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A new module for on-line manipulation and display of molecular information in the brain architecture management system

A new module for on-line manipulation and display of molecular information in the brain... A new “Molecules” module of the Brain Architecture Management System (BAMS; http://brancusi.usc.edu/bkms) is described. With this module, BAMS becomes the first online know ledge management system to handle central nervous system (CNS) region and celltype chemoarchitectonic data in the context of axonal connections between regions and cell types, in multiple species. The “Molecules” module implements a general knowledge representation schema for data and metadata collated from published and unpublished material, and allows insertion of complex reports about the presence of molecules collated from the literature. For different CNS neural regions and cell types the module's database structure includes representation of molecule expression revealed by various techniques including in situ hybridization and immunohistochemistry, molecule coexpression and time-dependent level changes, and physiological state of subjects. The metadata representation allows online comparison and evaluation of inserted experiments, and “Molecules” structure allows rapid development of data transfer protocols enabling neuroinformatics visualization tools to display gene expression patterns residing in BAMS, in terms of levels of expressed molecules and in situ hybridization data. The module's web interface allows users to construct lists of CNS regions containing a molecule (depending on physiological state), retrieve further details about inserted records, compare time-dependent data within and across experiments, reconstruct gene expression patterns and construct complex reports from individual experiments. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Neuroinformatics Springer Journals

A new module for on-line manipulation and display of molecular information in the brain architecture management system

Neuroinformatics , Volume 4 (4) – Apr 11, 2007

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Publisher
Springer Journals
Copyright
Copyright © 2006 by Humana Press Inc.
Subject
Chemistry; Biotechnology; Engineering, general; Neurology
ISSN
1539-2791
eISSN
1559-0089
DOI
10.1385/NI:4:4:275
pmid
17142838
Publisher site
See Article on Publisher Site

Abstract

A new “Molecules” module of the Brain Architecture Management System (BAMS; http://brancusi.usc.edu/bkms) is described. With this module, BAMS becomes the first online know ledge management system to handle central nervous system (CNS) region and celltype chemoarchitectonic data in the context of axonal connections between regions and cell types, in multiple species. The “Molecules” module implements a general knowledge representation schema for data and metadata collated from published and unpublished material, and allows insertion of complex reports about the presence of molecules collated from the literature. For different CNS neural regions and cell types the module's database structure includes representation of molecule expression revealed by various techniques including in situ hybridization and immunohistochemistry, molecule coexpression and time-dependent level changes, and physiological state of subjects. The metadata representation allows online comparison and evaluation of inserted experiments, and “Molecules” structure allows rapid development of data transfer protocols enabling neuroinformatics visualization tools to display gene expression patterns residing in BAMS, in terms of levels of expressed molecules and in situ hybridization data. The module's web interface allows users to construct lists of CNS regions containing a molecule (depending on physiological state), retrieve further details about inserted records, compare time-dependent data within and across experiments, reconstruct gene expression patterns and construct complex reports from individual experiments.

Journal

NeuroinformaticsSpringer Journals

Published: Apr 11, 2007

References