Plant Name Services Using Tropicos

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

Tropicos History
Originated in 1982 to capture specimen label data
Opened to Web in 1996
Dr. Robert Magill, ca. 1984, with Tropicos hardware.

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

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

Tropicos – 2002

Tropicos - 2006

Tropicos – 2011

Data sharing & integration Names Specimens Plant Names Plant Names Specimens Descriptions Occurrences of Plant Names Protologue Citations Plant Names

services.tropicos.org

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

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

Tropicos API Key Request

Services Are Explained Online

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>

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>

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)

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)

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)

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

Taxonomic Name Resolution Service (TNRS)
Partnership between:
Innovative tool for the computer-assisted standardization of plant scientific names
http://tnrs.iplantcollaborative.org

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”

TNRS Matching Workflow

TNRS in action http://tnrs.iplantcollaborative.org

Download CSV, same info as displayed online:

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

Acknowledgements And the thousands of botanists who have contributed time & data in support of Tropicos.

Questions?
Chuck Miller VP-IT and Chief Information Officer E-mail: [email_address]
http://tropicos.org http://services.tropicos.org

Plant Name Services Using Tropicos

by Chris Freeland on Aug 01, 2011

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