ThePlanteomeProjectLaurelCooper,AustinMeier,JustinL.
Elser,JustinPreece,XuXu,RyanS.
Kitchen,BotongQu,EugeneZhang,SinisaTodorovic,PankajJaiswalOregonStateUniversity,Corvallis,OR,USAMarie-AngéliqueLaporte,ElizabethArnaudBioversityInternational,Montpellier,FranceSethCarbon,ChrisMungallLawrenceBerkeleyNationalLaboratory,Berkeley,CA,USABarrySmithUniversityatBuffalo,Buffalo,NY,USAGeorgiosGkoutosUniversityofBirmingham,UKandUniversityofAberystwyth,UKJohnDoonanUniversityofAberystwyth,UKAbstract—ThePlanteomeprojectisacentralizedonlineplantinformaticsportalwhichprovidessemanticintegrationofwidelydiversedatasetswiththegoalofplantimprovement.
Traditionalplantbreedingmethodsforcropimprovementmaybecombinedwithnext-generationanalysismethodsandautomatedscoringoftraitsandphenotypestodevelopimprovedvarieties.
ThePlanteomeproject(www.
planteome.
org)developsandhostsasuiteofreferenceontologiesforplantsassociatedwithagrowingcorpusofgenomicsdata.
Dataannotationslinkingphenotypesandgermplasmtogenomicsresourcesareachievedbydatatransformationandmappingspecies-specificcontrolledvocabulariestothereferenceontologies.
Analysisandannotationtoolsarebeingdevelopedtofacilitatestudiesofplanttraits,phenotypes,diseases,genefunctionandexpressionandgeneticdiversitydataacrossawiderangeofplantspecies.
TheprojectdatabaseandtheonlineresourcesprovideresearcherstoolstosearchandbrowseandaccessremotelyviaAPIsforsemanticintegrationinannotationtoolsanddatarepositoriesprovidingresourcesforplantbiology,breeding,genomicsandgenetics.
Keywords—ontology;traitsphenotype;semantic;dataintegration,plantsI.
INTRODUCTIONA.
RationaleItisestimatedthattheworldpopulationisprojectedtoreach9.
6billionpeopleinnextfewdecades(http://www.
wri.
org/blog/2013/12/global-food-challenge-explained-18-graphics).
Therefore,thechallengeishowtofeedthisgrowingpopulation,whileprotectingtheearth'senvironment.
Traditionalplantbreedingmethodsforplantimprovementmaybecombinedwithnext-generationanalysismethods,includingthehigh-throughputandautomatedscoringoftraitsandphenotypestodevelopimprovedvarieties.
Datafromhigh-throughputsequencing,transcriptomic,proteomic,phenomicandgenomeannotationprojectscanbelinkedtogermplasmresourcesthroughtheuseofinteroperable,referencevocabularies(ontologies).
Inthisway,theknowledgegainedfromthenext-generationdatacanbeutilizedforcropimprovement.
B.
WhatisthePlanteomeThePlanteomeProject(www.
planteome.
org)isacentralizedonlineinformaticsportalanddatabase,consistingofasuiteofreferenceontologiesforplants,anassociatedcorpusofplantgenomicsandphenomicsdata,andtoolsfordataanalysisandannotation.
Analysesofthesedatasetsfromgeneticandgenomicstudieshavethepotentialtoimproveourunderstandingofthemolecularbasisofeconomicallyrelevanttraits.
Inordertoutilizethisdata,researchersmustbeabletoconnecttherelevantplanttraitsofinteresttothespatialandtemporalexpressionpatternsofgenes,andelucidatetheirrolesinbiologicalprocessesinplants.
C.
GoalsofthePlanteomeProject:1.
Asuiteofinterrelatedreferenceontologiestodescribemajorknowledgedomainsofplantbiology,comprisingplantphenotypeandtraits,environments,andbioticandabioticstresses.
2.
Standards,workflowsandtoolsforannotationofplantgenomicsdata,andmetadataforcurationandimprovedannotationofgenes,genomes,phenotypeandgermplasm.
3.
ThePlanteomebrowseranddatabase,acentralized,onlineinformaticsportalandrepositorywherereferenceontologiesforplantsareusedtoaccessdataresourcesforplanttraits,phenotypes,diseases,geneexpressionandgeneticdiversitydataacrossawiderangeofplantspecies.
4.
OutreachinvolvingtheplantresearchcommunityandK-12andundergraduatestudents.
II.
THESCOPEOFTHEPLANTEOMEThescopeoftheontologiesinthePlanteomeprojectrangesfromabroadoverviewofplantenvironmentsandtaxonomy,tothecellularandmolecularlevelofexpressedgenesandtheirbiologicalfunctions.
ThePlanteomeontologies,describedinmoredetailbelow,consistofthePlantOntology(PO)[1-6],PlantTraitOntology(TO)[7,8],thePlantEnvironmentOntology(EO)[7]andthePlantStressOntology(PSO).
ThePlanteomeprojectimportsandintegrateswithrelevantreferenceontologiesdevelopedbycollaboratinggroups;theGeneOntology(GO)[9,10],thePhenotypicQualitiesOntology(PATO)[11],theEnvironmentOntology(ENVO)[12],andtheChemicalEntitiesofBiologicalInterest(ChEBI)[13].
Inaddition,thePlanteomeintegratesandmapsspecies-orclade-specificapplicationontologiesdevelopedbytheCropOntology(CO)project[14].
Togetherthissuiteofreferenceontologiescanbeusedtofullyannotateandlinktogetherthevitalplantknowledgedomain.
Thecentralreferenceontologyforplantanatomyandplantdevelopmentalstages,thePlantOntology(PO)[1-6]grewoutoftheneedtocreateassociationsbetweenstandardizedterminologyforplantsandgenomicsdata,andwasbasedtheworkdonetodeveloptheGeneOntologyinthelate1990s[9,10].
ThePOisrecognizedworldwideasthereferenceontologyforplantstructuresanddevelopmentalstages,andislinkedtodatafromawidevarietyofplants,fromtraditionalmodelspeciestothecropplantsthatfeedtheworld'sgrowingpopulation.
Plantimprovementreliesonanalysesofplanttraitsandphenotypes.
Forthesepurposes,thePlantTraitOntology(TO)[9,10]describesawiderangeofprecomposedplanttraitsconsistentwithEntity(E)-Quality(Q)statementsandleadstoanunderstandingofthemolecularprocessesthatunderliethem.
Eachtraitisameasurableorobservablecharacteristicofaplantstructure(PO:000901),aplantcellularcomponent(GO:0005575),oraplantstructuredevelopmentstage(PO:0009012),aswellasplantbiologicalprocesses(GO:0008150)andmolecularfunctions(GO:0003674).
TheTOencompassesninebroad,upper-levelcategoriesofplanttraits:biochemicaltrait(TO:0000277),biologicalprocesstrait(TO:0000283),plantgrowthanddevelopmenttrait(TO:0000357),plantmorphologytrait(TO:0000017),qualitytrait(TO:0000597),statureorvigortrait(TO:0000133),sterilityorfertilitytrait(TO:0000392),stresstrait(TO:0000164)andyieldtrait(TO:0000371).
ThePlantEnvironmentOntology(EO)isusedtodescribetheplantgrowthconditionsandstudytypesandcanbecombinedwiththetermsfromtheotherreferenceontologiestofullyannotateaplantphenotypedescription.
Inadditiontothereferenceontologies,thePlanteomeworkscloselywithdevelopersofthespecies-specificvocabulariessuchastheCropOntology[14]tointegratetheirterms,createmappingstothereferenceontologiesandlinkphenotypesandgermplasmtogenomicsresources.
III.
DEVELOPMENTOFTHEPLANTEOMEONTOLOGYNETWORKThedevelopmentofthePlanteomeProjectontologynetworkisafundamentalchangeinthewayofthinkingaboutontologiesforplants.
Inthepreviousproject,thePlantOntology(http://www.
plantontology.
org/),asinglereferenceontologywasdevelopedandusedtoannotateplantgenomicdatatoontologytermsdescribingplantstructuresandplantdevelopmentalstages.
Theadditionoftheotherreferenceandspecies-specifcontologiesforplantsenrichestheannotationenvironmentsoamorecompletepictureofthemetadataofplantpheotypescanbeexpressed.
Inordertocreatethenetwork,ontologytermsintheTOandthespecies-specifccroptraitontologieshavebeen'decomposed'intothecorrespondingEntity(E)-Quality(Q)statementswhichutilizetermsfromtheotherreferenceontologies,suchasPOandGOfortheentitiesandPATOforthequalities.
Inthisway,anetworkisformedwhichlinksallthevariousontologiestogether.
Oneofthelessonslearnedindevelopingthisnetworkisthatsomeofthereferenceontologiesandvocabulariesdevelopedbyourcollaborators(suchasChEBI,andtheNCBITaxonomy)aresolargethattheyarecumbersometodisplayonourbrowser.
Forthese,wehavedevelopedscripttoextractarelevant"slim"versionwhichcontainstheneededterms.
IV.
PLANTEOMEANNOTATIONDATABASEThePlanteomedatabaseprovidesontologytermsanddefinitionsalongwiththeassociated'annotations'[15],betweentheontologytermsanddatasourcedfromnumerousplantgenomicsdatasets.
ThePlanteome1.
0BetaRelease(Nov.
2015)containsabout47millionannotationslinkingreferenceontologytermstodataobjectsrepresentinggenes,genemodels,proteins,RNAs,germplasmandquantitativetraitloci(QTLs)from87differentplantspecies.
Thesedataarecurrentlycontributedby29differentdatasources.
Planteomecuratorsandresearchersatvariouscollaboratingdatabasegroupsworkcloselytodeveloptheannotationfilesinthestandardizeddataformatdatabase.
Thedatabaseisaccessibleonline(http://planteome.
org/)andalsoavailableforbulkdownload(http://palea.
cgrb.
oregonstate.
edu/viewsvn/associations/).
TheannotationdatabaseincludesfunctionalGeneOntologyannotationsfor60species.
Thesepredictionsweredoneusingtwomethods.
ThefirstmethodutilizedanInterProScan[16]toidentifyproteindomains.
TheresultinganalysisfileswerethenparsedtoassociatetheproteindomainstoGOterms.
ThesecondmethodwastoprojectontologyannotationsbasedonFig.
1.
AnnotationofRicebrd1mutantwithreferenceontologytermstocapturethephenotype.
Thericeplantimageisadaptedwithpermissionfrom[19]JohnWileyandSons.
orthologytoArabidopsisthalianagenes.
OrthologywaspredictedwithInParanoid[17],aprogramthattakesreciprocalBLASToutputandusespairwisesimilarityscorestodetermineorthologousclustersofgenes.
Thisisfollowedbycreatinggenesuperclustersbypoolingspecies-pairclusterswithcommongenes.
Theorthologoussuperclustersofthe60specieswerecomparedwiththeknownannotationfilesforArabidopsisthalianaforGO,andnewannotationfilesweregenerated.
PlanteomeistheonlyonlinesourceprovidingGOfunctionalannotationofgenesidentifiedformanyofthesespecies.
V.
CASESTUDYEXAMPLE:PHENOTYPEANNOTATIONOFRICEBRASSINOSTEROID(BR)-DEFICIENTDWARFMUTANTBrassinosteroid(BR)-deficient(brd1)dwarfmutantsofricewerecharacterizedtodeterminetherolesthatBRsplayinnormalplantgrowthanddevelopmentinamonocotplant[19].
Fig.
1showsanexampleofhowthereferenceontologiescanbeusedtoannotatethephenotypeofa(BR)-Deficientdwarfmutantrice,brd1-1.
ThisimageisacompliationofontologytermsfromvariousPlanteomereferenceontologiesthathavebeenusedtoannotatetheexpressionofbrd1(Os03g0602300)inthePlanteomedatabase.
Theseannotationswerecontributedfromavarietyofsources,suchasGramene(http://www.
gramene.
org/),EnsemblPlants(http://plants.
ensembl.
org/index.
html),andTheRiceAnnotationProject(RAP)(http://rapdb.
dna.
affrc.
go.
jp/)andcanbeusedtodescribeallaspectsofthebrd1mutantphenotype.
GatheringtheannotationstogetherinaunifiedplatformsuchasthePlanteomeallowsthedatatobemadeaccessibleandfacilitatesgenediscoverythroughinter-andintra-speciescomparisons.
VI.
PLANTEOMETOOLSFORCOLLABORATIONANDONTOLOGYINTEGRATIONThePlanteomeprojectisdevelopinganumberoftoolstoincreaseaccesstotheontologytermsandtoincreasetheinteroperabilityoftheannotateddata.
AllthePlanteomeontologiesarepublicallyavailableandaremaintainedatthePlanteomeGitHubsite(https://github.
com/Planteome)forsharingandtrackingrevsions.
Thissitefacilitatescommunityfeedback;userscanmakecomments,requesttermsandsuggestchangestothePlanteomeontologies.
Inaddition,thePlanteomeGitHubsitealsofeaturesspecies-specificvocabulariessuchasthosefromCropOntology(http://www.
cropontology.
org/).
AnothernewtoolwhichisunderdevelopmentisaTraitOntology-specific(http://to.
termgenie.
org/)instanceoftheTermGenietool[20].
TermGenieusesapattern-basedapproachtorapidlygeneratenewtermsandplacethemappropriatelywithintheontologystructure.
AlltermsarereviewedbyaPlanteomecuratorbeforethefinalcommittotheontology.
TermGeniecanbeusedtoquicklyobtainaTOtermforannotation,ifanappriopriateonedoesnotalreadyexist.
Planteomeisdevelopinganapplicationprogramminginterface(API)thatwillallowcollaboratorstoaccessandusethehosteddataintheirwebsitesandapplications.
ThefirsttwoAPImethods–currentlyaccessiblefromthePlanteomedevelopmentenvironment–queryPlanteome-hostedontologiesforterms,termdefinitions,andotherattributes,returningtheminJSONformat.
The"search"methodisfastenoughtobeusedinanautocompletesearchbox.
AllthePlanteomereferenceandspecies-specificontologiesareavailablethroughtheAPIservice.
Currently,theAPIonlyservestheterminformation,butthePlanteomeprojectplanstoaddAPImethodstoaccessannotationdata,aswell.
ThePlanteomeprojectiscollaboratingwiththeBisqueImageAnalysisEnvironment(CenterforBio-ImageInformatics,UCSB;http://www.
cyverse.
org/bisque)onintegratedimagesegmentationandontologyannotationfeatures.
ThePlanteomeprojectalreadyhostssuchatoolasadesktopapplication;AnnotationofImageSegmentswithOntologies(AISO;http://planteome.
org/node/3),butwewishtomoveitsfunctionalityonlineasamodulewithinBisque,takingadvantageofitssharedCyVerseauthentication,datastore,andcomputationinfrastructure.
Theontologydataitselfwillbeservedfromexternalservices,suchasthePlanteomeAPI.
VII.
CONCLUSIONSThePlanteomeprojectisacentralizedonlineplantinformaticsportalandwhichintegratesreferenceontologiesforplants,andspecies-specificcontrolledvocabularieswithalargeandgrowingcorpusofplantgenomicsdata.
Thisplatformprovidessemanticintegrationofwidelydiversedatasetswiththegoalofplantimprovement.
ACKNOWLEDGMENTFundingforthePlanteomeprojectisprovidedbytheNationalScienceFoundationawardIOS#1340112REFERENCES[1]Jaiswal,P,SAvraham,KIlic,EAKellogg,SMcCouch,APujar,etal.
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