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ORCIDJournal of Biomedical Semantics, Volume 4
Volume 4, 2013
- Stephen T. Wu, Vinod Kaggal, Dmitriy Dligach, James J. Masanz
, Pei J. Chen, Lee Becker, Wendy Webber Chapman, Guergana K. Savova, Hongfang Liu, Christopher G. Chute:
A common type system for clinical natural language processing. 1 - Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana, Chris Mungall, Alejandro Rodríguez González, Mark D. Wilkinson:
OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. 2 - Kavishwar B. Wagholikar, Manabu Torii, Siddhartha Jonnalagadda, Hongfang Liu:
Pooling annotated corpora for clinical concept extraction. 3 - Tor Johan Mikael Karlsson, Oswaldo Trelles:
MAPI: a software framework for distributed biomedical applications. 4 - Richard D. Boyce, John R. Horn, Oktie Hassanzadeh, Anita de Waard, Jodi Schneider, Joanne S. Luciano, Majid Rastegar-Mojarad, Maria Liakata:
Dynamic enhancement of drug product labels to support drug safety, efficacy, and effectiveness. 5 - The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies. 6
- Georgios Kontonatsios, Ioannis Korkontzelos, BalaKrishna Kolluru, Paul Thompson, Sophia Ananiadou:
Deploying and sharing U-Compare workflows as web services. 7 - Yasunori Yamamoto, Atsuko Yamaguchi, Akinori Yonezawa:
Building Linked Open Data towards integration of biomedical scientific literature with DBpedia. 8 - Alexandre Riazanov, Artjom Klein, Arash Shaban-Nejad, Gregory W. Rose, Alan J. Forster, David L. Buckeridge, Christopher J. O. Baker:
Semantic querying of relational data for clinical intelligence: a semantic web services-based approach. 9 - Patrick Lambrix, Valentina Ivanova:
A unified approach for debugging is-a structure and mappings in networked taxonomies. 10 - Guoqian Jiang, Harold R. Solbrig, Christopher G. Chute:
Using Semantic Web technology to support icd-11 textual definitions authoring. 11 - María Pérez Catalán, Rafael Berlanga Llavori, Ismael Sanz, María José Aramburu:
BioUSeR: A semantic-based tool for retrieving Life Science web resources driven by text-rich user requirements. 12 - Carissa A. Park, Susan M. Bello, Cynthia L. Smith, Zhi-Liang Hu, Diane H. Munzenmaier, Rajni Nigam, Jennifer R. Smith, Mary Shimoyama, Janan T. Eppig, James M. Reecy:
The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. 13 - Saeed Hassanpour, Martin J. O'Connor, Amar K. Das:
A semantic-based method for extracting concept definitions from scientific publications: evaluation in the autism phenotype domain. 14 - Terry F. Hayamizu, Michael N. Wicks, Duncan Davidson, Albert Burger, Martin Ringwald, Richard A. Baldock:
EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. 15 - Pantelis Topalis, Elvira Mitraka, Vicky Dritsou, Emmanuel Dialynas, Christos Louis:
IDOMAL: the malaria ontology revisited. 16 - Olivier Dameron, Paolo Besana, Oussama Zekri, Annabel Bourde, Anita Burgun, Marc Cuggia:
OWL model of clinical trial eligibility criteria compatible with partially-known information. 17 - Paul N. Schofield, John P. Sundberg, Beth A. Sundberg, Colin McKerlie, Georgios V. Gkoutos:
The mouse pathology ontology, MPATH; structure and applications. 18 - Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Antonio Jimeno-Yepes, Ian Lewin:
Monitoring named entity recognition: the League Table. 19 - Paola Roncaglia, Maryann E. Martone, David P. Hill, Tanya Z. Berardini, Rebecca E. Foulger, Fahim T. Imam, Harold J. Drabkin, Christopher J. Mungall, Jane Lomax:
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. 20 - Catia M. Machado, Ana T. Freitas, Francisco M. Couto:
Enrichment analysis applied to disease prognosis. 21 - Bernard de Bono, Pierre Grenon, Richard A. Baldock, Peter Hunter:
Functional tissue units and their primary tissue motifs in multi-scale physiology. 22 - Mathias Brochhausen, Martin N. Fransson, Nitin Kanaskar, Mikael Eriksson, Roxana Merino-Martinez, Roger A. Hall, Loreana Norlin, Sanela Kjellqvist, Maria Hortlund, Umit Topaloglu, William R. Hogan, Jan-Eric Litton:
Developing a semantically rich ontology for the biobank-administration domain. 23 - Christian Knüpfer, Clemens Beckstein:
Function of dynamic models in systems biology: linking structure to behaviour. 24 - Georg Fuellen, Ludger Jansen, Ulf Leser, Andreas Kurtz:
Using ontologies to study cell transitions. 25 - Jennifer R. Smith, Carissa A. Park, Rajni Nigam, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Timothy Lowry, Victoria Petri, Jeff de Pons, Marek Tutaj, Weisong Liu, Elizabeth A. Worthey, Mary Shimoyama, Melinda R. Dwinell:
The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications. 26 - Irena Spasic, Robert Mark Greenwood, Alun D. Preece, Nick Francis, Glyn Elwyn:
FlexiTerm: a flexible term recognition method. 27 - Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno-Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin:
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. 28 - Anika Oellrich, Christoph Grabmüller, Dietrich Rebholz-Schuhmann:
Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP. 29 - David Osumi-Sutherland, Steven J. Marygold, Gillian H. Millburn, Peter McQuilton, Laura Ponting, Raymund Stefancsik, Kathleen Falls, Nicholas H. Brown, Georgios V. Gkoutos:
The Drosophila phenotype ontology. 30 - Erik Segerdell, Virgilio G. Ponferrada, Christina James-Zorn, Kevin A. Burns, Joshua D. Fortriede, Wasila M. Dahdul, Peter D. Vize, Aaron M. Zorn:
Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. 31 - Marta Costa, Simon Reeve, Gary Grumbling, David Osumi-Sutherland:
The Drosophila anatomy ontology. 32 - Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala, Hongfang Liu:
Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. 33 - Peter E. Midford, Thomas Dececchi, James P. Balhoff, Wasila M. Dahdul, Nizar Ibrahim, Hilmar Lapp, John G. Lundberg, Paula M. Mabee, Paul C. Sereno, Monte Westerfield, Todd J. Vision, David C. Blackburn:
The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. 34 - Michaela Gündel, Erfan Younesi, Ashutosh Malhotra, Jiali Wang, Hui Li, Bijun Zhang, Bernard de Bono, Heinz-Theodor Mevissen, Martin Hofmann-Apitius:
HuPSON: the human physiology simulation ontology. 35 - Rajni Nigam, Diane H. Munzenmaier, Elizabeth A. Worthey, Melinda R. Dwinell, Mary Shimoyama, Howard J. Jacob:
Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD. 36 - Paolo Ciccarese, Stian Soiland-Reyes, Khalid Belhajjame, Alasdair J. G. Gray, Carole A. Goble, Tim Clark:
PAV ontology: provenance, authoring and versioning. 37 - Kevin M. Livingston, Michael Bada, Lawrence E. Hunter, Karin Verspoor:
Representing annotation compositionality and provenance for the Semantic Web. 38 - Kiyoko F. Aoki-Kinoshita, Jerven T. Bolleman, Matthew P. Campbell, Shin Kawano, Jin-Dong Kim, Thomas Lütteke, Masaaki Matsubara, Shujiro Okuda, René Ranzinger, Hiromichi Sawaki, Toshihide Shikanai, Daisuke Shinmachi, Yoshinori Suzuki, Philip V. Toukach, Issaku Yamada, Nicolle H. Packer, Hisashi Narimatsu:
Introducing glycomics data into the Semantic Web. 39 - Erica Marcos, Bin Zhao, Yongqun He:
The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. 40 - Daniel L. Cook, Maxwell Lewis Neal, Fred L. Bookstein, John H. Gennari:
Ontology of physics for biology: representing physical dependencies as a basis for biological processes. 41 - Mark Jensen, Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William D. Duncan, Patrick Ray, Bianca Weinstock-Guttman, Barry Smith, Alan Ruttenberg, Kinga Szigeti, Alexander D. Diehl:
The neurological disease ontology. 42 - Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J. Mungall, Suzanna E. Lewis:
The environment ontology: contextualising biological and biomedical entities. 43 - Josh Hanna, Eric Joseph, Mathias Brochhausen, William R. Hogan:
Building a drug ontology based on RxNorm and other sources. 44
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