BISEL

INCF Logo BISEL, lead by Dr. Albert Burger, has been inolved in the International Neuroinformatics Coordinating Facility (INCF) programme for some time.

The INCF fosters worldwide collaboration and data sharing in neuroscience in order to advance understanding of the human brain and its diseases. Based in Sweden, it has National Nodes in 14 countries world-wide.

One of the INCF's goals is the creation of a mechanism to map spatial atlases for rodents. There are a number of potential methods of linking the data:

using structure-structure mappings based on anatomy;
using lexical analysis e.g. linking the future midbrain in the Edinburgh Mouse Atlas (EMAP) to the midbrain in the Allen Brain Atlas (ABA);
mapping the 4D space, possibly by mapping each 4D model into the Waxholm Space first (Johnson G. A., et al. Waxholm Space: An image-based reference for coordinating mouse brain research - Paper).

BISEL plays an active role in the development of an EMAP hub as part of its commitment to the INCF's Digital Atlasing Infrastructure Task Force. The insight gained in this work is brought to bare on the standards document being produced by this task force.

Additionally, Dr. Albert Burger is member of the Representation and Deployment Task Force that is part of the Program on Ontologies of Neural Structures (PONS).

BISEL's initial involvement with the INCF was through a six-month project, funded under the International Neuroinformatics Coordinating Facility (INCF) programme to establish Standards and Guidelines for Digital Brain Atlasing.

The aim of the project was to develop an insight into the issues related to linking Neurological gene expression information held in separate Atlases. The use case that drove the project was the creation of a demonstrator prototype which integrated data from EMAP and Edinburgh Mouse Atlas Gene Expression (EMAGE) database with ABA. This illustrated the potential benefits of comparing gene expression data for the mouse brain across distributed data sets, in addition to highlighting a number of underlying technical issues.

Links:

INCF - International Neuroinformatics Coordinating Facility:
http://www.incf.org
The Digital Brain Atlas Programme:
http://www.incf.org/about/programs/atlasing/digital-brain-atlasing
The Standards and Guidelines Subgroup:
http://www.incf.org/about/programs/atlasing/digital-brain-atlasing-standards-and-guidelines
NIF - Neuroscience Information Framework:
http://nif.nih.gov
Allen Brain Atlas:
http://www.brain-map.org
EMAP:
http://emouseatlas.org
EMAGE:
http://genex.hgu.mrc.ac.uk/emage

Biomedical Informatics Systems Engineering Laboratory