iPlant TNRS
24
iPlant's Taxonomic Name Resolu3on Service Naim Matasci BIO5 / The iPlant Collabora3ve
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iPlant TNRS presentation for phylotatsic
Transcript of iPlant TNRS
iPlant's Taxonomic Name Resolu3on Service
Naim Matasci BIO5 / The iPlant Collabora3ve
Ancestral state of Hawaiian lobelioids
Lobelia niihauensis (Image: David Eickhoff)
Cyanea leptostegia (Image: Karl Magnacca)
(Schulter et al. 1997, Paradis 2004)
Con3nuous Ancestral Character Es3ma3on
?
Obtain sequences • GetSeq
Align sequences • Muscle
Build Tree • FastTree
(aML) • Ninja (NJ) • PHYLIP
(MP, NJ, ML)
• RAxML (ML)
Visualize Tree
• iPlant Tree Viewer
Integrate Data
• Lopper • TNRS
Run Analysis • CACE • DACE • Contrast • OUch • Picante • Penalized
likelihood
Obstacles !"#$%&'()'*'$+,&,!"#$%&'(-&%%",'!"#$%&'(.%"/&'01"+2&,3/$1'2"%"#$%&'()'*'&$+,&,3/$1'2"%"#$%&'(1'4/",2'456,!"#$%&'(567"%$*4'!"#$%&'(6*44"&8$,!"#$%&'(+&&5'*$+,&,9/&.5'1&'(&+,&.+&,9/&.5'1&'(/"4)&&:$%&,,$'(/562&8",7$/1':$%&,,$'(,*#4"/8'2';6'+$'(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
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
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
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 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
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
Obtain sequences • GetSeq
Align sequences • Muscle
Build Tree • FastTree
(aML) • Ninja (NJ) • PHYLIP
(MP, NJ, ML)
• RAxML (ML)
Visualize Tree
• iPlant Tree Viewer
Integrate Data
• Lopper • TNRS
Run Analysis • CACE • DACE • Contrast • OUch • Picante • Penalized
likelihood
Trematolobelia kauaiensisBrighamia rockiiCyanea hirtellaCyanea acuminataClermontia faurieiClermontia arborescensClermontia kakeanaClermontia parvifloraDelissea leptostegiaCyanea coriaceaBrighamia insignisDelissea rhytidospermaDelissea subcordataTrematolobelia macrostachysLobelia hypoleucaNeowimmeria yuccoidesGaleatella gloria montisLobelia niihauensisLobelia villosaLobelia kauaensis
maxHeight.m
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0.822
0.454
0.881
0.996
0.958
0.750
0.993
0.959
0.839
0.992
0.937
0.757
0.986
0.970
0.931
0.977
1.000
0.426
1.000
0
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Issues
• Plants only – cross-‐code homonyms • Lexical reconcilia3on – Chondodendron tomentosum R. P. aff. = Chondodendron tomentosum Ruiz & Pav.
• API • Performance (caching)
