Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

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module implements a general knowledge representation schema for data and metadata collated from published and unpublished material, and allows insertion of complex reports about the presence of molecules collated from the literature.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

Bota, Mihail; Swanson, Larry
Neuroinformatics , Volume 4 (4) – Apr 11, 2007
Download PDF
24 pages

Loading next page...
 
/lp/springer-journals/a-new-module-for-on-line-manipulation-and-display-of-molecular-xMDL5pBnHP
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

Neuroinformatics – Springer Journals

Published: Apr 11, 2007

References

  • From gene networks to brain networks
    Bota, M.; Dong, H. W.; Swanson, L. W.
  • The Brain Architecture Management System
    Bota, M.; Dong, H. W.; Swanson, L. W.
  • Integrating Databases and Expert Systems for the Analysis of Brain Structures: Connections, Similarities and Homologies
    Bota, M.; Arbib, M. A.
  • Handbook of Chemical Neuroanatomy vol. 13: The Primate Nervous System, part I
    Bowden, D. M.; Martin, R. F.
  • Neuro Names 2002
    Bowden, D. M.; Dubach, F. M.
  • Specificity controls for immunocytochemical methods
    Burry, R. W.
  • Computing the Brain: A Guide to Neuroinformatics
    Burns, G. A. P. C.
  • Neurotransmitter receptor for binding
    Burt, D. R.
  • Onine retrieval, processing, and visualization of primate connectivity data from the CoCoMac Database
    Kötter, R.
  • Neurotransmitter receptor binding
    Kuhar, M. J.
  • Neurotransmitter receptor mapping by autoradiography and other methods
    Kuhar, M. J.; Souza, E. B.; Unnerstall, J. R.
  • A multimodal, multidimensional atlas of the C57BL/6J mouse brain
    MacKenzie-Graham, A.; Lee, E. F.; Dinov, I. D.
  • The informatics of a C57BL/6J mouse brain atlas
    MacKenzie-Graham, A.; Jones, E. S.; Shattuck, D. W.; Dinov, I. D.; Bota, M.; Toga, A. W.
  • An open letter to our readers on the use of antibodies
    Saper, C. B.
  • Magic peptides, magic antibodies: guidelines for appropriate controls for immunohistochemistry
    Saper, C. B.; Sawchenko, P. E.
  • Brain Maps: Structure of the Rat Brain
    Swanson, L. W.
  • What is the brain?
    Swanson, L. W.
  • Brain Mapping: The Applications
    Swanson, L. W.
  • Differential steroid hormone and neural influences on peptide mRNA levels in CRH cells of the paraventricular nucleus: a hybridization histochemical study in the rat
    Swanson, L. W.; Simmons, D. M.
  • Distribution of alpha 2, alpha 3, alpha 4, and beta 2 neuronal nicotinic receptor subunit mRNAs in the central nervous system: a hybridization histochemical study in the rat
    Wada, E.; Wada, K.; Boulter, J.
  • Interactions between heterotypic stressors and corticosterone reveal integrative mechanisms for controlling corticotropin-releasing hormone gene expression in the rat paraventricular nucleus
    Watts, A. G.; Sanchez-Watts, G.
  • Methods in neurosciences
    Watts, A. G.; Swanson, L. W.