overview plantcollections – publish information about public garden collections – using existing...
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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
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PlantCollections• Collaboration of 18 public
gardens 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
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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)
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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
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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
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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
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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
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Search with Thumbnail response
http://services.morphbank.net/mbSearch page
RSS Feed
Cooliris link
Results page
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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
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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>Calamagrostis canadensis with id 140441</title> <author>Morphbank</author> <media:thumbnail url="http://www.morphbank.net/?
id=141256&imgType=thumb"/> <media:content url="http://www.morphbank.net/?id=141256&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>Calamagrostis canadensis with id 140442</title> <author>Morphbank</author> <media:thumbnail url="http://www.morphbank.net/?
id=141257&imgType=thumb"/> <media:content url="http://www.morphbank.net/?id=141257&imgType=jpg"/> <georss:point>63.75 -146.0</georss:point>
</item>