AIMC Topic: Biological Ontologies
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Knowledge retrieval from PubMed abstracts and electronic medical records with the Multiple Sclerosis Ontology.
PloS one
Feb 9, 2015
BACKGROUND: In order to retrieve useful information from scientific literature and electronic medical records (EMR) we developed an ontology specific for Multiple Sclerosis (MS).
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.
Database : the journal of biological databases and curation
Feb 4, 2015
The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to assess the evidence of an interaction occurring in ...
Describing the breakbone fever: IDODEN, an ontology for dengue fever.
PLoS neglected tropical diseases
Feb 3, 2015
BACKGROUND: Ontologies represent powerful tools in information technology because they enhance interoperability and facilitate, among other things, the construction of optimized search engines. To address the need to expand the toolbox available for ...
Aber-OWL: a framework for ontology-based data access in biology.
BMC bioinformatics
Jan 28, 2015
BACKGROUND: Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within t...
PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease.
Database : the journal of biological databases and curation
Jan 28, 2015
Rats have been used extensively as animal models to study physiological and pathological processes involved in human diseases. Numerous rat strains have been selectively bred for certain biological traits related to specific medical interests. Recent...
ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life.
Bioinformatics (Oxford, England)
Jan 24, 2015
UNLABELLED: The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centr...
Ontology-based data integration between clinical and research systems.
PloS one
Jan 14, 2015
Data from the electronic medical record comprise numerous structured but uncoded elements, which are not linked to standard terminologies. Reuse of such data for secondary research purposes has gained in importance recently. However, the identificati...
Exploiting Semantic Web Technologies to Develop OWL-Based Clinical Practice Guideline Execution Engines.
IEEE journal of biomedical and health informatics
Dec 18, 2014
Computerizing paper-based CPG and then executing them can provide evidence-informed decision support to physicians at the point of care. Semantic web technologies especially web ontology language (OWL) ontologies have been profusely used to represent...
Recognizing lexical and semantic change patterns in evolving life science ontologies to inform mapping adaptation.
Artificial intelligence in medicine
Dec 6, 2014
BACKGROUND: Mappings established between life science ontologies require significant efforts to maintain them up to date due to the size and frequent evolution of these ontologies. In consequence, automatic methods for applying modifications on mappi...
ADReCS: an ontology database for aiding standardization and hierarchical classification of adverse drug reaction terms.
Nucleic acids research
Oct 31, 2014
Adverse drug reactions (ADRs) are noxious and unexpected effects during normal drug therapy. They have caused significant clinical burden and been responsible for a large portion of new drug development failure. Molecular understanding and in silico ...
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