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  1. Experimental research on the automatic extraction of information about mutations from texts is greatly hindered by the lack of consensus evaluation infrastructure for the testing and benchmarking of mutation t...

    Authors: Artjom Klein, Alexandre Riazanov, Matthew M Hindle and Christopher JO Baker

    Citation: Journal of Biomedical Semantics 2014 5:11

    Content type: Research

    Published on:

  2. Systematic representation of information related to genetic and non-genetic variations is required to allow large scale studies, data mining and data integration, and to make it possible to reveal novel relati...

    Authors: Mauno Vihinen

    Citation: Journal of Biomedical Semantics 2014 5:9

    Content type: Software

    Published on:

  3. Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information. With the currently existing wealth of formalised knowledge, the ability to ...

    Authors: Razan Paul, Tudor Groza, Jane Hunter and Andreas Zankl

    Citation: Journal of Biomedical Semantics 2014 5:8

    Content type: Research

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  4. The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hier...

    Authors: Victoria Petri, Pushkala Jayaraman, Marek Tutaj, G Thomas Hayman, Jennifer R Smith, Jeff De Pons, Stanley JF Laulederkind, Timothy F Lowry, Rajni Nigam, Shur-Jen Wang, Mary Shimoyama, Melinda R Dwinell, Diane H Munzenmaier, Elizabeth A Worthey and Howard J Jacob

    Citation: Journal of Biomedical Semantics 2014 5:7

    Content type: Research

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  5. Terminologies that account for variation in language use by linking synonyms and abbreviations to their corresponding concept are important enablers of high-quality information extraction from medical texts. D...

    Authors: Aron Henriksson, Hans Moen, Maria Skeppstedt, Vidas Daudaravičius and Martin Duneld

    Citation: Journal of Biomedical Semantics 2014 5:6

    Content type: Research

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  6. The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHac...

    Authors: Toshiaki Katayama, Mark D Wilkinson, Kiyoko F Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts…

    Citation: Journal of Biomedical Semantics 2014 5:5

    Content type: Review

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  7. Epidemiology is a data-intensive and multi-disciplinary subject, where data integration, curation and sharing are becoming increasingly relevant, given its global context and time constraints. The semantic ann...

    Authors: Catia Pesquita, João D Ferreira, Francisco M Couto and Mário J Silva

    Citation: Journal of Biomedical Semantics 2014 5:4

    Content type: Research

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  8. Identifying phrases that refer to particular concept types is a critical step in extracting information from documents. Provided with annotated documents as training data, supervised machine learning can autom...

    Authors: Manabu Torii, Kavishwar Wagholikar and Hongfang Liu

    Citation: Journal of Biomedical Semantics 2014 5:3

    Content type: Research

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  9. Natural human languages show a power law behaviour in which word frequency (in any large enough corpus) is inversely proportional to word rank - Zipf’s law. We have therefore asked whether similar power law be...

    Authors: Leila R Kalankesh, John P New, Patricia G Baker and Andy Brass

    Citation: Journal of Biomedical Semantics 2014 5:2

    Content type: Research

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  10. The diverse set of human brain structure and function analysis methods represents a difficult challenge for reconciling multiple views of neuroanatomical organization. While different views of organization are...

    Authors: B Nolan Nichols, Jose LV Mejino, Landon T Detwiler, Trond T Nilsen, Maryann E Martone, Jessica A Turner, Daniel L Rubin and James F Brinkley

    Citation: Journal of Biomedical Semantics 2014 5:1

    Content type: Database

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  11. We built the Drug Ontology (DrOn) because we required correct and consistent drug information in a format for use in semantic web applications, and no existing resource met this requirement or could be altered...

    Authors: Josh Hanna, Eric Joseph, Mathias Brochhausen and William R Hogan

    Citation: Journal of Biomedical Semantics 2013 4:44

    Content type: Research

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  12. As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growi...

    Authors: Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J Mungall and Suzanna E Lewis

    Citation: Journal of Biomedical Semantics 2013 4:43

    Content type: Research

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  13. 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

    Content type: Database

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  14. 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

    Content type: Research

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  15. 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

    Content type: Research

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  16. 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

    Content type: Short Report

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  17. 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

    Content type: Research

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  18. 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

    Content type: Research

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  19. 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

    Content type: Database

    Published on:

  20. 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

    Content type: Research

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  21. 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

    Content type: Database

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  22. 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

    Content type: Research

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  23. 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

    Content type: Research

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  24. 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

    Content type: Research

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  25. 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

    Content type: Research

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  26. 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

    Content type: Research

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  27. 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

    Content type: Research

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  28. 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

    Content type: Research

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  29. 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

    Content type: Research

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  30. 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

    Content type: Research

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  31. 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

    Content type: Research

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  32. 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

    Content type: Research

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  33. 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

    Content type: Database

    Published on:

  34. 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

    Content type: Software

    Published on:

  35. 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

    Content type: Database

    Published on:

  36. 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

    Content type: Research

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  37. 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

    Content type: Short Report

    Published on:

  38. 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

    Content type: Short Report

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  39. 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

    Content type: Research

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  40. 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

    Content type: Database

    Published on:

  41. 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

    Content type: Research

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  42. 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

    Content type: Proceedings

    Published on:

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

  43. 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

    Content type: Commentary

    Published on:

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

  44. 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

    Content type: Proceedings

    Published on:

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

  45. 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

    Content type: Proceedings

    Published on:

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

  46. 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

    Content type: Introduction

    Published on:

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

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