AIMC Topic: Biological Ontologies

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Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.

Database : the journal of biological databases and curation
Bio-ontologies provide terminologies for the scientific community to describe biomedical entities in a standardized manner. There are multiple initiatives that are developing biomedical terminologies for the purpose of providing better annotation, da...

Integrating ontologies of rare diseases and radiological diagnosis.

Journal of the American Medical Informatics Association : JAMIA
PURPOSE: The author sought to integrate an ontology of rare diseases with a large ontological model of radiological diagnosis.

MorphoCol: An ontology-based knowledgebase for the characterisation of clinically significant bacterial colony morphologies.

Journal of biomedical informatics
BACKGROUND: One of the major concerns of the biomedical community is the increasing prevalence of antimicrobial resistant microorganisms. Recent findings show that the diversification of colony morphology may be indicative of the expression of virule...

Assessing the impact of case sensitivity and term information gain on biomedical concept recognition.

PloS one
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 ...

Innovative Bayesian and parsimony phylogeny of dung beetles (coleoptera, scarabaeidae, scarabaeinae) enhanced by ontology-based partitioning of morphological characters.

PloS one
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
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
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
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
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...