cladewww.meansys

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.
,2005.
PlantOntology(PO):AControlledVocabularyofPlantStructuresandGrowthStages.
CompFunctGenomics,.
6(7--‐8):p.
388-97(references)[2]Pujar,A,PJaiswal,EAKellogg,KIlic,LVincent,SAvraham,etal.
2006.
Whole-‐plantgrowthstageontologyforangiospermsanditsapplicationinplantbiology.
PlantPhysiol,142(2):p.
414--‐28.
[3]Ilic,K,EAKellogg,PJaiswal,FZapata,PFStevens,LPVincent,etal.
,2007.
Theplantstructureontology,aunifiedvocabularyofanatomyandmorphologyofafloweringplant.
PlantPhysiol.
143(2):p.
587--‐599.
[4]Avraham,S,CWTung,KIlic,PJaiswal,EAKellogg,SMcCouch,etal.
,2008.
ThePlantOntologyDatabase:acommunityresourceforplantstructureanddevelopmentalstagescontrolledvocabularyandannotations.
NucleicAcidsRes.
,36(Databaseissue):p.
D449--‐54.
.
[5]CooperL,WallsRL,ElserJ,GandolfoMA,StevensonDW,SmithB,etal.
(2013)ThePlantOntologyasatoolforcomparativeplantanatomyandgenomicanalyses.
PlantandCellPhysiology54:e1–e1[6]CooperLandJaiswalP(2016)ThePlantOntology:AToolforPlantGenomics.
InDEdwards,ed,PlantBioinformatics.
SpringerNewYork,pp89–114[7]JaiswalP,WareD,NiJ,ChangK,ZhaoW,SchmidtS,etal.
(2002)Gramene:developmentandintegrationoftraitandgeneontologiesforrice.
ComparativeandFunctionalGenomics3:132–136.
[8]ArnaudE,CooperL,ShresthaR,MendaN,NelsonRT,MatteisL,etal.
(2012)TowardsareferencePlantTraitOntologyformodelingknowledgeofplanttraitsandphenotypes.
ProceedingsoftheInternationalConferenceonKnowledgeEngineeringandOntologyDevelopment.
Barcelona,Spain,pp220–225.
[9]AshburnerM,BallCA,BlakeJA,BotsteinD,ButlerH,CherryJM,etal.
(2000)GeneOntology:toolfortheunificationofbiology.
NatGenet25:25–29.
[10]TheGeneOntologyConsortium(2014)GeneOntologyConsortium:goingforward.
NucleicAcidsResearch.
doi:10.
1093/nar/gku1179.
[11]GkoutosG,GreenE,MallonA-M,HancockJ,DavidsonD(2004)Usingontologiestodescribemousephenotypes.
GenomeBiol6:R8[12]ButtigiegP,MorrisonN,SmithB,MungallC,LewisS(2013)Theenvironmentontology:contextualisingbiologicalandbiomedicalentities.
JournalofBiomedicalSemantics4:43[13]HastingsJ,OwenG,DekkerA,EnnisM,KaleN,MuthukrishnanV,etal.
(2016)ChEBIin2016:Improvedservicesandanexpandingcollectionofmetabolites.
NucleicAcidsResearch44:D1214–D1219[14]Shrestha,R,Davenport,GFBruskiewich,R,Arnaud,E.
(2011)Developmentofcropontologyforsharingcropphenotypicinformation.
Droughtphenotypingincrops:fromtheorytopractice.
pp171–179[15]HillDP,SmithB,McAndrews-HillMS,BlakeJ(2008)GeneOntologyannotations:whattheymeanandwheretheycomefrom.
BMCBioinformatics9:S2[16]QuevillonE,SilventoinenV,PillaiS,etal.
2005.
InterProScan:proteindomainsidentifier.
NucleicAcidsResearch.
33(WebServerissue):W116-W120.
doi:10.
1093/nar/gki442.
[17]RemmM,StormCEVandSonnhammerELL(2001).
AutomaticClusteringofOrthologsandIn-paralogsfromPairwiseSpeciesComparisons.
JMB,314:1041-1052.
[18]Altschul,SF,Madden,TL,Schffer,AA,Zhang,J,Zhang,Z,Miller,W,etal.
(1997).
GappedBLASTandPSI-BLAST:anewgenerationofproteindatabasesearchprograms.
NucleicAcidsRes.
25:3389-3402.
[19]Hong,Z,Ueguchi-Tanaka,M,Shimizu-Sato,S,Inukai,Y,Fujioka,S,Shimada,Y,etal(2002)Loss-of-functionofaricebrassinosteroidbiosyntheticenzyme,C-6oxidase,preventstheorganizedarrangementandpolarelongationofcellsintheleavesandstem.
ThePlantJournal32:495–508[20]Dietze,H,Berardini,T,Foulger,R,Hill,D,Lomax,J,OsumiSutherland,D,RoncagliaP,MungallC(2014)TermGenie-Awebapplicationforpattern-basedontologyclassgeneration.
JournalofBiomedicalSemantics5:48[21]LingutlaN,PreeceJ,TodorovicS,CooperL,MooreL,JaiswalP(2014)AISO:AnnotationofImageSegmentswithOntologies.
JournalofBiomedicalSemantics5:50