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“solve”bigdataproblems.Although,muchofdatascienceinnovationfocusesonhardware,cloud computing,andnovelalgorithmstosolveBD2Kproblems,thecriticalissuesremainatthelevelof theutilityofthedata(eg,simplification)addressedinthisimportantbookbyBerman.

DataSimplification provideseasy,freesolutionstotheunintendedconsequencesofdatacomplexity.Thisbookshouldbethefirst(andprobablymostimportant)guidetosuccessinthedatasciences. Iwillbeprovidingcopiestomytrainees,programmers,analysts,andfaculty,asrequiredreading.

MichaelJ.Becich,MD,PhD

AssociateVice-ChancellorforInformaticsintheHealthSciences ChairmanandDistinguishedUniversityProfessor,DepartmentofBiomedicalInformatics Director,CenterforCommercialApplication(CCA)ofHealthcareData UniversityofPittsburghSchoolofMedicine

purposes,canbecreatedforasingledocumentordataset.Asdataaccrues,indexescanbe updated.Whendatasetsarecombined,theirrespectiveindexescanbemerged.Agoodwayofthinking aboutindexesisthatthedocumentcontainsallofthecomplexity;theindexcontainsallofthe simplicity.Datascientistswhounderstandhowtocreateanduseindexeswillbeinthebestposition tosearch,retrieve,andanalyzetextualdata.Methodsareprovidedforautomaticallycreatingcustomizedindexesdesignedforspecificanalyticpursuitsandforbindingindextermstostandard nomenclatures.

Chapter4,UnderstandingYourData,describeshowdatacanbequicklyassessed,priortoformal quantitativeanalysis,todevelopsomeinsightintowhatthedatameans.Afewsimplevisualization tricksandsimplestatisticaldescriptorscangreatlyenhanceadatascientist’sunderstandingofcomplex andlargedatasets.Varioustypesofdataobjects,suchastextfiles,images,andtime-seriesdata,canbe profiledwithasummarysignaturethatcapturesthekeyfeaturesthatcontributetothebehaviorand contentofthedataobject.Suchprofilescanbeusedtofindrelationshipsamongdifferentdataobjects, ortodeterminewhendataobjectsarenotcloselyrelatedtooneanother.

Chapter5,IdentifyingandDeidentifyingData,tacklesoneofthemostunder-appreciatedandleast understoodissuesindatascience.Measurements,annotations,properties,andclassesofinformationhave noinformationalmeaningunlesstheyareattachedtoanidentifierthatdistinguishesonedataobjectfrom allotherdataobjects,andthatlinkstogetheralloftheinformationthathasbeenorwillbeassociatedwith theidentifieddataobject.Themethodofidentificationandtheselectionofobjectsandclassestobeidentifiedrelatesfundamentallytotheorganizationalmodelofcomplexdata.Ifthesimplifyingstepofdata identificationisignoredorimplementedimproperly,datacannotbeshared,andconclusionsdrawnfrom thedatacannotbebelieved.Allwell-designedinformationsystemsare,attheirheart,identificationsystems:waysofnamingdataobjectssothattheycanberetrieved.Onlywell-identifieddatacanbeusefully deidentified.Thischapterdiscussesmethodsforidentifyingdataanddeidentifyingdata.

Chapter6,GivingMeaningtoData,exploresthemeaningofmeaning,asitappliestocomputer science.Weshalllearnthatdata,byitself,hasnomeaning.Itisthejobofthedatascientisttoassign meaningtodata,andthisisdonewithdataobjects,triples,andclassifications(seeGlossaryitems, Data object, Triple, Classification, Ontology).Unfortunately,courseworkintheinformationsciencesoften omitsdiscussionofthecriticalissueof"datameaning";advancingfromdatacollectiontodataanalysis withoutstoppingtodesigndataobjectswhoserelationshipstootherdataobjectsaredefinedanddiscoverable.Inthischapter,readerswilllearnhowtoprepareandclassifymeaningfuldata.

Chapter7,Object-OrientedData,showshowwecanunderstanddata,usingafewelegantcomputationalprinciples.Modernprogramminglanguages,particularlyobject-orientedprogramminglanguages,useintrospectivedata(ie,thedatawithwhichdataobjectsdescribethemselves)tomodify theexecutionofaprogramatrun-time;anelegantprocessknownasreflection.Usingintrospection andreflection,programscanintegratedataobjectswithrelateddataobjects.Theimplementations ofintrospection,reflectionandintegration,areamongthemostimportantachievementsinthefield ofcomputerscience.

Chapter8,ProblemSimplification,demonstratesthatitisjustasimportanttosimplifyproblemsas itistosimplifydata.Thisfinalchapterprovidessimplebutpowerfulmethodsforanalyzingdata,withoutresortingtoadvancedmathematicaltechniques.Theuseofrandomnumbergeneratorstosimulate thebehaviorofsystems,andtheapplicationofMonteCarlo,resampling,andpermutativemethodsto awidevarietyofcommonproblemsindataanalysis,willbediscussed.Theimportanceofdata reanalysis,followingpreliminaryanalysis,isemphasized.

case,itwouldbeimpossibletoproduceanyvalidresultsbasedonastudyofpatientsdiagnosedasMFH.The resultswouldbeabiasedandirreproduciblecacophonyofdatacollectedacrossdifferent,andundetermined, classesoftumors.Believeitornot,thisspecificexample,oftheblendedMFHclassoftumors,isselected fromthereal-lifeannalsoftumorbiology.30, 31 Theliteratureisrifewithresearchofdubiousquality,based onpoorlydesignedclassificationsandblendedclasses.Adetaileddiscussionofthistopicisfoundin Section6.5,PropertiesthatCrossMultipleClasses.Onecaveat.Effortstoeliminateclassblendingcan becounterproductiveifundertakenwithexcesszeal.Forexample,inanefforttoreduceclassblending, aresearchermaychoosegroupsofsubjectswhoareuniformwithrespecttoeveryknownobservableproperty.Forexample,supposeyouwanttoactuallycompareappleswithoranges.Toavoidclassblending,you mightwanttomakeverysurethatyourapplesdonotincludedanykumquats,orpersimmons.Youshouldbe certainthatyourorangesdonotincludeanylimesorgrapefruits.Imaginethatyougoevenfurther,choosing onlyapplesandorangesofonevariety(eg,Macintoshapplesandnaveloranges),size(eg10cm),andorigin (eg,California).Howwillyourcomparisonsapplytothevarietiesofapplesandorangesthatyouhaveexcludedfromyourstudy?Youmayactuallyreachconclusionsthatareinvalidandirreproducibleformore generalizedpopulationswithineachclass.Inthiscase,youhavesucceededineliminatedclassblending, attheexpenseoflosingrepresentativepopulationsoftheclasses.See Simpson’sparadox.

ChildClass Thedirectorfirstgenerationsubclassofaclass.Sometimesreferredtoasthedaughterclassor,less precisely,asthesubclass.See Parentclass.See Classification.

Class Aclassisagroupofobjectsthatshareasetofpropertiesthatdefinetheclassandthatdistinguishthemembersoftheclassfrommembersofotherclasses.Theword"class,"lowercase,isusedasageneralterm.The word"Class,"uppercase,followedbyanuppercasenoun(egClassAnimalia),representsaspecificclasswithin aformalclassification.See Classification Classification Asysteminwhicheveryobjectinaknowledgedomainisassignedtoaclasswithinahierarchyof classes.Thepropertiesofsuperclassesareinheritedbythesubclasses.Everyclasshasoneimmediatesuperclass(ie,parentclass),althoughaparentclassmayhavemorethanoneimmediatesubclass(ie,childclass). Objectsdonotchangetheirclassassignmentinaclassification,unlesstherewasamistakeintheassignment. Forexample,arabbitisalwaysarabbit,anddoesnotchangeintoatiger.Classificationscanbethoughtofas thesimplestandmostrestrictivetypeofontology,andservetoreducethecomplexityofaknowledgedomain.32 Classificationscanbeeasilymodeledinanobject-orientedprogramminglanguageandarenonchaotic (ie,calculationsperformedonthemembersandclassesofaclassificationshouldyieldthesameoutput,each timethecalculationisperformed).Aclassificationshouldbedistinguishedfromanontology.Inanontology,a classmayhavemorethanoneparentclassandanobjectmaybeamemberofmorethanoneclass.Aclassificationcanbeconsideredaspecialtypeofontologywhereineachclassislimitedtoasingleparentclass andeachobjecthasmembershipinoneandonlyoneclass.See Nomenclature.See Thesaurus.See Vocabulary. See Classification.See Dictionary.See Terminology.See Ontology.See Parentclass.See Childclass.See Superclass.See Unclassifiableobjects.

Coding Theterm"coding"hasthreeverydifferentmeanings;dependingonwhichbranchofscienceinfluences yourthinking.Forprogrammers,codingmeanswritingthecodethatconstitutesacomputerprogrammer. Forcryptographers,codingissynonymouswithencrypting(ie,usingaciphertoencodeamessage).Formedics, codingiscallinganemergencyteamtohandleapatientinextremis.Forinformaticiansandlibraryscientists, codinginvolvesassigninganalphanumericidentifier,representingaconceptlistedinanomenclature,toa term.Forexample,asurgicalpathologyreportmayincludethediagnosis,"Adenocarcinomaofprostate." AnomenclaturemayassignacodeC4863000thatuniquelyidentifiestheconcept"Adenocarcinoma."Coding thereportmayinvolveannotatingeveryoccurrenceoftheword"Adenocarcinoma"withthe"C4863000"identifier.Foradetailedexplanationofcoding,anditsimportanceforsearchingandretrievingdata,seethefulldiscussioninSection3.4,"AutoencodingandIndexingwithNomenclatures."See Autocoding.See Nomenclature CommandLine Instructionstotheoperatingsystem,thatcanbedirectlyenteredasalineoftextfromtheasystemprompt(eg,theso-calledCprompt,"c:\>",inWindowsandDOSoperatingsystems;theso-calledshell prompt,"$",inLinux-likesystems).

CommandLineUtility Programslackinggraphicuserinterfacesthatareexecutedviacommandlineinstructions. Theinstructionsforautilityaretypicallycouchedasaseriesofarguments,onthecommandline,followingthe nameoftheexecutablefilethatcontainstheutility.See Utility.

DataQualityAct IntheU.S.,thedatauponwhichpublicpolicyisbasedmusthavequalityandmustbeavailable forreviewbythepublic.Simplyput,publicpolicymustbebasedonverifiabledata.TheDataQualityActof 2002,requirestheOfficeofManagementandBudgettodevelopgovernment-widestandardsfordataquality.33

DataObject Adataobjectiswhateverisbeingdescribedbythedata.Forexample,ifthedatais"6feettall," thenthedataobjectisthepersonorthingtowhich"6feettall"applies.Minimally,adataobjectisa metadata/datapair,assignedtoauniqueidentifier(ie,atriple).Inpractice,themostcommondataobjects aresimpledatarecords,correspondingtoarowinaspreadsheetoralineinaflat-file.Dataobjectsinobjectorientedprogramminglanguagestypicallyencapsulateseveralitemsofdata,includinganobjectname,an objectuniqueidentifier,multipledata/metadatapairs,andthenameoftheobject’sclass.See Triple .See Identifier.See Metadata

DataRepurposing Involvesusingolddatainnewways,thatwerenotforeseenbythepeoplewhooriginally collectedthedata.Datarepurposingcomesinthefollowingcategories:(1)Usingthepreexistingdatato askandanswerquestionsthatwerenotcontemplatedbythepeoplewhodesignedandcollectedthedata; (2)Combiningpreexistingdatawithadditionaldata,ofthesamekind,toproduceaggregatedatathatsuits anewsetofquestionsthatcouldnothavebeenansweredwithanyoneofthecomponentdatasources;(3) Reanalyzingdatatovalidateassertions,theories,orconclusionsdrawnfromtheoriginalstudies;(4)Reanalyzingtheoriginaldatasetusingalternateorimprovedmethodstoattainoutcomesofgreaterprecisionorreliabilitythantheoutcomesproducedintheoriginalanalysis;(5)Integratingheterogeneousdatasets(ie,data setswithseeminglyunrelatedtypesofinformation),forthepurposeanansweringquestionsordeveloping conceptsthatspandiversescientificdisciplines;(6)Findingsubsetsinapopulationoncethoughttobehomogeneous;(7)Seekingnewrelationshipsamongdataobjects;(8)Creatingon-the-fly,noveldatasetsthrough datafilelinkages;(9)Creatingnewconceptsorwaysofthinkingaboutoldconcepts,basedonareexamination ofdata;(10)Fine-tuningexistingdatamodels;and(11)Startingoverandremodelingsystems.34 See Heterogeneousdata.

Dictionary Aterminologyorwordlistaccompaniedbyadefinitionforeachitem.See Nomenclature.See Vocabulary.See Terminology.

ExeFile Afilewiththefilenamesuffix".exe".Incommonparlance,filenameswiththe".exe"suffixareexecutablecode.See Executablefile

ExecutableFile Afilethatcontainscompiledcomputercodethatcanbereaddirectlyfromthecomputer’sCPU, withoutinterpretationbyaprogramminglanguage.AlanguagesuchasCwillcompileCcodeintoexecutables. Scriptinglanguages,suchasPerl,Python,andRubyinterpretplain-textscriptsandsendinstructionstoaruntimeengine,forexecution.Becauseexecutablefileseliminatetheinterpretationstep,theytypicallyrunfaster thanplain-textscripts.See Exefile.

FOSS Freeandopensourcesoftware.EquivalenttoFLOSS(FreeLibreOpenSourceSoftware),anabbreviation thattradesredundancyforinternationalappeal.See FreeSoftwareMovementversusOpenSourceInitiative. FreeSoftwareMovementVersusOpenSourceInitiative Beyondtrivialsemantics,thedifferencebetweenfree softwareandopensourcesoftwarerelatestotheessentialfeaturenecessaryfor"opensource"software(ie, accesstothesourcecode)andtothedifferentdistributionlicensesoffreesoftwareandopensourcesoftware. Sticklersinsistthatfreesoftwarealwayscomeswithpermissiontomodifyandredistributesoftwareinaprescribedmannerasdiscussedinthesoftwarelicense;apermissionnotalwaysgrantedinopensourcesoftware. Inpractice,thereisverylittledifferencebetweenfreesoftwareandopensourcesoftware.RichardStallmanhas writtenanessaythatsummarizesthetwodifferentapproachestocreatingfreesoftwareandopensource software.35

FreeSoftware Theconceptoffreesoftware,aspopularizedbytheFreeSoftwareFoundation,referstosoftware thatcanbeusedfreely,withoutrestriction.Theterm"free"doesnotnecessarilyrelatetotheactualcostofthe software.

Namespace Anamespaceistherealminwhichametadatatagapplies.Thepurposeofanamespaceistodistinguishmetadatatagsthathavethesamename,butadifferentmeaning.Forexample,withinasingleXMLfile, themetadatatag"date"maybeusedtosignifyacalendardate,orthefruit,orthesocialengagement.Toavoid confusion,metadatatermsareassignedaprefixthatisassociatedwithaWebdocumentthatdefinestheterm (ie,establishesthetag’snamespace).Inpracticalterms,atagthatcanhavedifferentdescriptivemeaningsin differentcontextsisprovidedwithaprefixthatlinkstoawebdocumentwhereinthemeaningofthetag,asit appliesintheXMLdocumentisspecified.

Nomenclature Anomenclaturesisalistingoftermsthatcoveralloftheconceptsinaknowledgedomain.A nomenclatureisdifferentfromadictionaryforthreereasons:(1)thenomenclaturetermsarenotannotated withdefinitions,(2)nomenclaturetermsmaybemulti-word,and(3)thetermsinthenomenclatureare limitedtothescopeoftheselectedknowledgedomain.Inaddition,mostnomenclaturesgroupsynonyms underagroupcode.Forexample,afoodnomenclaturemightcollectsubmarine,hoagie,po’boy,grinder, hero,andtorpedounderanalphanumericcodesuchas"F63958".Nomenclaturessimplifytextualdocuments byunitingsynonymoustermsunderacommoncode.Documentsthathavebeencodedwiththesamenomenclaturecanbeintegratedwithotherdocumentsthathavebeensimilarlycoded,andqueriesconducted oversuchdocumentswillyieldthesameresults,regardlessofwhichtermisentered(ie,asearchforeither hoagie,orpo’boywillretrievethesameinformation,ifbothtermshavebeenannotatedwiththesynonym code,"F63948").Optimally,thecanonicalconceptslistedinthenomenclatureareorganizedintoahierarchicalclassification.38,39 See Coding.See Autocoding.

Nonatomicity Nonatomicityistheassignmentofacollectionofobjectstoasingle,compositeobject,thatcannot befurthersimplifiedorsensiblydeconstructed.Forexample,thehumanbodyiscomposedoftrillionsof individualcells,eachofwhichlivesforsomelengthoftime,andthendies.Manyofthecellsinthebody arecapableofdividingtoproducemorecells.Inmanycases,thecellsofthebodythatarecapableofdividing canbeculturedandgrowninplasticcontainers,muchlikebacteriacanbeculturedandgrowninPetridishes.If thehumanbodyiscomposedofindividualcells,whydowehabituallythinkofeachhumanasasingleliving entity?Whydon’twethinkofhumansasbagsofindividualcells?Perhapsthereasonstemsfromthe coordinatedresponsesofcells.Whensomeonestepsonthecellsofyourtoe,thecellsinyourbrainsensepain, thecellsinyourmouthandvocalcordssayouch,andanarmyofinflammatorycellsrushtothesceneofthe crime.Thecellsinyourtoearenotcapableofregisteringanactionablecomplaint,withoutagreatdealof assistance.Anotherreasonthatorganisms,composedoftrillionsoflivingcells,aregenerallyconsideredtohave nonatomicity,probablyrelatestothe"species"conceptinbiology.Everycellinanorganismdescendedfrom thesamezygote,andeveryzygoteineverymemberofthesamespeciesdescendedfromthesameancestral organism.Hence,thereseemstobelittlebenefittoassigninguniqueentitystatustotheindividualcellsthat composeorganisms,whentheclassstructurefororganismsisbasedondescentthroughzygotes.See Species. Notation3 Alsocalledn3.Asyntaxforexpressingassertionsastriples(uniquesubject+metadata+data).Notation 3expressesthesameinformationasthemoreformalRDFsyntax,butn3iseasierforhumanstoread.40 RDFand n3areinterconvertible,andeitheronecanbeparsedandequivalentlytokenized(ie,brokenintoelementsthatcan bereorganizedinadifferentformat,suchasadatabaserecord).See RDF.See Triple.

Ontology Anontologyisacollectionofclassesandtheirrelationshipstooneanother.Ontologiesareusuallyrulebasedsystems(ie,membershipinaclassisdeterminedbyoneormoreclassrules).Twoimportantfeatures distinguishontologiesfromclassifications.Ontologiespermitclassestohavemorethanoneparentclass.For example,theclassofautomobilesmaybeadirectsubclassof"motorizeddevices"andadirectsubclassof "mechanizedtransporters."Inaddition,aninstanceofaclasscanbeaninstanceofanynumberofadditional classes.Forexample,aLamborghinimaybeamemberofclass"automobiles"andofclass"luxuryitems."This meansthatthelineageofaninstanceinanontologycanbehighlycomplex,withasingleinstanceoccurringin multipleclasses,andwithmanyconnectionsbetweenclasses.Becauserecursiverelationsarepermitted,itis possibletobuildanontologywhereinaclassisbothanancestorclassandadescendantclassofitself.Aclassificationisahighlyrestrainedontologywhereininstancescanbelongtoonlyoneclass,andeachclassmay haveonlyoneparentclass.Becauseclassificationshaveanenforcedlinearhierarchy,theycanbeeasily

modeled,andthelineageofanyinstancecanbetracedunambiguously.See Classification.See Multiclass classification.See Multiclassinheritance

OpenAccess Adocumentisopenaccessifitscompletecontentsareavailabletothepublic.Openaccessapplies todocumentsinthesamemannerasopensourceappliestosoftware.

OpenSource Softwareisopensourceifthesourcecodeisavailabletoanyonewhohasaccesstothesoftware.See Opensourcemovement.See Openaccess

OpenSourceMovement Opensourcesoftwareissoftwareforwhichthesourcecodeisavailable.TheOpen SourceSoftwaremovementisanoffspringoftheFreeSoftwaremovement.Althoughagooddealoffreesoftwareisno-costsoftware,theintendedmeaningoftheterm"free"isthatthesoftwarecanbeusedwithoutrestrictions.TheOpenSourceInitiativepostsanopensourcedefinitionRopaRandalistofapprovedlicensesthat canbeattachedtoopensourceproducts.

ParentClass Theimmediateancestor,orthenext-higherclass(ie,thedirectsuperclass)ofaclass.Forexample, intheclassificationoflivingorganisms,ClassVertebrataistheparentclassofClassGnathostomata.Class GnathostomataistheparentclassofClassTeleostomi.Inaclassification,whichimposessingleclassinheritance,eachchildclasshasexactlyoneparentclass;whereasoneparentclassmay haveseveraldifferent childclasses.Furthermore,someclasses,inparticular thebottomclassinthelineage,havenochildclasses (ie,aclassneednotalwaysbeasuperclassofotherclasses).Aclasscanbedefinedbyitsproperties,its membership(ie,theinstancesthatbelongtotheclass),andbythenameofitsparentclass.Whenwelist alloftheclassesinaclassification,inanyorder,wecanalwaysreconstructthecompleteclasslineage, intheircorrectlineageandbranchings,ifweknowthenameofeachclass’sparentclass.See Instance See Childclass.See Superclass .

RDF ResourceDescriptionFramework(RDF)isasyntaxinXMLnotationthatformallyexpressesassertionsas triples.TheRDFtripleconsistsofauniquelyidentifiedsubjectplusametadatadescriptorforthedataplusa dataelement.Triplesarenecessaryandsufficienttocreatestatementsthatconveymeaning.Triplescanbe aggregatedwithothertriplesfromthesamedatasetorfromotherdatasets,solongaseachtriplepertains toauniquesubjectthatisidentifiedequivalentlythroughthedatasets.EnormousdatasetsofRDFtriples canbemergedorfunctionallyintegratedwithothermassiveorcomplexdataresources.ForadetaileddiscussionseeOpenSourceToolsfor Chapter6,"SyntaxforTriples."See Notation3.See Semantics.See Triple See XML

RDFSchema ResourceDescriptionFrameworkSchema(RDFS).Adocumentcontainingalistofclasses,their definitions,andthenamesoftheparentclass(es)foreachclass.InanRDFSchema,thelistofclassesis typicallyfollowedbyalistofpropertiesthatapplytooneormoreclassesintheSchema.Tobeuseful, RDFSchemasarepostedontheInternet,asaWebpage,withauniqueWebaddress.Anyonecanincorporate theclassesandpropertiesofapublicRDFSchemaintotheirownRDFdocuments(publicorprivate)bylinking namedclassesandproperties,intheirRDFdocument,tothewebaddressoftheRDFSchemawheretheclasses andpropertiesaredefined.See Namespace.See RDFS.

RDFS SameasRDFSchema.

Reflection Aprogrammingtechniquewhereinacomputerprogramwillmodifyitself,atrun-time,basedoninformationitacquiresthroughintrospection.Forexample,acomputerprogrammayiterateoveracollectionofdata objects,examiningtheself-descriptiveinformationforeachobjectinthecollection(ie,objectintrospection).If theinformationindicatesthatthedataobjectbelongstoaparticularclassofobjects,thentheprogrammaycalla methodappropriatefortheclass.Theprogramexecutesinamannerdeterminedbydescriptiveinformation obtainedduringrun-time;metaphoricallyreflectinguponthepurposeofitscomputationaltask.See Introspection.

Reproducibility Reproducibilityisachievedwhenrepeatstudiesproducethesameresults,overandover.Reproducibilityiscloselyrelatedtovalidation,whichisachievedwhenyoudrawthesameconclusions,fromthe data,overandoveragain.Implicitintheconceptof"reproducibility"isthattheoriginalresearchmustsomehowconveythemeansbywhichthestudycanbereproduced.Thisusuallyrequiresthecarefulrecordingof methods,algorithms,andmaterials.Insomecases,reproducibilityrequiresaccesstothedataproducedinthe originalstudies.Ifthereisnofeasiblewayforscientiststoundertakeareconstructionoftheoriginalstudy,orif

theresultsobtainedintheoriginalstudycannotbeobtainedinsubsequentattempts,thenthestudyisirreproducible.Iftheworkisreproduced,buttheresultsandtheconclusionscannotberepeated,thenthestudyis consideredinvalid.See Validation.See Verification.

Script Ascriptisaprogramthatiswritteninplain-text,inasyntaxappropriateforaparticularprogramming language,thatneedstobeparsedthroughthatlanguage’sinterpreterbeforeitcanbecompiledandexecuted. Scriptstendtorunabitslowerthanexecutablefiles,buttheyhavetheadvantagethattheycanbeunderstoodby anyonewhoisfamiliarwiththescript’sprogramminglanguage.Scriptscanbeidentifiedbytheso-calledshebanglineatthetopofthescript.See Shebang.See Executablefile.See Haltingascript.

Semantics Thestudyofmeaning(Greekroot,semantikos,signficantmeaning).Inthecontextofdatascience,semanticsisthetechniqueofcreatingmeaningfulassertionsaboutdataobjects.Ameaningfulassertion,asused here,isatripleconsistingofanidentifieddataobject,adatavalue,andadescriptorforthedatavalue.Inpractical terms,semanticsinvolvesmakingassertionsaboutdataobjects(ie,makingtriples),combiningassertionsabout dataobjects(ie,mergingtriples),andassigningdataobjectstoclasses;hencerelatingtriplestoothertriples.Asa wordofwarning,fewinformaticianswoulddefinesemanticsintheseterms,butmostdefinitionsforsemantics arefunctionallyequivalenttothedefinitionofferedhere.Mostlanguageisunstructuredandmeaningless.Considertheassertion:Samistired.Thisisanadequatelystructuredsentencewithasubjectverbandobject.Butwhat isthemeaningofthesentence?TherearealotofpeoplenamedSam.WhichSamisbeingreferredtointhis sentence?WhatdoesitmeantosaythatSamistired?Is"tiredness"aconstitutivepropertyofSam,ordoes itonlyapplytospecificmoments?Ifso,forwhatmomentintimeistheassertion,"Samistired"actuallytrue? Toacomputer,meaningcomesfromassertionsthathaveaspecific,identifiedsubjectassociatedwithsomesensiblepieceoffullydescribeddata(metadatacoupledwiththedataitdescribes).See Triple.See RDF.

Shebang StandardscriptswritteninRuby,Perl,orPythonallbeginwithashebang,acolloquialismreferringto theconcatenationofthepoundcharacter,"#"(knownbythemusically-inclinedasaSHarpcharacter),followed byanexclamationsign,"!"(connotingasurpriseorabang).Atypicalshebangline(ie,topline)forPerl,Ruby, Python,andBashscriptsis:

#!/usr/local/bin/perl

#!/usr/local/bin/ruby

#!/usr/local/bin/python

#!/usr/local/bin/sh

Ineachcase,theshebangisfollowedbythedirectorypathtothescript,andthisistraditionallyfollowedby optionalprogrammingargumentsspecifictoeachlanguage.Theshebangline,thoughessentialinsomeUnixlikesystems,isunnecessaryintheWindowsoperatingsystem.Inthisbook,Iusetheshebanglinetoindicate, ataglance,thelanguageinwhichascriptiscomposed.

Simpson’sParadox Occurswhenacorrelationthatholdsintwodifferentdatasetsisreversedifthedatasetsare combined.Forexample,baseballplayerAmayhaveahigherbattingaveragethanplayerBforeachoftwo seasons,butwhenthedataforthetwoseasonsarecombined,playerBmayhavethehigher2-seasonaverage. Simpson’sparadoxisjustoneexampleofunexpectedchangesinoutcomewhenvariablesareunknowingly hiddenorblended.41

Species Speciesisthebottom-mostclassofanyclassificationorontology.Becausethespeciesclasscontainsthe individualobjectsoftheclassification,itistheonlyclasswhichisnotabstract.Thespecialsignificanceofthe speciesclassisbestexemplifiedintheclassificationoflivingorganisms.Everyspeciesoforganismcontains individualsthatshareacommonancestralrelationshiptooneanother.Whenwelookatagroupofsquirrels,we knowthateachsquirrelinthegrouphasitsownuniquepersonality,itsownuniquegenes(ie,genotype),andits ownuniquesetofphysicalfeatures(ie,phenotype).Moreover,althoughtheDNAsequencesofindividual squirrelsareunique,weassumethatthereisacommonalitytothegenomeofsquirrelsthatdistinguishesit fromthegenomeofeveryotherspecies.Ifweusethemoderndefinitionofspeciesasanevolvinggenepool,

weseethatthespeciescanbethoughtofasabiologicallifeform,withsubstance(apopulationofpropagating genes),andafunction(evolvingtoproducenewspecies).42–44 Putsimply,speciesspeciate;individualsdonot. Asacorollary,speciesevolve;individualssimplypropagate.Hence,thespeciesclassisaseparablebiological unitwithformandfunction.We,asindividuals,arefocusedonthelivesofindividualthings,andwemustbe remindedoftheroleofspeciesinbiologicalandnonbiologicalclassifications.TheconceptofspeciesisdiscussedingreaterdetailinSection6.4.See Blendedclass.See Nonatomicity

Specification Aspecificationisaformalmethodfordescribingobjects(physicalobjectssuchasnutsandboltsor symbolicobjects,suchasnumbers,orconceptsexpressedastext).Ingeneral,specificationsdonotrequirethe inclusionofspecificitemsofinformation(ietheydonotimposerestrictionsonthecontentthatisincludedinor excludedfromdocuments),andspecificationsdonotimposeanyorderofappearanceofthedatacontainedin thedocument(ie,youcanmixupandrearrangespecifiedobjects,ifyoulike).Specificationsarenotgenerally certifiedbyastandardsorganization.Theyaregenerallyproducedbyspecialinterestorganizations,andthe legitimacyofaspecificationdependsonitspopularity.ExamplesofspecificationsareRDF(ResourceDescriptionFramework)producedbytheW3C(WorldWideWebConsortium),andTCP/IP(TransferControl Protocol/InternetProtocol),maintainedbytheInternetEngineeringTaskForce.Themostwidelyimplemented specificationsaresimpleandeasilyimplemented.See Specificationversusstandard.

SpecificationVersusStandard Datastandards,ingeneral,tellyouwhatmustbeincludedinaconformingdocument,and,inmostcases,dictatestheformatofthefinaldocument.Inmanyinstances,standardsbarinclusionof anydatathatisnotincludedinthestandard(eg,youshouldnotincludeastronomicaldatainanclinicalx-ray report).Specificationssimplyprovideaformalwayfordescribingthedatathatyouchoosetoincludeinyour document.XMLandRDF,asemanticdialectofXML,areexamplesofspecifications.Theybothtellyou howdatashouldberepresented,butneithertellyouwhatdatatoinclude,orhowyourdocumentordatasetshould appear.Filesthatcomplywithastandardarerigidlyorganizedandcanbeeasilyparsedandmanipulatedbysoftwarespecificallydesignedtoadheretothestandard.Filesthatcomplywithaspecificationaretypicallyselfdescribingdocumentsthatcontainwithinthemselvesalltheinformationnecessaryforahumanoracomputer toderivemeaningfromthefilecontents.Intheory,filesthatcomplywithaspecificationcanbeparsedandmanipulatedbygeneralizedsoftwaredesignedtoparsethemarkuplanguageofthespecification(eg,XML,RDF)and toorganizethedataintodatastructuresdefinedwithinthefile.Therelativestrengthsandweaknessesofstandards andspecificationsarediscussedinSection2.6,"SpecificationsGood,StandardsBad."See XML.See RDF.

Superclass Anyoftheancestralclassesofasubclass.Forexample,intheclassificationoflivingorganisms,the classofvertebratesisasuperclassoftheclassofmammals.Theimmediatesuperclassofaclassisitsparent class.Incommonparlance,whenwespeakofthesuperclassofaclass,weareusuallyreferringtoitsparent class.See Parentclass

Syntax Syntaxisthestandardformorstructureofastatement.WhatweknowasEnglishgrammarisequivalentto thesyntaxfortheEnglishlanguage.CharlesMeaddistinctlysummarizedthedifferencebetweensyntaxand semantics:"Syntaxisstructure;semanticsismeaning."45 See Semantics.

TaxonomicOrder Inbiologicaltaxonomy,thehierarchicallineageoforganismsaredividedintoadescending listofnamedorders:Kingdom,Phylum(Division),Class,Order,Family,andGenus,Species.Aswehave learnedmoreandmoreabouttheclassesoforganisms,moderntaxonomistshaveaddedadditionalranksto theclassification(eg,supraphylum,subphylum,suborder,infraclass,etc.).Wasthisreallynecessary?All ofthistaxonomiccomplexitycouldbeavertedbydroppingnamedranksandsimplyreferringtoeveryclass as"Class."Modernspecificationsforclasshierarchies(eg,RDFSchema)encapsulateeachclasswiththename ofitssuperclass.Wheneveryobjectyieldsitsclassandsuperclass,itispossibletotraceanyobject’sclass lineage.Forexample,intheclassificationoflivingorganisms,ifyouknowthenameoftheparentforeach class,youcanwriteasimplescriptthatgeneratesthecompleteancestrallineageforeveryclassandspecies withintheclassification.46 See Class.See Taxonomy.See RDFSchema.See Species Taxonomy Ataxonomyisthecollectionofnamedinstances(classmembers)inaclassificationoranontology. Whenyouseeaschematicshowingclassrelationships,withindividualclassesrepresentedbygeometric shapesandtherelationshipsrepresentedbyarrowsorconnectinglinesbetweentheclasses,thenyouare

essentiallylookingatthestructureofaclassification,minusthetaxonomy.Youcanthinkofbuildingataxonomyastheactofpouringallofthenamesofalloftheinstancesintotheirproperclasses.Ataxonomyis similartoanomenclature;thedifferenceisthatinataxonomy,everynamedinstancemusthaveanassigned class.See Taxonomicorder

Terminology Thecollectionofwordsandtermsusedinsomeparticulardiscipline,field,orknowledgedomain. Nearlysynonymouswithvocabularyandwithnomenclature.Vocabularies,unliketerminologies,arenottobe confinedtothetermsusedinaparticularfield.Nomenclatures,unliketerminologies,usuallyaggregateequivalenttermsunderacanonicalsynonym.

Thesaurus Avocabularythatgroupstogethersynonymousterms.Athesaurusisverysimilartoanomenclature. Therearetwominordifferences.Nomenclaturesincludedmulti-wordterms;whereasathesaurusistypically composedofone-wordterms.Inaddition,nomenclaturesaretypicallyrestrictedtoawell-definedtopicor knowledgedomain(eg,namesofstars,infectiousdiseases,etc.).See Nomenclature.See Vocabulary.See Classification.See Dictionary.See Terminology.See Ontology

Triple Incomputersemantics,atripleisanidentifieddataobjectassociatedwithadataelementandthedescriptionofthedataelement.Inthecomputerscienceliterature,thesyntaxforthetripleiscommonlydescribedas: subject,predicate,object,whereinthesubjectisanidentifier,thepredicateisthedescriptionoftheobject,and theobjectisthedata.Thedefinitionoftriple,usinggrammaticalterms,canbeoff-puttingtothedatascientist, whomaythinkintermsofspreadsheetentries:akeythatidentifiesthelinerecord,acolumnheadercontaining themetadatadescriptionofthedata,andacellthatcontainsthedata.Inthisbook,thethreecomponentsofa triplearedescribedas:(1)theidentifierforthedataobject,(2)themetadatathatdescribesthedata,and(3)the dataitself.Intheory,alldatasets,databases,andspreadsheetscanbeconstructedordeconstructedascollectionsoftriples.See Introspection.See Dataobject.See Semantics.See RDF.See Meaning UnclassifiableObjects Classificationscreateaclassforeveryobjectandtaxonomiesassigneachandeveryobjecttoitscorrectclass.Thismeansthataclassificationisnotpermittedtocontainunclassifiedobjects;aconditionthatputsfussytaxonomistsinanuntenableposition.Supposeyouhaveanobject,andyousimplydonot knowenoughabouttheobjecttoconfidentlyassignittoaclass.Or,supposeyouhaveanobjectthatseemstofit morethanoneclass,andyoucan’tdecidewhichclassisthecorrectclass.Whatdoyoudo?Historically,scientistshaveresortedtocreatinga"miscellaneous"classintowhichotherwiseunclassifiableobjectsaregivena temporaryhome,untilmoresuitableaccommodationscanbeprovided.Ihavespokenwithnumerousdata managers,andeveryoneseemstobeofamindthat"miscellaneous"classes,createdasastopgapmeasure, serveausefulpurpose.Notso.Historically,thepromiscuousapplicationof"miscellaneous"classeshave proventobeahugeimpedimenttotheadvancementofscience.Inthecaseoftheclassificationoflivingorganisms,theclassofprotozoansstandsasacaseinpoint.ErnstHaeckel,aleadingbiologicaltaxonomistinhis time,createdtheKingdomProtista(ie,protozoans),in1866,toaccommodateawidevarietyofsimpleorganismswithsuperficialcommonalities.Haeckelhimselfunderstoodthattheprotistswereablendedclassthat includedunrelatedorganisms,buthebelievedthatfurtherstudywouldresolvetheconfusion.Inasense, hewasright,buttheprocesstookmuchlongerthanhehadanticipated;occupyinggenerationsoftaxonomists overthefollowing150years.Today,KingdomProtistanolongerexists.Itsmembershavebeenreassignedto otherclasses.Nonetheless,textbooksofmicrobiologystilldescribetheprotozoans,justasthoughthisname continuedtooccupyalegitimateplaceamongterrestrialorganisms.Inthemeantime,therapeuticopportunities foreradicatingso-calledprotozoalinfections,usingclass-targetedagents,havenodoubtbeenmissed.47 You mightthinkthatthecreationofaclassoflivingorganisms,withnoestablishedscientificrelationtothereal world,wasarareandancienteventintheannalsofbiology,havinglittleornochanceofbeingrepeated.Notso. Aspecialpseudoclassoffungi,deuteromyctetes(spelledwithalowercase"d,"signifyingitsquestionablevalidityasatruebiologicclass)hasbeencreatedtoholdfungiofindeterminatespeciation.Atpresent,thereare severalthousandsuchfungi,sittinginataxonomiclimbo,waitingtobeplacedintoadefinitivetaxonomic class.47, 48 See Blendedclass.

UndifferentiatedSoftware Intellectualpropertydisputeshavedrivendeveloperstodividesoftwareintotwocategories:undifferentiatedsoftwareanddifferentiatedsoftware.Undifferentiatedsoftwarecomprisesthefundamentalalgorithmsthateveryoneuseswhenevertheydevelopanewsoftwareapplication.Itisinnobody’s interesttoassignpatentstobasicalgorithmsandtheirimplementations.Nobodywantstodevotetheircareers toprosecutingordefendingtenuouslegalclaimsovertheownershipofthefundamentalbuildingblocksof computerscience.Differentiatedsoftwarecomprisescustomizedapplicationsthataresufficientlynewand differentfromanyprecedingproductthatpatentprotectionwouldbereasonable.

Utility Inthecontextofsoftware,autilityisanapplicationthatisdedicatedtoperformingonespecifictaskvery wellandveryfast.Inmostinstances,utilitiesareshortprograms,oftenrunningfromthecommandline,and thuslackinganygraphicuserinterface.Manyutilitiesareavailableatnocost,withopensourcecode.Ingeneral,simpleutilitiesarepreferabletomultipurposesoftwareapplications.29 Remember,anapplicationthat claimstodoeverythingfortheuseris,mostoften,anapplicationthatrequirestheusertodoeverything fortheapplication. See Commandline.See Commandlineutility

Validation Validationistheprocessthatcheckswhethertheconclusionsdrawnfromdataanalysisarecorrect.49 Validationusuallystartswithrepeatingthesameanalysisofthesamedata,usingthemethodsthatwereoriginallyrecommended.Obviously,ifadifferentsetofconclusionsisdrawnfromthesamedataandmethods,the originalconclusionscannotbevalidated.Validationmayinvolveapplyingadifferentsetofanalyticmethods tothesamedata,todetermineiftheconclusionsareconsistent.Itisalwaysreassuringtoknowthatconclusions arerepeatable,withdifferentanalyticmethods.Inprioreras,experimentswerevalidatedbyrepeatingtheentireexperiment,thusproducinganewsetofobservationsforanalysis.Manyoftoday’sscientificexperiments arefartoocomplexandcostlytorepeat.Insuchcases,validationrequiresaccesstothecompletecollectionof theoriginaldata,andtothedetailedprotocolsunderwhichthedatawasgenerated.Oneofthemostuseful methodsofdatavalidationinvolvestestingnewhypotheses,basedontheassumedvalidityoftheoriginal conclusions.Forexample,ifyouweretoacceptDarwin’sanalysisofbarnacledata,leadingtohistheory ofevolution,thenyouwouldexpecttofindachronologichistoryoffossilsinascendinglayersofshale.This wasthecase;thus,paleontologistsstudyingtheBurgessshalereservesprovidedsomevalidationtoDarwin’s conclusions.Validationshouldnotbemistakenforproof.Nonetheless,therepeatabilityofconclusions,over time,withthesameordifferentsetsofdata,andthedemonstrationofconsistencywithrelatedobservations,is aboutallthatwecanhopeforinthisimperfectworld.See Verification.See Reproducibility.

Verification Theprocessbywhichdataischeckedtodeterminewhetherthedatawasobtainedproperly(ie, accordingtoapprovedprotocols),andthatthedataaccuratelymeasuredwhatitwasintendedtomeasure, onthecorrectspecimens,andthatallstepsindataprocessingweredoneusingwell-documentedprotocols. Verificationoftenrequiresalevelofexpertisethatisatleastashighastheexpertiseoftheindividuals whoproducedthedata.49 Dataverificationrequiresafullunderstandingofthemanystepsinvolvedindata collectionandcanbeatime-consumingtask.Inonecelebratedcase,inwhichtwostatisticiansrevieweda microarraystudyperformedatDukeUniversity,thetimedevotedtotheirverificationeffortwas reportedtobe2000hours.50 Toputthisstatementinperspective,theofficialwork-year,accordingtothe U.S.OfficeofPersonnelManagement,is2087hours.Verificationisdifferentfromvalidation.Verification isperformedondata;validationisdoneontheresultsofdataanalysis.See Validation.See Microarray See Introspection.

Vocabulary Acomprehensivecollectionofthewordsandtheirassociatedmeanings.Insomequarters,"vocabulary"and"nomenclature"areusedinterchangeably,buttheyaredifferentfromoneanother.Nomenclatures typicallyfocusontermsconfinedtooneknowledgedomain.Nomenclaturestypicallydonotcontaindefinitionsforthecontainedterms.Nomenclaturestypicallygrouptermsbysynonymy.Lastly,nomenclaturesincludemulti-wordterms.Vocabulariesarecollectionsofsinglewords,culledfrommultipleknowledge domains,withtheirdefinitions,andassembledinalphabeticorder.See Nomenclature.See Thesaurus.See Taxonomy.See Dictionary.See Terminology.

XML AcronymforeXtensibleMarkupLanguage,asyntaxformarkingdatavalueswithdescriptors (ie,metadata).Thedescriptorsarecommonlyknownastags.InXML,everydatavalueisenclosedbya start-tag,containingthedescriptorandindicatingthatavaluewillfollow,andanend-tag,containingthesame descriptorandindicatingthatavalueprecededthetag.Forexample: <name>ConradNervig </name >.The enclosinganglebrackets,"<>",andtheend-tagmarker,"/",arehallmarksofHTMLandXMLmarkup.This simplebutpowerfulrelationshipbetweenmetadataanddataallowsustoemploymetadata/datapairsasthough eachwereaminiaturedatabase.ThesemanticvalueofXMLbecomesapparentwhenwebindametadata/data pairtoauniqueobject,formingaso-calledtriple.See Triple.See Meaning.See Semantics.See HTML.

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Data simplification : taming information with open source tools 1st edition berman - Instantly acces

Red Zone: A Steamy Instalove

Notices

REFERENCES

AuthorBiography