incf digital atlasing infrastructure: an overview
TRANSCRIPT
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INCF Digital Atlasing Infrastructure:An Overview
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Central role of WHS space
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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
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Managing multiple data types
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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
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Demonstration
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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!
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Demo overview
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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
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INCF Central, and INCF Services and Hubs
INCF Central:
Service registry,Registry of
spaces,Metadata catalog
ABA Service
WHSService
UCSDService
EMAGEService
Other…
Other…
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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
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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)
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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
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Discussion