needs and progress: summary flexible, powerful, modular atlas interface, and a query gateway to...

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


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



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


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


User can query by Concept or Spatial Query and visualize in zViewer


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




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



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

needs and progress: summary flexible, powerful, modular atlas interface, and a query gateway to...

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