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Ontologies for Bioinformatics

Bioinformatics and Biology Insights, 2008
The past twenty years have witnessed an explosion of biological data in diverse database formats governed by heterogeneous infrastructures. Not only are semantics (attribute terms) different in meaning across databases, but their organization varies ...
Nadine Schuurman, Agnieszka Leszczynski
doaj   +2 more sources

A Guideline-Oriented Ontological Decision Support System for Diagnosis and Treatment of Urinary Incontinence (UrInO-DSS): A System Framework

Journal of Urological Surgery, 2023
Objective: To design an ontology-based clinical decision support system based on a clinical guideline for urinary incontinence.Materials and Methods:The study will be conducted in four phases: Updating the adapted clinical guideline for urinary ...
Fatemeh Sadeghi-Ghyassi, Shahla Damanabi, Leila R. Kalankesh, Stijn Van de Velde, Mohammad-Reza Feizi-Derakhshi, Sakineh Hajebrahimi   +5 more
doaj   +1 more source

The ontology of biological sequences

BMC Bioinformatics, 2009
Background Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins.
Kelso Janet, Hoehndorf Robert, Herre Heinrich   +2 more
doaj   +1 more source

IntegromeDB: an integrated system and biological search engine

BMC Genomics, 2012
Background With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Description Here, we present an
Baitaluk Michael, Kozhenkov Sergey, Dubinina Yulia, Ponomarenko Julia   +3 more
doaj   +1 more source

Content and quality of physical activity ontologies: a systematic review

International Journal of Behavioral Nutrition and Physical Activity, 2023
Introduction Ontologies are a formal way to represent knowledge in a particular field and have the potential to transform the field of health promotion and digital interventions.
Maya Braun, Stéphanie Carlier, Femke De Backere, Annick De Paepe, Marie Van De Velde, Delfien Van Dyck, Marta M. Marques, Filip De Turck, Geert Crombez   +8 more
doaj   +1 more source

Biomedical ontologies and their development, management, and applications in and beyond China

Journal of Bio-X Research, 2019
. Since the boom of biomedical big data studies, various big data processing technologies have been developed rapidly. As an important form of knowledge representation, ontology has become an important means for the utilization and integration of ...
Hongjie Pan, Yan Zhu, Sheng Yang, Zhigang Wang, Wei Zhou, Yongqun He, Xiaolin Yang   +6 more
doaj   +1 more source

The Ontology for Biomedical Investigations. [PDF]

PLoS ONE, 2016
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted.
Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H Brush, Bill Bug, Marcus C Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Daniel Schober, Barry Smith, Larisa N Soldatova, Christian J Stoeckert, Chris F Taylor, Carlo Torniai, Jessica A Turner, Randi Vita, Patricia L Whetzel, Jie Zheng   +43 more
doaj   +1 more source

clusterProfiler: an R package for comparing biological themes among gene clusters.

Omics, 2012
Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment ...
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing‐Yu He   +3 more
semanticscholar   +1 more source

The role of ontologies in biological and biomedical research: a functional perspective

Briefings Bioinform., 2015
Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena ...
R. Hoehndorf, P. Schofield, G. Gkoutos
semanticscholar   +1 more source

A Tool for Collaborative Construction of Large Biological Ontologies

International Conference on Database and Expert Systems Applications, 2006
In order for ontologies to be broadly useful to the scientific community, they need to capture knowledge and expertise of multiple experts and research groups.
Jie Bao, Zhilian Hu, Doina Caragea, J. Reecy, Vasant G Honavar   +4 more
semanticscholar   +1 more source