iPlant TNRS

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iPlant TNRS presentation for phylotatsic

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iPlant TNRS

  1. 1. iPlants  Taxonomic  Name  Resolu3on   Service   Naim  Matasci   BIO5  /  The  iPlant  Collabora3ve  
  2. 2. Ancestral  state  of  Hawaiian  lobelioids  Lobelia  niihauensis  (Image:  David  Eickhoff)   Cyanea  leptostegia  (Image:  Karl  Magnacca)  
  3. 3. Con3nuous  Ancestral  Character  Es3ma3on     ?  (Schulter  et  al.  1997,  Paradis  2004)  
  4. 4. Obtain   Align   Build  Tree   sequences   sequences   •  FastTree  •  GetSeq   •  Muscle   (aML)   •  Ninja  (NJ)   •  PHYLIP   (MP,  NJ,   ML)   •  RAxML   (ML)   Visualize   Integrate   Run  Analysis   Tree   Data   •  CACE  •  iPlant   •  Lopper   •  DACE   Tree   •  TNRS   •  Contrast   Viewer   •  OUch   •  Picante   •  Penalized   likelihood  
  5. 5. Obstacles   !"#$%&()*$+,&, !"#$%&(-&%%", !"#$%&(.%"/&01"+2&, 3/$12"%"#$%&()*&$+,&, 3/$12"%"#$%&(14/",2456, !"#$%&(567"%$*4 !"#$%&(6*44"&8$, !"#$%&(+&&5*$+,&, 9/&.51&(&+,&.+&, 9/&.51&(/"4)&& :$%&,,$(/562&8",7$/1 :$%&,,$(,*#4"/82 ;6+$(7&%", ;6+$(4*1&+2 ;6+$(5&/2$%% ;6+$(4"/&4$ ;6+$(%$72",2$.& ;%$/1"+2&())$+ ;%$/1"+2&(7/-&<%"/ ;%$/1"+2&(/#"/$,4$+, ;%$/1"+2&(<*/&$&Number  of  taxa   Taxa  names  
  6. 6. Taxonomic  uncertainty  1.  Non-­‐existent  names   •  Misspellings   •  Contamina3on   •  Annota3ons   •  Morphospecies   •  Digi3za3on  issues  (frame  shi[s,  character  encoding) Lexical  variants  (digi3za3on  conven3ons)  2.  Synonymy   •  Nomenclatural  synonyms   •  Taxonomic  synonyms  /  concepts  3.  Misiden3fica3ons,  incomplete  iden3fica3ons    
  7. 7. a)  Centaurium  curvistamineum   (Wi`r.)  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  Wi`r.   (1886)   h)  Erythraea  minima  Howell  (1901)   i)  Erythraea  muhlenbergii  Griseb.   (1839)  Image:  Gordon  Leppig  &  Andrea  J.  Pickart  
  8. 8. How  to  figure  that  out?  …or  ask  around  at  My-­‐Plant.org  
  9. 9. Original  Use  Case  –  Density  Plots  (BIEN/NCEAS)   Makemake  at  de.wikipedia  
  10. 10. Hans  Hillewaert  
  11. 11. Taxonomic  Name  Resolu3on  Service  •  Computer  assisted  standardiza3on  of  plant   names  •  Corrects  spelling  errors  and  alterna3ve   spellings  to  a  standard  list  of  names  •  Convert  out-­‐of-­‐date  names  to  currently   accepted  names  
  12. 12. Lobelia  kauaensis  Lobelia  villosa  Galeatella  gloria-­‐mon3s  Trematolobelia  kauaiensis  Trematolobelia  macrostachys  Lobelia  hypoleuca  Neowimmeria  yuccoides  Lobelia  niihauensis  Brighamia  insignis  Brighamia  rockii  Delissea  rhy3dosperma  Delissea  subcordata  Cyanea  acuminata  Cyanea  hirtella  Cyanea  coriacea  Delissea  leptostegia  Clermon3a  kakeana  Clermon3a  parviflora  Clermon3a  arborescens  Clermon3a  fauriei  
  13. 13. Obtain   Align   Build  Tree   sequences   sequences   •  FastTree  •  GetSeq   •  Muscle   (aML)   •  Ninja  (NJ)   •  PHYLIP   (MP,  NJ,   ML)   •  RAxML   (ML)   Visualize   Integrate   Run  Analysis   Tree   Data   •  CACE  •  iPlant   •  Lopper   •  DACE   Tree   •  TNRS   •  Contrast   Viewer   •  OUch   •  Picante   •  Penalized   likelihood  
  14. 14. maxHeight.m1412 1.000 ●Lobelia kauaensis ●10 ●Lobelia villosa 8 0.426 ●Lobelia niihauensis 0.937 ● 6 ● 0.977 ●Galeatella gloria montis ● 4 1.000 ●Neowimmeria yuccoides 2 ● 0.757 ●Lobelia hypoleuca 0 ● ●Trematolobelia macrostachys 0.986 ●0.931 ●Delissea subcordata ● 0.970 ● ●Delissea rhytidosperma ●Brighamia insignis 0.822 ● 0.992 ●Cyanea coriacea ● ●Delissea leptostegia 0.750 0.839 ●Clermontia parviflora ● ● 0.959 ● ●Clermontia kakeana 0.993 0.996 ● ●Clermontia arborescens ● ●Clermontia fauriei 0.881 ● 0.958 ●Cyanea acuminata ● 0.454 ●Cyanea hirtella ● ●Brighamia rockii ●Trematolobelia kauaiensis
  15. 15. Issues  •  Plants  only  –  cross-­‐code  homonyms  •  Lexical  reconcilia3on   –  Chondodendron  tomentosum  R.  P.  aff.  =   Chondodendron  tomentosum  Ruiz  &  Pav.  •  API  •  Performance  (caching)    

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