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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. Content type: Research

    One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preser...

    Authors: Kristina M Hettne, Harish Dharuri, Jun Zhao, Katherine Wolstencroft, Khalid Belhajjame, Stian Soiland-Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, Lourdes Verdes-Montenegro, Julian Garrido, David de Roure, Oscar Corcho, Graham Klyne, Reinout van Schouwen, Peter A C ‘t Hoen…

    Citation: Journal of Biomedical Semantics 2014 5:41

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  19. Content type: Research

    The scientific names of plants and animals play a major role in Life Sciences as information is indexed, integrated, and searched using scientific names. The main problem with names is their ambiguous nature, ...

    Authors: Nina Laurenne, Jouni Tuominen, Hannu Saarenmaa and Eero Hyvönen

    Citation: Journal of Biomedical Semantics 2014 5:40

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  20. Content type: Research

    Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their abi...

    Authors: Robert W Thacker, Maria Cristina Díaz, Adeline Kerner, Régine Vignes-Lebbe, Erik Segerdell, Melissa A Haendel and Christopher J Mungall

    Citation: Journal of Biomedical Semantics 2014 5:39

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  21. Content type: Research

    We evaluate the application of the Emotion Ontology (EM) to the task of self-reporting of emotional experience in the context of audience response to academic presentations at the International Conference on B...

    Authors: Janna Hastings, Andy Brass, Colin Caine, Caroline Jay and Robert Stevens

    Citation: Journal of Biomedical Semantics 2014 5:38

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  22. Content type: Database

    Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two year...

    Authors: Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Terrence F Meehan, Alexander D Diehl, Uma D Vempati, Stephan C Schürer, Chao Pang, James Malone, Helen Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H Brush…

    Citation: Journal of Biomedical Semantics 2014 5:37

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  23. Content type: Research

    The Adverse Event Reporting System (AERS) is an FDA database providing rich information on voluntary reports of adverse drug events (ADEs). Normalizing data in the AERS would improve the mining capacity of the...

    Authors: Liwei Wang, Guoqian Jiang, Dingcheng Li and Hongfang Liu

    Citation: Journal of Biomedical Semantics 2014 5:36

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  24. Content type: Research

    Spatial terminology is used in anatomy to indicate precise, relative positions of structures in an organism. While these terms are often standardized within specific fields of biology, they can differ dramatic...

    Authors: Wasila M Dahdul, Hong Cui, Paula M Mabee, Christopher J Mungall, David Osumi-Sutherland, Ramona L Walls and Melissa A Haendel

    Citation: Journal of Biomedical Semantics 2014 5:34

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  25. Content type: Research

    A huge amount of associations among different biological entities (e.g., disease, drug, and gene) are scattered in millions of biomedical articles. Systematic analysis of such heterogeneous data can infer nove...

    Authors: Yuji Zhang, Cui Tao, Guoqian Jiang, Asha A Nair, Jian Su, Christopher G Chute and Hongfang Liu

    Citation: Journal of Biomedical Semantics 2014 5:33

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  26. Content type: Research

    Biological databases vary enormously in size and data complexity, from small databases that contain a few million Resource Description Framework (RDF) triples to large databases that contain billions of triple...

    Authors: Hongyan Wu, Toyofumi Fujiwara, Yasunori Yamamoto, Jerven Bolleman and Atsuko Yamaguchi

    Citation: Journal of Biomedical Semantics 2014 5:32

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  27. Content type: Research

    In the past years, significant progress has been made to develop and use experimental settings for extensive data collection on tobacco smoke exposure and tobacco smoke exposure-associated diseases. Due to the...

    Authors: Erfan Younesi, Sam Ansari, Michaela Guendel, Shiva Ahmadi, Chris Coggins, Julia Hoeng, Martin Hofmann-Apitius and Manuel C Peitsch

    Citation: Journal of Biomedical Semantics 2014 5:31

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  28. Content type: Research

    A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical int...

    Authors: Yongqun He, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith

    Citation: Journal of Biomedical Semantics 2014 5:29

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  29. Content type: Research

    Scientific publications are documentary representations of defeasible arguments, supported by data and repeatable methods. They are the essential mediating artifacts in the ecosystem of scientific communicatio...

    Authors: Tim Clark, Paolo N Ciccarese and Carole A Goble

    Citation: Journal of Biomedical Semantics 2014 5:28

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  30. Content type: Proceedings

    Matching and comparing sequence annotations of different reference sequences is vital to genomics research, yet many annotation formats do not specify the reference sequence types or versions used. This makes ...

    Authors: Zuotian Tatum, Marco Roos, Andrew P Gibson, Peter EM Taschner, Mark Thompson, Erik A Schultes and Jeroen FJ Laros

    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):S6

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    This article is part of a Supplement: Volume 5 Supplement 1

  31. Content type: Proceedings

    The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary d...

    Authors: Saminda Abeyruwan, Uma D Vempati, Hande Küçük-McGinty, Ubbo Visser, Amar Koleti, Ahsan Mir, Kunie Sakurai, Caty Chung, Joshua A Bittker, Paul A Clemons, Steve Brudz, Anosha Siripala, Arturo J Morales, Martin Romacker, David Twomey, Svetlana Bureeva…

    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):S5

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    This article is part of a Supplement: Volume 5 Supplement 1

  32. Content type: Proceedings

    The molecular etiology is still to be identified for about half of the currently described Mendelian diseases in humans, thereby hindering efforts to find treatments or preventive measures. Advances, such as n...

    Authors: Anika Oellrich, Sebastian Koehler, Nicole Washington, Chris Mungall, Suzanna Lewis, Melissa Haendel, Peter N Robinson and Damian Smedley

    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):S4

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    This article is part of a Supplement: Volume 5 Supplement 1

  33. Content type: Proceedings

    With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ...

    Authors: Emily Merrill, Stéphane Corlosquet, Paolo Ciccarese, Tim Clark and Sudeshna Das

    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):S3

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    This article is part of a Supplement: Volume 5 Supplement 1

  34. Content type: Proceedings

    Ontologies encode relationships within a domain in robust data structures that can be used to annotate data objects, including scientific papers, in ways that ease tasks such as search and meta-analysis. Howev...

    Authors: Chayan Chakrabarti, Thomas B Jones, George F Luger, Jiawei F Xu, Matthew D Turner, Angela R Laird and Jessica A Turner

    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):S2

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    This article is part of a Supplement: Volume 5 Supplement 1

  35. Content type: Proceedings

    Accounts of evidence are vital to evaluate and reproduce scientific findings and integrate data on an informed basis. Currently, such accounts are often inadequate, unstandardized and inaccessible for computat...

    Authors: Christian Bölling, Michael Weidlich and Hermann-Georg Holzhütter

    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):S1

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    This article is part of a Supplement: Volume 5 Supplement 1

  36. Content type: Introduction

    Over the 16 years, the Bio-Ontologies SIG at ISMB has provided a forum for vibrant discussions of the latest and most innovative advances in the research area of bio-ontologies, its applications to biomedicine...

    Authors: Larisa N Soldatova, Philippe Rocca-Serra, Michel Dumontier and Nigam H Shah

    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):I1

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    This article is part of a Supplement: Volume 5 Supplement 1

  37. Content type: Research

    Semantic Category Disambiguation (SCD) is the task of assigning the appropriate semantic category to given spans of text from a fixed set of candidate categories, for example Protein to “Fibrin”. SCD is relevant ...

    Authors: Pontus Stenetorp, Sampo Pyysalo, Sophia Ananiadou and Jun’ichi Tsujii

    Citation: Journal of Biomedical Semantics 2014 5:26

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  38. Content type: Database

    Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descrip...

    Authors: James Malone, Andy Brown, Allyson L Lister, Jon Ison, Duncan Hull, Helen Parkinson and Robert Stevens

    Citation: Journal of Biomedical Semantics 2014 5:25

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  39. Content type: Research

    Hospital documents contain free text describing the most important facts relating to patients and their illnesses. These documents are written in specific language containing medical terminology related to hos...

    Authors: Małgorzata Marciniak and Agnieszka Mykowiecka

    Citation: Journal of Biomedical Semantics 2014 5:24

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  40. Content type: Research

    Recently, exchanging data and information has become a significant challenge in medicine. Such data include abnormal states. Establishing a unified representation framework of abnormal states can be a difficul...

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

    Citation: Journal of Biomedical Semantics 2014 5:23

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  41. Content type: Research

    Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Mult...

    Authors: Melissa A Haendel, James P Balhoff, Frederic B Bastian, David C Blackburn, Judith A Blake, Yvonne Bradford, Aurelie Comte, Wasila M Dahdul, Thomas A Dececchi, Robert E Druzinsky, Terry F Hayamizu, Nizar Ibrahim, Suzanna E Lewis, Paula M Mabee, Anne Niknejad, Marc Robinson-Rechavi…

    Citation: Journal of Biomedical Semantics 2014 5:21

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  42. Content type: Research

    Multiple models of anatomy have been developed independently and for different purposes. In particular, 3D graphical models are specially useful for visualizing the different organs composing the human body, w...

    Authors: Olivier Palombi, Federico Ulliana, Valentin Favier, Jean-Claude Léon and Marie-Christine Rousset

    Citation: Journal of Biomedical Semantics 2014 5:20

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  43. Content type: Research

    Due to human variations in genetic susceptibility, vaccination often triggers adverse events in a small population of vaccinees. Based on our previous work on ontological modeling of genetic susceptibility to ...

    Authors: Yu Lin and Yongqun He

    Citation: Journal of Biomedical Semantics 2014 5:19

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  44. Content type: Research

    Pharmacovigilance is the activity related to the collection, analysis and prevention of adverse drug reactions (ADRs) induced by drugs. This activity is usually performed within dedicated databases (national, ...

    Authors: Marie Dupuch, Laëtitia Dupuch, Thierry Hamon and Natalia Grabar

    Citation: Journal of Biomedical Semantics 2014 5:18

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  45. Content type: Editorial

    The 2013 “Vaccine and Drug Ontology Studies” (VDOS 2013) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have contributed to dramatic i...

    Authors: Cui Tao, Yongqun He and Sivaram Arabandi

    Citation: Journal of Biomedical Semantics 2014 5:16

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