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A Web Based Tool For the Detection and Analysis of
AvianInfluenza Outbreaks From
Internet News SourcesIan Turton and Andrew
MurdochGeoVISTA Center
Penn State University
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Flight?
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Summary
• Who we are?• Why we did it?• What is Avian Flu?• What we did?• How we did it?• Did it work?• What will we do next?
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Who we are?
• Ian – Senior Research Associate in GeoVISTA
Center– E-Education Fellow in Dutton E-
Education Institute.
• Andrew– MGIS Student (graduated in Summer
2008)– GIS Developer at ArcBridge Consulting
and Training
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What we did?
• Andrew needed a project for Ian’s course on web mapping, and later for his capstone project (like a dissertation).
• Ian had an interest in extracting geographic information from unstructured text.
• Picked the spread of Avian Influenza and how to map it automatically from news reports.
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What is Avian Flu?
• Avian flu or Bird flu is a virus
• Most scary strain is H5N1 but there are many others.
• ~60% death rate in humans.
• Currently no (or very limited) human to human transmission.
Picture by Quiplash! CCbyA
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What we did?
• Designed and built a system to automatically read internet news articles and map them for us so we could gain a better understanding of how avian flu is spreading on a day to day basis.
• Set it running to see how it did• Tweaked it a bit as we saw how it
worked
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How we did it?
• Data sources• Data processing tools• GeoCoding tools• Web Mapping tools
– Server– Client
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Data Sources
• Official Avian Flu sites– WHO – PROMED
• Internet News sites– Google News– Feedburner
• Collected as RSS feeds
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Why does this work?
• Media panic/interest leads to widespread reporting of any avian flu story.
• Use of medical blogs like PROMED also helps overcome government restrictions on reporting.
Pictures: ianstacey, quiplash, Incessantflux CCbyA
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What is RSS?
• Really Simple Syndication
• RDF Site Summary• A standardized XML
file for passing information about web log (blog) updates.
• You normally view RSS feeds in a feed reader
• We wrote programs to read for us.
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Finding the geography
• Step one extract the place names, named entity extraction– Custom tools– Reuters’ Calais system– MetaCarta – GeoNames.org
• GeoCode the places, disambiguate London, Washington etc– Custom tools– MetaCarta– GeoNames.org
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Well that can’t be too hard?
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Web Mapping Server
• Open Web Mapping Standards from the OGC (allows others to use our data).
• Open Source tools (we’re a poor university).
• Store the data points and news text in PostGIS (free spatial database).
• GeoServer to serve maps from the DB to web (and desktop) clients.
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Mapping Client
• Remember our end users are epidemiologists not GIS users so stick with a web browser as client.
• OpenLayers (www.openlayers.org)– JavaScript library that implements the
OGC WMS and WFS standards our server uses.
– Allows rapid construction of an interactive web map by relative novice developers.
– The finished map looks a lot like a Google map so users can use it easily.
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The Map
Choice of background layersChoice of feeds
http://www.experimental.geovista.psu.edu/andrew/html/avian_influenza_map.html
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Zoom and Pan
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Time Line
• We are also interested in change over time.
• Added SIMILE Timeline from MIT– JavaScript tool allows user to scroll
through time or date stamped information
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Link to external pages
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Query the map
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Did it work?
• Yes,• Well mostly, • Well some of the time!• We can take news feeds, geocode
them and draw maps in a web browser.
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What didn’t work?
• News sources and even medical feeds contain too many items that are about avian flu in a general sense but not actually about an outbreak.– Conferences about avian flu– Vaccine news– Reports of other influenza outbreaks– Reports of other infectious diseases
(“unlike avian flu…”
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What will we do next?
• Improved selection of RSS items• Bayesian classifier
– Train on a selection of “good” and “bad” items
– Allow user to rate articles
• Non-negative matrix factorization– Clusters similar items based on word
usage– Help overcome repeated reports
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What will we do next?
• Continue to improve the GeoCoder– Better disambiguation algorithms.– Allow user to rate the accuracy of
locations found in reports.
• Improve User Interface– Better selection of points of interest
using timeline – Replace SIMILE with custom time bar
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Conclusions
• It is possible to construct an online automated system that can read news articles from professional and general news feeds and map them in a way that allows experts and members of the public to track the spread of avian flu outbreaks.
• There is still much work that can be carried out to improve this work.