Tipsfortaxonomic

cleaningwiththeTNRS

BradBoyleUniversityofArizona

9January2016

Taxonomiccleaning

• Whybother?• Taxonomicscrubbingapplications• Generalglitchesandgotchas• TNRSglitchesandgotchas• Pre-processing• Post-processing• Understandingtheoutput

Taxonomiccleaning:whybother?

HieronymaoblongaWidespreadtropicaltree

Taxonomiccleaning:whybother?

HieronymaoblongaWidespreadtropicaltree

HieronymapoasanaSynonymofHieronymaoblonga,oncethought tobeendemictoCostaRica

Taxonomiccleaning:whybother?

HieronymaoblongaWidespreadtropicaltree

HieronymapoasanaSynonymofHieronymaoblonga,oncethought tobeendemictoCostaRica

HyeronimaoblongaHieronimaoblonga

CommonmisspellingsofHieronymaoblonga

Whybother?

10%“bad”names

Whybother?

Overlapbetweendatabasesonly3%!

Whybother?

400%increaseinoverlap

Taxonomiccleaningapplications

• TNRS• (http://tnrs.iplantcollaborative.org/index.html)

• TaxonStand• http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2012.00232.x/full

• GlobalNameResolver• http://resolver.globalnames.org/

• PlantMiner• http://www.plantminer.com/

• Manyothers…

Generalarchitecture

• Nameparser– Breaksupandclassifiesnamecomponents

HieronimapoasanaStandley

Specificepithet

Genus Authority

Generalarchitecture

• Nameresolver– Matchesthenametoreferencedatabase– Triesfuzzymatchingifexactmatchfails

HieronimapoasanaStandley

HieronymapoasanaStandl.

Misspelled

Correctspelling(aspublished)

Generalarchitecture

• Taxonomicstatus&synonymconversion– Someapplicationsdonodothislaststep

HieronymapoasanaStandl.

Hieronymaoblonga(Tul.)Müll.Arg.

Synonym

Currentlyacceptedname

ExampleworkflowwithTNRSAPI

• Script:tnrs_api_example.R• Steps:1. Extractthenames2. Turnintoastringseparatedbycommas3. URL-encodeandsendtotheTNRSAPI4. ConvertthereturnedJSONtodataframe5. Updateyournames

ProsandConsofTNRSAPI• Advantages

– Fast,simple,fullyautomated• Disadvantages

– Can’tadjustallsettingsavailableinwebinterface– UsesTropicosasonlysource– Can’ttakeadvantageofwebinterfacetoinspectresults,choosealternativematchesandresearchnames

– Can’taccessdownloadoptionsavailableinwebinterface

– Parse-onlyoptionnotavailable

ExamplebasicworkflowwithTNRSwebinterface

• Script:tnrs_gui_example.R• Steps:1. ExtractnamestoCSVfilewithtwocolumns:UniqueID&

names2. UploadtoTNRSusingbulk“UploadandSubmitList”tab,

checkingbox“Myfilecontainsanidentifierasfirstcolumn”3. Adjustnameprocessingsettingsandsubmit4. Inspectresultsonline,selectingalternatematchesif

appropriate5. Downloadresults,usingoptions:Bestmatchesonly,

Detailedresults,UTF-8format6. ImportTNRSresultsastab-delimittedfile7. RemainingprocessingasforAPI

ProsandConsofTNRSWebInterface

• Disadvantages– Notfullyautomated

• Advantages– Canadjustnameresolutionsettings– Morenameresolutionsources– Usewebinterfacetoinspectresults,choosealternativematchesandresearchnames

– Selectanddownloadalternativematchesonthefly– Moredownloadoptions,including“Allmatches”(usefulifyoudon’tlikehowTNRSchoosesbestmatchandwanttoscriptityourself)

– Parse-onlymore(usefulforcomparingpartoforiginalnametomatchedname)

TNRSTips&Gotchas

• Tip:Pre-pendfamilytonametopreventmatchingsimilarnamesindifferentfamilies

• Gotcha:IfyouwanttouseThePlantList,*always*selectTPL+ILDIS+GCCtogether

• Tip:ResearchanynamewhereTaxonomicStatus<>AcceptedorSynonym

• Gotcha:Evenacceptednamescanbewrong!

TaxonomicStatusTaxonomicStatusreferstotheMatchedName

• Accepted:Goodtogo!• Synonym:Goodtogo,aslongasacceptednamesupplied• Noopinion:Couldbegoodorbadname.RESEARCHIT• Invalid:Nevervalidlypublished.DON’TUSE• Illegitimate:Violatesnomenclaturalrules.DON’TUSE• Rejectedname:Rejectedbynomenclaturalcommittee.DON’TUSE

• Misappliedname:Commonlymisappliedtothethewrongspecies.Mayormaynotbecorrect.RESEARCHIT

Evenacceptednamescanbewrong!

Name submitted Tropicos The Plant List

Henriettea fascicularis =Henriettella fascicularis =Henriettella fascicularis

Henriettea ramiflora Accepted Accepted

Henriettea succosa Accepted Accepted

Henriettella fascicularis Accepted Accepted

Henriettella tuberculosa Accepted =Henriettea tuberculosa

Actually,allbelonginHenriettea