Data integration with the help of the INCF Digital Atlasing Infrastructure
The goal of the INCF Digital Atlasing Program is to make the rapidly growing collection of multidimensional data widely accessible and useable to the international scientific community. A milestone of this project, the integration of three major online mouse brain resources, has now been achieved.
Digital brain atlases are useful as references, analysis tools and data integration frameworks for applications in neuroscience. Atlases and supporting tools are therefore crucial resources in facilitating and promoting data sharing. With the advance of informatics in the life sciences, neuroscientists have advocated the use of digital atlases as gateways to data of multiple modalities and from distributed locations. This infrastructure places digital atlases as hubs of a system that allows easy access to data and tools from multiple sources, and in addition, facilitates scientific discovery, data analysis and standardization. Such a framework would be both helpful to individual neuroscientists and a powerful tool for furthering neuroinformatics research.
Dr. Lydia Ng,
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.
One of the key accomplishments of the INCF Digital Atlasing Program is a standardized digital atlasing framework for sharing rodent brain data, consisting of Waxholm Space (WHS) and a supporting web-based Digital Atlasing Infrastructure (DAI). The Waxholm Space (WHS) is a spatial standard, a virtual coordinate system that unifies 3D mouse brain data from different formats and online atlases. It was developed by the INCF Standards in Digital Atlasing Task Force, based on recommendations from community representatives. The Digital Atlasing Infrastructure (DAI) supports use of the WHS via web services that allow researchers to transform images from their own data format to that of a collaborator, and to integrate different types of data from several sources at once.
Together, the WHS and DAI enable the integration of data from genetic, anatomical and functional imaging studies of the mouse brain, as well as convenient access to the data and easy conversion between data formats.
In addition, the WHS and DAI are designed so that it is reasonably straightforward to add other resources to the framework. Use of WHS data and the DAI are provided freely to the international research community.
Prof. Richard Baldock,
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.
Three major online mouse brain resources - the Allen Mouse Brain Atlas, the Edinburgh Mouse Atlas Project, and an effort from University of California San Diego (primarily the Cell Centered Database) - are now integrated with the INCF Digital Atlasing Infrastructure, working together and accessible from multiple software clients. Any client that is WHS aware and uses components of the DAI may now access these resources. This interoperability will facilitate future research as well as increase the value of previously acquired data.
Work on a corresponding Waxholm Space framework for the rat is underway in Norway, under the direction of Prof. Jan Bjaalie at the Institute of Basic Medical Sciences, University of Oslo.
Prof. Jan G. Bjaalie,
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.
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A symmetrical Waxholm canonical mouse brain for NeuroMaps (2011) Bowden DM, Johnson GA, Zaborsky L, Green WD, Moore E, Badea A, Dubach MF, Bookstein FL. J Neurosci Methods vol. 195(2):170-5.
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