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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. Content type: Research

    Personalized drug prescription can be benefited from the use of intelligent information management and sharing. International standard classifications and terminologies have been developed in order to provide ...

    Authors: Charalampos Doulaverakis, George Nikolaidis, Athanasios Kleontas and Ioannis Kompatsiaris

    Citation: Journal of Biomedical Semantics 2014 5:13

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  30. Content type: Database

    The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description ...

    Authors: Michel Dumontier, Christopher JO Baker, Joachim Baran, Alison Callahan, Leonid Chepelev, José Cruz-Toledo, Nicholas R Del Rio, Geraint Duck, Laura I Furlong, Nichealla Keath, Dana Klassen, James P McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D Wilkinson…

    Citation: Journal of Biomedical Semantics 2014 5:14

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  31. Content type: Review

    Over the past 15 years, the biomedical research community has increased its efforts to produce ontologies encoding biomedical knowledge, and to provide the corresponding infrastructure to maintain them. As ont...

    Authors: Robert Hoehndorf, Melissa Haendel, Robert Stevens and Dietrich Rebholz-Schuhmann

    Citation: Journal of Biomedical Semantics 2014 5:15

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  32. Content type: Research

    Experimental research on the automatic extraction of information about mutations from texts is greatly hindered by the lack of consensus evaluation infrastructure for the testing and benchmarking of mutation t...

    Authors: Artjom Klein, Alexandre Riazanov, Matthew M Hindle and Christopher JO Baker

    Citation: Journal of Biomedical Semantics 2014 5:11

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  33. Content type: Research

    The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular anatomy and development of the zebrafish, Dan...

    Authors: Ceri E Van Slyke, Yvonne M Bradford, Monte Westerfield and Melissa A Haendel

    Citation: Journal of Biomedical Semantics 2014 5:12

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  34. Content type: Research

    Authors of biomedical publications use gel images to report experimental results such as protein-protein interactions or protein expressions under different conditions. Gel images offer a concise way to commun...

    Authors: Tobias Kuhn, Mate Levente Nagy, ThaiBinh Luong and Michael Krauthammer

    Citation: Journal of Biomedical Semantics 2014 5:10

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  35. Content type: Software

    Systematic representation of information related to genetic and non-genetic variations is required to allow large scale studies, data mining and data integration, and to make it possible to reveal novel relati...

    Authors: Mauno Vihinen

    Citation: Journal of Biomedical Semantics 2014 5:9

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  36. Content type: Research

    Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information. With the currently existing wealth of formalised knowledge, the ability to ...

    Authors: Razan Paul, Tudor Groza, Jane Hunter and Andreas Zankl

    Citation: Journal of Biomedical Semantics 2014 5:8

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  37. Content type: Research

    Terminologies that account for variation in language use by linking synonyms and abbreviations to their corresponding concept are important enablers of high-quality information extraction from medical texts. D...

    Authors: Aron Henriksson, Hans Moen, Maria Skeppstedt, Vidas Daudaravičius and Martin Duneld

    Citation: Journal of Biomedical Semantics 2014 5:6

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  38. Content type: Research

    The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hier...

    Authors: Victoria Petri, Pushkala Jayaraman, Marek Tutaj, G Thomas Hayman, Jennifer R Smith, Jeff De Pons, Stanley JF Laulederkind, Timothy F Lowry, Rajni Nigam, Shur-Jen Wang, Mary Shimoyama, Melinda R Dwinell, Diane H Munzenmaier, Elizabeth A Worthey and Howard J Jacob

    Citation: Journal of Biomedical Semantics 2014 5:7

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  39. Content type: Review

    The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHac...

    Authors: Toshiaki Katayama, Mark D Wilkinson, Kiyoko F Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts…

    Citation: Journal of Biomedical Semantics 2014 5:5

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  40. Content type: Research

    Epidemiology is a data-intensive and multi-disciplinary subject, where data integration, curation and sharing are becoming increasingly relevant, given its global context and time constraints. The semantic ann...

    Authors: Catia Pesquita, João D Ferreira, Francisco M Couto and Mário J Silva

    Citation: Journal of Biomedical Semantics 2014 5:4

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  41. Content type: Research

    Identifying phrases that refer to particular concept types is a critical step in extracting information from documents. Provided with annotated documents as training data, supervised machine learning can autom...

    Authors: Manabu Torii, Kavishwar Wagholikar and Hongfang Liu

    Citation: Journal of Biomedical Semantics 2014 5:3

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  42. Content type: Research

    Natural human languages show a power law behaviour in which word frequency (in any large enough corpus) is inversely proportional to word rank - Zipf’s law. We have therefore asked whether similar power law be...

    Authors: Leila R Kalankesh, John P New, Patricia G Baker and Andy Brass

    Citation: Journal of Biomedical Semantics 2014 5:2

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  43. Content type: Database

    The diverse set of human brain structure and function analysis methods represents a difficult challenge for reconciling multiple views of neuroanatomical organization. While different views of organization are...

    Authors: B Nolan Nichols, Jose LV Mejino, Landon T Detwiler, Trond T Nilsen, Maryann E Martone, Jessica A Turner, Daniel L Rubin and James F Brinkley

    Citation: Journal of Biomedical Semantics 2014 5:1

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  44. Content type: Research

    We built the Drug Ontology (DrOn) because we required correct and consistent drug information in a format for use in semantic web applications, and no existing resource met this requirement or could be altered...

    Authors: Josh Hanna, Eric Joseph, Mathias Brochhausen and William R Hogan

    Citation: Journal of Biomedical Semantics 2013 4:44

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  45. Content type: Research

    As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growi...

    Authors: Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J Mungall and Suzanna E Lewis

    Citation: Journal of Biomedical Semantics 2013 4:43

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