BAMS is also an online knowledge management system designed to handle neurobiological information at different levels of organization of the vertebrate nervous system (NS). It handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of the vertebrate NS: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.

BAMS invites and encourages neuroscientists to help populate BAMS with connectivity and cell type data. This is the only way such an ambitious undertaking can move toward being comprehensive.

BAMS: general structure
The structure of BAMS is modular, with the Brain Parts module as the center of the system. Brain parts are uniquely defined by a tuplet made of the name of the part, the nomenclature used to identify and name it, the nomenclature version, and species. A brain nomenclature is defined as an internally consistent set of terms used to name a part of the CNS. The number of terms included in a nomenclature is variable (at least one), and the nomenclature version uniquely specifies the set. Usually a brain nomenclature is associated with a brain atlas, but this does not constitute a constraint for inserting it. The constraints that are taken into account are the internal consistency of terms, whether the reference is original research, and the brain region names are associated with textual definitions, or at least depicted on a brain atlas.

The other modules of BAMS are Connections, Relations, Cell Types, and Molecules.
Connections module of BAMS holds data and metadata about macroscopic neuroanatomical projections between brain regions. Any neuroanatomical projection can be represented in BAMS by a set of more than 40 attributes. Details about this module can be found in Bota et al. 2005.
The Relations module stores qualitative spatial relations between brain regions, as well as cited references.
The Cell Types module allows insertion of names and definitions of neuron types and classes, as well as relations between them, as collated from references. The module also records neuron populations attributes, such as position within brain region, density and pattern of staining. It also includes a neurons classification schema, which allows specification of criteria used to hierarchically organize neuron nomenclatures. See Bota & Swanson, 2007 for details.
The Molecules module represents data and metadata as collated from the literature and pertaining to brain regions or neurons that are recorded in different physiological states: normal and manipulated. Molecules are classified in two general classes: cell associated and releasable by neurons. The cell associated class is further divided in classes accepted by the IUPHAR nomenclature (http://www.iuphar-db.org/index.jsp).

The Molecules module allows insertion of quantitative and qualitative attributes as identified using radioactive tracers, immunohistochemistry, or gene expression. It also includes a comprehensive schema for metadata representation . A full description of this module can be found in Bota & Swanson, 2006.

If you would like to set up an account in the system to insert data either in the public part of BAMS, or in the personal account, please contact the system administrator. If you are registered as a collator of BAMS, you can start inserting gene expression data in your Personal account. If you would like to use the newly implemented Personal Workspace, to receive updates about new features and tools added to BAMS, or to know when new data is inserted please go to the Registration page. You can use the Personal Workspace to save your searches of brain regions, neuroanatomical connections, and molecules.