 4:40

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  4. Content type: Short Report

    Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycolipi...

    Authors: Kiyoko F Aoki-Kinoshita, Jerven Bolleman, Matthew P Campbell, Shin Kawano, Jin-Dong Kim, Thomas Lütteke, Masaaki Matsubara, Shujiro Okuda, Rene Ranzinger, Hiromichi Sawaki, Toshihide Shikanai, Daisuke Shinmachi, Yoshinori Suzuki, Philip Toukach, Issaku Yamada, Nicolle H Packer…

    Citation: Journal of Biomedical Semantics 2013 4:39

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  5. Content type: Research

    Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple...

    Authors: Paolo Ciccarese, Stian Soiland-Reyes, Khalid Belhajjame, Alasdair JG Gray, Carole Goble and Tim Clark

    Citation: Journal of Biomedical Semantics 2013 4:37

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  6. Content type: Research

    Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. ...

    Authors: Michaela Gündel, Erfan Younesi, Ashutosh Malhotra, Jiali Wang, Hui Li, Bijun Zhang, Bernard de Bono, Heinz-Theodor Mevissen and Martin Hofmann-Apitius

    Citation: Journal of Biomedical Semantics 2013 4:35

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  7. Content type: Research

    Though the annotation of digital artifacts with metadata has a long history, the bulk of that work focuses on the association of single terms or concepts to single targets. As annotation efforts expand to capt...

    Authors: Kevin M Livingston, Michael Bada, Lawrence E Hunter and Karin Verspoor

    Citation: Journal of Biomedical Semantics 2013 4:38

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  8. Content type: Database

    The Rat Genome Database (RGD) (http://​rgd.​mcw.​edu/​) is the premier site for comprehensive data on the different strains of the laboratory rat (Rattus n...

    Authors: Rajni Nigam, Diane H Munzenmaier, Elizabeth A Worthey, Melinda R Dwinell, Mary Shimoyama and Howard J Jacob

    Citation: Journal of Biomedical Semantics 2013 4:36

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  9. Content type: Database

    A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, ...

    Authors: Peter E Midford, Thomas Alex Dececchi, James P Balhoff, Wasila M Dahdul, Nizar Ibrahim, Hilmar Lapp, John G Lundberg, Paula M Mabee, Paul C Sereno, Monte Westerfield, Todd J Vision and David C Blackburn

    Citation: Journal of Biomedical Semantics 2013 4:34

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  10. Content type: Research

    Ontologies are useful in many branches of biomedical research. For instance, in the vaccine domain, the community-based Vaccine Ontology (VO) has been widely used to promote vaccine data standardization, integ...

    Authors: Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala and Hongfang Liu

    Citation: Journal of Biomedical Semantics 2013 4:33

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  11. Content type: Research

    The African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Xenopus research contributes to the understanding of genetic, developmental and molecular mechanisms underlying...

    Authors: Erik Segerdell, Virgilio G Ponferrada, Christina James-Zorn, Kevin A Burns, Joshua D Fortriede, Wasila M Dahdul, Peter D Vize and Aaron M Zorn

    Citation: Journal of Biomedical Semantics 2013 4:31

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  12. Content type: Research

    Anatomy ontologies are query-able classifications of anatomical structures. They provide a widely-used means for standardising the annotation of phenotypes and expression in both human-readable and programmati...

    Authors: Marta Costa, Simon Reeve, Gary Grumbling and David Osumi-Sutherland

    Citation: Journal of Biomedical Semantics 2013 4:32

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  13. Content type: Research

    Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to...

    Authors: David Osumi-Sutherland, Steven J Marygold, Gillian H Millburn, Peter A McQuilton, Laura Ponting, Raymund Stefancsik, Kathleen Falls, Nicholas H Brown and Georgios V Gkoutos

    Citation: Journal of Biomedical Semantics 2013 4:30

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  14. Content type: Research

    Large-scale mutagenesis projects are ongoing to improve our understanding about the pathology and subsequently the treatment of diseases. Such projects do not only record the genotype but also report phenotype...

    Authors: Anika Oellrich, Christoph Grabmüller and Dietrich Rebholz-Schuhmann

    Citation: Journal of Biomedical Semantics 2013 4:29

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  15. Content type: Research

    The identification of protein and gene names (PGNs) from the scientific literature requires semantic resources: Terminological and lexical resources deliver the term candidates into PGN tagging solutions and t...

    Authors: Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno Yepes, Robert Hoehndorf, Rolf Backofen and Ian Lewin

    Citation: Journal of Biomedical Semantics 2013 4:28

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  16. Content type: Research

    The increasing amount of textual information in biomedicine requires effective term recognition methods to identify textual representations of domain-specific concepts as the first step toward automating its s...

    Authors: Irena Spasić, Mark Greenwood, Alun Preece, Nick Francis and Glyn Elwyn

    Citation: Journal of Biomedical Semantics 2013 4:27

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  17. Content type: Research

    Biobanks are a critical resource for translational science. Recently, semantic web technologies such as ontologies have been found useful in retrieving research data from biobanks. However, recent research has...

    Authors: Mathias Brochhausen, Martin N Fransson, Nitin V Kanaskar, Mikael Eriksson, Roxana Merino-Martinez, Roger A Hall, Loreana Norlin, Sanela Kjellqvist, Maria Hortlund, Umit Topaloglu, William R Hogan and Jan-Eric Litton

    Citation: Journal of Biomedical Semantics 2013 4:23

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  18. Content type: Research

    Enrichment analysis is well established in the field of transcriptomics, where it is used to identify relevant biological features that characterize a set of genes obtained in an experiment.

    Authors: Catia M Machado, Ana T Freitas and Francisco M Couto

    Citation: Journal of Biomedical Semantics 2013 4:21

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  19. Content type: Research

    The Clinical Measurement Ontology (CMO), Measurement Method Ontology (MMO), and Experimental Condition Ontology (XCO) were originally developed at the Rat Genome Database (RGD) to standardize quantitative rat ...

    Authors: Jennifer R Smith, Carissa A Park, Rajni Nigam, Stanley JF Laulederkind, G Thomas Hayman, Shur-Jen Wang, Timothy F Lowry, Victoria Petri, Jeff De Pons, Marek Tutaj, Weisong Liu, Elizabeth A Worthey, Mary Shimoyama and Melinda R Dwinell

    Citation: Journal of Biomedical Semantics 2013 4:26

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  20. Content type: Research

    Understanding, modelling and influencing the transition between different states of cells, be it reprogramming of somatic cells to pluripotency or trans-differentiation between cells, is a hot topic in current...

    Authors: Georg Fuellen, Ludger Jansen, Ulf Leser and Andreas Kurtz

    Citation: Journal of Biomedical Semantics 2013 4:25

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  21. Content type: Database

    The Gene Ontology (GO) (http://​www.​geneontology.​org/​) contains a set of terms for describing the activity and actions of gene products across all kingd...

    Authors: Paola Roncaglia, Maryann E Martone, David P Hill, Tanya Z Berardini, Rebecca E Foulger, Fahim T Imam, Harold Drabkin, Christopher J Mungall and Jane Lomax

    Citation: Journal of Biomedical Semantics 2013 4:20

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  22. Content type: Research

    Clinical trials are important for patients, for researchers and for companies. One of the major bottlenecks is patient recruitment. This task requires the matching of a large volume of information about the pa...

    Authors: Olivier Dameron, Paolo Besana, Oussama Zekri, Annabel Bourdé, Anita Burgun and Marc Cuggia

    Citation: Journal of Biomedical Semantics 2013 4:17

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  23. Content type: Software

    Named entity recognition (NER) is an essential step in automatic text processing pipelines. A number of solutions have been presented and evaluated against gold standard corpora (GSC). The benchmarking against...

    Authors: Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Antonio Jimeno Yepes and Ian Lewin

    Citation: Journal of Biomedical Semantics 2013 4:19

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  24. Content type: Database

    The capture and use of disease-related anatomic pathology data for both model organism phenotyping and human clinical practice requires a relatively simple nomenclature and coding system that can be integrated...

    Authors: Paul N Schofield, John P Sundberg, Beth A Sundberg, Colin McKerlie and Georgios V Gkoutos

    Citation: Journal of Biomedical Semantics 2013 4:18

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  25. Content type: Short Report

    With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on I...

    Authors: Pantelis Topalis, Elvira Mitraka, Vicky Dritsou, Emmanuel Dialynas and Christos Louis

    Citation: Journal of Biomedical Semantics 2013 4:16

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  26. Content type: Short Report

    The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy provides a standard nomenclature for describing normal and mutant mouse embryo anatomy. The ontology forms the core of the EMAP ...

    Authors: Terry F Hayamizu, Michael N Wicks, Duncan R Davidson, Albert Burger, Martin Ringwald and Richard A Baldock

    Citation: Journal of Biomedical Semantics 2013 4:15

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  27. Content type: Research

    A variety of informatics approaches have been developed that use information retrieval, NLP and text-mining techniques to identify biomedical concepts and relations within scientific publications or their sent...

    Authors: Saeed Hassanpour, Martin J O’Connor and Amar K Das

    Citation: Journal of Biomedical Semantics 2013 4:14

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  28. Content type: Database

    The use of ontologies to standardize biological data and facilitate comparisons among datasets has steadily grown as the complexity and amount of available data have increased. Despite the numerous ontologies ...

    Authors: Carissa A Park, Susan M Bello, Cynthia L Smith, Zhi-Liang Hu, Diane H Munzenmaier, Rajni Nigam, Jennifer R Smith, Mary Shimoyama, Janan T Eppig and James M Reecy

    Citation: Journal of Biomedical Semantics 2013 4:13

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  29. Content type: Research

    Open metadata registries are a fundamental tool for researchers in the Life Sciences trying to locate resources. While most current registries assume that resources are annotated with well-structured metadata,...

    Authors: María Pérez, Rafael Berlanga, Ismael Sanz and María José Aramburu

    Citation: Journal of Biomedical Semantics 2013 4:12

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  30. Content type: Proceedings

    The World Wide Web has become a dissemination platform for scientific and non-scientific publications. However, most of the information remains locked up in discrete documents that are not always interconnecte...

    Authors: L Jael Garcia Castro, C McLaughlin and A Garcia

    Citation: Journal of Biomedical Semantics 2013 4(Suppl 1):S5

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    This article is part of a Supplement: Volume 4 Supplement 1

  31. Content type: Proceedings

    Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving reca...

    Authors: Daniel Eisinger, George Tsatsaronis, Markus Bundschus, Ulrich Wieneke and Michael Schroeder

    Citation: Journal of Biomedical Semantics 2013 4(Suppl 1):S3

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    This article is part of a Supplement: Volume 4 Supplement 1

  32. Content type: Proceedings

    A key activity for life scientists in this post “-omics” age involves searching for and integrating biological data from a multitude of independent databases. However, our ability to find relevant data is hamp...

    Authors: Alison Callahan, José Cruz-Toledo and Michel Dumontier

    Citation: Journal of Biomedical Semantics 2013 4(Suppl 1):S1

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    This article is part of a Supplement: Volume 4 Supplement 1

  33. Content type: Proceedings

    The theory of probability is widely used in biomedical research for data analysis and modelling. In previous work the probabilities of the research hypotheses have been recorded as experimental metadata. The o...

    Authors: Larisa N. Soldatova, Andrey Rzhetsky, Kurt De Grave and Ross D King

    Citation: Journal of Biomedical Semantics 2013 4(Suppl 1):S7

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    This article is part of a Supplement: Volume 4 Supplement 1

  34. Content type: Commentary

    Ontologies categorize entities, express relationships between them, and provide standardized definitions. Thus, they can be used to present and enforce the specific relationships between database components. T...

    Authors: Randi Vita, James A. Overton, Jason A. Greenbaum, Alessandro Sette and Bjoern Peters

    Citation: Journal of Biomedical Semantics 2013 4(Suppl 1):S6

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    This article is part of a Supplement: Volume 4 Supplement 1

  35. Content type: Proceedings

    The Gene Ontology and its associated annotations are critical tools for interpreting lists of genes. Here, we introduce a method for evaluating the Gene Ontology annotations and structure based on the impact t...

    Authors: Erik L Clarke, Salvatore Loguercio, Benjamin M Good and Andrew I Su

    Citation: Journal of Biomedical Semantics 2013 4(Suppl 1):S4

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    This article is part of a Supplement: Volume 4 Supplement 1

  36. Content type: Proceedings

    As the number and size of biological knowledge resources for physiology grows, researchers need improved tools for searching and integrating knowledge and physiological models. Unfortunately, current resources...

    Authors: Daniel L. Cook, Maxwell L. Neal, Robert Hoehndorf, Georgios V. Gkoutos and John H. Gennari

    Citation: Journal of Biomedical Semantics 2013 4(Suppl 1):S2

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    This article is part of a Supplement: Volume 4 Supplement 1

  37. Content type: Introduction

    Over the 15 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 2013 4(Suppl 1):I1

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    This article is part of a Supplement: Volume 4 Supplement 1

  38. Content type: Research

    Clinical Intelligence, as a research and engineering discipline, is dedicated to the development of tools for data analysis for the purposes of clinical research, surveillance, and effective health care manage...

    Authors: Alexandre Riazanov, Artjom Klein, Arash Shaban-Nejad, Gregory W Rose, Alan J Forster, David L Buckeridge and Christopher JO Baker

    Citation: Journal of Biomedical Semantics 2013 4:9

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  39. Content type: Research

    There is a growing need for efficient and integrated access to databases provided by diverse institutions. Using a linked data design pattern allows the diverse data on the Internet to be linked effectively an...

    Authors: Yasunori Yamamoto, Atsuko Yamaguchi and Akinori Yonezawa

    Citation: Journal of Biomedical Semantics 2013 4:8

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  40. Content type: Software

    U-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. U-Compare contains a large library of components that are tuned to the biomedical domain. U...

    Authors: Georgios Kontonatsios, Ioannis Korkontzelos, BalaKrishna Kolluru, Paul Thompson and Sophia Ananiadou

    Citation: Journal of Biomedical Semantics 2013 4:7

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  41. Content type: Review

    BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and access...

    Authors: Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau…

    Citation: Journal of Biomedical Semantics 2013 4:6

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  42. Content type: Research

    Out-of-date or incomplete drug product labeling information may increase the risk of otherwise preventable adverse drug events. In recognition of these concerns, the United States Federal Drug Administration (...

    Authors: Richard D Boyce, John R Horn, Oktie Hassanzadeh, Anita De Waard, Jodi Schneider, Joanne S Luciano, Majid Rastegar-Mojarad and Maria Liakata

    Citation: Journal of Biomedical Semantics 2013 4:5

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  43. Content type: Research

    The availability of annotated corpora has facilitated the application of machine learning algorithms to concept extraction from clinical notes. However, high expenditure and labor are required for creating the...

    Authors: Kavishwar B Wagholikar, Manabu Torii, Siddhartha R Jonnalagadda and Hongfang Liu

    Citation: Journal of Biomedical Semantics 2013 4:3

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  44. Content type: Software

    Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in partic...

    Authors: Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Chris Mungall, Erick Antezana, Alejandro Rodríguez González and Mark D Wilkinson

    Citation: Journal of Biomedical Semantics 2013 4:2

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