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Plant Name Services Using Tropicos

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Plant Name Services Using Tropicos

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

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