AIMC Topic: Biological Ontologies

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Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis.

Proteomics
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 ...

Transformation of standardized clinical models based on OWL technologies: from CEM to OpenEHR archetypes.

Journal of the American Medical Informatics Association : JAMIA
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...

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

Database : the journal of biological databases and curation
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
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
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
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)
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
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...