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GeneNetwork SQL connection MBAT Release 11/05 Test Version of CCDB BAMS hierarchies URL Access In Addition: Paxinos contours from SmartAtlas 3 separate atlases
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Needs and Progress: Summary• Flexible, powerful, modular atlas interface, and a query gateway to multiple
types of data (GeneNetwork, Barlow, Smith, CCDB, Gensat, ABA, etc.) e.g. MBAT’2007
• 2D and 3D integration in the viewer in MBAT’2007• Query atlases and images by location spatial registry • Query images by labels and annotations, taking into account annotation and
label semantics e.g. Phenote-SA integration • Upload and registration tools enhanced with spatial and semantic
registration (e.g. microarray + AID + image registration workflow) • Images and mosaics are often large (2Gb+) specialized toolkits, clusters
(e.g. image registration workflow) • Delivering images or fragments to atlases regardless of image size e.g.
ArcIMS/IWS servers• Support for images at multiple scales alignment and translation services,
IWS-based viz• Integrating different atlases via state exchange e.g. Atlas Interop API
Outside Sources
Internal Sources
MBAT Query Interfaces
MBAT data visualization interfaces
Infrastructure
sources
Access Services
Community Standard for
Access
OverviewConnection type
Web-baseddata upload
Interface
TestDatabase
GeneNetwork
SQL connection
MBAT Release 11/05
Test Version of
CCDB
BAMShierarchie
s
URL Access
URL Access
In Addition:• Paxinos contours from
SmartAtlas• 3 separate atlases
MicroarrayDatabases
GeneNetwork
MBAT Release 11/06
Test Version of
CCDB
BIRN Microarray
MicroarrayUpload
Interface
BarlowDatabase
SmithDatabase
URL access
Mediator/webservices
BAMShierarchie
sSQL connection
URL Access
In Addition:• technical documents• interface additions• look changes• Gene Expression Query
Interface• Atlas API integration and
connection to ArcIMS server
MBAT 2007 Plans, Advanced Query
Concept Query Interface
zViewer 2D images (integrated into a MBAT window)
Spatial QueryInterface
Gene Expression Explorer (can be visualized in MBAT)
Information Query Interface
MBAT has different query interfaces to bring together different types of data within the context of a digital atlas. Results are integrated into MBAT as much as possible with plans for improvement
Nearly all BIRN resources shown in the following slides are or will be accessible to the public
Concept Query InfrastructureUCLA & CC
Term Source
Database
Search the DB at that column for results
matching the query
Mediator
Gives the column and DB information
matched to that TERM(BIRNLex/Bonfire)
•Holds some underlying “business logic” for the Query interface-categorizes data types and search criteria. •Move functionality to this over time
Example: User generates a query for calb1 in C57BL/6 in BIRN Microarray DB and GeneNetwork.
(Metadata Database holds information for Interface to formulate Query)
1) Query Term Source DB for terminology from different sources calb1 and C57BL/6, and the output is:
DATASOURCE = TABLE NAME FIELD NAME Gene Network = “Gene table” “genesymbol” Microarray = “UAD_probe_term” “key=GeneSymbol”2) (Optional) Query Term Source DB for all fields of
“Table Name”3) To generate this query to mediator, “get all fields =
Calb1 in the given Table of each DataSource”4) Query mediator for all the matching results
This infrastructure:• Easier for the User• Expandable• More comprehensive searches of
multiple sources• Start migrating functionality from
Interface to Server after Fall• If on Server, easier for others to
use our infrastructure
MetadataDatabase
Concept Query Interface
Spatial Query InfrastructureUCLA & UCSD
ImageMetadata
Retrieve Images
Spatial Registry ArcIMS
Images
Atlas API
webservices
Atlas Interoperabiity Server
Atla
s AP
I
• User can query with ROI• Uses Atlas
Interoperability Server and API
• Visualize images using zViewer
zViewer 2D images (integrated into a MBAT window)
Spatial QueryInterface
InformationSources
Information Query UCLA, USC, CC
BAMs
BonFire
JDBC
webservicesMediator/webservices
User can query two different information sources depending on needs of user
1) ontologies: useful for defining what a user means by a term and mapping data across data sources
2) BAMs information: connections, molecules and cells in different areas (It is unlikely we will have the needed time to make the necessary changes to expand this by the fall release-we will need to decide if we want to include it at all)
Information Query Interface
MicroarrayDatabases
GeneNetwork
Microarray Data Handling UCLA, UTHSC
BIRN Microarray
MicroarrayUpload
Interface
BarlowDatabase
SmithDatabase
MAGE XML
New 2007:• MAGE compatible-facilitates
compatibility with other microarray sources
• Expanded Query of DBs• More easily expandable to
other sources• More robust process• More flexible queries
Gene Expression Explorer (can be visualized in MBAT)
URL access
Mediator/webservices
Microarray
Annotation
Database
Concept Query Interface
ImageMetadata
Retrieve Images
Spatial Registry
2D Image Data Handling UCLA, UCSD (CCDB, ArcIMS), Neurcommons (ABA), Stott Parker (Gensat)
ArcIMS Images
Atlas API
ABA Images
Gensat Images
CCDB images
Neuro-Commons
Implement Stott’s
Gensat DB
CCDB
webservices
RDF/Sparql
webservices
URL accessMediator/webservices
2DRegistrationWorkflow
zViewer 2D images (integrated into a MBAT window)
User can query by Concept or Spatial Query and visualize in zViewer
Concept Query Interface
Spatial QueryInterface Atlas
Interoperabiity Server
2005 New in 2006 New in 2007Data types •MR volumes (Analyze,
MINC, Caltech, Duke) •TIFF•.pic (biorad)
•Integrated label Format created (hierarchy, and synchronization of BG and atlas labels)
Nifti
Data Sources for Query
•BAMs (v1)•WebQTL(v1 now GeneNetwork)•CCDB (test site)
•BIRN Microarray DB (B) (created source for upload and immediate query)
•ABA (B)•GENSAT (B)•Barlow DB (Mediator) (B)•ArcIMS (spatial) (B)•BIRN Microarray DB (v1)•GeneNetwork (v2)•CCDB (v1)•BONFIRE (B)•BAMs (v1.5)
Functionality •BrainGraph (BG)•Multiple atlases•EM/Cell tool-CCDB test site•3D surface viewer•Label drawing•BAMS connection (v1)•WebQTL client (v1)•Reorient tool•Open Duke big volumes
•BG-color (match labels)•BG + tree view•Maximum intensity Projection (especially useful for cell volumes)•Create file from main window•Gene Expression query tool (multiple sources)•Docking (B)
•Launch window (B)•Workspaces (B)•Query Data (cross data type) (B)•4 up view (B)•Gene Expression image analysis (B)•Search by ROI (B)•Create Atlas Workspace (B)•Connection to upload sites (B)
Inter-operability
Atlas Interoperability API developed and used for synchronization with SmartAtlas and ability to access contours and some spatially-related information (used for CCDB test connection)
•Create stereotaxic atlas (aid interoperability)•Volumetric Atlas adopted that can be used to cross data types•Technical Specifications move towards standards•Remote load NeuroTerrain Atlas (B)
•Anatomical structures from BIRNLex•Atlas interoperability Server developed for transforms between different atlases•Moving towards BIRN MAGE format for microarray•Metadata DB for Query Application (B)• Move towards use of Concept Term Mapper and Mediator to aid with different terminology in sources
3D Databases
CCDB
What’s next: Connection to 3D data sources
UCLA
NeuroTerrain Server
Caltech
Duke
AID
• The concept query infrastructure will be expanded to include 3D volume data sources
• NeuroTerrain in conjunction with the Atlas Interoperability Infrastructure may facilitate quick visualization of slices of 3D volumes (possibly used for the spatial query)
• Mapping these data into the 3D space will require extension of the Atlas Interoperability Infrastructure
URL accessMediator/webservices
Concept Query Interface
Spatial QueryInterface
Atlas Interoperabiity Server
Atlas API
What’s next: Visualization of 2D in 3D atlas
Atlas API
• We will develop a standard for opening 2D images in 3D atlas space and make the process available to others
• As atlases are added to Atlas Interoperability infrastructure, associated 2D data may be visualized within the context of other atlases (as with the ArcIMS data)
• These data may be queried with the spatial Query Interface• Mapping these data to atlases will require extension of the Atlas Interoperability Infrastructure• Potential candidates include our current 2D data sources, Erh-Fang’s embryonic work, EMAP
Atlas Interoperabiity Server
Spatial QueryInterface
Registered 2D Datasets
ArcIMS Other 2D data?
What’s next: Easier upload, processing, and analysis of gathered data
3D MRUpload
Interface
Connectionto CCDBUpload
Access to pre-processing
programs
Databases
CCDB
AID
Access to Analysis
Tools
Ability to upload and immediately visualize data within the context of MBAT will depend on easy mapping to BIRNLex or spatial registration of images. Added functionality may require mapping the database to the BIRN CC Term Source Index/Mediator Databases
Spatial Registry