Data integration with the help of the INCF Digital Atlasing Infrastructure

Dr. Lydia Ng,
Director of Atlas Development,
Allen Institute for Brain Science

Working on the Allen Mouse Brain Atlas has taught me the power of combining datasets to mine for information and to discover new relationships. Linking and layering other data sources in addition to the existing expression data is the logical next step. Doing so requires the construction of spatial and/or ontological relationship between data from disparate sources but creating these links is very difficult to do without commonly agreed models. 

An atlas-based data sharing hub has the potential of streamlining this process: instead of having to determine a multitude of source-to-source relationships, each source need to only do a one-time connection to a standard canonical space. The challenge here is in identifying a widely applicable reference space. 

Making data accessible to the scientific community is a central tenet of the Institute’s mission. Our participation includes registering our 3D atlas to the canonical space and help with developing web services to allow links from external data to our anatomical and gene expression data.

Prof. Richard Baldock,
Head of Biomedical Systems Analysis,
MRC Human Genetics Unit

Once you get to the organ level of biological organisation, you need atlases. An atlas serves as an organizing principle, or framework, that stretches all the way from basic biology to medical data in the clinic and ultimately to an individual patient. In the brain, a lot of function has to do with spatial properties like connectivity and structure. The atlasing hub acts as a focus through which spatial data can be exchanged, and even more important, compared. Enabling people to share data and make comparative analyses is critical.

The EMAP project has been running for a long time. It is all about the mouse embryo, which is very space dependent because of patterning to drive the developmental process. This has given us lots of experience in mapping and transforming spatially complex data, and this experience is what we bring to the Digital Atlasing project. 

I think INCF can be very proud that it is leading the way in tackling integration of spatial data; the DAI is pioneering and setting important standards for biomedical research.

Prof. Jan G. Bjaalie,
Inst. of Basic Medical Sciences, University of Oslo

Brain atlases are among the most important neuroscience tools. They exist in different formats, and are heavily used and cited. Researchers use atlases to prepare experiments and to analyse data collected from experiments. Traditionally you would go to a few standard resources for all of these tasks and look up additional information in research articles. With digital atlasing, several atlases displaying a broader range of information are made available. With the new common atlasing framework introduced by the INCF, researchers will be able to make better use of their data, and perform more powerful experiments and analyses. It will be easier to compare and interpret data, and to share data with the community.

The Waxholm Space gives you a recipe and instructions for how to apply a coordinate system onto any brain of a given species. Waxholm space has already been adapted to a mouse reference data set and we are currently doing the same for the rat, a low-hanging fruit since the logic for the Waxholm Space applies to all species. The important thing to realize is that it does not stop there, with a single ‘Waxholm Mouse’ or ‘Waxholm Rat’; we would like to see Waxholm Space applied to many reference brains holding different data modalities – as many as you want.

There are good reasons for the ‘Waxholm Rat’: Previously published data from the rat brain would be more accessible if they were made available in the Waxholm Space framework, and several new disease models offer exciting opportunities for future studies.