IPlant's Taxonomic Name Resolution Service Naim Matasci BIO5 / The iPlant Collaborative.

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Presentation transcript:

iPlant's Taxonomic Name Resolution Service Naim Matasci BIO5 / The iPlant Collaborative

The Problem – Taxonomic Uncertainty Solanum lycopersicum Lycopersycon lycopersicum Lycopersycon esculentum Solanum lycopersicon?

Taxonomic uncertainty 1.Non-existent names Misspellings Contamination Annotations Morphospecies Digitization issues (frame shifts, character encoding)Lexical variants (digitization conventions) 2.Synonymy Nomenclatural synonyms Taxonomic synonyms / concepts 3.Misidentifications, incomplete identifications

a) Centaurium curvistamineum (Wittr.) Abrams (1951) b) Centaurium minimum (Howell) Piper (1915) c) Centaurium muhlenbergii (Griseb.) Wight ex Piper (1906) d) Centaurium muhlenbergii (Griseb.) Wight ex Piper forma albiflorum (Suksd.) St. John (1937) e) Centaurium muhlenbergii (Griseb.) Wight ex Piper var. albiflorum Suksd. (1927) f) Centaurodes muhlenbergii (Griseb.) Kuntze (1891) g) Erythraea curvistaminea Wittr. (1886) h) Erythraea minima Howell (1901) i) Erythraea muhlenbergii Griseb. (1839) Image: Gordon Leppig & Andrea J. Pickart

How to figure that out? …or ask around at My-Plant.org

Makemake at de.wikipedia Original Use Case – Density Plots (BIEN/NCEAS)

Hans Hillewaert

Taxonomic Name Resolution Service Computer assisted standardization of plant names Corrects spelling errors and alternative spellings to a standard list of names Convert out-of-date names to currently accepted names

Where is my plant!!! It's all wrong!!!

Future More sources – Standard source import with DwC support Better performance TNRastic API Integration with Global Names components

Web: Code: ource/TNRS API (provisional): TNRastic API:

Brad Boyle Brian Enquist Juan Antonio Raygoza Garay Nicole Hopkins Zhenyuan Lu Martha Narro Shannon Oliver William Piel Jill Yarmchuk Bob Magill (Missouri Botanical Garden) Chris Freeland (Missouri Botanical Garden) Chuck Miller (Missouri Botanical Garden) Peter Jorgensen (Missouri Botanical Garden) Amy Zanne (University of Missouri, St. Louis) Peter Stevens (Missouri Botanical Garden) Jay Paige (Missouri Botanical Garden) Bob Peet (University of North Carolina at Chapel Hill) Paul Morris (Harvard University) Alan Paton (Kew Royal Botanic Gardens and their International Plant Names Index) Tony Rees (Commonwealth Scientific and Industrial Research Organisation) Michael Giddens ( Dmitry Mozzherin (Global Biodiversity Information Facility) David Remsen (Global Biodiversity Information Facility) David Patterson (Encyclopedia of Life) Cam Webb (Harvard University) Missouri Botanical Garden (Tropicos) Funding provided by the National Science Foundation Plant Cyberinfrastructure Program (grant #DBI ).