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Neuroinformatics: a Spotlight on Various Databases and the Importance of Their Integration Erica Sequeira and Saraswathy Nagendran*

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Neuroinformatics: a Spotlight on Various Databases and the Importance of Their Integration Erica Sequeira and Saraswathy Nagendran* Original Article Neuroinformatics: A Spotlight on Various Databases and the Importance of Their Integration Erica Sequeira and Saraswathy Nagendran* SVKM`s NMIMS Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, Vile Parle (W), Mumbai, India ABSTRACT Brain is one of the most complex organs of the body and thus the challenge in neuroscience would seem the effort of understanding the complex structure, function, and development of the nervous system in healthy as well as diseased condition. Such understanding requires the integration of huge amounts of heterogeneous and complex data collected at various levels of investigation. Neuroinformatics combines neuroscience with information science/technology and deals with the creation and maintenance of web accessible databases that will be required to achieve such integration. There is significant interest amongst neuroscientists in sharing neuroscience data and analytical tools which provides the opportunity to differently re- Address for analyze previously collected data and encourage new neuroscience Correspondence interpretations that facilitates further development. However, information is usually stored in various databases, managed by SVKM`s NMIMS heterogeneous database management systems or files, spreadsheets Shobhaben Pratapbhai etc. which results into inaccuracy and inconsistencies in data Patel School of acquisition and processing, lack of coordination resulting in Pharmacy and duplication of efforts and of resources. Thus an integration of Technology databases is a vital solution to these problems. This article, analyses Management, Vile various databases in the field of neuroscience along with the Parle (W), Mumbai, importance of integration of databases. India. E-mail: saraswathy76 Keywords: Neuroscience, Databases, Nervous system, Brain, @gmail.com Information technology. INTRODUCTION Neuroinformatics as a field for decade witnessed a development which understanding the nervous system in healthy involved dealing with the complex types of as well as the diseased condition was data that is required during the research. In initiated in the early 19001. The subsequent 2000, a paper had suggested that databases American Journal of Phytomedicine and Clinical Therapeutics www.ajpct.org Nagendran et al_____________________________________________ ISSN 2321 – 2748 were needed to organize the numerous Neuroinformatics databases databases and tools2. Around 2004, a database (SfN (Society for Neuroscience) Brain imaging database Neuroscience Database Gateway 2007)3 that Current techniques in brain imaging emerged to satisfy this need. Many are divided into mainly two different areas, investigators realized that the computer was firstly, structural imaging technique for a vital tool to keep a track of the series of studying the anatomy of the brain, for letters that represented the base sequence example, computerized tomography (CT) and that makes up the nucleic acids (e.g. GCAT) magnetic resonance imaging (MRI) and or the sequence of amino acids that makes secondly, functional imaging techniques for up the protein molecule4-7. European studying its functions or the connectivity of Molecular Biology laboratory’s EMBL- the brain, for example, functional magnetic Bank and the National Center for resonance imaging (fMRI), positron emission Biotechnology Information GenBank, were tomography (PET), and diffusion tensor launched in the early 1980s for databases of imaging (DTI). genes8,9. Neuroinformatics is a field that capitalizes on the potential synergies Brain-development.org between neuroscience and information It is a part of the research project in technology (IT) such as: deals with the the Imperial college London which contains application of advanced IT methods to deal datasets of over 600 MRI images of healthy with the flood of neuroscientific data by subjects which utilizes T1 T2 and PD developing and applying data analysis weighted images, MRA images, DTI images, methods for the study of the brain; by and Diffusion weighted images of normal and providing both analytical and numerical healthy human brains. It also gives the tools for theoretically modeling brain demographic information of each subject11. function; and by exploiting our insights into the principles underlying brain function to Brainmuseum.org develop new IT technologies. With the It is a public web site that provides the development of many methods of studying images and the information of well preserved, the brain, researchers have studied the brain sectioned and stained brains of over 100 using various technologies such as magnetic species of mammals including humans. resonance imaging (MRI), functional Stained sections of several species such as magnetic resonance imaging (fMRI), and humans, chimpanzees, monkeys, carnivores, computerized tomography (CT) to study rodents, California sea lion, Big brown bat, functions, connectivity, and structures of the American badger, American Racoon, yellow brain; microarray, in situ hybridization mongoose, zebra, cow and Atlantic Bottle (ISH) and next generation sequencing nose Dolphin is available and it explains how (NGS) to study the molecular state of the the evolution of brain occurred12. brain; electroencephalography (EEG) and magnetoencephalography (MEG) to study Harvard whole brain atlas the electrophysiology of the brain10. Thus, It is a comprehensive and a well neuroscience has become essential to the designed site that contains a huge compilation neuroscience investigators and clinicians for of modern cross sectional signaling including conducting scientific inquiry, understanding CT, MRI and SPECT in health and diseased the cause and pathogenesis of a brain condition of brains such as cerebrovascular disorder and practicing medicine. diseases, neoplastic diseases, degenerative AJPCT[2][8][2014]976-984 Nagendran et al_____________________________________________ ISSN 2321 – 2748 diseases, and infections and inflammatory and integrated due to the complexity and diseases13. diversity of it. In spite of all these difficulties some databases and tools are developed and Brainmap.org available now. It is a database of published functional and structural neuroimaging experiments with NeuroElectro coordinate-based results (x, y, z) in Talairach It is a database describing the or Montreal Neurological Institute (MNI) electrophysiology properties of different space. It involves the development of neuron types so as to understand the role of software and tools to share neuroimaging diversity across neuron types. Using a results and enable meta-analysis of studies of combination of manual and automated human brain function and structure in healthy methods it describes a methodology to curate and diseased subjects14. the neuron electrophysiology information into a centralized database and facilitates the Brainmaps.org discovery of neuron-to-neuro relationships18. It is an interactive multiresolution next generation brain atlas that is based on Code Analysis, Modeling and Repository for over 20 million megapixels of submicron E-Neuroscience (CARMEN) Project resolution, annotated, scanned images of It provides a web based portal serial sections of both primates, e.g. Homo platform through which users can share and sapiens and non-primate brain, e.g. Carassius collaboratively exploit data such as the neural auratus. In addition, it also contains activity recording including signals and series connectivity maps, Connectomes.org of some of images; analysis code and expertise in species such as Caenorhabditis elegans15,16. neuroscience19. Neuromorpho.org Collaborative Research in Computational It is the largest public repository of 3- Neuroscience (CRNCS) D digital neuronal reconstruction and It provides a forum of discussion over associated metadata. It is an inventory that electrophysiological datasets as well as contains 7,986 digitally reconstructed neurons involved in sharing data. Data sets of this and is associated with peer-reviewed forum include the visual cortex, auditory publications, it can be used for analysis, cortex, hippocampus, eye movements, lateral visualization and modelling of neuronal geniculate nucleus in the mouse. It gives data17. information about data collection, experimental conditions, identifying the Electrophysiological databases species, surgical procedures and the special Brains achieve efficient functioning recording techniques20. due to different neurons that serve distinct computational role. One striking way in Brain connectivity databases which the neuron types differ is their To transfer information between electrophysiological properties. Electro- anatomical structures of a brain, the brain is physiology of the brain is an important aspect wired with a dense network of electrical since the biological information is converted signals such as the axonal connections and into electrical signals for the brain to interpret. synapses. But there are many connections However there are no firm standards how between the brain components of various electrophysiological data is to be described scales to an entire brain regional scale, and AJPCT[2][8][2014]976-984 Nagendran et al_____________________________________________ ISSN 2321 – 2748 different technologies are required for the BAMS is that it has atlas and parsing engine. analysis of each scale of connection. The parsing engine makes connectivity map Connectomes are divided to micro containing brain regions and connection connectome and macro connectome on the strength.
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