iPlants Taxonomic Name Resolution               Service            Naim Matasci    BIO5 / The iPlant Collaborative
The Problem – Taxonomic Uncertainty             Lycopersycon esculentum   Solanum lycopersicum                            ...
Taxonomic uncertainty1. Non-existent names  •   Misspellings  •   Contamination      •   Annotations      •   Morphospecie...
a) Centaurium curvistamineum                                               (Wittr.) Abrams (1951)                         ...
How to figure that out?…or ask around at My-Plant.org
Original Use Case – Density Plots (BIEN/NCEAS)  Makemake at de.wikipedia
Hans Hillewaert
Taxonomic Name Resolution Service• Computer assisted standardization of plant  names• Corrects spelling errors and alterna...
Its all wrong!!!Where is my plant!!!
Future• More sources  – Standard source import with DwC support• Better performance• TNRastic API• Integration with Global...
• Web: http://tnrs.iplantc.org/• Code:  https://github.com/iPlantCollaborativeOpenS  ource/TNRS• API (provisional): http:/...
Brad Boyle                                  Paul Morris (Harvard University)Brian Enquist                               Al...
iPlant Taxonomic Name Resolution Service v. 3
iPlant Taxonomic Name Resolution Service v. 3
iPlant Taxonomic Name Resolution Service v. 3
iPlant Taxonomic Name Resolution Service v. 3
iPlant Taxonomic Name Resolution Service v. 3
iPlant Taxonomic Name Resolution Service v. 3
iPlant Taxonomic Name Resolution Service v. 3
iPlant Taxonomic Name Resolution Service v. 3
iPlant Taxonomic Name Resolution Service v. 3
iPlant Taxonomic Name Resolution Service v. 3
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iPlant Taxonomic Name Resolution Service v. 3

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Presentation of the new features available in the 3.0 release of the iPlant TNRS

Published in: Technology, Self Improvement
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iPlant Taxonomic Name Resolution Service v. 3

  1. 1. iPlants Taxonomic Name Resolution Service Naim Matasci BIO5 / The iPlant Collaborative
  2. 2. The Problem – Taxonomic Uncertainty Lycopersycon esculentum Solanum lycopersicum Lycopersycon lycopersicum Solanum lycopersicon?
  3. 3. Taxonomic uncertainty1. Non-existent names • Misspellings • Contamination • Annotations • Morphospecies • Digitization issues (frame shifts, character encoding)Lexical variants (digitization conventions)2. Synonymy • Nomenclatural synonyms • Taxonomic synonyms / concepts3. Misidentifications, incomplete identifications
  4. 4. 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
  5. 5. How to figure that out?…or ask around at My-Plant.org
  6. 6. Original Use Case – Density Plots (BIEN/NCEAS) Makemake at de.wikipedia
  7. 7. Hans Hillewaert
  8. 8. 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
  9. 9. Its all wrong!!!Where is my plant!!!
  10. 10. Future• More sources – Standard source import with DwC support• Better performance• TNRastic API• Integration with Global Names components
  11. 11. • Web: http://tnrs.iplantc.org/• Code: https://github.com/iPlantCollaborativeOpenS ource/TNRS• API (provisional): http://goo.gl/XnUiH• TNRastic API: http://goo.gl/Z7Fkc
  12. 12. Brad Boyle Paul Morris (Harvard University)Brian Enquist Alan Paton (Kew Royal Botanic GardensJuan Antonio Raygoza Garay and their International Plant Names Index)Nicole Hopkins Tony Rees (Commonwealth Scientific andZhenyuan Lu Industrial Research Organisation)Martha Narro Michael Giddens (www.silverbiology.com)Shannon Oliver Dmitry Mozzherin (Global BiodiversityWilliam Piel Information Facility)Jill Yarmchuk David Remsen (Global Biodiversity Information Facility)Bob Magill (Missouri Botanical Garden) David Patterson (Encyclopedia of Life)Chris Freeland (Missouri Botanical Cam Webb (Harvard University)Garden)Chuck Miller (Missouri Botanical Garden) Missouri Botanical Garden (Tropicos)Peter Jorgensen (Missouri BotanicalGarden) Funding provided by the National ScienceAmy Zanne (University of Missouri, St. Foundation Plant CyberinfrastructureLouis) Program (grant #DBI-0735191).Peter Stevens (Missouri Botanical Garden)Jay Paige (Missouri Botanical Garden)Bob Peet (University of North Carolina atChapel Hill)

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