INCF Digital Atlasing Infrastructure: An Overview

Central role of WHS space

INCF DAI Architecture: WHS-aware APIs Internet Atlas Resource Atlas Resource WHS API … … Atlas Resource Atlas Resource WHS API Compute Resource Compute Resource WHS API … … Compute Resource Compute Resource WHS API INCF WHS Ontology Server INCF WHS Ontology Server INCF WHS Resource Registry INCF WHS Resource Registry WHS-aware Integration Resources WHS-aware Integration Resources WHS-aware Applications/Tools WHS-aware Applications/Tools

Managing multiple data types

Servers & Databases MicroarrayImaging Informatio n Spatial registry Spatial Transformations + metadata Image APIs Integrate Spatial Integration Semantic Integration Database Integration Standards Data Upload Client Integration APIs AnalyzeVisualize Query Register to Atlas Microarray APIs INCF-DAI: Path to Adoption

Demonstration

Demo Contributors Neuroscience 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 team Hardware and server setup: Larry Lui (UCSD) Architecture: Albert, Fons, Jyl, Mike, Janis, Ilya Thanks to Jyl and Janis for coordination!

Demo overview

Atlas Services ABA ServiceWHS ServiceUCSD ServiceEMAGE Service Core Services GetCapabilities, DescribeProcess Known coordinate spaces ABAvoxel, AGEA, ABAreference WHSPaxinosEMAP LookupGetStructureNameBy POI Coordinate translations WHS  AGEA, ABAreference   ABAvoxel, AGEA   ABAvoxel Paxinos   WHSEMAP   WHS Other, based on POI Get2DImageAtPOI, GetCorrelationMap, GetGenesByPOI Get2DImageAtPOIGet2DImageAtPOI, GetGenesByPOI Based on structure 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 WHS Service UCSD Service EMAGE Service Other…

Atlasing Hubs User Interface EMAGE: INCF Hub webservices WHS canonical space and dataset Standard terminologies Standard services and exchange schemas WHS canonical space and dataset Standard terminologies Standard services and exchange schemas INCF Spatial Server Atlasing Infrastructure webservices INCF Concept Server INCF Registry webservices ABA: INCF Hub webservices UCSD: INCF Hub webservices INCF DAI Infrastructure Components Present information about atlasing hubs Query atlasing hubs All components built on standards Harvest metadata from 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 novel 3D Atlas Integration application The system is extensible

Discussion