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Andrew Murdoch Avian Influenza 20080414
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Andrew Murdoch Avian Influenza 20080414



Open Source software presentation - Avian Influenza RSS geocoding and Internet map display

Open Source software presentation - Avian Influenza RSS geocoding and Internet map display



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Andrew Murdoch Avian Influenza 20080414 Andrew Murdoch Avian Influenza 20080414 Presentation Transcript

  • Avian influenza RSS web mapping exploring geographic and temporal aspects of outbreak events Andrew Murdoch & Ian Turton September 2007
  • Presentation Overview
    • Goals
    • Background info on terms
    • Project Plan
      • Problems Faced
      • Unfinished Business
    • 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
  • Initial mockup:
  • Screenshot of application http://www.experimental.geovista.psu.edu/andrew/html/avian_influenza_map.html
  • Initial 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).
  • Project tasks
    • Data Ingest and Processing
    • GeoServer Administration tasks
    • OpenLayers Client setup and customization
    • Initial tasks completed (prior to FOSS4G conference)
      • Historical and nightly data import
      • Basic data display
    • Subsequent tasks completed
      • Scheduled hourly import of RSS data
      • Prevented duplicate entries stored in PostGIS
      • SIMILE timeline integration / GeoJSON format conversion
      • Drilldown to HTML records from map RSS events
  • 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 (Center for International Earth Science Information Network (CIESIN) data), extents defined and map control tools chosen. (NASA JPL MODIS data was unavailable)
  • Initial tasks completed
    • 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
  • Subsequent tasks completed
    • Added hourly Java import to PostGIS tables for two RSS datafeeds (WHO UN data and Feedburner news aggregator).
    • Edited Java code to prevent duplicate GeoRSS points from being imported into the same PostGIS table. This is important as the RSS feeds are checked hourly.
    • Converted GeoServer WMS output to GeoJSON format to download onto client machine. This is then integrated with the MIT SIMILE Timeline tool. Too many points downloaded causes some web browsers to stall or produce error messages.
    • Edited Java import code to only show actual locations of Avian Influenza outbreaks (not conference locations, health organization locations, etc.) This was problematic as there are no “guaranteed” valid keywords for outbreak events that aren’t also referenced in non-outbreak news items. I filtered on the keyword “update”, which seemed to be used as a UN convention for situation updates on human cases of Avian Influenza.
    • Customized OpenLayers client to allow user to “drill down” to linked HTML files for each Avian Influenza outbreak event point.
  • 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. These were then converted into many single points in the PostGIS table, all referring to the same news item.
    • 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).
    • Unable to use Google background maps because of problem with GeoServer software.
    • Unable to create new PostgreSQL views querying the data to show Avian Influenza fatalities, non-fatal sickness and outbreaks among bird populations. This could potentially be handled as a follow-on exercise in parsing keywords from the RSS news entries.
  • Unfinished Business
    • Data filtering
    • Set user-defined time ranges for timeline tool
    • Sort drill-down list of events by date. Highlight events that fall within the current timeline range
    • Incorporate Google background maps
  • Data Filtering not completed
    • Ideally, 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. Currently the only filter is hard-coded in the data ingest java class to find UN-WHO “situation updates”.
    • This could help make the Feedburner RSS feed more useful as it currently has too many duplicate or similar entries every day.
    • Subject matter experts could be called on to guide the choice of keywords.
  • Google Maps integration
    • Unable to incorporate Google Maps background layers because of problems with the current version of GeoServer (which is used to display the RSS point events and background layers).
  • Live Demo
    • Display UN WHO data
    • Drill down to HTML page for each event location
    • Highlight events from a chosen date range
  • 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?