Journal of Biomedical Semantics

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Towards improving phenotype representation in OWL
Journal of Biomedical Semantics - Tập 3 - Trang 1-17 - 2012
Frank Loebe, Frank Stumpf, Robert Hoehndorf, Heinrich Herre
Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. The Entity-Quality (EQ) formalism is a means to describe complex phenotypes based on one or more affected entities and a quality. EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies. ...... hiện toàn bộ
Neural side effect discovery from user credibility and experience-assessed online health discussions
Journal of Biomedical Semantics - Tập 11 Số 1 - 2020
Van-Hoang Nguyen, Kazunari Sugiyama, Min-Yen Kan, Kishaloy Halder
AbstractBackgroundHealth 2.0 allows patients and caregivers to conveniently seek medical information and advice via e-portals and online discussion forums, especially regarding potential drug side effects. Although online health communities are helpful platforms for obtaining non-professional opinions, they pose risks in communica...... hiện toàn bộ
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing
Journal of Biomedical Semantics - Tập 14 - Trang 1-14 - 2023
Antonio Jose Jimeno Yepes, Karin Verspoor
Information pertaining to mechanisms, management and treatment of disease-causing pathogens including viruses and bacteria is readily available from research publications indexed in MEDLINE. However, identifying the literature that specifically characterises these pathogens and their properties based on experimental research, important for understanding of the molecular basis of diseases caused by...... hiện toàn bộ
Natural language processing algorithms for mapping clinical text fragments onto ontology concepts: a systematic review and recommendations for future studies
Journal of Biomedical Semantics - Tập 11 - Trang 1-21 - 2020
Martijn G. Kersloot, Florentien J. P. van Putten, Ameen Abu-Hanna, Ronald Cornet, Derk L. Arts
Free-text descriptions in electronic health records (EHRs) can be of interest for clinical research and care optimization. However, free text cannot be readily interpreted by a computer and, therefore, has limited value. Natural Language Processing (NLP) algorithms can make free text machine-interpretable by attaching ontology concepts to it. However, implementations of NLP algorithms are not eval...... hiện toàn bộ
Improving reusability along the data life cycle: a regulatory circuits case study
Journal of Biomedical Semantics - Tập 13 - Trang 1-15 - 2022
Marine Louarn, Fabrice Chatonnet, Xavier Garnier, Thierry Fest, Anne Siegel, Catherine Faron, Olivier Dameron
In life sciences, there has been a long-standing effort of standardization and integration of reference datasets and databases. Despite these efforts, many studies data are provided using specific and non-standard formats. This hampers the capacity to reuse the studies data in other pipelines, the capacity to reuse the pipelines results in other studies, and the capacity to enrich the data with ad...... hiện toàn bộ
Building Linked Open Data towards integration of biomedical scientific literature with DBpedia
Journal of Biomedical Semantics - Tập 4 - Trang 1-7 - 2013
Yasunori Yamamoto, Atsuko Yamaguchi, Akinori Yonezawa
There is a growing need for efficient and integrated access to databases provided by diverse institutions. Using a linked data design pattern allows the diverse data on the Internet to be linked effectively and accessed efficiently by computers. Previously, we developed the Allie database, which stores pairs of abbreviations and long forms (LFs, or expanded forms) used in the life sciences. LFs de...... hiện toàn bộ
Section level search functionality in Europe PMC
Journal of Biomedical Semantics - Tập 6 - Trang 1-5 - 2015
Şenay Kafkas, Xingjun Pi, Nikos Marinos, Francesco Talo’, Andrew Morrison, Johanna R McEntyre
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 Europe PMC that allows selected sections of full text articles to be searched, including figures and reference lists. Users can now search particular parts of an article, reducing noise and a...... hiện toàn bộ
OWL model of clinical trial eligibility criteria compatible with partially-known information
Journal of Biomedical Semantics - Tập 4 - Trang 1-10 - 2013
Olivier Dameron, Paolo Besana, Oussama Zekri, Annabel Bourdé, Anita Burgun, Marc Cuggia
Clinical trials are important for patients, for researchers and for companies. One of the major bottlenecks is patient recruitment. This task requires the matching of a large volume of information about the patient with numerous eligibility criteria, in a logically-complex combination. Moreover, some of the patient’s information necessary to determine the status of the eligibility criteria may not...... hiện toàn bộ
A task-based approach for Gene Ontology evaluation
Journal of Biomedical Semantics - Tập 4 - Trang 1-11 - 2013
Erik L Clarke, Salvatore Loguercio, Benjamin M Good, Andrew I Su
The Gene Ontology and its associated annotations are critical tools for interpreting lists of genes. Here, we introduce a method for evaluating the Gene Ontology annotations and structure based on the impact they have on gene set enrichment analysis, along with an example implementation. This task-based approach yields quantitative assessments grounded in experimental data and anchored tightly to ...... hiện toàn bộ
Topics in machine learning for biomedical literature analysis and text retrieval
Journal of Biomedical Semantics - Tập 3 Số S3 - 2012
Rezarta Islamaj Doğan, Lana Yeganova
Tổng số: 347   
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