The TNRS: a Taxonomic Name Resolution Service for Plants

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iPlant presentation given at iEvoBio 2011

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The TNRS: a Taxonomic Name Resolution Service for Plants

  1. 1. The TNRS: a Taxonomic Name Resolution Service for Plants Naim Matasci (nmatasci@iplantcollaborative.org) The iPlant Collaborative iEvoBio 2011 Jun 21-22, 2011
  2. 2. What is iPlant?
  3. 3. Discovery Environment http://www.iplantcollaborative.org/discovery-environment-preview-access
  4. 4.
  5. 6. Taxonomic uncertainty <ul><li>Non-existent names </li></ul><ul><ul><li>Misspellings </li></ul></ul><ul><ul><li>Contamination </li></ul></ul><ul><ul><ul><li>Annotations </li></ul></ul></ul><ul><ul><ul><li>Morphospecies </li></ul></ul></ul><ul><ul><ul><li>Digitization issues (frame shifts, character encoding)Lexical variants (digitization conventions) </li></ul></ul></ul><ul><li>Synonymy </li></ul><ul><ul><li>Nomenclatural synonyms </li></ul></ul><ul><ul><li>Taxonomic synonyms / concepts </li></ul></ul><ul><li>Misidentifications, incomplete identifications </li></ul>
  6. 7. 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
  7. 8. How to figure that out? … or ask around at My-Plant.org
  8. 9. Makemake at de.wikipedia
  9. 10. Non-existent names: Herbarium specimens <ul><li>*New World plant specimens, 34 herbaria, simple match against IPNI and TROPICOS, excluding authors </li></ul>Total specimens: <ul><ul><li>1.1 million </li></ul></ul>Unique species names: <ul><ul><li>53,052 </li></ul></ul>Published names (legitimate & illegitimate): <ul><ul><li>44,532 </li></ul></ul>Misspelled names: <ul><ul><ul><ul><li>9371 (18%) </li></ul></ul></ul></ul>Specimens with misspelled names: <ul><ul><ul><ul><li>101,237 (9%) </li></ul></ul></ul></ul>
  10. 11. Hans Hillewaert
  11. 13. Taxonomic Name Resolution Service <ul><li>Computer assisted standardization of plant names </li></ul><ul><li>Corrects spelling errors and alternative spellings to a standard list of names </li></ul><ul><li>Convert out-of-date names to currently accepted names </li></ul>
  12. 17. Availability Source code (3-clause BSD) http://github.com/iPlantCollaborativeOpenSource/TNRS Web + API instructions http://tnrs.iplantcollaborative.org
  13. 22. Availability Source code (3-clause BSD) http://github.com/iPlantCollaborativeOpenSource/TNRS Web + API instructions http://tnrs.iplantcollaborative.org Questions, suggestions, collaborations [email_address]

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