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.orghttp://services.tropicos.org

Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://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 NamesSpecimensDescriptions

Occurrences of Plant Names

ProtologueCitations

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 Life176,280 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 actionhttp://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 MillerVP-IT and Chief Information OfficerE-mail: [email protected]

http://tropicos.orghttp://services.tropicos.org

plant name services using tropicos

Technology

tropicos names

tropicos services

tropicos apis

list names

support of tropicos

tropicos history

tropicos hardware

common names