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  1. Content type: Review

    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

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  2. Content type: Software

    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

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  3. Content type: Research

    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

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  4. Content type: Software

    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

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  5. Content type: Research article

    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

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  6. Content type: Short Report

    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

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  7. Content type: Research

    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

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  8. Content type: Research Article

    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

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  9. Content type: Research

    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

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  10. Content type: Research article

    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

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  11. Content type: Research Article

    Phenotypes form the basis for determining the existence of a disease against the given evidence. Much of this evidence though remains locked away in text – scientific articles, clinical trial reports and elect...

    Authors: Nigel Collier, Anika Oellrich and Tudor Groza

    Citation: Journal of Biomedical Semantics 2015 6:24

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  12. Content type: Research article

    Mild traumatic brain injury (mTBI) has high prevalence in the military, among athletes, and in the general population worldwide (largely due to falls). Consequences can include a range of neuropsychological di...

    Authors: Michael J Cairelli, Marcelo Fiszman, Han Zhang and Thomas C Rindflesch

    Citation: Journal of Biomedical Semantics 2015 6:25

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  13. Content type: Research Article

    Discovering gene interactions and their characterizations from biological text collections is a crucial issue in bioinformatics. Indeed, text collections are large and it is very difficult for biologists to fu...

    Authors: Peggy Cellier, Thierry Charnois, Marc Plantevit, Christophe Rigotti, Bruno Crémilleux, Olivier Gandrillon, Jiří Kléma and Jean-Luc Manguin

    Citation: Journal of Biomedical Semantics 2015 6:27

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  14. Content type: Research article

    While the association between a drug and an adverse event (ADE) is generally detected at the level of individual drugs, ADEs are often discussed at the class level, i.e., at the level of pharmacologic classes ...

    Authors: Rainer Winnenburg, Alfred Sorbello and Olivier Bodenreider

    Citation: Journal of Biomedical Semantics 2015 6:18

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  15. Content type: Research Article

    Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information. The community-driven ontology curation process, however, ignores the possib...

    Authors: Tudor Groza, Tania Tudorache, Peter N Robinson and Andreas Zankl

    Citation: Journal of Biomedical Semantics 2015 6:21

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  16. Content type: Research Article

    Model repositories such as BioModels Database provide computational models of biological systems for the scientific community. These models contain rich semantic annotations that link model entities to concept...

    Authors: Rebekka Alm, Dagmar Waltemath, Markus Wolfien, Olaf Wolkenhauer and Ron Henkel

    Citation: Journal of Biomedical Semantics 2015 6:20

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  17. Content type: Review

    Establishing robust links among gene expression, pathways and phenotypes is critical for understanding diseases and developing treatments. In recent years there have been many efforts to develop the computatio...

    Authors: Irene Papatheodorou, Anika Oellrich and Damian Smedley

    Citation: Journal of Biomedical Semantics 2015 6:17

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  18. Content type: Research Article

    There is an increasing recognition of the need for the data capture phase of clinical studies to be improved and for more effective sharing of clinical data. The Health Care and Life Sciences community has emb...

    Authors: Hugo Leroux and Laurent Lefort

    Citation: Journal of Biomedical Semantics 2015 6:16

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  19. Content type: Research article

    Electronic Health Records (EHRs) contain a wealth of information useful for studying clinical phenotype-genotype relationships. Severity is important for distinguishing among phenotypes; however other severity...

    Authors: Mary Regina Boland, Nicholas P Tatonetti and George Hripcsak

    Citation: Journal of Biomedical Semantics 2015 6:14

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  20. Content type: Research Article

    Ontologies play a major role in life sciences, enabling a number of applications, from new data integration to knowledge verification. SNOMED CT is a large medical ontology that is formally defined so that it ...

    Authors: Alina Petrova, Yue Ma, George Tsatsaronis, Maria Kissa, Felix Distel, Franz Baader and Michael Schroeder

    Citation: Journal of Biomedical Semantics 2015 6:22

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  21. Content type: Software

    We develop medical-specialty specific ontologies that contain the settled science and common term usage. We leverage current practices in information and relationship extraction to streamline the ontology deve...

    Authors: Kristina Doing-Harris, Yarden Livnat and Stephane Meystre

    Citation: Journal of Biomedical Semantics 2015 6:15

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  22. Content type: Research Article

    With the increasing presence of biomedical data sources on the Internet more and more research effort is put into finding possible ways for integrating and searching such often heterogeneous sources. Ontologie...

    Authors: Patrick Lambrix, Fang Wei-Kleiner and Zlatan Dragisic

    Citation: Journal of Biomedical Semantics 2015 6:12

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  23. Content type: Research

    The NDF-RT (National Drug File Reference Terminology) is an ontology, which describes drugs and their properties and supports computerized physician order entry systems. NDF-RT’s classes are mostly specified u...

    Authors: Rainer Winnenburg, Jonathan M Mortensen and Olivier Bodenreider

    Citation: Journal of Biomedical Semantics 2015 6:13

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  24. Content type: Research article

    A vast array of data is about to emerge from the large scale high-throughput mouse knockout phenotyping projects worldwide. It is critical that this information is captured in a standardized manner, made acces...

    Authors: Cynthia L Smith and Janan T Eppig

    Citation: Journal of Biomedical Semantics 2015 6:11

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  25. Content type: Research

    Engineered nanomaterials (ENMs) are being developed to meet specific application needs in diverse domains across the engineering and biomedical sciences (e.g. drug delivery). However, accompanying the exciting...

    Authors: Janna Hastings, Nina Jeliazkova, Gareth Owen, Georgia Tsiliki, Cristian R Munteanu, Christoph Steinbeck and Egon Willighagen

    Citation: Journal of Biomedical Semantics 2015 6:10

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  26. Content type: Research

    Most computational methods that predict protein function do not take advantage of the large amount of information contained in the biomedical literature. In this work we evaluate both ontology term co-mention ...

    Authors: Christopher S Funk, Indika Kahanda, Asa Ben-Hur and Karin M Verspoor

    Citation: Journal of Biomedical Semantics 2015 6:9

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  27. Content type: Research article

    Chronic obstructive pulmonary disease (COPD) is a life-threatening lung disorder whose recent prevalence has led to an increasing burden on public healthcare. Phenotypic information in electronic clinical reco...

    Authors: Xiao Fu, Riza Batista-Navarro, Rafal Rak and Sophia Ananiadou

    Citation: Journal of Biomedical Semantics 2015 6:8

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  28. Content type: Software

    As the availability of open access full text research articles increases, so does the need for sophisticated search services that make the most of this new content. Here, we present a new feature available in ...

    Authors: Şenay Kafkas, Xingjun Pi, Nikos Marinos, Francesco Talo’, Andrew Morrison and Johanna R McEntyre

    Citation: Journal of Biomedical Semantics 2015 6:7

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  29. Content type: Software

    Semantic similarity measures over phenotype ontologies have been demonstrated to provide a powerful approach for the analysis of model organism phenotypes, the discovery of animal models of human disease, nove...

    Authors: Robert Hoehndorf, Michael Gruenberger, Georgios V Gkoutos and Paul N Schofield

    Citation: Journal of Biomedical Semantics 2015 6:6

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  30. Content type: Research

    Data from high throughput experiments often produce far more results than can ever appear in the main text or tables of a single research article. In these cases, the majority of new associations are often arc...

    Authors: Eleni Mina, Mark Thompson, Rajaram Kaliyaperumal, Jun Zhao, van Eelke der Horst, Zuotian Tatum, Kristina M Hettne, Erik A Schultes, Barend Mons and Marco Roos

    Citation: Journal of Biomedical Semantics 2015 6:5

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  31. Content type: Software

    It is time-consuming to build an ontology with many terms and axioms. Thus it is desired to automate the process of ontology development. Ontology Design Patterns (ODPs) provide a reusable solution to solve a ...

    Authors: Zuoshuang Xiang, Jie Zheng, Yu Lin and Yongqun He

    Citation: Journal of Biomedical Semantics 2015 6:4

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  32. Content type: Review

    Linked Data has gained some attention recently in the life sciences as an effective way to provide and share data. As a part of the Semantic Web, data are linked so that a person or machine can explore the web...

    Authors: Kiyoko F Aoki-Kinoshita, Akira R Kinjo, Mizuki Morita, Yoshinobu Igarashi, Yi-an Chen, Yasumasa Shigemoto, Takatomo Fujisawa, Yukie Akune, Takeo Katoda, Anna Kokubu, Takaaki Mori, Mitsuteru Nakao, Shuichi Kawashima, Shinobu Okamoto, Toshiaki Katayama and Soichi Ogishima

    Citation: Journal of Biomedical Semantics 2015 6:3

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  33. Content type: Research

    Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used bey...

    Authors: Junguk Hur, Arzucan Özgür, Zuoshuang Xiang and Yongqun He

    Citation: Journal of Biomedical Semantics 2015 6:2

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  34. Content type: Research

    In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe P...

    Authors: Şenay Kafkas, Jee-Hyub Kim, Xingjun Pi and Johanna R McEntyre

    Citation: Journal of Biomedical Semantics 2015 6:1

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  35. Content type: Research

    Using knowledge representation for biomedical projects is now commonplace. In previous work, we represented the knowledge found in a college-level biology textbook in a fashion useful for answering questions. ...

    Authors: Vinay K Chaudhri, Daniel Elenius, Andrew Goldenkranz, Allison Gong, Maryann E Martone, William Webb and Neil Yorke-Smith

    Citation: Journal of Biomedical Semantics 2014 5:51

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  36. Content type: Software

    Large quantities of digital images are now generated for biological collections, including those developed in projects premised on the high-throughput screening of genome-phenome experiments. These images ofte...

    Authors: Nikhil Tej Lingutla, Justin Preece, Sinisa Todorovic, Laurel Cooper, Laura Moore and Pankaj Jaiswal

    Citation: Journal of Biomedical Semantics 2014 5:50

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  37. Content type: Software

    Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontolo...

    Authors: Heiko Dietze, Tanya Z Berardini, Rebecca E Foulger, David P Hill, Jane Lomax, David Osumi-Sutherland, Paola Roncaglia and Christopher J Mungall

    Citation: Journal of Biomedical Semantics 2014 5:48

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  38. Content type: Research

    In this paper, we show how we have applied the Clinical Narrative Temporal Relation Ontology (CNTRO) and its associated temporal reasoning system (the CNTRO Timeline Library) to trend temporal information with...

    Authors: Kim Clark, Deepak Sharma, Rui Qin, Christopher G Chute and Cui Tao

    Citation: Journal of Biomedical Semantics 2014 5:49

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  39. Content type: Research

    The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to catalogue genetic mutations responsible for cancer using genome analysis techniques. One of the aims of this project is to c...

    Authors: Muhammad Saleem, Shanmukha S Padmanabhuni, Axel-Cyrille Ngonga Ngomo, Aftab Iqbal, Jonas S Almeida, Stefan Decker and Helena F Deus

    Citation: Journal of Biomedical Semantics 2014 5:47

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  40. Content type: Software

    Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier t...

    Authors: Alejandro Rodríguez González, Alison Callahan, José Cruz-Toledo, Adrian Garcia, Mikel Egaña Aranguren, Michel Dumontier and Mark D Wilkinson

    Citation: Journal of Biomedical Semantics 2014 5:46

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  41. Content type: Software

    Phenex (http://​phenex.​phenoscape.​org/​) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutio...

    Authors: James P Balhoff, Wasila M Dahdul, T Alexander Dececchi, Hilmar Lapp, Paula M Mabee and Todd J Vision

    Citation: Journal of Biomedical Semantics 2014 5:45

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  42. Content type: Research

    We are currently facing a proliferation of heterogeneous biomedical data sources accessible through various knowledge-based applications. These data are annotated by increasingly extensive and widely dissemina...

    Authors: Gayo Diallo

    Citation: Journal of Biomedical Semantics 2014 5:44

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  43. Content type: Research

    Bacterial identification and characterization at subspecies level is commonly known as Microbial Typing. Currently, these methodologies are fundamental tools in Clinical Microbiology and bacterial population g...

    Authors: Cátia Vaz, Alexandre P Francisco, Mickael Silva, Keith A Jolley, James E Bray, Hannes Pouseele, Joerg Rothganger, Mário Ramirez and João A Carriço

    Citation: Journal of Biomedical Semantics 2014 5:43

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  44. Content type: Software

    In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however,...

    Authors: Mikel Egaña Aranguren, Alejandro Rodríguez González and Mark D Wilkinson

    Citation: Journal of Biomedical Semantics 2014 5:42

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