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Journal of Biomedical Semantics

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  1. Content type: Research

    In biomedical applications where the size and complexity of SNOMED CT become problematic, using a smaller subset that can act as a reasonable substitute is usually preferred. In a special class of use cases—li...

    Authors: Pablo López-García and Stefan Schulz

    Citation: Journal of Biomedical Semantics 2016 7:56

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  2. Content type: Research

    Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analys...

    Authors: Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith and Yongqun He

    Citation: Journal of Biomedical Semantics 2016 7:53

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  3. Content type: Research

    Gene Ontology (GO) terms represent the standard for annotation and representation of molecular functions, biological processes and cellular compartments, but a large gap exists between the way concepts are rep...

    Authors: Christopher S. Funk, K. Bretonnel Cohen, Lawrence E. Hunter and Karin M. Verspoor

    Citation: Journal of Biomedical Semantics 2016 7:52

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  4. Content type: Research

    Ontologies are widely used both in the life sciences and in the management of public and private companies. Typically, the different offices in an organization develop their own models and related ontologies t...

    Authors: Giandomenico Pozza, Stefano Borgo, Alessandro Oltramari, Laura Contalbrigo and Stefano Marangon

    Citation: Journal of Biomedical Semantics 2016 7:51

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  5. Content type: Research

    We developed the Apollo Structured Vocabulary (Apollo-SV)—an OWL2 ontology of phenomena in infectious disease epidemiology and population biology—as part of a project whose goal is to increase the use of epide...

    Authors: William R. Hogan, Michael M. Wagner, Mathias Brochhausen, John Levander, Shawn T. Brown, Nicholas Millett, Jay DePasse and Josh Hanna

    Citation: Journal of Biomedical Semantics 2016 7:50

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  6. Content type: Research

    The increasing number of open-access ontologies and their key role in several applications such as decision-support systems highlight the importance of their validation. Human expertise is crucial for the vali...

    Authors: Asma Ben Abacha, Julio Cesar Dos Reis, Yassine Mrabet, Cédric Pruski and Marcos Da Silveira

    Citation: Journal of Biomedical Semantics 2016 7:48

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  7. Content type: Research

    Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repo...

    Authors: Luke Slater, Georgios V. Gkoutos, Paul N. Schofield and Robert Hoehndorf

    Citation: Journal of Biomedical Semantics 2016 7:49

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  8. Content type: Research

    The Ontology of Medically Related Social Entities (OMRSE) was initially developed in 2011 to provide a framework for modeling demographic data in Resource Description Framework/Web Ontology Language. It is bui...

    Authors: Amanda Hicks, Josh Hanna, Daniel Welch, Mathias Brochhausen and William R. Hogan

    Citation: Journal of Biomedical Semantics 2016 7:47

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  9. Content type: Research

    Open model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time, leading to different model versions. Taken together, the underlying...

    Authors: Martin Scharm, Dagmar Waltemath, Pedro Mendes and Olaf Wolkenhauer

    Citation: Journal of Biomedical Semantics 2016 7:46

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  10. Content type: Research

    Neurodegenerative diseases are incurable and debilitating indications with huge social and economic impact, where much is still to be learnt about the underlying molecular events. Mechanistic disease models co...

    Authors: Anandhi Iyappan, Shweta Bagewadi Kawalia, Tamara Raschka, Martin Hofmann-Apitius and Philipp Senger

    Citation: Journal of Biomedical Semantics 2016 7:45

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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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