Mouse BIRN — Tools Primer
The Mouse BIRN focuses on multimodal digital atlases and associated tools as a framework to integrate data from multiple sources and of different types in a meaningful manner. With the proper infrastructure, atlases can act as an intuitive interface to visualize, share, analyze, and mine this multi-scale data. We are using this approach to coordinate disparate forms of data and present them in a clear and meaningful manner, in an environment that facilitates data sharing.
What types of data is Mouse BIRN currently working on integrating into this infrastructure?
The Mouse BIRN focuses on many diverse data types including various types of MR imaging, light and electron microscopy, and microarray data. Processed or derived data includes segmentations, atlases, and surfaces.While we are mainly focused on the adult mouse, we have members of our group working on development as well as other species. Data protocols used by member of Mouse BIRN may be found here.
What tools do you offer to process data?
The Mouse BIRN Atlasing Toolkit (MBAT) currently has the ability for a user to create their own labels and segmentations which they may wish to use to create their own atlas. In addition, several groups within Mouse BIRN run complex processing procedures that include both manual and automatic processing steps. For processing of the different data types, tools created by the Mouse BIRN groups are accessible on the Mouse BIRN wiki. We are working on offering complete automated processing steps to the rest of the scientific community in a simplified manner.
What types of data can currently be uploaded to this infrastructure?
Mouse BIRN is developing upload steps so any scientist may use our resources as we develop them. Currently, we offer the ability for anyone to upload processed gene expression microarray data. This fall, we will offer the ability to upload histological images, and many other types of light and electron microscopy images and correlated imaging (http://ccdb.ucsd.edu/data.html#contributing).
What tools does Mouse BIRN offer to organize and manage data?
We rely heavily on BIRN”s controlled vocabulary, BIRNLex for building our upload processes and other terminology accessed by our tools.
We adopt community standard formats for data exchange and when needed, help create these standards.
In addition to the resources offered above, we offer the BrainGraph tool in MBAT which allows a user to visualize and navigate structural hierarchies, but these may be used to visualize and navigate any type of hierarchy. In addition, we offer the BrainGraph editor which allows anyone to create their own hierarchy.
How may I integrate my own data source with this infrastructure?
There are multiple resources our group and the rest of BIRN are developing to facilitate integrating and expanding this infrastructure, including:
- Register databases with the BIRN CC Mediator
- Conceptual mapping of data using BIRNLex
- Common data models and APIs for data exchange
- Atlasing interoperability server and API
The best methods for interoperability with an existing database will vary.
How may I access Mouse BIRN data?
One of the main goals of the Mouse BIRN collaboration is to make query and access to multiple data types and sources easy and intuitive within the context of a digital atlas. To meet these needs, we offer the Mouse BIRN Atlasing Toolkit (MBAT) which currently has some query options, and which will be expanded this fall. In addition, several datasets are available for download from the BIRN Data Repository.
What other data sources may I access through this infrastructure?
MBAT currently accesses several data sources, including many for which we do not offer upload. This is specifically to allow access to multiple types of data for comparison.
Current data sources include:
- GeneNetwork
- BIRN Microarray Database
- Several Microarray Databases registered through the BIRN Mediator
- The Cell Centered Database (CCDB)
Data sources added this fall will include data from:
- Spatially registered histologic images from SmartAtlas and ArcIMS
- Allen Brain Atlas data through a database developed by NeuroCommons
It will also include these information sources:
- BIRN’s Bonfire Ontology Manager
- The Brain Architecture Management System (BAMS)
May I visualize my own data using MBAT?
MBAT may be used to visualize several different image volume and surface formats, as well as .pic and .tiff files. The full list of supported files may be found at http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/FileFormats.
What Analyses Tools does Mouse BIRN offer?
We are currently expanding MBAT’s analysis tools for gene expression and image data. GeneNetwork offers sophisticated statistical tools for examining gene expression differences in genetic reference populations.
How do I share my data after this process?
All BIRN tools are being developed so a scientist may choose to publish their data and make it publicly accessible. You may share your data through the BDR or MBAT.