Nervous System Database (NSD): data integration spanning molecular and system levels
The nervous system and, in particular, the brain is the most complex biological structure known. In order to investigate this system it is important to adopt a strategy that encompasses the different "levels" of nervous system structure and functioning. These levels correspond to different scales: from molecular components to molecular systems, from single neuron to neural networks. Moreover, the use of mathematical models, which allow both the studies about the properties of such complex systems and the prediction of their behaviour, becomes a crucial aspect.
A multidisciplinary and integrative approach is therefore essential to face the study of the nervous system. First of all, it is important to organize available data in an easily accessible way, storing in a unique repository the contributions of different scientific communities that work on specific aspects.
The presented work deals with the data integration concerning the human nervous system: knowledge about biological components, such as genes and proteins, are collected together with information at the system level, such as protein networks and molecular pathways, that are relevant for a better exploration of neural systems. Crucial aspects of the developed resource mainly consist in providing an ontological framework for the biological components annotations, and in including a models oriented section, where several mathematical models are collected.
For what concerns the first feature, the annotations stored in NSD are associated to ontological terms: this solution provides a semantic layer to improve data storage, accessibility and sharing and represents an instrument to identify relations among biological components. Exploited ontologies, in OBO (Open Biomedical Ontologies) format, cover all levels of molecular biology and are among the most known and widely used bioinformatics resources.
Regarding the second feature, the database includes implemented, reconstructed or simply listed models which represent the state of the art of the nervous system modelling at different scales and with different perspectives: the classical computational neuroscience approach, oriented to single neuron and neuron network scale, is coupled to the system biology approach, that is grounded on molecules and studies molecular systems that arise from the relationship among DNA, RNA molecules, proteins, metabolites and other cellular components.
The implemented database provides several methods for managing data collected within the resource. The query and browsing systems supplies information about gene functions, processes where they are involved and their spatial localization. Taking advantage from protein-protein interactions data the resource provides a way to characterize poorly annotated components or to predict protein complexes. Moreover, by analysing the distribution of the annotations among a gene set, genes with similar properties can be identified, such as those that encode the same domain or that belong to the same biochemical pathway. Coupling this information with other data it is possible to assemble analysis pipelines, for example to compare annotations of proteins that physically interact with a queried one.
In conclusion, NSD represents a bioinformatics innovative resource, which integrates data from different scales to provide a more complete knowledge within the human nervous system field of study.
Conference:
Neuroinformatics 2009, Pilsen, Czechia, 6 Sep - 8 Sep, 2009.
Presentation Type:
Poster Presentation
Topic:
Infrastructural and portal services
Citation:
Mosca
E,
Alfieri
R,
Viti
F,
Merelli
I and
Milanesi
L
(2019). Nervous System Database (NSD): data integration spanning molecular and system levels.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2009.
doi: 10.3389/conf.neuro.11.2009.08.121
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Received:
26 May 2009;
Published Online:
09 May 2019.
*
Correspondence:
Ettore Mosca, ITB-CNR, Segrate, Italy, ettore.mosca@itb.cnr.it