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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. Content type: Research

    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

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  18. Content type: Research

    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

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  19. Content type: Database

    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

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  20. Content type: Research

    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

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  21. Content type: Research

    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

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  22. Content type: Research

    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

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  23. Content type: Short report

    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

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  24. Content type: Research

    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

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  25. Content type: Research

    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

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  26. Content type: Research

    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

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  27. Content type: Research

    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

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  28. Content type: Research

    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

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  29. Content type: Research

    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

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  30. Content type: Research

    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

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  31. Content type: Research

    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

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  32. Content type: Software

    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

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  33. Content type: Software

    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

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  34. Content type: Research

    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

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  35. Content type: Research

    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

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  36. Content type: Research

    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

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

  37. Content type: Research

    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

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  38. Content type: Editorial

    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

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  39. Content type: Research

    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

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  40. Content type: Research

    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

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

  41. Content type: Review

    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

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  42. Content type: Database

    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

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  43. Content type: Research

    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

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