Avian influenza RSS web mapping exploring geographic

and temporal aspects of outbreak events

Andrew Murdoch & Ian TurtonSeptember 2007

Presentation Overview

• Abstract

• Goals

• What is Avian Influenza?

• What is RSS?

• What tools were used?

• Project Plan

• Summary

Goals

• Provide a tool for viewing and analyzing spatial and temporal data.

• Link RSS text information with geographic map and timeline of events– Primary goal: Display human infection cases

and confirmed human deaths caused by avian influenza H5N1 virus

– Secondary goal: Display outbreaks of H5N1 virus among avian species (wild and domestic)

Potential uses• This type of tool could potentially be used

to disseminate information for other data sets that have both a geographic and temporal aspect. Applications include disaster event mapping, migration pattern mapping, and other disease outbreak mapping.

What is Avian Influenza?

–Also known as “bird flu”–Common name for disease caused by

H5N1 influenza virus–Transmitted to humans by infected wild

and domestic birds–Rarely transmitted from person to

person (currently only in isolated cases)

Human Mortality

• “H5N1 flu is a concern due to the global spread of H5N1 that constitutes a pandemic threat. The majority of H5N1 flu cases have been reported in southeast and east Asia.”

• Human mortality rate averages 61% percent on average since first diagnosed human infections in 2003.– www.wikipedia.org (

http://en.wikipedia.org/wiki/Human_mortality_from_H5N1) Accessed 14 July 2007

What is RSS?

• “RSS (which, in its latest format, stands for "Really Simple Syndication") is a family of web feed formats used to publish frequently updated content such as blog entries, news headlines or podcasts. An RSS document, which is called a "feed," "web feed," or "channel," contains either a summary of content from an associated web site or the full text. RSS makes it possible for people to keep up with their favorite web sites in an automated manner that's easier than checking them manually.”• www.wikipedia.org (http://en.wikipedia.org/wiki/RSS)

Accessed 14 July 2007

RSS data sources

• Avian Influenza data sources– World Health Organization (WHO)

http://www.who.int/csr/disease/avian_influenza/en/index.html

– General news sources• http://www.reuters.com• http://www.cnn.com

What Open Source tools will be used?

• GeoServer – “Middleware” server software that supports multiple data input and output formats “connecting from legacy databases to many diverse clients”. Written in Java.

• (http://geoserver.org/)

• OpenLayers – Presentation layer software for displaying map data in modern web browsers. Written in JavaScript.

• (http://www.openlayers.org/)

What Open Source tools will be used?

• PostGIS – “PostGIS adds support for geographic objects to the PostgreSQL object-relational database. In effect, PostGIS "spatially enables" the PostgreSQL server, allowing it to be used as a backend spatial database for geographic information systems (GIS), much like ESRI's SDE or Oracle's Spatial extension.”– (http://postgis.refractions.net/)

What Open Source tools will be used?

• GeoNames.org – “The Geonames "RSS to GeoRSS Converter" reads the entries of an RSS feed and searches the Geonames Database to find a location for the entry text.” It is a web service that geocodes text RSS and outputs a georeferenced RSS feed with latitude and longitude coordinates.– (http://www.geonames.org/)

• MIT SIMILE project Timeline tool – A JavaScript based interactive timeline tool for visualizing temporal data.– (http://simile.mit.edu/timeline/)

SIMILE Timeline tool

What is different about this proposed application than most “mashup” mapping websites?

• Uses Open Source tools• Link between map display and interactive

timeline tool• Display of live and historical RSS feed info

that originally had only a limited geographic component (country name and state/province name)

• Unique data visualization tool

Mockup:

Project Plan

• Investigate data sources• Evaluate Open Source software tools• Install and test Open Source software “stack”

– Test Geonames.org ability to georeference WHO avian influenza RSS feed

• Store historical WHO RSS feed info in PostGIS database– Filter items with keywords

• Link PostGIS (database) to GeoServer (middleware) to OpenLayers (presentation)

• Link to multiple RSS feeds (WHO, US Govt., General news feeds)

• Integrate SIMILE Timeline tool to synchronize with map display

Anticipated Results:

• At the conclusion of the capstone project there will be a web site hosted at the Penn State GeoVista center which provides a window onto ongoing avian influenza events worldwide. The website will show the geographic distribution of new and historical avian influenza events drawn from RSS feeds from the World Health Organization and general news services. Avian influenza events will be classified on the map by the severity of event (deaths, non-lethal human infection, poultry outbreak or migratory bird infections). The web site will allow a user to specify which RSS feeds to display on the map and allow users to view events within a specified time window (or view only the latest avian influenza events).

Progress to date:

• Historical (back to 2005) WHO RSS data imported to PostGIS data table for display in OpenLayers through GeoServer.

• Nightly WHO RSS feeds imported into PostGIS data table.

• Data displayed as GeoServer WMS through simple OpenLayers interface.

Problems faced

• Difficulty importing historical RSS feed info from WHO RSS data source.

• Lack of well-documented example applications using OpenLayers.

• We found it necessary to create non-standard “multi-point” GeoRSS items to represent avian influenza event updates.

• Difficulty representing GeoRSS data as PostGIS data.• Different datasource requirements for OpenLayers GIS

view and MIT SIMILE Timeline view (XML/JSON vs. WMS/WFS). Conflicting GeoJSON interfaces (OpenLayers and GeoServer).

Data ingest and processing

• One Java class is used to read a URL of an RSS feed and parse locations referenced in the text of the RSS feed as well as linked HTML files. A GeoRSS XML file is output with points for each location referred to in the RSS feed.

• Another Java class is used to import the GeoRSS XML file into a geospatially aware PostGIS PostgreSQL table.

• These two Java classes are referenced by a UNIX shell script that is called nightly by a scheduled “crontab” job.

PostGIS data filtering

• Once the PostGIS table has been setup and data has been imported from the Java GeoRSS converter, the new table can be filtered in a view to eliminate most unwanted location references. Current filter looks for human outbreak events.

GeoServer administration tasks

• A PostGIS datastore is established, a style SLD is created and a featuretype is defined for the filtered PostGIS data.

OpenLayers client setup

• The GeoServer data layer is added as a transparent WMS service.

• A WMS background data layer is chosen (NASA JPL MODIS data), extents defined and map control tools chosen.

Data displayed through OpenLayers

What Next?• Add nightly Java import, PostGIS table and GeoServer featuretype

data layer for Reuters News RSS feed.• Edit Java code to prevent duplicate GeoRSS points from being

imported into the same PostGIS table.• Convert GeoServer WMS/WFS output to GeoJSON format for

download onto client machine. This can then be integrated with the MIT SIMILE Timeline tool without needing to use a WFS data layer with many repeated GetFeature requests to a remote server. Everything can be handled on the client.

• Edit Java import code to only show actual locations of Avian Influenza outbreaks (not conference locations, health organization locations, etc.)

• Create new PostgreSQL views querying the data to show Avian Influenza fatalities, non-fatal sickness and outbreaks among bird populations. These can be displayed as separate data layers on the OpenLayers map.

• Customize OpenLayers client to allow user to “drill down” to linked HTML files for each Avian Influenza outbreak event point.

Summary

• You can geocode and map an RSS feed using open source and custom tools.

• This can provide useful monitoring tools for non-geospatial experts in a variety of fields.

• Integrating different varieties of open source software projects is a difficult endeavor but this project may only have been possible with these open source tools.

• Questions?