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COMMENTARYOpenAccessChemicaldatumentsasscientificenablersHenrySRzepaAbstractThisarticleisanattempttoconstructachemicaldatumentasameansofpresentinginsightsintochemicalphenomenainascientificjournal.
AnexplorationoftheinteractionspresentinasmallfragmentofduplexZ-DNAandthenatureofthecatalyticcentreofacarbon-dioxide/alkeneepoxidealternatingco-polymerisationispresentedinthisdatument,withexamplesoftheuseofthreesoftwaretools,onebasedonJava,theothertwousingJavascriptandHTML5technologies.
Theimplicationsfortheevolutionofscientificjournalsarediscussed.
BackgroundChemicalsciencesareoftenconsideredtostandatthecrossroadsofpathstomanydisciplines,includingmo-lecularandlifesciences,materialsandpolymersciences,physics,mathematicalandcomputersciences.
Asare-searchdiscipline,chemistryhasitselfevolvedoverthelastfewdecadestofocusitsmetaphoricalmicroscopeonbothfarlargerandmorecomplexmolecularsystemsthanpreviouslyattempted,aswellasuncoveringafarmoresubtleunderstandingofthequantummechanicalunderpinningsofeventhesmallestofmolecules.
Boththeseextremes,andeverythinginbetween,relyheavilyondata.
Datainturnisoftenpresentedintheformofvisualortemporalmodelsthatareconstructedtoillus-tratemolecularbehaviourandthescientificsemantics.
Inthepresentarticle,Iarguethatthemechanismsforsharingboththeunderlyingdata,andthe(semantic)modelsbetweenscientistsneedtoevolveinparallelwiththeincreasingcomplexityofthesemodels.
Putsimply,themainexchangemechanism,thescientificjournal,isaccepted[1]asseriouslylaggingbehindinitsfitnessforpurpose.
Itisinurgentneedofreinvention;oneexperi-mentinsuchwaspresentedasadata-richchemicalexploratorium[2].
Mycasehereinthisarticlewillbebasedonmyrecentresearchexperiencesintwospecificareas.
ThefirstinvolvesadetailedanalysisoftheinnerkerneloftheZ-DNAduplexusingmoderntechniquesforinterpretingtheelectronicpropertiesofamolecule.
Thesecondrecountstheexperienceslearntfrommodel-lingthecatalysedalternatingco-polymerisationofanal-keneepoxideandcarbondioxide.
Anattemptwillherebemadetopresentbothstoriesintheformofachemicaldatument.
Thisportmanteauwordreferstoadata-richdocument,andisusedheretomeanadocumentthatdescribesastoryofchemicalre-searchinamannerwhichallowsthedataunderpinningthediscoursetobeprovidedasanintegralpartofthatstory.
Althoughthetermdatumentwasoriginallyexpli-citlycoinedinascientificcontextin2004[3],arguablythefirsttruedatumentonthetopicofmolecularsciencewaspublishedinamainstreampeer-reviewedchemistryjournalhadappearedasearlyas2001[4].
Thislatterart-iclehasseveralunusualattributes.
Itattractedaneditor-ialcomment[5]thatdescribesthearticleasan"interestingexperiment",butwhichalsoconcludesthat"itwasn'teasytodealwithbyanymeans",referringtotheproductionprocess.
Inthissense,thisarticlewasalsoarguablyaheadofitstime,sinceitrequiredanearlybetaversionofaWebbrowsertoexposetheavailabledatatothereader(InternetExplorer6.
0or6.
5)usingacombinationofXMLasthecarrierofthedata/contentandXSLTstylesheetstotransformthisforbrowserpres-entation.
Modernbrowserssupportnewerversionsofthestandardsusedfortheseoperationsandsome11yearson,theoriginalarticlenowneeds"maintenance"torecovertheseaspects.
Butnevertheless,thedatacon-tainedwithit,expressedinXMLandCML[6]astheprinciplecarrierofchemicalinformationretainsallofitsoriginalsemanticmeanings,anditisspecificallythepresentationallayerthatrequiresthemaintenance.
Thisofitselfraisessomeinterestingissueswhichwillneedtobeaddressedinthefuture.
Inturn,itmayalsomeanthatthepresentationalmechanismsusedinthecurrentarticlemayequallyneedcurationinthefuture.
Inthelast11yearsnevertheless,mademajoradvancesinthisCorrespondence:rzepa@imperial.
ac.
ukDepartmentofChemistry,ImperialCollegeLondon,SouthKensingtonCampus,London,UK2012Rzepa;licenseeChemistryCentralLtd.
ThisisanOpenAccessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense(http://creativecommons.
org/licenses/by/2.
0),whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited.
RzepaJournalofCheminformatics2012,5:6http://www.
jcheminf.
com/content/5/1/6areaofsemanticscientificpublishinghavebeenmade,andthereaderisreferredtoseveralexcellentreviewsofthisareaforfurtherinformation[7,8].
Case1.
TheinnersecretsofthestructureofZ-DNAInapreviousarticleonthetopic[9],IrecountedhowearlypapersdescribingthemolecularstructureoftheDNAdouble-helixwerequitedata-impoverished.
Theissuerelatedtowhythismoleculeadoptedaleftorrighthandedhelicalwindandwhatthefactorsinfluencingthisbalancemighthavebeen.
Toanalysethesefeaturesrequiresevaluatingthewavefunctionofa(smallfrag-ment)ofthesystem.
Thisistheninspectedfornotonlytheelectronicinteractionsbetweencovalentbondsthemselvesbutalsothenatureofanyclose(non-cova-lent)contactsbetweenpairsofatomswhichdonotclas-sifyasbondsorappearinabondconnectiontable(andarethereforeun-indexedandhenceneglected)[2].
Twoanalyticaltoolswereutilisedandtheresultsarepresentedhere.
1.
Thefirstwasaso-calledNatural-bond-orbitalanalysis[10,11],thebasisofwhichistotransformthecomputedwavefunctionofthemoleculeintolocalisedfunctionscalledNBOs,whichtaketwobasicforms.
Thefirsthasatwo-electronoccupancy,andisdeemedtobeapotentialdonorofthesetwoelectrons(BD).
ThesecondisanNBOwithzero-electronoccupancy,andwhichisdeemedtobeanacceptorofelectrons(BD*).
TheextenttowhichthelatterinfluencestheformerisquantifiedbyaperturbationenergyE(2).
ThemagnitudeofthisterminturndependsonboththedifferenceinenergybetweenthetwointeractingNBOsandthedegreeofoverlapbetweenthem.
Whilsttheformercanbeexpressedsimplybyanenergy,thelatterlendsitselftovisualpresentationasasetofoverlappingiso-surfaces.
2.
TheNBOprocedure,bydefinition,exploreshowbondsBDinteractwithanti-bonds,BD*,withinamolecule.
Butalmostasimportantaretheregionswhichconventionallyarenotdefinedasbonds,butareinsteadreferredtoasnon-covalentinteractionswithinamolecule.
Ahydrogenbondisoneexampleofthistype,buttheycanalsorefertoweakerinteractions.
Itisimportanttoappreciatethatalthoughanysinglesuchinteractionmaybequiteweak,repeatedoccurrenceinalargemoleculewilltendtoaccumulatetheeffect.
ThisNCIprocedure[12-14]involvescomputingthereduced(electron)densitygradientisosurfacesforthemoleculeinquestion,andfilteringtherangeofthisvaluetothatwhichfocusesonlyontheweaklyinteractingregions.
Afurtherproperty(thedensityLaplacian)canbeusedinconjunctionwithcolourcodingoftheisosurfacetoindicatewhethertheinteractionisattractiveorrepulsive.
Again,thisisacomplexvisualsurfacegeneratedfromacomputedmolecularwavefunction.
Youmightappreciatethatcommunicatingthesecon-ceptstothereaderusingmerelydescriptivetextandstaticdiagrams(eventheuseofcolourbyauthorsindiagramscanincurverysubstantial/additionalcostschargedbythepublisher)maybeverylimiting.
Ofcourse,Ihavealsoselectedthisexampleforpreciselysuchdifficulty,andtointroducehowadatumentmightgoalongwaytowardsaddressingthisproblem.
Case2.
Unravellingthemechanismofco-polymerisationsOptimisingtheeffectiveuseofcarbondioxideasaC1feedstockformanufacturingpolymersisapressingsci-entificchallenge[15].
Theanswerliesinunderstandingthecomplexcatalyticchemistriesofquitelargemolecu-larsystems.
Thesechemistriescanincreasinglybesuc-cessfullymodelledusingmodernquantumchemicaltheories.
Thecapabilitytoaddressthesecomplexcata-lyticsystemsfirstemergedaround2002when,insome-thingofatour-de-forceforthatperiod,Morokumaandco-workersreportedtheirexplorationofthemechanismofZinc(II)-catalysedalternatingco-polymerisationofcarbondioxidewithcyclohexeneepoxide[16].
Theob-jectivethenwastodeveloparationalexplanationforwhythepolymeralternated,i.
e.
byadditionofonemol-eculeofcarbondioxidemonomerwasinvariablyfol-lowedbyonemoleculeofcyclohexeneepoxide,andthenagainbyCO2.
By2012thecomplexityandsubtlenatureofthechallengehadincreased,thechallengenowbeinganunderstanding[17]ofhowasymmetricinduc-tionintheresultingpolymercanbeachieved.
Answer-ingsuchquestionsinvolvesadetailedandintricateknowledgeofthereacting(covalentorionic)bondsthemselvesand(aswiththeDNAprojectdiscussedabove)thenatureofthenon-covalentinteractions[12-14].
Themodelonebuildstoexploresuchaspectsmaycontainupto200atoms(inapolymerofcourse,itispotentiallymuchlarger,andonehastotruncatethemodeltomangeableproportions).
Twoexamplesofthiscomplexityareshownbelow(Figures1and2).
Firstly,Ishouldstatethatthisarticleistypicaloftheperiod(ameretenyearsago),wherebylimitationsonthepagelengthprecludedinclusionofanytablesofcoordinates(=data)associatedwiththisfigure.
Seekingtoexploretheattributesofthebondsandappropriatenon-covalentinteractionsrequiresdata.
Itwashoweverreasonablycommoninthatperiod,butcertainlynotmandatory,forsuchdatatobeincludedinthesupport-inginformation(noteitisstyledasinformation,notRzepaJournalofCheminformatics2012,5:6Page2of11http://www.
jcheminf.
com/content/5/1/6data).
Inthisparticularinstance,nosuchinformationisactuallyavailable.
Evenin2011whenanotherarticleonthistopicwaspublished[18],andforwhichsupportinginformationwasavailable,onefindsapaucityofthetypeofdatarequiredtoreconstituteanyofthemodelsonwhichalltheassertionsinthebodyofthearticlearebased.
Unliketheareaofcrystallography,wheredatade-positionismandatory[19],nosuchrequirementsexistformanyotherareasofdata-richchemistry,includinge.
g.
forcomputationalchemistry.
Thefiguresthemselves(Figure1)containinformationthatonlyahumancouldattributemeaningto(thefigurescouldnotforexamplebeautomaticallyminedforinformationinthemannerthategtheOSCARpro-ject[20]hasdemonstrated).
Eventhisauthor(asahuman),struggledtoreconstituteausablemodelfromthesefigures.
Thereisindeedsomenumericalinforma-tionassociated(notethattextminingsoftwarecannotaccessthisinformation)withthefigure,styledinlight-faceandboldface(eachbeingtheresultofusingadiffer-enttheoreticalmethod,asexplainedintheoriginalfigurecaption).
butforasystemwithperhaps100atoms(countingtheactualnumberfromthefigureisessen-tiallyimpossible),thisrepresentsonly7ofthe294(=3N-6)variablesrequiredtopreciselydefinethethreedimensionalmodel.
Otherannotationsarepresentinthefigure;thedesignationback-sideorfront-sideattackhaveasemanticmeaningthatisnotimmediatelyobvioustosomeonenotveryfamiliarwiththeoriginalresearch.
Oneofthediagrams(Figure2)haslinescarryingarrow-heads,theother(Figure1)doesnot.
Althoughnotexplainedinthefigurecaption,anexperienced(human)computationalchemistcanneverthelessinfertheseman-ticsthatthesearenormalvibrationalmodedisplacementvectors.
Furthermoreitislikelythatthisparticularmodeisselectedbecauseitrepresentsthevibrationfor(har-monic)motionoftheatomsatthetransitionstateforthereaction.
Thesevectorsmayormaynotbemass-weighted,sotheirlengthmaycarrynosignificance.
Onemightassociatethisfeaturewiththe(non-minable)textbelowitindicatingthatthe(imaginary)wavenumberofthismodeis61.
8icm-1.
Onemightinferthatthedia-graminwhichsuchvectorsareabsent(Figure1)isnotatransitionstate,butanequilibriumstructureinwhichallthenormalmodesarerealandnotimaginary.
Thatisalotofimplicitsemantics,whicha(trained)humancancopewith,butwhichagainamachineisunlikelyto.
Ihavegoneintothisonefigureinsomedetail,notatalltocriticisetheauthorsforprovidingadeficientfigure,buttoillustratetheextenttowhichthedatafromwhichthemodelcanbebuiltislacking,togetherwiththesemanticsneededtoputthatdatatogooduse.
Theprecedinganalysisofthesearticles[16,17,20]origi-natedasanoutcomeoftheexplorationofthemechanismofthisreaction[15].
Inordertocomparenewmodelswiththeearlierones,itwasessentialtoanalysetheinformationcarriedinFigures1and2,inparticularwhetherthesys-temshowninthesefiguresrepresentedamonoorabi-metallicsystem.
Becauseoftheparticularprojectionontotwodimensionsusedinthepublishedfigures,itwasnotpossibletoestablishwithabsolutecertaintywhetherasec-ondZnatommightbepresent,butbeobscuredintheFigure1Modelformetalcatalysedco-polymerisationofepoxideandcarbondioxideshowinganintermediateinthemechanism.
Figure2Modelformetalcatalysedco-polymerisationofepoxideandcarbondioxideshowingatransitionstateinthemechanism.
RzepaJournalofCheminformatics2012,5:6Page3of11http://www.
jcheminf.
com/content/5/1/6figure.
Afteraboutanhourofsuchanalysis,akey(seman-tic)connectionwasmade,therealisationthatbimetallicmodelshadonlybeenexplicitlydiscussedintheliteraturefromtheyear2003onwards.
Fromthischronology,itwaspossibletoconcludethatitwasprobablethatthe2002modeldidnotrepresentabimetallicsystem.
Unfortu-nately,therewerenodatapresentedintheformofatomlistswhichwouldhaveinstantlyclarifiedthisaspect.
DiscussionWhenitcametocommunicatingourownresearchesonthesetopics[15],itwasimperativethatweshouldexplorehowtonotpropagatethedifficultiesweourselveshadexperiencedwiththeearlierliteratureontofuturereadersofourownarticle.
Howcouldtheappropriatedata(andsemantics)beincorporatedintoajournalarticlein2012Onepublisherisalreadymakingavirtueofthisaspectinadvertisingthe-article-of-the-future[21].
Thesearticlesfeaturedata-basedcomponentssuchascompoundinfor-mation,experimentalflowchartsandembeddedvideo(althoughpotentiallydatarich,thisdatacanoftenbeinaccessibleinthesamesensethatwasdiscussedforFigures1and2.
Ananimationforexamplecanonlybeviewedfromtheauthor'spredeterminedviewpoint,andnotfromthereader's).
Atthetimeofwriting,therearenoexamplesofarticles-of-the-future[21]suitablefordescrib-ingthetypeofresearchdiscussedabove.
Infact,wehadstartedanexplorationin2006[22]ofdata-richarticleswhichcontainedso-calledweb-enhancedobjects(tablesandfigures)inconjunctionwithotherpublishers[23].
Theseconstitutedatumentsinthesensethatnotonlycanahumaneasilyre-usethedatacarriedinsuchanarticle,butintheorysocoulda(muchmorepedantic)softwareagenttaskedtominethedata.
SuchminingisfacilitatedbyusingXHTMLtoexpressthedatument(PDFversionsofthearticleswerealsomadeavailablebythepublisher,butthesemanticdata-enrichmentisnotpresentintheseversions).
Thesearticleshoweverwerenotoptimisedfortheirsemanticattributes.
Our2001datument[4]wasexpressedentirelyinXML,andpresentedtothereaderbyanon-the-flytransformationofthatXMLusingappropri-ateXSLTstylesheets.
Our2006+web-enhancedfiguresandtablesacceptedthepracticalrealitythatpublisherswerenotyetreadytoacceptXML/XSLTsubmissions,aswellastheobservationthatveryfewauthorshadthetimeandskillstoauthordatumentsinthisformat.
ThedigitaldatarepositoryanddatasemanticsItisimportanttodistinguishbetweendataandthewrapperbywhichitispresentedtothe(human)reader.
Thereareseveralconsiderations.
1.
Therawunprocesseddatamaybetoolargetoreasonablyincludeinadatument.
2.
Oritmaytakealotofprocessingpower,orrequirecomplexcomputercode,totransformthedataintoameaningfulvisualappearance.
3.
Therawdatamayhavenometa-dataassociatedwithit,andhencemaynotbesemanticallyprocessableorsearchable.
Theexpedientadoptedhereistoincludeatleastsuffi-cientwell-structured(i.
e.
XML-based)datatoallowre-generationoftheoriginal(large)datasetwithalmostnoeffortrequiredtoachievethis.
Ifthetransformationofthedataforvisualpresentationisitselftoocomplextobehandledbyabrowserinreal-time,thentheresultofthattransformcanitselfbeincludedinthedatument(againideallyasanXMLdataset).
Finally,tocompletetheutilityofthedatument,the(possiblylarge)inputsandoutputsfromwhichthedatasetderivescanbelinkedtoadigitalrepositorywherethesemanticenrich-mentcanbeaddedinalargelyautomaticmanner.
Thisinturnwouldalloweitherhumansorsoftwareagentstoprocessthemifdesired.
Examplesofdigitalrepositoriescontainingmoleculardata1.
TheDSpace-basedSPECTRarepository[24].
Eachentryhereiscreatedfromrawdatafiles,andthemetadataisaddedbypost-processedrecognitionofregularpatternsinthedata,alongwithmeta-datacapturedfromtheuserorsystemattimeofdeposition.
Theresultingdata-collectionisidentifiedwithauniquehandle,whichcanberesolvedbythesameresourceasthedigitalobjectidentifier(DOI)nowubiquitouslyusedinjournalarticlessuchastheoneyouarecurrentreading.
Atypicalsetofmeta-dataandrawdataforthetypeofcalculationreportedinthisarticlecanbeseeninFigure3.
TherawfilesthemselvesareassociatedwithappropriateMIMEtypes[25]toenableautomatedprocessingwhendownloaded.
Theentirecollectioniscreatedautomaticallyfromthejobsubmissionportalusedtocreatethedatainthefirstplace,ensuringitisasfreeofhumanerroraspossible.
Theuniquemoleculeidentifiers(theInChIKey)arecapturedasassignedtoDublin-corefields,andcanalsoservewellasnodesinanRDFdescription[26],althoughDspaceitselfcannotbeusedtoinvokeasemanticquerybasedonsuchRDFdeclarations.
2.
Figshare[27]isanew,moregeneraldatarepository,carryingmuchthesamemeta-dataastheDSpaceexample(Figure4).
IttooassociatesaDOIwiththedataset,andcanbeusedinthesamemanner.
3.
ChemPound[28]wasdesignedspecificallytoarchivechemicalinformation,andgeneratesmeta-dataforRDFdeclarationatamuchmorefinelygrainedlevel.
RzepaJournalofCheminformatics2012,5:6Page4of11http://www.
jcheminf.
com/content/5/1/6Forexample,thefinaltotalenergyinaquantummechanicalcalculationisidentifiedandassociatedwithanRDFtriple.
ThechempoundrepositoryisalsotheonlyonespecificallydesignedforRDF-SPARQLlikesemanticqueriesofthetriplestore.
Unlikethefirsttworepositorieshowever,Chempounddoesnot(yet)generateauniquehandleforidentificationofeachentry.
ExamplesofdigitalrepositoriescontainingothertypesofdataExamplesofotherprojectsfordepositingandcuratingdataincludeDataOne[29],Dryad[30](anotherDSpace-basedrepository),DataCite[31](whichalsoprovidesDOIidentifiersforeachcollection)andDataShare(anonlinedigitalrepositoryofmulti-disciplinaryresearchdatasetsproducedattheUniversityofEdinburgh)[32].
Therearealsoseparateinitiativesfordevelopingstan-dardsforthedepositionandsearchingofdata[33].
Itisbecomingclearthatsuchrepositoriesarebifurcatingintotwotypes;thoseforgeneraldatathatcarryonlygeneralmeta-datadescriptorsforthecontent,andsubject-specificrepositorieswhichservetoharvestmuchmorefinelytunedmeta-data,inturnallowingmuchmorespecificsearchesoftherepositorytobemade.
Ifthefragmentationintoincreasinglysubject-specificcontentcontinues,thenthechallengewillrefocusonsearchingacrossdifferentrepositoriesforrelateddatasetsbetweenwhichtheremaybevaluablesynergies.
Twoexamplesofhowsuchastrategymaybedeployedarediscussednext.
TheJava-baseddatumentTransclusionof(chemical)data-objectsintoHTMLpagesforhumanstoreadhasevolvedinthreephases.
Oneoftheearliestwasintroducedaround1996andbene-fitedfromtheclosephysicalproximityinSanFranciscooftwocommercialorganisations,NetscapeandMDLLtdandtheearlierpublicationofanarticleonthetopic[34].
Thereaderhadtodownloadthesoftware(Chime)andinstalliteachcomputertheywishedtouse.
ThiswasreplacedafewyearslaterbytheuseofJava,wherebythenecessarysoftwarearchive(.
jar)isdownloadedautomaticallywhenthedata-objectisloaded.
ThismodeisusedtoFigure3AdatarepositoryentryinDSpace,showingassociatedchemicalmetadata.
Theoriginalcanberetrievedathandle:10042/20199.
RzepaJournalofCheminformatics2012,5:6Page5of11http://www.
jcheminf.
com/content/5/1/6thepresentdayonmostconventionaloperatingsys-temsandisillustratedbelow.
Itmakesuseofadigit-allysigned.
jarfile,whichallowsdatatobeextractedfromthedisplaybytheuser(hencetheprompttheuserreceivestoacceptthedatumentsourcewhenitisloaded).
AnexampleofthisisillustratedinAdditionalfile1:Interactivitybox1.
TheHTML5baseddatumentThismodeofpresentationtakesadvantageofthenewgenerationofmobiledevicessuchastouch-screentablets.
Italsopresentsastrategyforbrowseranddeviceindependence,sincetheredoesseemtobeatrendto-wardsincreasedadoptionofstandardscenteredaroundHTML5forbothbrowsersandthedevicestheyrunon.
Inthisregard,thedesignofmobiledevicesappearstobeevolvingawayfromdependencyonpower-consumingsoftwareenvironmentssuchasJava,andtowardsdata-handlingenvironmentssuchasJSON[35]andJava-script,utilisinglightweightgraphicsrenderingsbasedonWebGLincombinationwithHTML5thatcantakefulladvantageofsuchanenvironment.
AnadvantageoverFigure4AdatarepositoryentryinFigshare,showingassociatedchemicalmetadata.
Theoriginalcanberetrievedatdoi:10.
6084/m9.
figshare.
95816.
RzepaJournalofCheminformatics2012,5:6Page6of11http://www.
jcheminf.
com/content/5/1/6aJava-basedsolutionisthatthenecessarydisplaycodeismuchsmallerandrunsnativelywithinthebrowserra-therthanasaJavavirtualenvironment.
Twosuchimple-mentationsforHTML5areChemDoodle[36]andGLMol[37],forwhichexamplesofdifferenttypesoftranscludeddataAdditionalfiles2-4(InteractivityBoxes)areshownbelow[38].
Datacanalsobeflexiblyretrievedfromsuchobjects[39].
AcomparisonbetweenthestaticFigures1and2andthedata-richinteractivityboxesservestoillus-tratehowanenhancedperceptionbyreadercanbeachie-vedwhentheyareallowedtointeractwiththedatument.
TheauthoringperspectiveIshouldalsodescribetheexperienceofcreatingsuchfiguresfromanauthor'sperspective.
Thedata-carryingcomponentsareembeddedintheformofscripts,whichthemselvesarecanberegardedbytheauthoras(publisher-provided)templates,andtheonlyrealtaskistoprovideappropriatevariablenames.
1.
Additionalfile1:Interactivitybox1iscreatedusingascriptforadevice-sensitivedisplay,whichsupportseitheraJava-basedJmolapplet,oraJavascript-basedChemDoodlecanvas:Figure3=Jmol.
getApplet("Figure3",Info1)Jmol.
script(Figure3,"loaddna_mo148.
cub.
xyz;backgroundimage'helix-back.
jpg';spin5;#alt:LOADdna_mo148.
cub.
xyz")2.
ThelinksintheinteractivityboxofFigure3arecreatedas:(View/downloadmodel)3.
Additionalfile2:Interactivitybox2iscreatedusingjustaJavascript-basedChemDoodlecanvas;if(ChemDoodle.
RzepaJournalofCheminformatics2012,5:6Page7of11http://www.
jcheminf.
com/content/5/1/6RzepaJournalofCheminformatics2012,5:6Page8of11http://www.
jcheminf.
com/content/5/1/6featureDetection.
supports_webgl()){vartransformBallAndStick1=newChemDoodle.
TransformCanvas3D('transformBallAndStick1',550,450);transformBallAndStick1.
specs.
projectionWidthHeightRatio_3D=550/450;transformBallAndStick1.
specs.
set3DRepresentation('BallandStick');4.
TransformBallAndStick1.
specs.
backgroundColor='white';varmolFile=httpGet('datument.
mol');varmolecule=ChemDoodle.
readMOL(molFile,2);transformBallAndStick1.
loadMolecule(molecule);}else{document.
write('');}Theimportantvariablesintheabovearesimplythenamesofthedatafile(e.
g.
datument.
mol).
Otherimportantattributessuchasthesizeofthecanvasetc.
canbedefinedusinginformationarrays(e.
g.
Info1).
Suchscriptsareeasilywrappedintoe.
g.
HTML5componentssuchaswidgets(interactive,andpotentially3Dobjects),whichinturncanbeabsorbedintoauthoringenvironments(suchasiBooksauthor)[40]astranscludedobjects,acategorythatalsoincludestables,chartsandimagemedia.
Whilsttheaveragecompositorofascientificarticleiscurrentlywellacquaintedwiththelattertype,familiaritywiththeconceptofincludinge.
g.
adata-handlingwidgetmaywellbecomeaskillessentialtoauthoringthesciencearticleofthefuture.
Perhapsthemostrealisticstartingpointmightbetoen-courage(require)Ph.
D.
thesestobepreparedandexam-inedinsuchenhancedformats.
Certainlyitisincreasinglyarequirementimposedbyexaminerstohaveavailablethedataunderlyingthethesesindigita,easilyviewedform.
ItisalsobecomingacceptedthatthesescancontainDOIresol-verstopertinentdata-setssupportingtheresearchbeingexamined.
Theconversionofsuchmaterialintojournalarticlesmightnotthenappearachallenge.
ConclusionsTheeverincreasingmolecularcomplexityofmodernchemistrypresentsinterestingnewchallengesforhowtheunderlyingmodelsmaybestbesharedbetweenscientists.
Aresearchershouldnothavetousewhatmayamounttoinspiredguessworktoreconstitutesuchamodelfromajournalarticle.
HereIhavetakentwoexamplesofcomplexmolecularstructuresandbyem-beddingdescriptivedatawithinthisarticle,havecreatedaworkingtool,adatumentfortheresearcher.
Inotedearlierthatoneoftheissuesthatneedsaddressingiswhetherthenecessarytoolsfordoingsowouldbeac-cessiblefortheaveragescientificauthor.
Thisparticulardatumentwasinfactwrittenandassembledoveraperiodoftwodays,althoughseveralofitscomponentswerealreadyavailable(havingbeenpreparedaspartofteachingnotesonconformationalanalysisforlecturesRzepaJournalofCheminformatics2012,5:6Page9of11http://www.
jcheminf.
com/content/5/1/6deliveredbytheauthor).
Higherordertools(suchasAppleiBooksauthor[40])showhowsomeofthefunc-tionalityneededcouldbeabsorbedintoasimpletousetool.
Anothersourceofpublishabledatumentsmightcomefromthenewgenerationsofelectroniclaboratorynotebooksinchemistry,andthesearealsoincreasinglyinterfacingtodigitalrepositories.
Therearealsosignsthatafteralonginductionperiod,somepublishersarestartingtoadoptsuchtechnologiesforjournalpublication.
Buttherearealsodangers.
Forexample,willadatumentsimplycometobetreatedasarights-manageddocument,withboththefulltextandthedataardentlyprotectedbythepublisher'scommer-cialmodelWillsuchenrichedpublicationsresultinsig-nificantlymoreexpensivejournalsWillpublishersallowdatumentstobeminedfortheirdatabysoftwareagents[20]suchasOSCARAndcanadatumentbeappropri-atelycuratedtoensureaccessibilitylongintothefutureTheseareimportantissues,butwemustensurethatresolutionincludesactiveparticipationfromboththeauthorsofscientificdatumentsandtheirconsumers.
CompetinginterestsTheauthordeclaresthattheyhavenocompetinginterests.
AcknowledgementsIwouldliketoespeciallythankBobHanson,KevinTheisenandTakanoriNakaneforhelpfulassistancewithJmol(andtheassociatedscriptsfordevice-sensitivity)ChemDoodleandGLmolrespectivelyandtherefereesforhelpfulcomments.
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