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 Overview Connection type Web-based data upload Interface Web-based data upload Interface Test Database

GeneNetwork SQL connection MBAT Release 11/05 Test Version of CCDB BAMS hierarchies URL Access In Addition: Paxinos contours from SmartAtlas 3 separate atlases

Microarray Databases GeneNetwork MBAT Release 11/06 Test Version of CCDB BIRN Microarray Upload Interface Microarray Upload Interface Barlow Database Smith Database URL access Mediator/webservices BAMS hierarchies SQL 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 Query Interface 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 Infrastructure UCLA & 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 Metadata Database Concept Query Interface

Spatial Query Infrastructure UCLA & UCSD Image Metadata Retrieve Images Spatial Registry ArcIMS Images Atlas API webservices Atlas Interoperabiity Server Atlas API User can query with ROI Uses Atlas Interoperability Server and API Visualize images using zViewer zViewer 2D images (integrated into a MBAT window) Spatial Query Interface

Information Sources Information Query UCLA, USC, CC BAMs BonFire JDBC webservices Mediator/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

Microarray Databases GeneNetwork Microarray Data Handling UCLA, UTHSC BIRN Microarray Upload Interface Microarray Upload Interface Barlow Database Smith Database 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

Image Metadata 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 access Mediator/webservices 2D Registration Workflow 2D Registration Workflow zViewer 2D images (integrated into a MBAT window) User can query by Concept or Spatial Query and visualize in zViewer Concept Query Interface Spatial Query Interface Atlas Interoperabiity Server

2005New in 2006New in 2007 Data 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 access Mediator/webservices Concept Query Interface Spatial Query Interface 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 Query Interface Registered 2D Datasets ArcIMS Other 2D data?

What’s next: Easier upload, processing, and analysis of gathered data 3D MR Upload Interface 3D MR Upload Interface Connection to CCDB Upload Connection to CCDB Upload 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