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  1. Content type: Research

    Vaccine has been one of the most successful public health interventions to date. However, vaccines are pharmaceutical products that carry risks so that many adverse events (AEs) are reported after receiving va...

    Authors: Junxiang Wang, Liang Zhao, Yanfang Ye and Yuji Zhang

    Citation: Journal of Biomedical Semantics 2018 9:19

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  2. Content type: Research

    In recent years, Twitter has been applied to monitor diseases through its facility to monitor users’ comments and concerns in real-time. The analysis of tweets for disease mentions should reflect not only user...

    Authors: Joana M. Barros, Jim Duggan and Dietrich Rebholz-Schuhmann

    Citation: Journal of Biomedical Semantics 2018 9:18

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  3. Content type: Research

    Adverse drug reactions (ADRs), also called as drug adverse events (AEs), are reported in the FDA drug labels; however, it is a big challenge to properly retrieve and analyze the ADRs and their potential relati...

    Authors: Junguk Hur, Arzucan Özgür and Yongqun He

    Citation: Journal of Biomedical Semantics 2018 9:17

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  4. Content type: Research

    Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of usin...

    Authors: Stefan Kropf, Alexandr Uciteli, Katrin Schierle, Peter Krücken, Kerstin Denecke and Heinrich Herre

    Citation: Journal of Biomedical Semantics 2018 9:16

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  5. Content type: Research

    Prompted by the frequency of concomitant use of prescription drugs with natural products, and the lack of knowledge regarding the impact of pharmacokinetic-based natural product-drug interactions (PK-NPDIs), t...

    Authors: John Judkins, Jessica Tay-Sontheimer, Richard D. Boyce and Mathias Brochhausen

    Citation: Journal of Biomedical Semantics 2018 9:15

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  6. Content type: Research

    Inherited mutations in glyco-related genes can affect the biosynthesis and degradation of glycans and result in severe genetic diseases and disorders. The Glyco-Disease Genes Database (GDGDB), which provides i...

    Authors: Elena Solovieva, Toshihide Shikanai, Noriaki Fujita and Hisashi Narimatsu

    Citation: Journal of Biomedical Semantics 2018 9:14

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  7. Content type: Research

    Automatic identification of term variants or acceptable alternative free-text terms for gene and protein names from the millions of biomedical publications is a challenging task. Ontologies, such as the Cardio...

    Authors: Mercedes Arguello Casteleiro, George Demetriou, Warren Read, Maria Jesus Fernandez Prieto, Nava Maroto, Diego Maseda Fernandez, Goran Nenadic, Julie Klein, John Keane and Robert Stevens

    Citation: Journal of Biomedical Semantics 2018 9:13

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  8. Content type: Review

    Natural language processing applied to clinical text or aimed at a clinical outcome has been thriving in recent years. This paper offers the first broad overview of clinical Natural Language Processing (NLP) f...

    Authors: Aurélie Névéol, Hercules Dalianis, Sumithra Velupillai, Guergana Savova and Pierre Zweigenbaum

    Citation: Journal of Biomedical Semantics 2018 9:12

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  9. Content type: Research

    The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed...

    Authors: Mengyi Zhao, Songmao Zhang, Weizhuo Li and Guowei Chen

    Citation: Journal of Biomedical Semantics 2018 9:11

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  10. Content type: Research

    The Gene Ontology (GO) consists of over 40,000 terms for biological processes, cell components and gene product activities linked into a graph structure by over 90,000 relationships. It has been used to annota...

    Authors: David J. Osumi-Sutherland, Enrico Ponta, Melanie Courtot, Helen Parkinson and Laura Badi

    Citation: Journal of Biomedical Semantics 2018 9:10

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  11. Content type: Research

    Pathogenesis of inflammatory diseases can be tracked by studying the causality relationships among the factors contributing to its development. We could, for instance, hypothesize on the connections of the pat...

    Authors: Asan Agibetov, Ernesto Jiménez-Ruiz, Marta Ondrésik, Alessandro Solimando, Imon Banerjee, Giovanna Guerrini, Chiara E. Catalano, Joaquim M. Oliveira, Giuseppe Patanè, Rui L. Reis and Michela Spagnuolo

    Citation: Journal of Biomedical Semantics 2018 9:9

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  12. Content type: Research

    Treatment of type 2 diabetes mellitus (T2DM) is a complex problem. A clinical decision support system (CDSS) based on massive and distributed electronic health record data can facilitate the automation of this...

    Authors: Shaker El-Sappagh, Daehan Kwak, Farman Ali and Kyung-Sup Kwak

    Citation: Journal of Biomedical Semantics 2018 9:8

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  13. Content type: Research

    Relation extraction from biomedical publications is an important task in the area of semantic mining of text. Kernel methods for supervised relation extraction are often preferred over manual feature engineeri...

    Authors: Nagesh C. Panyam, Karin Verspoor, Trevor Cohn and Kotagiri Ramamohanarao

    Citation: Journal of Biomedical Semantics 2018 9:7

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  14. Content type: Research

    The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the ba...

    Authors: Viktor Senderov, Kiril Simov, Nico Franz, Pavel Stoev, Terry Catapano, Donat Agosti, Guido Sautter, Robert A. Morris and Lyubomir Penev

    Citation: Journal of Biomedical Semantics 2018 9:5

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  15. Content type: Research

    Biomedical ontologies pose several challenges to ontology matching due both to the complexity of the biomedical domain and to the characteristics of the ontologies themselves. The biomedical tracks in the Onto...

    Authors: Daniel Faria, Catia Pesquita, Isabela Mott, Catarina Martins, Francisco M. Couto and Isabel F. Cruz

    Citation: Journal of Biomedical Semantics 2018 9:4

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  16. Content type: Review

    Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interop...

    Authors: Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A. Overton and Edison Ong

    Citation: Journal of Biomedical Semantics 2018 9:3

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  17. Content type: Research

    Traditionally text mention normalization corpora have normalized concepts to single ontology identifiers (“pre-coordinated concepts”). Less frequently, normalization corpora have used concepts with multiple id...

    Authors: John D. Osborne, Matthew B. Neu, Maria I. Danila, Thamar Solorio and Steven J. Bethard

    Citation: Journal of Biomedical Semantics 2018 9:2

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  18. Content type: Research

    Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomica...

    Authors: Miguel Ángel Rodríguez-García, Georgios V. Gkoutos, Paul N. Schofield and Robert Hoehndorf

    Citation: Journal of Biomedical Semantics 2017 8:58

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  19. Content type: Research

    One important type of information contained in biomedical research literature is the newly discovered relationships between phenotypes and genotypes. Because of the large quantity of literature, a reliable aut...

    Authors: Maryam Khordad and Robert E. Mercer

    Citation: Journal of Biomedical Semantics 2017 8:57

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  20. Content type: Research

    The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important f...

    Authors: Ian Harrow, Ernesto Jiménez-Ruiz, Andrea Splendiani, Martin Romacker, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, James Malone and Arild Waaler

    Citation: Journal of Biomedical Semantics 2017 8:55

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  21. Content type: Research

    There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, ...

    Authors: Aisha Blfgeh, Jennifer Warrender, Catharien M. U. Hilkens and Phillip Lord

    Citation: Journal of Biomedical Semantics 2017 8:54

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  22. Content type: Research

    High-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these data together with biological knowledge is a critical issue in biology and requires ...

    Authors: Vincent J. Henry, Anne Goelzer, Arnaud Ferré, Stephan Fischer, Marc Dinh, Valentin Loux, Christine Froidevaux and Vincent Fromion

    Citation: Journal of Biomedical Semantics 2017 8:53

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