Project Overview

The Brain Architecture Project is a collaborative effort aimed at creating an integrated resource containing knowledge about nervous system architecture in multiple species, with a focus on mouse and human.

What is architecture? In its traditional setting of buildings, architecture may be defined as the shaping of space for human use.  In the case of nervous systems, “architecture” may be taken as the collection of structural elements that enable behaviors, both intrinsic and stimulus driven.  This architecture may be studied at different levels of organization: intracellular networks (gene regulatory networks as well as protein interaction networks), intra-cellular neural networks (local microcircuits, mesocircuits between anatomical regions) as well as organization on a larger scale of organ systems in the body (neuroendocrine and peripheral nervous systems).  Shaped by the evolutionary process, nervous system architecture enables behaviors important for survival and adaption to the environment.

Our knowledge about nervous system architecture is fragmented and incomplete.  For even the best studied rodent species, we only have a partial knowledge about brain connectivity.  Further, the knowledge that is present in the literature is spread across research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves.  The goal of the Brain Architecture Project is both to collate this information from the literature sources, and also to generate primary data sets that enable such information integration.  Some major subprojects are detailed below and others may be explored through the sub-menus on the portal.

Mouse Brain Architecture Project

This is a high throughput experimental project, the goal of which is to systematically do injection-based tractography in whole mouse brains, on a grid of injections that cover the whole brain. The motivation for this project can be found in this position paper (http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000334)

Further information about the MBAP may be found at the main website for the project.

Text Mining for Neuroanatomy

The large body of research articles and textbooks that describe neuroanatomy contain unstructured knowledge that can be extracted and placed into a structured database where it can be more readily examined.  One approach is to perform such information extraction manually, by individually reading and annotating all the relevant articles.  Alternatively, methods in natural language processing (NLP) can be used to greatly facilitate this process, and to provide tools that allow researchers to keep up with and examine the exponentially increasing body of literature.

We have manually curated a relatively small set of papers that describe classical neuroantomical methods applied to the human brain.  The extracted information is available in our Human Brain Connectivity Database.  Additionally, we have developed a specialized search engine to probe a large corpus of full-text articles using semantic queries related to brain architecture.

Analysis of Brain Wide Data Sets

One of the few existing examples of comprehensive, brain wide data sets is the Gene Expression Atlas for the Mouse Brain developed by the Allen Institute of Brain Sciences. Analysis of the co-expression patterns of genes in the mouse brain shows the utility of whole brain data sets. Applications were made to gene lists implicated in addiction and autism and some results are presented on this website.