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Journal of Biomedical Semantics


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  1. Content type: Research

    The motivation for the BioHub project is to create an Integrated Knowledge Management System (IKMS) that will enable chemists to source ingredients from bio-renewables, rather than from non-sustainable sources...

    Authors: Warren J. Read, George Demetriou, Goran Nenadic, Noel Ruddock, Robert Stevens and Jerry Winter

    Citation: Journal of Biomedical Semantics 2016 7:30

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  2. Content type: Research

    Neuropathy often occurs following drug treatment such as chemotherapy. Severe instances of neuropathy can result in cessation of life-saving chemotherapy treatment.

    Authors: Abra Guo, Rebecca Racz, Junguk Hur, Yu Lin, Zuoshuang Xiang, Lili Zhao, Jordan Rinder, Guoqian Jiang, Qian Zhu and Yongqun He

    Citation: Journal of Biomedical Semantics 2016 7:29

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  3. Content type: Database

    Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, s...

    Authors: Simon Jupp, James Malone, Tony Burdett, Jean-Karim Heriche, Eleanor Williams, Jan Ellenberg, Helen Parkinson and Gabriella Rustici

    Citation: Journal of Biomedical Semantics 2016 7:28

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  4. Content type: Research

    Biomedical event extraction is one of the key tasks in biomedical text mining, supporting various applications such as database curation and hypothesis generation. Several systems, some of which have been appl...

    Authors: Farrokh Mehryary, Suwisa Kaewphan, Kai Hakala and Filip Ginter

    Citation: Journal of Biomedical Semantics 2016 7:27

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  5. Content type: Research

    As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs re...

    Authors: Jingshan Huang, Fernando Gutierrez, Harrison J. Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Yu Lin, Bin Wu, Nisansa de Silva, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan…

    Citation: Journal of Biomedical Semantics 2016 7:25

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  6. Content type: Research

    In the United States, 795,000 people suffer strokes each year; 10–15 % of these strokes can be attributed to stenosis caused by plaque in the carotid artery, a major stroke phenotype risk factor. Studies compa...

    Authors: Danielle L. Mowery, Brian E. Chapman, Mike Conway, Brett R. South, Erin Madden, Salomeh Keyhani and Wendy W. Chapman

    Citation: Journal of Biomedical Semantics 2016 7:26

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  7. Content type: Short report

    The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data ...

    Authors: Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima and Toshimichi Fujiwara

    Citation: Journal of Biomedical Semantics 2016 7:16

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  8. Content type: Research

    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identificat...

    Authors: Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Yongqun He, Shaojie Zhang…

    Citation: Journal of Biomedical Semantics 2016 7:24

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  9. Content type: Research

    The public health initiatives for obesity prevention are increasingly exploiting the advantages of smart technologies that can register various kinds of data related to physical, physiological, and behavioural...

    Authors: Aleksandra Sojic, Walter Terkaj, Giorgia Contini and Marco Sacco

    Citation: Journal of Biomedical Semantics 2016 7:12

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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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

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