new approaches to gis and atlas production infrastructure for spatial data integration: across...

New Approaches to GIS and Atlas Production

Infrastructure for spatial data integration: across scales and projects

Ilya Zaslavsky David ValentineSan 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 statistics.

Source: Wikipedia: http://en.wikipedia.org/wiki/Atlas

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

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 usesUnified Medical Language System (UMLS) to query across multiple data sources and explore spatial relationships across brainslices indifferent 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-Javabased Web applicationfor ontology-awarediscovery andintegration of distributed multiscale braindata registeredto the commonstereotaxic 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

Semantic Mediation

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

Now at: http://www-apps.niehs.nih.gov/katrina/

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