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Plant Name Services Using Tropicos

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  • 1. PLANT NAME SERVICES USING TROPICOS Chuck Miller Vice President, IT & CIO Chris Freeland Director, Center for Biodiversity Informatics http://tropicos.org http://services.tropicos.org
  • 2. Tropicos History
    • Originated in 1982 to capture specimen label data
    • Opened to Web in 1996
    Dr. Robert Magill, ca. 1984, with Tropicos hardware.
  • 3. Stats *
    • Content
    • Names: 1,254,414
    • Specimens: 3,966,223
    • Images: 167,466
    • Publications: 47,561
    • References: 122,010
    • Common Names: 53,202
    • Usage
    • Visits / Month: 111,000
    • Visitors / Month: 38,000
    • Pageviews / Month: 1.4m
    * As of 20 July 2011
  • 4. Work completed since IBC 2005
    • Completed reengineering of entire system
      • Rich desktop client
      • Interactive web site: http://tropicos.org
      • Conversion of images to JPEG2000 format and high resolution viewer
      • Multi-processor, 64-bit servers
  • 5. Tropicos – 2002
  • 6. Tropicos - 2006
  • 7. Tropicos – 2011
  • 8. Data sharing & integration Names Specimens Plant Names Plant Names Specimens Descriptions Occurrences of Plant Names Protologue Citations Plant Names
  • 9. services.tropicos.org
  • 10. Tropicos Services:
    • List Names
    • Name Search
    • Get Summary
    • Get Synonyms
    • Get Accepted Names
    • Get Name Distributions
    • Get Name References
    • Get Name Images
    • Get Chrom. Counts
    • Get Higher Taxa
    • Get Specimens
    • Get Computed Acceptance
    • Get Computed Synonyms
    http://services.tropicos.org
  • 11. Tropicos API Key Request
    • Encourage use of APIs instead of screen scraping
      • Better performance for all users
    • Meant to help consumers, not restrict
      • Provides structured access to data
      • Enables more detailed stats & reporting
    • Key is assigned to an individual
    • UUID
      • e.g. D1CC4285-279D-4B5C-B469-861F4C1F4020
    • http://services.tropicos.org/help?requestkey
  • 12. Tropicos API Key Request
  • 13. Services Are Explained Online
  • 14. Name Services: Name Search
    • Pattern:
    • Name/Search?name={name}&type={type}&apikey={apikey}&format={format}
    • Example:
    • Name/Search?name=poa annua&type=wildcard &apikey=D1CC4285-279D-4B5C-B469-861F4C1F4020&format=xml
    • Sample Response:
    • <Names>
  <Name>
    <NameId>25509881</NameId>
    <ScientificName>Poa annua</ScientificName>
    <ScientificNameWithAuthors>Poa annua L.</ScientificNameWithAuthors>
    <Family>Poaceae</Family>
  </Name>
</Names>
  • 15. Name Services: Get Summary
    • Pattern:
    • Name/{id}?apikey={apikey}&format={format}
    • Example:
    • Name/25509881?apikey=D1CC4285-279D-4B5C-B469-861F4C1F4020&format=xml
    • Sample Response:
    • <Name>
  <NameId>25509881</NameId>
  <ScientificName>Poa annua</ScientificName>
  <ScientificNameWithAuthors>Poa annua L.</ScientificNameWithAuthors>
  <Family>Poaceae</Family>
  <SynonymCount>78</SynonymCount>
  <AcceptedNameCount>0</AcceptedNameCount>
</Name>
  • 16. Name Services: Get Synonyms
    • Pattern:
    • Name/{id}/Synonyms?apikey={apikey}&format={format}
    • Example:
    • Name/25509881/Synonyms?apikey=D1CC4285-279D-4B5C-B469-861F4C1F4020&format=xmlSample
    (1 of 3)
  • 17. Get Synonyms Response
    • <Synonyms>
  <Synonym>
    <SynonymName>
      <NameId>25503923 </NameId>
      <ScientificName>Aira pumila</ScientificName>
      <ScientificNameWithAuthors>Aira pumila Pursh</>
      <Family>Poaceae</Family>
    </SynonymName>
    <AcceptedName>
      <NameId>25509881</NameId>
      <ScientificName>Poa annua</ScientificName>
      <ScientificNameWithAuthors>Poa annua L.</ScientificNameWithAuthors>
      <Family>Poaceae</Family>
    </AcceptedName>
    (2 of 3)
  • 18. Get Synonyms Response
    • …
  <Reference>
   <ReferenceId>46337</ReferenceId>
   <PublicationId>605</PublicationId>
   <AuthorString>Soreng, R. J., L. M. Giussani & M. A. Negritto</AuthorString>
   <ArticleTitle>~Poa~. In Catalogue of New World Grasses</ArticleTitle>
   <Collation>48: 505-580</Collation>
   <AbbreviatedTitle>Contr. U.S. Natl. Herb.</AbbreviatedTitle>
   <YearPublished>2003</YearPublished>
 </Reference>
    •   </Synonym>
    • </Synonyms>
    (3 of 3)
  • 19. API Usage Stats Harvesting by Encyclopedia of Life 176,280 requests in one day All APIs combined have received more than 17mil requests since 1 Jan 2011 Sample: Get Synonyms
  • 20. Taxonomic Name Resolution Service (TNRS)
    • Partnership between:
    • Innovative tool for the computer-assisted standardization of plant scientific names
    http://tnrs.iplantcollaborative.org
  • 21. TNRS: Mechanics
    • Users input lists of names
      • Can submit 5,000 via online form or unlimited via CSV text file upload
    • Using data harvested from Tropicos’ APIs:
      • Name strings are compared to Tropicos names
      • When name matches are found, TNRS returns name details, synonymy & computed acceptance
      • When names are not matched, TNRS tries fuzzy matching to find near-miss variants
        • User submits “Poa anua” TNRS returns “Poa annua”
  • 22. TNRS Matching Workflow
  • 23. TNRS in action http://tnrs.iplantcollaborative.org
  • 24. Download CSV, same info as displayed online:
  • 25. Future
    • Organize & build toward Global Strategy for Plant Conservation Target 1: “ An online flora of all known plants. ”
    • Continued expansion of core Tropicos features
      • Living Collections
      • Phylogeny
    • More data, more projects
    • Work with TNRS to integrate The Plant List & other data sources for completeness
  • 26. Acknowledgements And the thousands of botanists who have contributed time & data in support of Tropicos.
  • 27. Questions?
    • Chuck Miller VP-IT and Chief Information Officer E-mail: [email_address]
    http://tropicos.org http://services.tropicos.org