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

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

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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?methods
  earchobjecttypeImagekeywordsctollimit100fir
  stResult200formatthumb
• 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/mb Search page
Cooliris link
RSS Feed
Results page
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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

• ltrss version"2.0" xmlnsgeorss"http//www.geor
  ss.org/georss" xmlnsmedia"http//search.yahoo.
  com/mrss/"gt ltchannelgt lttitlegtKeyword
  querylt/titlegt ltdescriptiongtSearch Results
  for keywords 'alaska' lt/descriptiongt ltitem
  group"UAM" type"Specimen"gt ltlinkgthttp//www.mo
  rphbank.net/?id140441lt/linkgt lttitlegtCalamagrost
  is canadensis with id 140441lt/titlegt
  ltauthorgtMorphbanklt/authorgt ltmediathumbnail
  url"http//www.morphbank.net/?id141256ampimgTy
  pethumb"/gt ltmediacontent url"http//www.morph
  bank.net/?id141256ampimgTypejpg"/gt
  ltgeorsspointgt63.7000007629395
  -141.860000610352lt/georsspointgt lt/itemgt
  ltitem group"UAM" type"Specimen"gt
  ltlinkgthttp//www.morphbank.net/?id140442lt/linkgt
  lttitlegtCalamagrostis canadensis with id
  140442lt/titlegt ltauthorgtMorphbanklt/authorgt
  ltmediathumbnail url"http//www.morphbank.net/?
  id141257ampimgTypethumb"/gt ltmediacontent
  url"http//www.morphbank.net/?id141257ampimgTy
  pejpg"/gt ltgeorsspointgt63.75
  -146.0lt/georsspointgt lt/itemgt