plant name services using tropicos
TRANSCRIPT
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.
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
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
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
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
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
Tropicos – 2002
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
Tropicos - 2006
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
Tropicos – 2011
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
Data sharing & integration
Names
Specimens
Plant Names
Plant NamesSpecimensDescriptions
Occurrences of Plant Names
ProtologueCitations
Plant Names
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
services.tropicos.org
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://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
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://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
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
Tropicos API Key Request
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
Services Are Explained Online
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
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>
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
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>
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
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)
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
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)
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
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)
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
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
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
Taxonomic Name Resolution Service (TNRS)
Partnership between:
Innovative tool for the computer-assisted standardization of plant scientific names
http://tnrs.iplantcollaborative.org
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.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”
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
TNRS Matching Workflow
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
TNRS in actionhttp://tnrs.iplantcollaborative.org
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
Download
CSV, same info as displayed online:
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
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
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
Acknowledgements
And the thousands of botanists who have contributed time & data in support of Tropicos.
Miller. 28 July 2011. IBC 2011, Melbourne. Tropicos: http://tropicos.org
Questions?
Chuck MillerVP-IT and Chief Information OfficerE-mail: [email protected]
http://tropicos.orghttp://services.tropicos.org