overview

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

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

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)

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

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

Search with Thumbnail response

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http://services.morphbank.net/mbSearch page

RSS Feed

Cooliris link

Results page

Cooliris Image Viewer

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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&amp;imgType=thumb"/> <media:content url="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>Calamagrostis canadensis with id 140442</title> <author>Morphbank</author> <media:thumbnail url="http://www.morphbank.net/?

id=141257&amp;imgType=thumb"/> <media:content url="http://www.morphbank.net/?id=141257&amp;imgType=jpg"/> <georss:point>63.75 -146.0</georss:point>

</item>

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