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  1. 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

    Content type: Software

    Published on:

  2. 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

    Content type: Research

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  3. 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

    Content type: Research

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  4. 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

    Content type: Research

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  5. 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

    Content type: Research

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  6. 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

    Content type: Research

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  7. 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

    Content type: Database

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  8. 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

    Content type: Research

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  9. 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

    Content type: Research

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  10. 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

    Content type: Research

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  11. 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

    Content type: Short report

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  12. 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

    Content type: Research

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  13. 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

    Content type: Research

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  14. Biobanking necessitates extensive integration of data to allow data analysis and specimen sharing. Ontologies have been demonstrated to be a promising approach in fostering better semantic integration of bioba...

    Authors: Mathias Brochhausen, Jie Zheng, David Birtwell, Heather Williams, Anna Maria Masci, Helena Judge Ellis and Christian J. Stoeckert Jr.

    Citation: Journal of Biomedical Semantics 2016 7:23

    Content type: Research

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  15. MicroRNAs are increasingly being appreciated as critical players in human diseases, and questions concerning the role of microRNAs arise in many areas of biomedical research. There are several manually curated...

    Authors: Samir Gupta, Karen E. Ross, Catalina O. Tudor, Cathy H. Wu, Carl J. Schmidt and K. Vijay-Shanker

    Citation: Journal of Biomedical Semantics 2016 7:9

    Content type: Research

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  16. Biomedical text mining may target various kinds of valuable information embedded in the literature, but a critical obstacle to the extension of the mining targets is the cost of manual construction of labeled ...

    Authors: Xu Han, Jung-jae Kim and Chee Keong Kwoh

    Citation: Journal of Biomedical Semantics 2016 7:22

    Content type: Research

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  17. In previous work, we built the Drug Ontology (DrOn) to support comparative effectiveness research use cases. Here, we have updated our representation of ingredients to include both active ingredients (and thei...

    Authors: Josh Hanna, Jiang Bian and William R. Hogan

    Citation: Journal of Biomedical Semantics 2016 7:7

    Content type: Research

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  18. To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts ...

    Authors: Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E. Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B. Gerstein, Andrew F. Hill, Robert R. Kitchen, Jan Lötvall, Tushar Patel…

    Citation: Journal of Biomedical Semantics 2016 7:19

    Content type: Research

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  19. MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium in...

    Authors: Carrine E. Blank, Hong Cui, Lisa R. Moore and Ramona L. Walls

    Citation: Journal of Biomedical Semantics 2016 7:18

    Content type: Research

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  20. The Simple Knowledge Organization System (SKOS) was introduced to the wider research community by a 2005 World Wide Web Consortium (W3C) working draft, and further developed and refined in a 2009 W3C recommend...

    Authors: Mike Conway, Artem Khojoyan, Fariba Fana, William Scuba, Melissa Castine, Danielle Mowery, Wendy Chapman and Simon Jupp

    Citation: Journal of Biomedical Semantics 2016 7:5

    Content type: Software

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  21. Authoring bio-ontologies is a task that has traditionally been undertaken by skilled experts trained in understanding complex languages such as the Web Ontology Language (OWL), in tools designed for such exper...

    Authors: Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen Parkinson and James Malone

    Citation: Journal of Biomedical Semantics 2016 7:17

    Content type: Software

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  22. There have been relatively few attempts to represent vision or blindness ontologically. This is unsurprising as the related phenomena of sight and blindness are difficult to represent ontologically for a varie...

    Authors: Patrick L. Ray, Alexander P. Cox, Mark Jensen, Travis Allen, William Duncan and Alexander D. Diehl

    Citation: Journal of Biomedical Semantics 2016 7:15

    Content type: Research

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  23. The Centre for Therapeutic Target Validation (CTTV - https://​www.​targetvalidation​.​org/​) was established to generate therapeutic target evidence from ge...

    Authors: Sirarat Sarntivijai, Drashtti Vasant, Simon Jupp, Gary Saunders, A. Patrícia Bento, Daniel Gonzalez, Joanna Betts, Samiul Hasan, Gautier Koscielny, Ian Dunham, Helen Parkinson and James Malone

    Citation: Journal of Biomedical Semantics 2016 7:8

    Content type: Research

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  24. Information about drug–drug interactions (DDIs) is crucial for computational applications such as pharmacovigilance and drug repurposing. However, existing sources of DDIs have the problems of low coverage, lo...

    Authors: Yaoyun Zhang, Heng-Yi Wu, Jingcheng Du, Jun Xu, Jingqi Wang, Cui Tao, Lang Li and Hua Xu

    Citation: Journal of Biomedical Semantics 2016 7:11

    Content type: Research

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    The Erratum to this article has been published in Journal of Biomedical Semantics 2016 7:21

  25. The Biomedical Research Integrated Domain Group (BRIDG) model is a formal domain analysis model for protocol-driven biomedical research, and serves as a semantic foundation for application and message developm...

    Authors: Guoqian Jiang, Julie Evans, Cory M. Endle, Harold R. Solbrig and Christopher G. Chute

    Citation: Journal of Biomedical Semantics 2016 7:10

    Content type: Research

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  26. The “Vaccine and Drug Ontology Studies” (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have been critical to prevent and treat ...

    Authors: Cui Tao, Yongqun He and Sivaram Arabandi

    Citation: Journal of Biomedical Semantics 2016 7:6

    Content type: Editorial

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  27. It has been shown that exergames have multiple benefits for physical, mental and cognitive health. Only recently, however, researchers have started considering them as health monitoring tools, through collecti...

    Authors: Giorgos Bamparopoulos, Evdokimos Konstantinidis, Charalampos Bratsas and Panagiotis D. Bamidis

    Citation: Journal of Biomedical Semantics 2016 7:4

    Content type: Research

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    The Erratum to this article has been published in Journal of Biomedical Semantics 2016 7:31

  28. Identifying partial mappings between two terminologies is of special importance when one terminology is finer-grained than the other, as is the case for the Human Phenotype Ontology (HPO), mainly used for rese...

    Authors: Ferdinand Dhombres and Olivier Bodenreider

    Citation: Journal of Biomedical Semantics 2016 7:3

    Content type: Research

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  29. Genotype-phenotype studies aim to identify causative relationships between genes and phenotypes. The International Mouse Phenotyping Consortium is a high throughput phenotyping program whose goal is to collect...

    Authors: Anika Oellrich, Terrence F. Meehan, Helen Parkinson, Sirarat Sarntivijai, Jacqueline K. White and Natasha A. Karp

    Citation: Journal of Biomedical Semantics 2016 7:2

    Content type: Review

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  30. MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s)...

    Authors: Randi Vita, James A. Overton, Emily Seymour, John Sidney, Jim Kaufman, Rebecca L. Tallmadge, Shirley Ellis, John Hammond, Geoff W. Butcher, Alessandro Sette and Bjoern Peters

    Citation: Journal of Biomedical Semantics 2016 7:1

    Content type: Database

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  31. The specification of metadata in clinical and epidemiological study projects absorbs significant expense. The validity and quality of the collected data depend heavily on the precise and semantical correct rep...

    Authors: Alexandr Uciteli and Heinrich Herre

    Citation: Journal of Biomedical Semantics 2015 6:41

    Content type: Research

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  32. The bio-ontologies and phenotypes special issue includes eight papers selected from the 11 papers presented at the Bio-Ontologies SIG (Special Interest Group) and the Phenotype Day at ISMB (Intelligent Systems...

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

    Citation: Journal of Biomedical Semantics 2015 6:40

    Content type: Review

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  33. Semantic web technologies have a tremendous potential for the integration of heterogeneous data sets. Therefore, an increasing number of widely used biological resources are becoming available in the RDF data ...

    Authors: Jesse CJ van Dam, Jasper J Koehorst, Peter J Schaap, Vitor AP Martins dos Santos and Maria Suarez-Diez

    Citation: Journal of Biomedical Semantics 2015 6:39

    Content type: Software

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  34. Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physicall...

    Authors: Pierre-Yves Rabattu, Benoit Massé, Federico Ulliana, Marie-Christine Rousset, Damien Rohmer, Jean-Claude Léon and Olivier Palombi

    Citation: Journal of Biomedical Semantics 2015 6:36

    Content type: Research

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  35. The increasing use of ontologies highlights the need for a library for working with ontologies that is efficient, accessible from various programming languages, and compatible with common computational platforms.

    Authors: Mikhail K. Levin and Lindsay G. Cowell

    Citation: Journal of Biomedical Semantics 2015 6:35

    Content type: Software

    Published on:

  36. Vaccines are one of the most important public health successes in last century. Besides effectiveness in reducing the morbidity and mortality from many infectious diseases, a successful vaccine program also re...

    Authors: Yuji Zhang, Puqiang Wu, Yi Luo and Cui Tao

    Citation: Journal of Biomedical Semantics 2015 6:33

    Content type: Research article

    Published on:

  37. The Genome Variant Format (GVF) uses the Sequence Ontology (SO) to enable detailed annotation of sequence variation. The annotation includes SO terms for the type of sequence alteration, the genomic features t...

    Authors: Fiona Cunningham, Barry Moore, Nicole Ruiz-Schultz, Graham RS Ritchie and Karen Eilbeck

    Citation: Journal of Biomedical Semantics 2015 6:32

    Content type: Short Report

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  38. Large quantities of biomedical data are being produced at a rapid pace for a variety of organisms. With ontologies proliferating, data is increasingly being stored using the RDF data model and queried using RD...

    Authors: Amir H. Asiaee, Todd Minning, Prashant Doshi and Rick L. Tarleton

    Citation: Journal of Biomedical Semantics 2015 6:31

    Content type: Research

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  39. The complexity and scale of the knowledge in the biomedical domain has motivated research work towards mining heterogeneous data from both structured and unstructured knowledge bases. Towards this direction, i...

    Authors: Dirk Weissenborn, Michael Schroeder and George Tsatsaronis

    Citation: Journal of Biomedical Semantics 2015 6:28

    Content type: Research Article

    Published on:

  40. In the clinical dentists and periodontal researchers’ community, there is an obvious demand for a systems model capable of linking the clinical presentation of periodontitis to underlying molecular knowledge. ...

    Authors: Asami Suzuki, Takako Takai-Igarashi, Jun Nakaya and Hiroshi Tanaka

    Citation: Journal of Biomedical Semantics 2015 6:30

    Content type: Research

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  41. There are numerous options available to achieve various tasks in bioinformatics, but until recently, there were no tools that could systematically identify mentions of databases and tools within the literature...

    Authors: Geraint Duck, Aleksandar Kovacevic, David L. Robertson, Robert Stevens and Goran Nenadic

    Citation: Journal of Biomedical Semantics 2015 6:29

    Content type: Research article

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