The Brain Architecture Management System

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The Brain Architecture Management System
http//brancusi.usc.edu/bkms
Mihail Bota NIBS
Program in Neurosciences USC
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What is the Brain Architecture Knowledge
Management System (BAMS) http//brancusi.usc.edu/
bkms an online environment for
storing retrieval of neurobiological
information collated from the literature or
inserted by users inference of relations
between brain parts and associated
data processing of experimental
neuroanatomical information The design and the
underlying conceptual framework of BAMS ensures
representation of data regardless of
the species nomenclature and across four
different levels of organization of the mammalian
CNS networks of brain structures brain
parts cell types molecules
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BAMS Object-Relationship Structure
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BAMS Object-Relationship Structure
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BAMS Object-Relationship Structure, Molecules
and Cell Types
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BAMS Object-Relationship Structure
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BAMS Object-Relationship Structure, Connections
Brain region A Nomenclature X
Brain region B Nomenclature X
Collator
Code Strain Sex Weight Age Annotations
Animal ID Topographical position injection
site/terminal Topological position injection
site/terminal Extension injection site/terminal
outside of target areas Hemisphere
injection/terminal Connection strength
(qualitative) Technique Type of
connection Numbers stained neurons in injection
site/terminal Percentage area/total numbers of
neurons of stained cells in injection
site/terminal Min/Max stained neurons in
injection site/terminal Min/Max percentage
area/total numbers of neurons of stained cells in
injection site/terminal Stained cells injection
site/terminal Atlas level Bregma Associated
annotation Part of a major fiber tract
Assignment criteria
Cell Type
Reference
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BAMS Object-Relationship Structure
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BAMS Object-Relationship Structure, Hierarchy
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BAMS Object-Relationship Structure
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BAMS Cell Classification Schema
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BAMS Data
BAMS contains data and support information
collated from more than 400 references 7000
names of brain parts collated from 11 different
neuroanatomical atlases of mice (Paxinos
Franklin, 2001 Hof et al. 2000) rats
(Swanson, 1992 Swanson, 1998 Swanson, 2004
Paxinos Watson, 1998) cats (Berman
Jones, 1982) macaques (Neuronames,
2002) humans (Nomina Anatomica 1895 Mai et
al. 1997 Neuronames 2002) 20,000 reports
of projections between brain nuclei pertaining to
the rat visual and limbic systems 3000 reports
of chemicals identified in different rat brain
regions and neurons reports of different cell
types of the rat brain