INCF Digital Atlasing Infrastructure:An Overview

Central role of WHS space

INCF DAI Architecture: WHS-aware APIs

InternetInternet

AtlasResource

AtlasResource

WHS APIWHS API

……

WHS APIWHS API

AtlasResource

AtlasResource

WHS APIWHS API

ComputeResourceComputeResource

WHS APIWHS API

……

WHS APIWHS API

ComputeResourceComputeResource

WHS APIWHS API

INCF WHSOntology

Server

INCF WHSOntology

Server

INCF WHSResourceRegistry

INCF WHSResourceRegistry

WHS-awareIntegration Resources

WHS-awareIntegration Resources

WHS-awareApplications/Tools

WHS-awareApplications/Tools

Managing multiple data types

Servers &Databases

Microarray

Imaging Information

Spatial registry

Spatial Transformations

+ metadata

+ metadata Im

age

APIs

IntegrateSpatial

Integration

SemanticIntegrati

on

DatabaseIntegration

Standards

Data Upload

Client

Integration

APIs

AnalyzeVisualizeQuery

Register to Atlas

Microarra

y

APIs

INCF-DAI: Path to Adoption

Demonstration

Demo ContributorsNeuroscience scenarios: Maryann Martone, Stephen Larson (UCSD), Jyl Boline

(Informed Minds), Lydia Ng and Mike Hawrylycz (Allen Institute), Al Johnson (Duke University)

WHS dataset: Al Johnson and Jeff Brandenburg (Duke University), Jonathan Nissanov and Pablo Burstein (Drexel University)

Other datasets and meshes: Maryann Martone and Stephen Larson (UCSD), Lydia Ng and Chris Lau (Allen Institute)

INCF Central and atlas service wrappers: Asif Memon (UCSD)INCF hubs and local services: Lydia Ng (Allen Institute), Albert Burger (MRC, UK),

Kenneth McLeod (Heriot-Watt Univ, UK), Asif Memon (UCSD)Spatial transformations and anatomic structure lookup: Lydia Ng (Allen

Institute), Steven Lamont and Alexander Young (UCSD)Representation of coordinate spaces: Alexander Young (UCSD)Client development: Stephen Larson and UCSD team; Seth Ruffins and UCLA teamHardware and server setup: Larry Lui (UCSD)Architecture: Albert, Fons, Jyl, Mike, Janis, Ilya

Thanks to Jyl and Janis for coordination!

Demo overview

Atlas ServicesABA Service WHS Service UCSD Service EMAGE Service

Core Services

GetCapabilities, DescribeProcess

GetCapabilities, DescribeProcess

GetCapabilities, DescribeProcess

GetCapabilities, DescribeProcess

Known coordinate spaces

ABAvoxel, AGEA, ABAreference

WHS Paxinos EMAP

Lookup GetStructureNameByPOI

GetStructureNameByPOI

GetStructureNameByPOI

GetStructureNameByPOI

Coordinate translations

WHS AGEA,ABAreference ABAvoxel,AGEA ABAvoxel

Paxinos WHS EMAP WHS

Other, based on POI

Get2DImageAtPOI, GetCorrelationMap, GetGenesByPOI

Get2DImageAtPOI Get2DImageAtPOI, GetGenesByPOI

Based on structure

GetGenesByStructure GetGenesByStructure

(As of August 2009; planned services in italic)

Service = some functionality that you can call over the web in a standard manner

INCF Central, and INCF Services and Hubs

INCF Central:

Service registry,Registry of

spaces,Metadata catalog

ABA Service

WHSService

UCSDService

EMAGEService

Other…

Other…

Atlasing Hubs

User Interface

EMAGE:INCF Hub

webservices

WHS canonical space and datasetStandard terminologies

Standard services and exchange schemas

INCF SpatialServer

Atlasing Infrastructure

webservices

INCF ConceptServer

INCF Registry

webservices webservices

ABA:INCF Hub

webservices

UCSD:INCF Hub

webservices

INCF DAI Infrastructure Components

Present informationabout atlasing hubs Query

atlasing hubs

All components built on standards

Harvest metadatafrom atlasing hubs

Spatial transformations enable positioning a point of interest (POI) at approximately the same location in different atlases.

Paxinos to WHS

(1.0,4.3,1.78)

(308,642,224)

WHS to

AGEA,ABAvoxel

(AGEA:3825,5650,4650)

ABAvoxel to ABAreference

(1.19,5.13,1.70)

Summary

• We developed concepts of INCF-DAI, atlas hubs and services, INCF Central server, and communications between them

• We built service-oriented architecture prototype for distributed digital atlases of mouse brain, that relies, where possible:– On standard service descriptions and exchange schemas– On standardized spaces, and a registry of spaces– On a collection of coordinate translation services, with WHS at the center– On standard terminology, with term cross-walks where needed

• The translation services have performed well, and several tools were built for testing their performance

• Data from several atlas hubs can be spatially integrated for the first time, via services and service chains

• The integration has been demonstrated with a novel3D Atlas Integration application

• The system is extensible

Discussion