New Approaches to GIS and Atlas Production Infrastructure for spatial data integration: across scales and projects Ilya Zaslavsky David Valentine San Diego Supercomputer Center

Outline  Atlas functionality  Smart Atlas Example  Atlas Infrastructure  Examples

What is an atlas?  An atlas is a collection of maps, typically of Earth or a region of Earth, but there are atlases of the other planets (and their satellites) in the solar system. Atlases have traditionally been bound into book form, but today many atlases are in multimedia formats. In addition to presenting geographic features and politicalboundaries, many atlases often feature geopolitical, social,religious and economic st atistics.mapsmultimediageographicpoliticalgeopoliticalsocialreligiouseconomicst atistics  Source: Wikipedia:

 a set of 2D images or a 3D volume in a specified coordinate system, with anatomic feature delineations, and a set of spatially registered annotations What is an atlas?

ESRI Health Sciences Brochure Presented at several GIS conferences: keynote at International Health GIS, 2004; Part of ESRI’s President’s address at GIS User Conference (2003), other…

Spatial Framework  Atlas integration requires the ability to specify location which can be specified in at least three ways, including: atlas coordinates ontology (e.g. label) spatial placement rules:  i.e. a defined region of interest (ROI) specified as a collection of spatial rules that sequentially narrow the ROI space, "within X" "between site2 and site 3" "adjacent to site4"

GIS Challenges (Brain Atlases)  Multiple collections of brain images/ atlases, but lack of interoperability across them At the database and catalog levels At the interface level  Queries such as:  “which atlas sources provide images for user-selected area of the brain at a given resolution”, or  “display image segmentations available in one atlas over a newly obtained image stored in a different location on the grid”, or  “compare protein distributions in a given area of the brain available at several atlas sources” cannot be answered without a dedicated infrastructure that supports spatial integration of brain data  Heterogeneity in: image formats – conventions – spatial registration – access, retrieval and display mechanisms The SMART Atlas is the prototype infrastructure to answer this challenge

SMaRT: Spatial Markup and Rendering Tool

Spatial Queries on Brain Structures, including 3D queries The Smart Atlas: Spatial Integration over Distributed Data WebStart from BIRN portal

Position Synchronization

Use of Ontologies to Link Features Structures on slices color coded by relationships contained in the UMLS SMART Atlas uses Unified Medical Language System (UMLS) to query across multiple data sources and explore spatial relationships across brain slices in different coordinate systems (eg, across species)

Spatial integration of distributed multiscale data The new version of the S.M.A.R.T. Brain Atlas is a MapObjects-Java based Web application for ontology- aware discovery and integration of distributed multiscale brain data registered to the common stereotaxic coordinate system.

Atlas Infrastructure

Interoperability Read data from other atlases/databases API for data retrieval and transformation Find relevant data in other atlases/ databases API for atlas catalogs View the region of interest in another atlas API for atlas state exchange

Examples

The STARE (Structural Analysis of the Retina) project, UCSD Foveal Coordinate System Background Coordinate System Veins Arteries Optic nerve Fovea Cotton-Wool Hemorrhages

Semantic Mediation

Drinking water surface intakes and Toxics Release Inventory (TRI) facilities Now at:

TRI facilities within 3 miles of user-entered address

TRI facilities within a mile of drinking water intakes

Environmental justice applications: social and demographic variables overlaid with environmental effects

Data download and metadata are available for all spatial layers

Geocommons  Finder! is a browser-based application for finding, organizing and sharing GeoData in common formats.

You can make a map from data

Or use a created map

Electronic Cultural Atlas Initiative

Issues  Semantics Multi-lingual  Formats What common formats:  Data Is a spreadsheet enough?  Spatial Sources  Basemaps  Use Cases to Define Functionality  Functionality Historical Place and Events (Gazetteer) Distribution formats and tools Accessibility  Does it need to be accessible in the field? Privacy/Protection  Hide locations of sites