2/3/2017 ResearchObjectsmyExperiment

ResearchObjects
FrommyExperiment

Contents
1ResearchObjects:TheBraindump
2FromWorkflowstoPacksonmyExperiment
3FromPackstoResearchObjects
4DefiningResearchObjects
4.1Replayablegobackandseewhathappened
4.2Repeatableruntheexperimentagain
4.3Reproduciblerunnewexperimenttoreproducetheresults
4.4Reusableuseaspartofnewexperiments
4.5Repurposeablereusethepiecesinanewexperiment
4.6Reliablerobustunderautomation

ResearchObjects:TheBraindump
DavidDeRoure,July2009

ThisisthemyExperimentstoryonResearchObjects.It'snottheonlytakeonthissubject!TheeLaboratory
groupshasbeenmeetingweekly,withrepresentativesofmyExperimentandmanyotherprojects,tobuildthe
biggerpicture.Thereareimportantmotivationscomingfromtheclinicaldomainandalsofromtheneedtohavea
commonobjecttoexchangebetweentheservicesthatmakeupeLaboratories.Wedon'taddressthesehere:thisis
ResearchObjectsaccordingtomyExperiment.

FromWorkflowstoPacksonmyExperiment
TheWeb2.0DesignPatterns(http://oreilly.com/web2/archive/whatisweb20.html)tellusthat"Dataisthenext
IntelInside",i.e.

Applicationsareincreasinglydatadriven.Therefore:Forcompetitiveadvantage,seektoowna
unique,hardtorecreatesourceofdata.

ThisremindsusthatthevaluepropositionofmanyWeb2sitesistheirexcellentsupportforonetypeofcontent.
Sowehavephotosonflickr(http://www.flickr.com),moviesonYouTube(http://www.youtube.com)andslideson
SlideShare(http://slideshare.net).And,whenwebeganmyExperiment,webecametheunique,hardtorecreate
sourceofscientificworkflowsspecificallyTaverna(http://taverna.org.uk)workflows.Weareproudtoholdthe
largestpubliccollectionofworkflowsavailable,andtohaveagrowingnumberofworkflowtypes,including
Microsoft'sTrident(http://www.microsoft.com/mscorp/tc/trident.mspx).

But,significantly,wealsorecognisedthataworkflowcanbeenrichedasasharableitembybundlingitwithsome
otherpieceswhichmakeupthe"experiment".Weobservethatresearchersdonotworkwithjustonecontenttype
andmoreoverthattheirdataisnotinjustoneplaceit'sdistributed,andsometimesquitemessytoo.Sowehave

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alsodevelopedsupportforpackscollectionsofitems,bothinsideandoutsidemyExperiment,whichcanbe
sharedasone.Ouruserinterfacemetaphorforpacksisfamiliarfromshoppingsiteslikeashoppingcartor
wishlist.

AnexcellentexampleofapackisPack55(http://www.myexperiment.org/packs/55),whichisPaulFisher'spack
forhistrypswork.Itcontainsworkflows,exampleinputandoutputdata,results,logs,PDFsofpapersandslides
asdepictedbelow.

Suchapackcapturesanexperiment,itcanbevalidated,it'sselfdescribedanditcanbeexportedwecouldsay
thatpacks"puttheexperimentintomyExperiment"!Thecollectionofpacksisgrowinginvarietyandnumber.For
examplethepackofallthepartsforapaper(http://www.myexperiment.org/packs/56)includesPaul'spack.There
arepacksofbenchmarkworkflows,packsofexampleworkflows,packsofpapersandslides.

FromPackstoResearchObjects
Aswehaveworkedwithourscientistsandresearcherswehavestudiedtheusecasesforpacksandwatchedhow
packsareactuallybeingused.Throughthiswehaverecognisedtheemergenceofanewformofdigitalobject
theResearchObject.Researchobjectsareanevolutionofpacksandprovidethesharable,reusabledigital
objectsthatenableresearchtoberecordedandreusedwhich,fundamentally,iswhatScienceandeResearch
involves.Infactitseemstousentirelylikelythat,inthefullnessoftime,objectssuchasthesewillreplace
academicpapersastheentitiesthatresearchersshare,becausetheyplugstraightintothetoolingofeResearch.It
isResearchObjectsratherthanpapersthatwillbecollectedinourrepositories.Aswellasaworkflowrepository,
myExperimenthasbecomeaprototypicalResearchObjectrepository.

ButwhatdotheseResearchObjectslooklike?Paulannotatedthepackwitharrowsandlabelsasshownbelow
thisisagoodexampleofwhatweneedinaResearchObject.

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AlsoDavidShottoninOxfordhasalsoprovidedanexcellentexampleofsemanticpublishing
(http://wiki.myexperiment.org/images/Shotton.png)whichcomesatthisfromtheotherendi.e.howdowe
augmentapaper.

Ourcurrentpackuserinterfacepermitsdescriptionsandcommentssothereisawayofexpressinginfreetextthe
relationshipofitemstoapack.Somedefactopracticesareemerging,suchashowpresentationsaredescribed.
Onepackcanbeincludedinanother.Butcurrentlywecan'treallyexpresstherelationshipsbetweenthingsin
packs,northerelationshipsbetweenpacksthemselves.Someofthoselabelswillbedomainspecificweare
implentingsupportforcontrolledvocabularies.Othersmaybemoregeneric,suchasbasicnotionsofprovenance.

Wehaveadatamodelwhichincludesworkflowsandpacksandwhichweareextendingtocapturethese
relationships.ObjectsfrommyExperimentcanbeobtainedinRDFfromrdf.myexperiment.org.Thedatamodel
usesamodularisedontologydesignedbyDavidNewmanwhichdrawsonDublinCore,FOAFandalsowithCarl
Lagoze'sOAIObjectReuseandExchange(http://www.openarchives.org/ore/)representation.We'reengagedwith
TimClark'sSWANSIOCwork(http://esw.w3.org/topic/HCLSIG/SWANSIOC),andalsowithLucMoreauand
hisOpenProvenanceModel(OPM)(http://openprovenance.org/)andYolandaGil'sproposedW3Cincubator
groupinprovenance.

Meanwhilewearealsogaining,fromourusers,asenseofwhatmakesagoodResearchObjectforexample,a
workflowcompletewithexampleinputandoutputdataprovidesameansofcheckingtheworkflowstilldoeswhat
itusedto(thankstoWernerMllerforhighlightingthisapproach).Onedayperhapswe'llhaveabarometertelling
youhowgoodyourResearchObjectis,likepasswordsecuritystrengthorfillingoutuserprofiles.

DefiningResearchObjects
TodefineaResearchObjectweneedtounderstanditscharacteristics.Weknowthattheyarefundamentallyabout
recordandreusewhichmeansrecordingresearchforanticipatedbutalsounanticipatedreuse,andthereinlines
thechallenge.

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We'veoccasionallyusedtheword"reproducible"inpresentations,andthereisaliteratureon"reproducible
research"(http://www.rrplanet.com/reproducibleresearchlibrum/viewtopic.php?f=30&t=77).WhenIwas
workingupmytalk(http://dl.getdropbox.com/u/1202407/Presentations/myExpESWC.ppt)forthepanelatESWC
2009(http://www.eswc2009.org/programmenu/panel)Itooktheprovocativepositionthatapaperisjustan
"archaichumanreadableformofaResearchObject",andthatinthefuturewewon'tsay"canIhaveacopyof
yourpaperplease"butrather"couldyousharethatresearchobjectwithmeplease?"TopresentthisIcreateda
slideofwordsbeginningwithR(infact,"Re.*")whichcharacterisebothfutureresearchandhenceaResearch
Object,andthishasevolvedthroughseveraltalks.

ThesearetheRsastheyarenow,onaWikipagesotheycancontinuetoevolveinpublic.Theyhavevariedin
numberbutsettleddownatsix:

Replayablegobackandseewhathappened

Experimentsareautomated.Theymighthappeninmillsecondsorinmonths.Eitherway,theabilitytoreplaythe
experiment,andtostudypartsofit,isessentialforhumanunderstandingofwhathappened.

Repeatableruntheexperimentagain

There'senoughinaResearchObjectfortheoriginalresearcherorotherstobeabletorepeattheexperiment,
perhapsyearslater,inordertoverifytheresultsorvalidatetheexperimentalenvironment.Andthescaleofdata
intensivesciencemeanslotsofrepetitionofprocessingtodealwiththedelugeofdataorindeedthedelugeof
methods.ResearchObjectsshouldhelpusscale.

Reproduciblerunnewexperimenttoreproducetheresults

Aseveryscientistknows,reproducibleisdifferenttorepeatable!Toreproduce(orreplicate)aresultisforsomeone
elsetostartwiththesamematerialsandmethodsandseeifapriorresultcanbeconfirmed.

Reusableuseaspartofnewexperiments

Oneexperimentmaycalluponanotheranexperimentmaybeusedinacontextotherthatthatinwhichitwas
originallyconceived.Byassemblingmethodsinthiswaywecanconductresearch,andaskresearchquestions,ata
higherlevel.Workflowsareagreatexample.

Repurposeablereusethepiecesinanewexperiment

Anexperimentwhichisablackboxisonlyreusaeableasablackbox.Byopeningthelidwefindparts,and
combinationsofparts,availableforreuse,andthewaytheyareassembledisacluetohowtheycanbereused.
Thismeanstheremustbeadequatedescriptioninsidethebox.Hencearesearchobjectisselfcontainedandself
describingitcontainsenoughmetadatatohavealltheabovecharacteristicsandforaeLabcomponentorservice
tomakesenseofit.(ComputerScientistshavean"Re"wordforthis"reflection",whichmeansyoucannotonly
runaResearchObjectlikeaprogrambutyoucanalsolookinsideitlikedata).

Reliablerobustunderautomation

Automationbringssystematicandunbiasedprocessing,andalso"unattendedexperiments"humanouttheloop.
Indataintensivescience,ResearchObjectspromotereliableexperiments,butalsotheymustbereliablefor
automatedrunning.

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