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  1. Content type: Research

    Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated...

    Authors: Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai and Kazuhiko Ohe

    Citation: Journal of Biomedical Semantics 2017 8:22

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  2. Content type: Research

    Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and in...

    Authors: Marcos Martínez-Romero, Clement Jonquet, Martin J. O’Connor, John Graybeal, Alejandro Pazos and Mark A. Musen

    Citation: Journal of Biomedical Semantics 2017 8:21

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  3. Content type: Software

    We present the Europe PMC literature component of Open Targets - a target validation platform that integrates various evidence to aid drug target identification and validation. The component identifies target-...

    Authors: Şenay Kafkas, Ian Dunham and Johanna McEntyre

    Citation: Journal of Biomedical Semantics 2017 8:20

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  4. Content type: Software

    Bio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automat...

    Authors: David Osumi-Sutherland, Melanie Courtot, James P. Balhoff and Christopher Mungall

    Citation: Journal of Biomedical Semantics 2017 8:18

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  5. Content type: Research

    Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing...

    Authors: Deepak K. Sharma, Harold R. Solbrig, Cui Tao, Chunhua Weng, Christopher G. Chute and Guoqian Jiang

    Citation: Journal of Biomedical Semantics 2017 8:19

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  6. Content type: Research

    Research for ontology evaluation is scarce. If biomedical ontological datasets and knowledgebases are to be widely used, there needs to be quality control and evaluation for the content and structure of the on...

    Authors: Muhammad Amith and Cui Tao

    Citation: Journal of Biomedical Semantics 2017 8:17

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  7. Content type: Research

    A standard task in pharmacogenomics research is identifying genes that may be involved in drug response variability, i.e., pharmacogenes. Because genomic experiments tended to generate many false positives, co...

    Authors: Kevin Dalleau, Yassine Marzougui, Sébastien Da Silva, Patrice Ringot, Ndeye Coumba Ndiaye and Adrien Coulet

    Citation: Journal of Biomedical Semantics 2017 8:16

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  8. Content type: Research

    Single Nucleotide Polymorphisms (SNPs) are among the most important types of genetic variations influencing common diseases and phenotypes. Recently, some corpora and methods have been developed with the purpo...

    Authors: Behrouz Bokharaeian, Alberto Diaz, Nasrin Taghizadeh, Hamidreza Chitsaz and Ramyar Chavoshinejad

    Citation: Journal of Biomedical Semantics 2017 8:14

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  9. Content type: Research

    Biomedical data, e.g. from knowledge bases and ontologies, is increasingly made available following open linked data principles, at best as RDF triple data. This is a necessary step towards unified access to b...

    Authors: Ali Hasnain, Qaiser Mehmood, Syeda Sana e Zainab, Muhammad Saleem, Claude Warren Jr, Durre Zehra, Stefan Decker and Dietrich Rebholz-Schuhmann

    Citation: Journal of Biomedical Semantics 2017 8:13

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  10. Content type: Software

    Integrating multiple sources of pharmacovigilance evidence has the potential to advance the science of safety signal detection and evaluation. In this regard, there is a need for more research on how to integr...


    Citation: Journal of Biomedical Semantics 2017 8:11

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  11. Content type: Research

    The Drug Ontology (DrOn) is an OWL2-based representation of drug products and their ingredients, mechanisms of action, strengths, and dose forms. We originally created DrOn for use cases in comparative effecti...

    Authors: William R. Hogan, Josh Hanna, Amanda Hicks, Samira Amirova, Baxter Bramblett, Matthew Diller, Rodel Enderez, Timothy Modzelewski, Mirela Vasconcelos and Chris Delcher

    Citation: Journal of Biomedical Semantics 2017 8:10

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  12. Content type: Research

    Analysing public opinions on HPV vaccines on social media using machine learning based approaches will help us understand the reasons behind the low vaccine coverage and come up with corresponding strategies t...

    Authors: Jingcheng Du, Jun Xu, Hsingyi Song, Xiangyu Liu and Cui Tao

    Citation: Journal of Biomedical Semantics 2017 8:9

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  13. Content type: Research

    Identifying incident cancer cases within a population remains essential for scientific research in oncology. Data produced within electronic health records can be useful for this purpose. Due to the multiplici...

    Authors: Vianney Jouhet, Fleur Mougin, Bérénice Bréchat and Frantz Thiessard

    Citation: Journal of Biomedical Semantics 2017 8:6

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  14. Content type: Research

    Several query federation engines have been proposed for accessing public Linked Open Data sources. However, in many domains, resources are sensitive and access to these resources is tightly controlled by stake...

    Authors: Yasar Khan, Muhammad Saleem, Muntazir Mehdi, Aidan Hogan, Qaiser Mehmood, Dietrich Rebholz-Schuhmann and Ratnesh Sahay

    Citation: Journal of Biomedical Semantics 2017 8:5

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  15. Content type: Research

    Ectopic pregnancy is a frequent early complication of pregnancy associated with significant rates of morbidly and mortality. The positive diagnosis of this condition is established through transvaginal ultraso...

    Authors: Ferdinand Dhombres, Paul Maurice, Stéphanie Friszer, Lucie Guilbaud, Nathalie Lelong, Babak Khoshnood, Jean Charlet, Nicolas Perrot, Eric Jauniaux, Davor Jurkovic and Jean-Marie Jouannic

    Citation: Journal of Biomedical Semantics 2017 8:4

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  16. Content type: Research

    Drug product data is available on the Web in a distributed fashion. The reasons lie within the regulatory domains, which exist on a national level. As a consequence, the drug data available on the Web are inde...

    Authors: Milos Jovanovik and Dimitar Trajanov

    Citation: Journal of Biomedical Semantics 2017 8:3

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  17. Content type: Research

    Biomedical ontologies aim at providing the most exhaustive and rigorous representation of reality as described by biomedical sciences. A large part of medical reasoning deals with diagnosis and is essentially ...

    Authors: Adrien Barton, Jean-François Ethier, Régis Duvauferrier and Anita Burgun

    Citation: Journal of Biomedical Semantics 2017 8:1

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  18. Content type: Research

    Semantic relatedness is a measure that quantifies the strength of a semantic link between two concepts. Often, it can be efficiently approximated with methods that operate on words, which represent these conce...

    Authors: Maciej Rybinski and José Francisco Aldana-Montes

    Citation: Journal of Biomedical Semantics 2016 7:67

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  19. Content type: Short Report

    This special issue covers selected papers from the 18th Bio-Ontologies Special Interest Group meeting and Phenotype Day, which took place at the Intelligent Systems for Molecular Biology (ISMB) conference in D...

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

    Citation: Journal of Biomedical Semantics 2016 7:66

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  20. Content type: Research

    The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, c...

    Authors: Robert Hoehndorf, Mona Alshahrani, Georgios V. Gkoutos, George Gosline, Quentin Groom, Thomas Hamann, Jens Kattge, Sylvia Mota de Oliveira, Marco Schmidt, Soraya Sierra, Erik Smets, Rutger A. Vos and Claus Weiland

    Citation: Journal of Biomedical Semantics 2016 7:65

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Page 3 of 16

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