DANI-Boy: A Data Access and Navigation Interface for Biology
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1
École Polytechnique Fédérale de Lausanne, Blue Brain Project, Switzerland
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2
École Polytechnique Fédérale de Lausanne, Brain Mind Institute, Switzerland
Biomedical laboratories are producing ever increasing amounts of data, yet tools used to annotate and link the data are not flexible enough to accommodate rapidly evolving community standards and the demands of data integration, analysis and model workflows. Experimenters produce data and annotate parts of a project while performing data gathering and analysis of other part while performing annotation on others. Data integration tools used in the bio-medical domain currently do not provide a flexible enough framework to keep up with evolving ontologies and the daily reality of data generation. The increasing pressure to publish well annotated data and provide links to existing ontologies and data repositories creates the opportunity for a new set of tools.
We present a prototype of a Data Access and Navigation Interface for Biology (DANI-Boy) which support the continuous integration and annotation data by allowing easy access to community developed ontologies while allowing enough flexibility to add information not yet standardized by a wider community. DANI-Boy was build on best data integration practices, allowing to build on existing resources, such as NeuroLex biomedical ontologies. Semantic Media Wiki (SMW) is used in the current version as a graphical user interface to facilitating the continuous refinement of data annotation and linking to ontologically defined entities. Python is used for various background processing tasks to facilitate information extraction, cross ontology matching and in providing an ontology anchored object API. The intent is to provide a more intuitive service model than the standard SPARQL services provided by SMW.
The present prototype offers access to integrated experimental data gathered over the course of multiple years in the exploration of Layer I cells and microcircuitry of the neocortex of a P14 rat. The example implementation shows how morphological, electrophysiological, molecular and connectivity data can be organized, explored, annotated and updated.
Keywords:
Semantic Web technologies,
ontologies,
data integration,
python,
Neuroscience
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Demo
Topic:
Infrastructural and portal services
Citation:
Telefont
M,
Muralidhar
S,
Richardet
R and
Hill
SL
(2013). DANI-Boy: A Data Access and Navigation Interface for Biology.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00072
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Received:
29 Apr 2013;
Published Online:
11 Jul 2013.
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Correspondence:
Mr. Martin Telefont, École Polytechnique Fédérale de Lausanne, Blue Brain Project, Lausanne, Vaud, 1015, Switzerland, martin.telefont@epfl.ch