Journal of Biomedical Semantics

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Assessment of NER solutions against the first and second CALBC Silver Standard Corpus
Journal of Biomedical Semantics - Tập 2 Số 5 - Trang 1-12 - 2011
Rebholz-Schuhmann, Dietrich, Yepes, Antonio Jimeno, Li, Chen, Kafkas, Senay, Lewin, Ian, Kang, Ning, Corbett, Peter, Milward, David, Buyko, Ekaterina, Beisswanger, Elena, Hornbostel, Kerstin, Kouznetsov, Alexandre, Witte, René, Laurila, Jonas B, Baker, Christopher JO, Kuo, Cheng-Ju, Clematide, Simone, Rinaldi, Fabio, Farkas, Richárd, Móra, György, Hara, Kazuo, Furlong, Laura I, Rautschka, Michael, Neves, Mariana Lara, Pascual-Montano, Alberto, Wei, Qi, Collier, Nigel, Chowdhury, Md Faisal Mahbub, Lavelli, Alberto, Berlanga, Rafael, Morante, Roser, Van Asch, Vincent, Daelemans, Walter, Marina, José Luís, van Mulligen, Erik, Kors, Jan, Hahn, Udo
Competitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is time-consuming and costly and the final corpus consists at the most of a few thousand documents annotated with a limited set of semantic groups. To overcome these shortcomings, the CALBC project partners ...... hiện toàn bộ
The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species
Journal of Biomedical Semantics - Tập 4 - Trang 1-9 - 2013
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 use of ontologies to standardize biological data and facilitate comparisons among datasets has steadily grown as the complexity and amount of available data have increased. Despite the numerous ontologies available, one area currently lacking a robust ontology is the description of vertebrate traits. A trait is defined as any measurable or observable characteristic pertaining to an organism or...... hiện toàn bộ
Using Semantic Web technology to support icd-11 textual definitions authoring
Journal of Biomedical Semantics - Tập 4 - Trang 1-9 - 2013
Guoqian Jiang, Harold R Solbrig, Christopher G Chute
The beta phase of the 11th revision of International Classification of Diseases (ICD-11) intends to accept public input through a distributed model of authoring. One of the core use cases is to create textual definitions for the ICD categories. The objective of the present study is to design, develop, and evaluate approaches to support ICD-11 textual definitions authoring using Semantic Web techno...... hiện toàn bộ
My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development
Journal of Biomedical Semantics - Tập 6 - Trang 1-15 - 2015
Pierre-Yves Rabattu, Benoit Massé, Federico Ulliana, Marie-Christine Rousset, Damien Rohmer, Jean-Claude Léon, Olivier Palombi
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 physically based modeling are used to assist the visualization and the simulation of virtual humans for numerous domains such as surgical simulation and learning. On the other side, the ontology-based...... hiện toàn bộ
BioUSeR: a semantic-based tool for retrieving Life Science web resources driven by text-rich user requirements
Journal of Biomedical Semantics - - 2013
María Calzada Pérez, Rafael Berlanga, Ismael Sanz, María José Aramburu
Networks of neuroinjury semantic predications to identify biomarkers for mild traumatic brain injury
Journal of Biomedical Semantics - Tập 6 - Trang 1-14 - 2015
Michael J Cairelli, Marcelo Fiszman, Han Zhang, Thomas C Rindflesch
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 disorders. Unfortunately, such neural injury often goes undiagnosed due to the difficulty in identifying symptoms, so the discovery of an effective biomarker would greatly assist diagnosis; how...... hiện toàn bộ
Towards natural language question generation for the validation of ontologies and mappings
Journal of Biomedical Semantics - Tập 7 - Trang 1-15 - 2016
Asma Ben Abacha, Julio Cesar Dos Reis, Yassine Mrabet, Cédric Pruski, Marcos Da Silveira
The increasing number of open-access ontologies and their key role in several applications such as decision-support systems highlight the importance of their validation. Human expertise is crucial for the validation of ontologies from a domain point-of-view. However, the growing number of ontologies and their fast evolution over time make manual validation challenging. We propose a novel semi-auto...... hiện toàn bộ
Establishing a distributed system for the simple representation and integration of diverse scientific assertions
Journal of Biomedical Semantics - Tập 1 - Trang 1-12 - 2010
Matthias Samwald, Holger Stenzhorn
Information technology has the potential to increase the pace of scientific progress by helping researchers in formulating, publishing and finding information. There are numerous projects that employ ontologies and Semantic Web technologies towards this goal. However, the number of applications that have found widespread use among biomedical researchers is still surprisingly small. In this paper w...... hiện toàn bộ
Learning from biomedical linked data to suggest valid pharmacogenes
Journal of Biomedical Semantics - Tập 8 - Trang 1-12 - 2017
Yassine Marzougui, Ndeye Coumba Ndiaye, Sébastien Da Silva, Patrice Ringot, Adrien Coulet, Kevin Dalleau
A standard task in pharmacogenomics research is identifying genes that may be involved in drug response variability, i.e., pharmacogenes. Because genomic experiments tended to generate many false positives, computational approaches based on the use of background knowledge have been proposed. Until now, only molecular networks or the biomedical literature were used, whereas many other resources are...... hiện toàn bộ
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