AIMC Topic: Biological Ontologies
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Assessing the impact of case sensitivity and term information gain on biomedical concept recognition.
PloS one
Mar 19, 2015
Concept recognition (CR) is a foundational task in the biomedical domain. It supports the important process of transforming unstructured resources into structured knowledge. To date, several CR approaches have been proposed, most of which focus on a ...
Comparing a knowledge-driven approach to a supervised machine learning approach in large-scale extraction of drug-side effect relationships from free-text biomedical literature.
BMC bioinformatics
Mar 18, 2015
BACKGROUND: Systems approaches to studying drug-side-effect (drug-SE) associations are emerging as an active research area for both drug target discovery and drug repositioning. However, a comprehensive drug-SE association knowledge base does not exi...
Innovative Bayesian and parsimony phylogeny of dung beetles (coleoptera, scarabaeidae, scarabaeinae) enhanced by ontology-based partitioning of morphological characters.
PloS one
Mar 17, 2015
Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-le...
Combining computational models, semantic annotations and simulation experiments in a graph database.
Database : the journal of biological databases and curation
Mar 8, 2015
Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems. However, their storage concepts support only restricted types of queries and ...
Feeding the human brain model.
Current opinion in neurobiology
Feb 26, 2015
The goal of the Human Brain Project is to develop, during the next decade, an infrastructure capable of simulating a draft human brain model based on available experimental data. One of the key issues is therefore to integrate and make accessible the...
Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies.
BMC medical informatics and decision making
Feb 22, 2015
BACKGROUND: Every year, hundreds of thousands of patients experience treatment failure or adverse drug reactions (ADRs), many of which could be prevented by pharmacogenomic testing. However, the primary knowledge needed for clinical pharmacogenomics ...
BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.
BMC bioinformatics
Feb 21, 2015
BACKGROUND: Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biol...
Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis.
Proteomics
Feb 20, 2015
The main result of a great deal of the published proteomics studies is a list of identified proteins, which then needs to be interpreted in relation to the research question and existing knowledge. In the early days of proteomics this interpretation ...
Inappropriate use of the term "cytotoxicity" in scientific literature.
Daru : journal of Faculty of Pharmacy, Tehran University of Medical Sciences
Feb 20, 2015
Transformation of standardized clinical models based on OWL technologies: from CEM to OpenEHR archetypes.
Journal of the American Medical Informatics Association : JAMIA
Feb 10, 2015
INTRODUCTION: The semantic interoperability of electronic healthcare records (EHRs) systems is a major challenge in the medical informatics area. International initiatives pursue the use of semantically interoperable clinical models, and ontologies h...
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