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Journal of Biomedical Semantics

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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. Content type: Research

    An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protoco...

    Authors: Olga Giraldo, Alexander García, Federico López and Oscar Corcho

    Citation: Journal of Biomedical Semantics 2017 8:52

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  15. Content type: Research

    One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has a...

    Authors: Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L. Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung…

    Citation: Journal of Biomedical Semantics 2017 8:50

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  16. Content type: Research

    Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to hete...

    Authors: Freddy Priyatna, Raul Alonso-Calvo, Sergio Paraiso-Medina and Oscar Corcho

    Citation: Journal of Biomedical Semantics 2017 8:49

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  17. Content type: Research

    In this paper, we describe a histological ontology of the human cardiovascular system developed in collaboration among histology experts and computer scientists.

    Authors: Claudia Mazo, Liliana Salazar, Oscar Corcho, Maria Trujillo and Enrique Alegre

    Citation: Journal of Biomedical Semantics 2017 8:47

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  18. Content type: Research

    Regional and epidemiological cancer registries are important for cancer research and the quality management of cancer treatment. Many technological solutions are available to collect and analyse data for cance...

    Authors: Angel Esteban-Gil, Jesualdo Tomás Fernández-Breis and Martin Boeker

    Citation: Journal of Biomedical Semantics 2017 8:46

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  19. Content type: Research

    In this paper we present the approach that we employed to deal with large scale multi-label semantic indexing of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge (...

    Authors: Yannis Papanikolaou, Grigorios Tsoumakas, Manos Laliotis, Nikos Markantonatos and Ioannis Vlahavas

    Citation: Journal of Biomedical Semantics 2017 8:43

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