Validating RDF Data

308 Pages·2017·2.505 MB·English

by  Jose Emilio Labra Gayo, Eric Prud’hommeaux, Iovka Boneva, Dimitris Kontokostas

Validating RDF Data
Jose Emilio Labra Gayo
UniversityofOviedo
Eric Prud’hommeaux
W3C/MITandMicelio
Iovka Boneva
UniversityofLille
Dimitris Kontokostas
UniversityofLeipzig
SYNTHESISLECTURESONSEMANTICWEB:
THEORYAND TECHNOLOGY#16
M
&C Morgan&cLaypool publishers
Copyright©2018byMorgan&Claypool
ValidatingRDFData
JoseEmilioLabraGayo,EricPrud’hommeaux,IovkaBoneva,andDimitrisKontokostas
www.morganclaypool.com
ISBN:9781681731643 paperback
ISBN:9781681731650 ebook
ISBN:9781681731667 e-pub
ABSTRACT
RDFandLinkedDatahavebroadapplicabilityacrossmanyfields,fromaircraftmanufacturing
to zoology. Requirements for detecting bad data differ across communities, fields, and tasks,
but nearly all involve some form of data validation. This book introduces data validation and
describesitspracticaluseinday-to-daydataexchange.
TheSemanticWeboffersabold,newtakeonhowtoorganize,distribute,index,andshare
data. Using Web addresses (URIs) as identifiers for data elements enables the construction of
distributeddatabasesonaglobalscale.LiketheWeb,theSemanticWebisheraldedasaninfor-
mationrevolution,andalsoliketheWeb,itisencumberedbydataqualityissues.Thequalityof
SemanticWebdataiscompromisedbythelackofresourcesfordatacuration,formaintenance,
andfordevelopinggloballyapplicabledatamodels.
Attheenterprisescale,theseproblemshaveconventionalsolutions.Masterdatamanage-
ment provides an enterprise-wide vocabulary, while constraint languages capture and enforce
data structures. Filling a need long recognized by Semantic Web users, shapes languages pro-
videmodelsandvocabulariesforexpressingsuchstructuralconstraints.
ThisbookdescribestwotechnologiesforRDFvalidation:ShapeExpressions(ShEx)and
Shapes Constraint Language (SHACL), the rationales for their designs, a comparison of the
two,andsomeexampleapplications.
KEYWORDS
RDF,ShEx,SHACL,shapeexpressions,shapesconstraintlanguage,dataquality,
webofdata,SemanticWeb,linkeddata
Contents
Preface ........................................................... xv
ForewordbyPhilArcher ...........................................xvii
ForewordbyTomBaker............................................ xix
ForewordbyDanBrickleyandLibbyMiller ........................... xxi
1 Introduction .......................................................1
1.1 RDFandtheWebofData ......................................... 1
1.2 RDF:TheGoodParts ............................................. 1
1.3 ChallengesforRDFAdoption ...................................... 3
1.4 StructureoftheBook.............................................. 5
1.5 ConventionsandNotation.......................................... 6
2 TheRDFEcosystem.................................................9
2.1 RDFHistory .................................................... 9
2.2 RDFDataModel................................................ 10
2.3 SharedEntitesandVocabularies .................................... 17
2.4 TechnologiesRelatedwithRDF .................................... 18
2.4.1 SPARQL................................................. 18
2.4.2 InferenceSystems:RDFSchemaandOWL..................... 20
2.4.3 LinkedData,JSON-LD,Microdata,andRDFa.................. 23
2.5 Summary ...................................................... 25
2.6 SuggestedReading ............................................... 25
3 DataQuality ......................................................27
3.1 Non-RDFSchemaLanguages ..................................... 28
3.1.1 UML .................................................... 28
3.1.2 SQLandRelationalDatabases................................ 29
3.1.3 XML .................................................... 31
3.1.4 JSON.................................................... 37
3.1.5 CSV..................................................... 39
3.2 UnderstandingtheRDFValidationProblem .......................... 40
3.3 PreviousRDFValidationApproaches................................ 45
3.3.1 Query-basedValidation ..................................... 45
3.3.2 Inference-basedApproaches.................................. 47
3.3.3 StructuralLanguages ....................................... 48
3.4 ValidationRequirements .......................................... 48
3.4.1 GeneralRequirements ...................................... 49
3.4.2 Graph-basedRequirements .................................. 49
3.4.3 RDFDataModelRequirements .............................. 50
3.4.4 Data-modeling-basedRequirements ........................... 50
3.4.5 ExpressivenessofSchemaLanguage ........................... 51
3.4.6 ValidationInvocationRequirements ........................... 52
3.4.7 UsabilityRequirements...................................... 52
3.5 Summary ...................................................... 52
3.6 SuggestedReading ............................................... 53
4 ShapeExpressions .................................................55
4.1 UseofShEx .................................................... 55
4.2 FirstExample ................................................... 56
4.3 ShEximplementations............................................ 58
4.4 TheShapeExpressionsLanguage ................................... 59
4.4.1 ShapeExpressionsCompactSyntax............................ 59
4.4.2 InvokingValidation......................................... 60
4.4.3 StructureofShapeExpressions ............................... 63
4.4.4 StartShapeExpression ...................................... 64
4.5 NodeConstraints ................................................ 65
4.5.1 Nodekinds ............................................... 67
4.5.2 Datatypes................................................. 68
4.5.3 FacetsonLiterals .......................................... 70
4.5.4 ValueSets ................................................ 73
4.6 Shapes......................................................... 78
4.6.1 TripleConstraints .......................................... 79
4.6.2 Groupings ................................................ 80
4.6.3 Cardinalities .............................................. 80
4.6.4 Choices .................................................. 82
4.6.5 NestedShapes ............................................. 84
4.6.6 InverseTripleConstraints.................................... 85
4.6.7 RepeatedProperties ........................................ 86
4.6.8 PermittingotherTriples ..................................... 87
4.7 References...................................................... 90
4.7.1 ShapeReferences........................................... 90
4.7.2 RecursionandCyclicReferences .............................. 91
4.7.3 ExternalShapes............................................ 92
4.7.4 LabeledTripleExpression ................................... 93
4.7.5 Annotations............................................... 94
4.8 LogicalOperators................................................ 95
4.8.1 Conjunction............................................... 95
4.8.2 Disjunction ............................................... 98
4.8.3 Negation ................................................ 101
4.9 ShapeMaps ................................................... 105
4.9.1 FixedShapeMaps......................................... 105
4.9.2 QueryShapeMaps ........................................ 106
4.9.3 ResultShapeMaps ........................................ 108
4.9.4 JSONRepresentation ...................................... 109
4.9.5 ChainingValidationWorkflows .............................. 110
4.10 SemanticActions ............................................... 110
4.11 ShExandInference ............................................. 111
4.12 Importingschemas.............................................. 113
4.13 RDFandJSON-LDSyntax ...................................... 114
4.14 Summary ..................................................... 116
4.15 SuggestedReading .............................................. 116
5 SHACL .........................................................119
5.1 SimpleExample ................................................ 119
5.2 SHACLImplementations ........................................ 122
5.3 BasicDefinitions:ShapesGraphs,Node,andPropertyShapes........... 124
5.4 ImportingotherShapesGraphs ................................... 125
5.5 ValidationReport ............................................... 126
5.6 Shapes........................................................ 129
5.6.1 Nodeshapes.............................................. 129
5.6.2 PropertyShapes........................................... 130
5.6.3 ConstraintComponents .................................... 131
5.6.4 HumanFriendlyMessages .................................. 133
5.6.5 DeclaringShapeSeverities .................................. 134
5.6.6 DeactivatingShapes ....................................... 135
5.7 TargetDeclarations ............................................. 137
5.7.1 TargetNode.............................................. 137
5.7.2 TargetClass.............................................. 138
5.7.3 ImplicitClassTarget....................................... 139
5.7.4 TargetSubjectsOf ........................................ 140
5.7.5 TargetObjectsOf ......................................... 141
5.8 Cardinality .................................................... 141
5.9 ConstraintsonValues............................................ 142
5.9.1 Datatypes................................................ 142
5.9.2 ClassofValues............................................ 145
5.9.3 NodeKinds .............................................. 146
5.9.4 SetsofValues............................................. 147
5.9.5 SpecificValue ............................................ 148
5.10 DatatypeFacets ................................................ 148
5.10.1ValueRanges ............................................. 149
5.10.2String-basedConstraints ................................... 149
5.10.3Language-basedConstraints ................................ 151
5.11 LogicalConstraints:and,or,not,xone .............................. 154
5.11.1AND ................................................... 154
5.11.2OR..................................................... 157
5.11.3ExactlyOne.............................................. 159
5.11.4Not..................................................... 162
5.11.5CombiningLogicalOperators ............................... 162
5.12 Shape-basedConstraints ......................................... 164
5.12.1ShapeReferencesandRecursion ............................. 166
5.12.2QualifiedValueShapes ..................................... 174
5.13 ClosedShapes ................................................. 177
5.14 PropertyPairConstraints......................................... 180
5.15 Non-validatingSHACLProperties................................. 182
5.16 SHACL-SPARQL ............................................. 184
5.16.1SPARQLConstraints...................................... 184
5.16.2SPARQL-basedConstraintComponents ...................... 185
5.17 SHACLandInferenceSystems.................................... 188
5.18 SHACLCompactSyntax ........................................ 190
5.19 SHACLRulesandAdvancedFeatures.............................. 190
5.20 SHACLJavascript .............................................. 193
5.21 Summary ..................................................... 194
5.22 SuggestedReading .............................................. 194
6 Applications .....................................................195
6.1 DescribingaLinkedDataPortal................................... 195
6.1.1 WebIndexinShEx ........................................ 197
6.1.2 WebIndexinSHACL...................................... 200
6.2 DescribingClinicalRecords—FHIR ............................... 204
6.2.1 FHIRasLinkedData...................................... 206
6.2.2 Consistencyconstraints..................................... 206
6.2.3 FHIR/RDFDevelopment .................................. 209
6.2.4 GenericProperties......................................... 210
6.3 SpringerNatureSciGraph ........................................ 212
6.4 DBpediaValidationUseCases .................................... 213
6.4.1 Ontology-basedValidation.................................. 213
6.4.2 RDFMappingsValidation .................................. 214
6.4.3 ValidatingLinkContributionswithSHACL ................... 215
6.4.4 OntologyValidationwithSHACL ........................... 216
6.5 ShExforShEx ................................................. 219
6.6 SHACLinSHACL............................................. 225
6.7 Summary ..................................................... 230
6.8 SuggestedReading .............................................. 231
7 ComparingShExandSHACL ......................................233
7.1 CommonFeatures .............................................. 233
7.2 SyntacticDifferences ............................................ 237
7.3 Foundation:Schemavs.Constraints ................................ 239
7.4 InvokingValidation ............................................. 240
7.5 ModularizationandReusability.................................... 242
7.6 Shapes,Classes,andInference..................................... 244
7.7 ViolationReportingandSeverities ................................. 246
7.8 DefaultCardinalities ............................................ 246
7.9 PropertyPaths ................................................. 247
7.10 Recursion ..................................................... 248
7.11 PropertyPairConstraintsandUniqueness ........................... 250
7.12 RepeatedProperties ............................................. 251
7.13 ExactlyOneandAlternatives ..................................... 254
7.14 TreatmentofClosedShapes ...................................... 257
7.15 StemsandStemRanges.......................................... 259
7.16 Annotations ................................................... 260
7.17 SemanticsandComplexity........................................ 261
7.18 ExtensionMechanisms .......................................... 262
7.19 ConclusionsandOutlook ........................................ 263
7.20 Summary ..................................................... 266
7.21 SuggestedReading .............................................. 266
A WebIndexinShEx ................................................267
B WebIndexinSHACL..............................................269
C ShExinShEx ....................................................275
D SHACLinSHACL ...............................................279
Bibliography .....................................................285
Preface
This book describes two languages for implementing constraints on RDF data, describing the
main features of both Shape Expressions (ShEx) and Shapes Constraint Language (SHACL)
from a user perspective, and also offering a comparison of the technologies. Throughout this
book,wedevelopa small number of examples that typify validation requirementsand demon-
strate how they can be met with ShEx and SHACL. The book is not intended to be a formal
specification of the languages, for which the interested reader can consult the corresponding
referencedocuments,butrather,itismeanttoserveasanintroductiontothetechnologieswith
somebackgroundabouttherationaleoftheirdesignandsomepointsofcomparison.
Chapter 1 provides a brief introduction to the topic. Chapter 2 presents a short
overviewoftheRDFdatamodelandRDF-relatedtechnologies;thischaptercouldbeskipped
byanyreaderwhoalreadyknowsRDForTurtle.Chapter3helpsthereadertounderstandwhat
toexpectfromdatavalidation.ItdescribestheproblemofRDFvalidationandsomeapproaches
thathavebeenproposed.Thisbookspecificallyreviewstwooftheseapproachesinfurtherdetail:
ShEx(Chapter4)andSHACL(Chapter5).Thesechaptersdescribeeachlanguageandprovide
apracticalintroductionusingexamples.Followingthediscussionofbothlanguages,Chapter6
presents some applications using either ShEx, SHACL, or both. Finally, Chapter 7 compares
ShExandSHACLandofferssomeconclusions.
The goal of this book is to serve as a practical introduction to ShEx and SHACL using
examples.Whileweomittedformaldefinitionsorspecifications,referencesforfurtherreading
can be found at the end of each chapter. We give a quick overview of some background and
related technologies so that readers without RDF knowledge can follow the book’s contents.
Also,itisnotnecessarytohaveanypriorknowledgeofprogrammingorontologiestounderstand
RDFvalidationtechnologies.Theintendedaudienceisanyoneinterestedindatarepresentation
andquality.
JoseEmilioLabraGayo,EricPrud’hommeaux,IovkaBoneva,andDimitrisKontokostas
July2017