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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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

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

  15. 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

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

  16. 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

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

  17. 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

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

  18. 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

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

  19. 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

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

  20. 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

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

  21. 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

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

  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. One challenge in reusing clinical data stored in electronic medical records is that these data are heterogenous. Clinical Natural Language Processing (NLP) plays an important role in transforming information i...

    Authors: Stephen T Wu, Vinod C Kaggal, Dmitriy Dligach, James J Masanz, Pei Chen, Lee Becker, Wendy W Chapman, Guergana K Savova, Hongfang Liu and Christopher G Chute
    Citation: Journal of Biomedical Semantics 2013 4:1
  30. Fever is one of the most common adverse events of vaccines. The detailed mechanisms of fever and vaccine-associated gene interaction networks are not fully understood. In the present study, we employed a genom...

    Authors: Junguk Hur, Arzucan Özgür, Zuoshuang Xiang and Yongqun He
    Citation: Journal of Biomedical Semantics 2012 3:18
  31. Structured Product Labeling (SPL) is a document markup standard approved by Health Level Seven (HL7) and adopted by United States Food and Drug Administration (FDA) as a mechanism for exchanging drug product i...

    Authors: Qian Zhu, Guoqian Jiang and Christopher G Chute
    Citation: Journal of Biomedical Semantics 2012 3:16
  32. The sheer amount of information about potential adverse drug events publishedin medical case reports pose major challenges for drug safety experts toperform timely monitoring. Efficient strategies for identifi...

    Authors: Harsha Gurulingappa, Abdul Mateen‐Rajpu and Luca Toldo
    Citation: Journal of Biomedical Semantics 2012 3:15
  33. Identification of drug-drug and drug-diseases interactions can pose a difficult problem to cope with, as the increasingly large number of available drugs coupled with the ongoing research activities in the pha...

    Authors: Charalampos Doulaverakis, George Nikolaidis, Athanasios Kleontas and Ioannis Kompatsiaris
    Citation: Journal of Biomedical Semantics 2012 3:14
  34. The U.S. FDA/CDC Vaccine Adverse Event Reporting System (VAERS) provides a valuable data source for post-vaccination adverse event analyses. The structured data in the system has been widely used, but the info...

    Authors: Cui Tao, Yongqun He, Hannah Yang, Gregory A Poland and Christopher G Chute
    Citation: Journal of Biomedical Semantics 2012 3:13
  35. Vaccines and drugs have contributed to dramatic improvements in public health worldwide. Over the last decade, there have been efforts in developing biomedical ontologies that represent various areas associate...

    Authors: Yongqun He, Luca Toldo, Gully Burns, Cui Tao and Darrell R Abernethy
    Citation: Journal of Biomedical Semantics 2012 3:12
  36. As the “omics” revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope...

    Authors: Pedro Lopes and José Luís Oliveira
    Citation: Journal of Biomedical Semantics 2012 3:11
  37. The ability to conduct genome-wide association studies (GWAS) has enabled new exploration of how genetic variations contribute to health and disease etiology. However, historically GWAS have been limited by in...

    Authors: Jyotishman Pathak, Richard C Kiefer, Suzette J Bielinski and Christopher G Chute
    Citation: Journal of Biomedical Semantics 2012 3:10
  38. The amount of data generated from genome-wide association studies (GWAS) has grown rapidly, but considerations for GWAS phenotype data reuse and interchange have not kept pace. This impacts on the work of GWAS...

    Authors: Tim Beck, Robert C Free, Gudmundur A Thorisson and Anthony J Brookes
    Citation: Journal of Biomedical Semantics 2012 3:9
  39. In this paper we demonstrate the usage of RIO; a framework for detecting syntactic regularities using cluster analysis of the entities in the signature of an ontology. Quality assurance in ontologies is vital ...

    Authors: Eleni Mikroyannidi, Robert Stevens, Luigi Iannone and Alan Rector
    Citation: Journal of Biomedical Semantics 2012 3:8
  40. One of the key pieces of information which biomedical text mining systems are expected to extract from the literature are interactions among different types of biomedical entities (proteins, genes, diseases, d...

    Authors: Simon Clematide and Fabio Rinaldi
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 3):S5

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

  41. There are several humanly defined ontologies relevant to Medline. However, Medline is a fast growing collection of biomedical documents which creates difficulties in updating and expanding these humanly define...

    Authors: Lana Yeganova, Won Kim, Donald C Comeau and W John Wilbur
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 3):S3

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

  42. We propose a method for automatic extraction of protein-specific residue mentions from the biomedical literature. The method searches text for mentions of amino acids at specific sequence positions and attempt...

    Authors: KE Ravikumar, Haibin Liu, Judith D Cohn, Michael E Wall and Karin Verspoor
    Citation: Journal of Biomedical Semantics 2012 3(Suppl 3):S2

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

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