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ORCIDJournal of Biomedical Semantics, Volume 5
Volume 5, 2014
- B. Nolan Nichols
, José L. V. Mejino Jr., Landon Detwiler, Trond T. Nilsen, Maryann E. Martone, Jessica A. Turner, Daniel L. Rubin, James F. Brinkley:
Neuroanatomical domain of the foundational model of anatomy ontology. 1 - Leila Kalankesh, John P. New, Patricia G. Baker, Andy Brass:
The languages of health in general practice electronic patient records: a Zipf's law analysis. 2 - Manabu Torii, Kavishwar B. Wagholikar, Hongfang Liu:
Detecting concept mentions in biomedical text using hidden Markov model: multiple concept types at once or one at a time? 3 - Catia Pesquita, João D. Ferreira, Francisco M. Couto, Mário J. Silva:
The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. 4 - 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, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Pier Luigi Buttigieg, Matthew P. Campbell, Yi-an Chen, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Alexandru Constantin:
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. 5 - Aron Henriksson, Hans Moen, Maria Skeppstedt, Vidas Daudaravicius, Martin Duneld:
Synonym extraction and abbreviation expansion with ensembles of semantic spaces. 6 - Victoria Petri, Pushkala Jayaraman, Marek Tutaj, G. Thomas Hayman, Jennifer R. Smith, Jeff de Pons, Stanley J. F. Laulederkind, Timothy Lowry, Rajni Nigam, Shur-Jen Wang, Mary Shimoyama, Melinda R. Dwinell, Diane H. Munzenmaier, Elizabeth A. Worthey, Howard J. Jacob:
The pathway ontology - updates and applications. 7 - Razan Paul, Tudor Groza, Jane Hunter, Andreas Zankl:
Semantic interestingness measures for discovering association rules in the skeletal dysplasia domain. 8 - Mauno Vihinen:
Variation ontology: annotator guide. 9 - Tobias Kuhn, Mate Levente Nagy, Thaibinh Luong, Michael Krauthammer:
Mining images in biomedical publications: Detection and analysis of gel diagrams. 10 - Artjom Klein, Alexandre Riazanov, Matthew M. Hindle, Christopher J. O. Baker:
Benchmarking infrastructure for mutation text mining. 11 - Ceri E. Van Slyke, Yvonne M. Bradford, Monte Westerfield, Melissa A. Haendel:
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. 12 - Charalampos Doulaverakis, George Nikolaidis, Athanasios Kleontas, Ioannis Kompatsiaris:
Panacea, a semantic-enabled drug recommendations discovery framework. 13 - Michel Dumontier, Christopher J. O. Baker, Joachim Baran, Alison Callahan, Leonid L. Chepelev, Jose Cruz-Toledo, Nicholas R. Del Rio, Geraint Duck, Laura Inés Furlong, Nichealla Keath, Dana Klassen, Jamie P. McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D. Wilkinson, Robert Hoehndorf:
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. 14 - Robert Hoehndorf, Dietrich Rebholz-Schuhmann, Melissa A. Haendel, Robert Stevens:
Thematic series on biomedical ontologies in JBMS: challenges and new directions. 15 - Cui Tao, Yongqun He, Sivaram Arabandi:
A 2013 workshop: vaccine and drug ontology studies (VDOS 2013). 16 - Despoina Magka, Markus Krötzsch, Ian Horrocks:
A rule-based ontological framework for the classification of molecules. 17 - Marie Dupuch, Laëtitia Dupuch, Thierry Hamon, Natalia Grabar:
Exploitation of semantic methods to cluster pharmacovigilance terms. 18 - Yu Lin, Yongqun He:
The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. 19 - Olivier Palombi, Federico Ulliana, Valentin Favier, Jean-Claude Léon, Marie-Christine Rousset:
My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models. 20 - Melissa A. Haendel, James P. Balhoff, Frederic B. Bastian, David C. Blackburn, Judith A. Blake, Yvonne M. Bradford, Aurélie Comte, Wasila M. Dahdul, Thomas Dececchi, Robert E. Druzinsky, Terry F. Hayamizu, Nizar Ibrahim, Suzanna E. Lewis, Paula M. Mabee, Anne Niknejad, Marc Robinson-Rechavi, Paul C. Sereno, Christopher J. Mungall:
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. 21 - George Karystianis, Iain E. Buchan, Goran Nenadic:
Mining characteristics of epidemiological studies from Medline: a case study in obesity. 22 - Yuki Yamagata, Kouji Kozaki, Takeshi Imai, Kazuhiko Ohe, Riichiro Mizoguchi:
An ontological modeling approach for abnormal states and its application in the medical domain. 23 - Malgorzata Marciniak, Agnieszka Mykowiecka:
Terminology extraction from medical texts in Polish. 24 - James Malone, Andy Brown, Allyson L. Lister, Jon C. Ison, Duncan Hull, Helen E. Parkinson, Robert Stevens:
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. 25 - Pontus Stenetorp, Sampo Pyysalo, Sophia Ananiadou, Jun'ichi Tsujii:
Generalising semantic category disambiguation with large lexical resources for fun and profit. 26 - Johannes Röhl, Ludger Jansen:
Why functions are not special dispositions: an improved classification of realizables for top-level ontologies. 27 - Tim Clark, Paolo Ciccarese, Carole A. Goble:
Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications. 28 - Yongqun He, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao, Barry Smith:
OAE: The Ontology of Adverse Events. 29 - Rainer Winnenburg, Olivier Bodenreider:
A framework for assessing the consistency of drug classes across sources. 30 - Erfan Younesi, Sam Ansari, Michaela Gündel, Shiva Ahmadi, Chris Coggins, Julia Hoeng, Martin Hofmann-Apitius, Manuel C. Peitsch:
CSEO - the Cigarette Smoke Exposure Ontology. 31 - Hongyan Wu, Toyofumi Fujiwara, Yasunori Yamamoto, Jerven T. Bolleman, Atsuko Yamaguchi:
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. 32 - Yuji Zhang, Cui Tao, Guoqian Jiang, Asha A. Nair, Jian Su, Christopher G. Chute, Hongfang Liu:
Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network. 33 - Wasila M. Dahdul, Hong Cui, Paula M. Mabee, Christopher J. Mungall, David Osumi-Sutherland, Ramona L. Walls, Melissa A. Haendel:
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. 34 - Marjan Alirezaie, Amy Loutfi:
Automated Reasoning using Abduction for Interpretation of Medical Signals. 35 - Liwei Wang, Guoqian Jiang, Dingcheng Li, Hongfang Liu:
Standardizing adverse drug event reporting data. 36 - Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma D. Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen E. Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa A. Haendel, Jie Zheng, Christian J. Stoeckert Jr., Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He:
CLO: The cell line ontology. 37 - Janna Hastings, Andy Brass, Colin Caine, Caroline Jay, Robert Stevens:
Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference. 38 - Robert W. Thacker, Maria Díaz, Adeline Kerner, Régine Vignes-Lebbe, Erik Segerdell, Melissa A. Haendel, Christopher J. Mungall:
The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. 39 - Nina Laurenne, Jouni Tuominen, Hannu Saarenmaa, Eero Hyvönen:
Making species checklists understandable to machines - a shift from relational databases to ontologies. 40 - Kristina M. Hettne, Harish Dharuri, Jun Zhao, Katherine Wolstencroft, Khalid Belhajjame, Stian Soiland-Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, Lourdes Verdes-Montenegro, Julián Garrido, David De Roure, Óscar Corcho, Graham Klyne, Reinout van Schouwen, Peter A. C. 't Hoen, Sean Bechhofer, Carole A. Goble, Marco Roos:
Structuring research methods and data with the research object model: genomics workflows as a case study. 41 - Mikel Egaña Aranguren, Alejandro Rodríguez González, Mark D. Wilkinson:
Executing SADI services in Galaxy. 42 - Cátia Vaz, Alexandre P. Francisco, Mickael Silva, Keith A. Jolley, James E. Bray, Hannes Pouseele, Jörg Rothgänger, Mário Ramirez, João A. Carriço:
TypOn: the microbial typing ontology. 43 - Gayo Diallo:
An effective method of large scale ontology matching. 44 - James P. Balhoff, Wasila M. Dahdul, Thomas Dececchi, Hilmar Lapp, Paula M. Mabee, Todd J. Vision:
Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. 45 - Alejandro Rodríguez González, Alison Callahan, José Cruz-Toledo, Adrian Garcia, Mikel Egaña Aranguren, Michel Dumontier, Mark D. Wilkinson:
Automatically exposing OpenLifeData via SADI semantic Web Services. 46 - Muhammad Saleem, Shanmukha S. Padmanabhuni, Axel-Cyrille Ngonga Ngomo, Aftab Iqbal, Jonas S. Almeida, Stefan Decker, Helena F. Deus:
TopFed: TCGA Tailored Federated Query Processing and Linking to LOD. 47 - Heiko Dietze, Tanya Z. Berardini, Rebecca E. Foulger, David P. Hill, Jane Lomax, David Osumi-Sutherland, Paola Roncaglia, Christopher J. Mungall:
TermGenie - A web application for pattern-based ontology class generation. 48 - Kimberly Clark, Deepak K. Sharma, Rui Qin, Christopher G. Chute, Cui Tao:
A use case study on late stent thrombosis for ontology-based temporal reasoning and analysis. 49 - Nikhil Lingutla, Justin Preece, Sinisa Todorovic, Laurel Cooper, Laura Moore, Pankaj Jaiswal:
AISO: Annotation of Image Segments with Ontologies. 50 - Vinay K. Chaudhri, Daniel Elenius, Andrew Goldenkranz, Allison Gong, Maryann E. Martone, William Webb, Neil Yorke-Smith:
Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks. 51
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