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Overview

Data Integration Services for Biodiversity Informatics: An Example from Plant Collections and Morphbank Greg Riccardi , Florida State University Boyce Tankersley, Chicago Botanic Garden. Overview. PlantCollections Publish information about public garden collections

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Overview

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  1. Data Integration Services for Biodiversity Informatics: An Example from Plant Collections and Morphbank Greg Riccardi, Florida State UniversityBoyce Tankersley, Chicago Botanic Garden

  2. Overview • PlantCollections • Publish information about public garden collections • Using existing infrastructure • Morphbank • Goals and capabilities of project • Recording support for scientific inference • Some examples of existing infrastructure that are easy to use • Emphasis on people and their interactions with information and each other

  3. PlantCollections • Collaboration of 18 publicgardens which aims to presentinformation about plant diversity • Publication of information from existing plant records: information about • DNA, images, seeds, herbarium vouchers, living plants • Use of existing technologies • BG Base and other primary plant record databases • Google Base as information repository • Morphbank as image repository • Web portal developed by Dave Vieglais and Pathfinder

  4. Morphbank Project • Repository of images of organisms • 220,000 images so far • Each image has a context: • Specimen, taxon, locality, specimen part, view angle, etc. • Repository of information related to the images • Specimens, localities, users, groups, taxa, annotations, collections • Owner, group, date, permissions • Unique identity for each object • All objects are connected through collections and associations (aka annotations)

  5. Morphbank Project • Improve support for specific biology research activities • Proposal addressed 3 specific research activities • Develop infrastructure • Those activities could be improved by a collaborative, Web-based information system • Involve a multi-disciplinary team • Biology: zoology, botany, paleontology • Computer Science • Information Science

  6. Creating an Information Model for PlantCollections • Survey of information managers from the gardens • What fields of data do they have? • Survey of users from 8 domains • Taxonomy, horticulture, conservation science, ecology, weed science, education, gardeners, garden visitors • What information do they need? • Committee to create federated schema • Evaluate surveys • Create criteria for inclusion based on availability and need riccardi@ci.fsu.edu

  7. Information Transfer in PlantCollections • BG Base databases (and others) have primary data • Dump to CSV file • Requires field selection • Transform to XML • Customized code • Push to Google Base • Standard • Google Base is the aggregator and publisher • Accept insert and update documents • Maintain information for Web sites • Morphbank is the image repository and publisher • BG Base databases export image and image metadata to Google Base • Google Base pushes image and metadata to Morphbank • Integration • Development of portal for search and display riccardi@ci.fsu.edu

  8. Existing Infrastructure for Image Display • Showing images through plugin • DO NOT TRY THIS NOW • Cooliris.com provides an image plugin • Page that shows images exposes an RSS feed using MediaRSS • RSS feed provides thumbnail and larger image for each item • Search page, result thumbnails and image display follow • Another example from http://services.morphbank.net/mb2 • http://services.morphbank.net/mb2/request?method=search&objecttype=Image&keywords=ctol&limit=100&firstResult=200&format=thumb • This URL is a search of Morphbank for CTOL (Cypriniformes Tree of Life) images with a presentation of the results as a thumbnail page

  9. Search with Thumbnail response http://services.morphbank.net/mb Search page Cooliris link RSS Feed Results page riccardi@ci.fsu.edu

  10. Cooliris Image Viewer riccardi@ci.fsu.edu

  11. riccardi@ci.fsu.edu

  12. Geolocating objects in Google Maps • Using GeoRSS namespace for presenting lat/long • Paste RSS feed URL into the Google Maps search field • Pins on map for each geolocated item • Each pin includes a link to the home page for the item

  13. riccardi@ci.fsu.edu

  14. Sample RSS Feed • <rss version="2.0" xmlns:georss="http://www.georss.org/georss" xmlns:media="http://search.yahoo.com/mrss/"> <channel> <title>Keyword query</title> <description>Search Results for keywords 'alaska' </description> <item group="UAM" type="Specimen"> <link>http://www.morphbank.net/?id=140441</link> <title>Calamagrostiscanadensis with id 140441</title> <author>Morphbank</author> <media:thumbnailurl="http://www.morphbank.net/?id=141256&amp;imgType=thumb"/> <media:contenturl="http://www.morphbank.net/?id=141256&amp;imgType=jpg"/> <georss:point>63.7000007629395 -141.860000610352</georss:point> </item> <item group="UAM" type="Specimen"> <link>http://www.morphbank.net/?id=140442</link> <title>Calamagrostiscanadensis with id 140442</title> <author>Morphbank</author> <media:thumbnailurl="http://www.morphbank.net/?id=141257&amp;imgType=thumb"/> <media:contenturl="http://www.morphbank.net/?id=141257&amp;imgType=jpg"/> <georss:point>63.75 -146.0</georss:point> </item> riccardi@ci.fsu.edu

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