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  1. Content type: Database

    The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and ex...

    Authors: Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky, Melissa A. Haendel, Judith A. Blake and Christopher J. Mungall

    Citation: Journal of Biomedical Semantics 2016 7:44

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  2. Content type: Research

    The ShARe/CLEF eHealth challenge lab aims to stimulate development of natural language processing and information retrieval technologies to aid patients in understanding their clinical reports. In clinical tex...

    Authors: Danielle L. Mowery, Brett R. South, Lee Christensen, Jianwei Leng, Laura-Maria Peltonen, Sanna Salanterä, Hanna Suominen, David Martinez, Sumithra Velupillai, Noémie Elhadad, Guergana Savova, Sameer Pradhan and Wendy W. Chapman

    Citation: Journal of Biomedical Semantics 2016 7:43

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  3. Content type: Research

    Biological sequences, such as proteins, have been provided with annotations that assign functional information. These functional annotations are associations of proteins (or other biological sequences) with de...

    Authors: Hugo P. Bastos, Lisete Sousa, Luka A. Clarke and Francisco M. Couto

    Citation: Journal of Biomedical Semantics 2016 7:41

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  4. Content type: Software

    Clinical Natural Language Processing (NLP) systems require a semantic schema comprised of domain-specific concepts, their lexical variants, and associated modifiers to accurately extract information from clini...

    Authors: William Scuba, Melissa Tharp, Danielle Mowery, Eugene Tseytlin, Yang Liu, Frank A. Drews and Wendy W. Chapman

    Citation: Journal of Biomedical Semantics 2016 7:42

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  5. Content type: Research

    There have been repeated initiatives to produce standard nosologies and terminologies for cutaneous disease, some dedicated to the domain and some part of bigger terminologies such as ICD-10. Recently, formall...

    Authors: Hannah M. Fisher, Robert Hoehndorf, Bruno S. Bazelato, Soheil S. Dadras, Lloyd E. King Jr., Georgios V. Gkoutos, John P. Sundberg and Paul N. Schofield

    Citation: Journal of Biomedical Semantics 2016 7:38

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  6. Content type: Research

    Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, the...

    Authors: Jerven T. Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul J. P. Bonnal, Robert Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama and Peter J. A. Cock

    Citation: Journal of Biomedical Semantics 2016 7:39

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  7. Content type: Research

    Clinical practice guidelines (CPGs) recommend pharmacologic treatments for clinical conditions, and drug structured product labels (SPLs) summarize approved treatment indications. Both resources are intended t...

    Authors: Tiffany I. Leung and Michel Dumontier

    Citation: Journal of Biomedical Semantics 2016 7:37

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  8. Content type: Software

    High throughput imaging is now available to many groups and it is possible to generate a large quantity of high quality images quickly. Managing this data, consistently annotating it, or making it available to...

    Authors: Solomon Adebayo, Kenneth McLeod, Ilinca Tudose, David Osumi-Sutherland, Tony Burdett, Richard Baldock, Albert Burger and Helen Parkinson

    Citation: Journal of Biomedical Semantics 2016 7:35

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  9. Content type: Research

    Computational comparative analysis of multiple genomes provides valuable opportunities to biomedical research. In particular, orthology analysis can play a central role in comparative genomics; it guides estab...

    Authors: Jesualdo Tomás Fernández-Breis, Hirokazu Chiba, María del Carmen Legaz-García and Ikuo Uchiyama

    Citation: Journal of Biomedical Semantics 2016 7:34

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  10. Content type: Research

    The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases inv...

    Authors: Mercedes Arguello Casteleiro, Julie Klein and Robert Stevens

    Citation: Journal of Biomedical Semantics 2016 7:33

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  11. Content type: Research

    Biomedical research usually requires combining large volumes of data from multiple heterogeneous sources, which makes difficult the integrated exploitation of such data. The Semantic Web paradigm offers a natu...

    Authors: María del Carmen Legaz-García, José Antonio Miñarro-Giménez, Marcos Menárguez-Tortosa and Jesualdo Tomás Fernández-Breis

    Citation: Journal of Biomedical Semantics 2016 7:32

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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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Page 5 of 17

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