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  1. Content type: Research

    Biobanking necessitates extensive integration of data to allow data analysis and specimen sharing. Ontologies have been demonstrated to be a promising approach in fostering better semantic integration of bioba...

    Authors: Mathias Brochhausen, Jie Zheng, David Birtwell, Heather Williams, Anna Maria Masci, Helena Judge Ellis and Christian J. Stoeckert Jr.

    Citation: Journal of Biomedical Semantics 2016 7:23

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  2. Content type: Research

    MicroRNAs are increasingly being appreciated as critical players in human diseases, and questions concerning the role of microRNAs arise in many areas of biomedical research. There are several manually curated...

    Authors: Samir Gupta, Karen E. Ross, Catalina O. Tudor, Cathy H. Wu, Carl J. Schmidt and K. Vijay-Shanker

    Citation: Journal of Biomedical Semantics 2016 7:9

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  3. Content type: Research

    Biomedical text mining may target various kinds of valuable information embedded in the literature, but a critical obstacle to the extension of the mining targets is the cost of manual construction of labeled ...

    Authors: Xu Han, Jung-jae Kim and Chee Keong Kwoh

    Citation: Journal of Biomedical Semantics 2016 7:22

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  4. Content type: Research

    In previous work, we built the Drug Ontology (DrOn) to support comparative effectiveness research use cases. Here, we have updated our representation of ingredients to include both active ingredients (and thei...

    Authors: Josh Hanna, Jiang Bian and William R. Hogan

    Citation: Journal of Biomedical Semantics 2016 7:7

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  5. Content type: Research

    To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts ...

    Authors: Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E. Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B. Gerstein, Andrew F. Hill, Robert R. Kitchen, Jan Lötvall, Tushar Patel…

    Citation: Journal of Biomedical Semantics 2016 7:19

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  6. Content type: Research

    MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium in...

    Authors: Carrine E. Blank, Hong Cui, Lisa R. Moore and Ramona L. Walls

    Citation: Journal of Biomedical Semantics 2016 7:18

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  7. Content type: Software

    The Simple Knowledge Organization System (SKOS) was introduced to the wider research community by a 2005 World Wide Web Consortium (W3C) working draft, and further developed and refined in a 2009 W3C recommend...

    Authors: Mike Conway, Artem Khojoyan, Fariba Fana, William Scuba, Melissa Castine, Danielle Mowery, Wendy Chapman and Simon Jupp

    Citation: Journal of Biomedical Semantics 2016 7:5

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  8. Content type: Software

    Authoring bio-ontologies is a task that has traditionally been undertaken by skilled experts trained in understanding complex languages such as the Web Ontology Language (OWL), in tools designed for such exper...

    Authors: Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen Parkinson and James Malone

    Citation: Journal of Biomedical Semantics 2016 7:17

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  9. Content type: Research

    There have been relatively few attempts to represent vision or blindness ontologically. This is unsurprising as the related phenomena of sight and blindness are difficult to represent ontologically for a varie...

    Authors: Patrick L. Ray, Alexander P. Cox, Mark Jensen, Travis Allen, William Duncan and Alexander D. Diehl

    Citation: Journal of Biomedical Semantics 2016 7:15

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  10. Content type: Research

    The Centre for Therapeutic Target Validation (CTTV - https://​www.​targetvalidation​.​org/​) was established to generate therapeutic target evidence from ge...

    Authors: Sirarat Sarntivijai, Drashtti Vasant, Simon Jupp, Gary Saunders, A. Patrícia Bento, Daniel Gonzalez, Joanna Betts, Samiul Hasan, Gautier Koscielny, Ian Dunham, Helen Parkinson and James Malone

    Citation: Journal of Biomedical Semantics 2016 7:8

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  11. Content type: Research

    Information about drug–drug interactions (DDIs) is crucial for computational applications such as pharmacovigilance and drug repurposing. However, existing sources of DDIs have the problems of low coverage, lo...

    Authors: Yaoyun Zhang, Heng-Yi Wu, Jingcheng Du, Jun Xu, Jingqi Wang, Cui Tao, Lang Li and Hua Xu

    Citation: Journal of Biomedical Semantics 2016 7:11

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    The Erratum to this article has been published in Journal of Biomedical Semantics 2016 7:21

  12. Content type: Research

    The Biomedical Research Integrated Domain Group (BRIDG) model is a formal domain analysis model for protocol-driven biomedical research, and serves as a semantic foundation for application and message developm...

    Authors: Guoqian Jiang, Julie Evans, Cory M. Endle, Harold R. Solbrig and Christopher G. Chute

    Citation: Journal of Biomedical Semantics 2016 7:10

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  13. Content type: Editorial

    The “Vaccine and Drug Ontology Studies” (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have been critical to prevent and treat ...

    Authors: Cui Tao, Yongqun He and Sivaram Arabandi

    Citation: Journal of Biomedical Semantics 2016 7:6

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  14. Content type: Research

    Identifying partial mappings between two terminologies is of special importance when one terminology is finer-grained than the other, as is the case for the Human Phenotype Ontology (HPO), mainly used for rese...

    Authors: Ferdinand Dhombres and Olivier Bodenreider

    Citation: Journal of Biomedical Semantics 2016 7:3

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  15. Content type: Research

    It has been shown that exergames have multiple benefits for physical, mental and cognitive health. Only recently, however, researchers have started considering them as health monitoring tools, through collecti...

    Authors: Giorgos Bamparopoulos, Evdokimos Konstantinidis, Charalampos Bratsas and Panagiotis D. Bamidis

    Citation: Journal of Biomedical Semantics 2016 7:4

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    The Erratum to this article has been published in Journal of Biomedical Semantics 2016 7:31

  16. Content type: Review

    Genotype-phenotype studies aim to identify causative relationships between genes and phenotypes. The International Mouse Phenotyping Consortium is a high throughput phenotyping program whose goal is to collect...

    Authors: Anika Oellrich, Terrence F. Meehan, Helen Parkinson, Sirarat Sarntivijai, Jacqueline K. White and Natasha A. Karp

    Citation: Journal of Biomedical Semantics 2016 7:2

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  17. Content type: Database

    MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s)...

    Authors: Randi Vita, James A. Overton, Emily Seymour, John Sidney, Jim Kaufman, Rebecca L. Tallmadge, Shirley Ellis, John Hammond, Geoff W. Butcher, Alessandro Sette and Bjoern Peters

    Citation: Journal of Biomedical Semantics 2016 7:1

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  18. Content type: Research

    The specification of metadata in clinical and epidemiological study projects absorbs significant expense. The validity and quality of the collected data depend heavily on the precise and semantical correct rep...

    Authors: Alexandr Uciteli and Heinrich Herre

    Citation: Journal of Biomedical Semantics 2015 6:41

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  19. Content type: Review

    The bio-ontologies and phenotypes special issue includes eight papers selected from the 11 papers presented at the Bio-Ontologies SIG (Special Interest Group) and the Phenotype Day at ISMB (Intelligent Systems...

    Authors: Larisa N. Soldatova, Nigel Collier, Anika Oellrich, Tudor Groza, Karin Verspoor, Philippe Rocca-Serra, Michel Dumontier and Nigam H. Shah

    Citation: Journal of Biomedical Semantics 2015 6:40

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  20. Content type: Software

    Semantic web technologies have a tremendous potential for the integration of heterogeneous data sets. Therefore, an increasing number of widely used biological resources are becoming available in the RDF data ...

    Authors: Jesse CJ van Dam, Jasper J Koehorst, Peter J Schaap, Vitor AP Martins dos Santos and Maria Suarez-Diez

    Citation: Journal of Biomedical Semantics 2015 6:39

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  21. Content type: Research

    Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physicall...

    Authors: Pierre-Yves Rabattu, Benoit Massé, Federico Ulliana, Marie-Christine Rousset, Damien Rohmer, Jean-Claude Léon and Olivier Palombi

    Citation: Journal of Biomedical Semantics 2015 6:36

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Page 6 of 17

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