A generic organ based ontology system, applied to vertebrate heart anatomy, development and physiology

Abstract

Summary We present a novel approach to modelling biological information using ontologies. The system interlinks three ontologies, comprising anatomical, developmental and taxonomical information, and includes instances of structures for different species. The framework is constructed for comparative analyses in the field of evolutionary development. We have applied the approach to the vertebrate heart and present four case studies of the functionality of the system, focusing on cross-species comparisons, developmental studies, physiological studies and 3D visualisation.

CytomicsDB: A Metadata-Based Storage and Retrieval Approach for High-Throughput Screening Experiments

“…The structure of the metadata proposed in this paper will further evolve to an ontology based framework. A new layer to the architecture will be added in order to perform semantic queries, turning the architecture to a web based interactive semantic platform for cytomics [1].…”

“…The metadata of an HTP experiment consists of a variety of types and formats and has been grouped in five levels as showed in Figure 1: Project, Experiment, Plate -Wells, Video/Images and Measurements. These levels contain each other in a cascade fashion, for instance: [1] Project. This level contains a title which describes the aim of the project, the duration, the author, etc.…”