Ist16-04 An introduction to RDF

E. Della Valle – http://emanueledellavalle.org - @manudellavalle

Interoperability and Semantic Technologies 2015-16An Introduction RDF

Emanuele Della ValleDEIB - Politecnico di Milanohttp://emanueledellavalle.org - @manudellavalle


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E. Della Valle – http://emanueledellavalle.org - @manudellavalle 3

Data Interchange: RDF


RDF in a nutshellLooking for a flexible data model Why

• Application are always changing(competitive environment)

• People are always adding more features• Graceful evolution is important

Optimal: relational model• Relational model is remarkably flexible• Supports graceful evolution

– Change => Add another table– Existing queries are unaffected

• Easily accommodates new data – Without affecting existing queries

• Allows data to be easily combined ("joined") in new ways• 25+ years of relational database experience

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RDF in a nutshellResource Description Framework The adaptation of the relational model to the Web give rise

to RDF From tuples to triples

Any relational data can be represented as triples• Row Key --> Subject• Column --> Property• Value --> Value

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RDF in a nutshellRepresenting relational data in RDF (almost) E.g., drug data

Represented in RDF (almost)

ID Category FormulaBB.2 Anxiolytic

sC16H21NO2

ID Name LangBB.2 Propranolol en

BB.2 Propranololo it

BB.2 プロプラノロール

jp

BB.2

Anxiolytics C16H21NO2 Propranolol Propranololo プロプラノロール

CategoryFormula

Is a Drug

Legend

resource

literal

Name

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Drug Drug Names


RDF in a nutshellRepresenting relational data in RDF (almost) Two important problems,

- internal IDs (e.g., BB.2)- internal names of schema element (e.g., Category)once out of the database become meaningless

RDF solves this problem by using URI• Internal ID should be replaced by URI• Internal schema names should be replaced by URI• Values do not (always) need to be URI-fied

http://bio2rdf.org/drugbank_drugs:DB00571

http://dbpedia.org/resource/Category:Anxiolytics

C16H21NO2

http://www.w3.org/2004/02/skos/core#subject

http://bio2rdf.org/drugbank_ontology:chemicalFormula

http://www.w3.org/2000/01/rdf-schema#label

http://bio2rdf.org/page/drugbank_ontology:drugs

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

Legend

resource

literal

Propranolol

Propranololo

プロプラノロール

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Which URI should we use?• Popular ones! Data merge will take place automatically!

RDF in a nutshellRepresenting data in RDF Q/A 1/3




+http://bio2rdf.org/drugbank_drugs:DB00571

http://dbpedia.org/ontology/knownFor




=http://dbpedia.org/ontology/knownFor

http://dbpedia.org/resource/James_W._Black

http://dbpedia.org/resource/James_W._Black

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Where do I find popular URIs?• Ontology Dowsing

– http://www.w3.org/wiki/Ontology_Dowsing

• 1st solution: you know them ;-)– RDF vocabulary already includes:

- rdf:type : the “instance of” relationship between an individual and its class

- rdf:Property : the “concept” of property– RDF comes along a schema description language (RDF-S)

- rdfs:Class : the “concept” of class- rdfs:subClassOf : the “is a” relationship between two classes- rdfs:label : the standard way to provide a human-readable label

– …

• 2nd you search for them– With specialized search engines (e.g., http://vocab.cc/ )– In popular repositories (e.g., http://lov.okfn.org/dataset/lov/ )– …


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http://www.w3.org/wiki/Ontology_Dowsing

http://vocab.cc/

http://lov.okfn.org/dataset/lov/


What is a value? When shall we URI-fy a value? • Literals cannot be used to merge different data set• E.g., what if we what to merge two resources based on their

labels?

– BRCA may refer to different thing on the Webe.g., try http://en.wikipedia.org/wiki/BRCA

• URI-fy any value that can be eventually used to merge different dataset and leave the other values as literals


BRCA


BRCA


+ = ?

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RDF in a nutshellOther data structure in RDF Trees can be represented in RDF

Anything can be represented in RDF

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RDF in a nutshellMulti Source Data Integration with RDF

Gene Ontology

rdf:type

iRefIndex

uniprot:P05067 Uniprot:P05067Interacts with

uniprot:P05067 Go:MembranelocatedIn

uniprot:Proteinrdf:type

Uniprot:P05067Interacts with

Go:MembranelocatedIn

uniprot:P05067

uniprot:P05067 uniprot:Protein

RDF


RDF in a nutshellSerializing RDF Three alternatives to write triples, in

1. RDF/XML: Standard serialization in XML<Description about=”subject”> <property>value</property></Description>– e.g., http://dbpedia.org/data/Propranolol.rdf – Check-out the triples using http://www.w3.org/RDF/Validator/

2. NTriples: Simple (verbose) reference serialization (for specifications only)

<http://...subject> <http://...predicate> “value” .– http://www.w3.org/RDF/Validator/ARPServlet?URI=http%3A%2F

%2Fdbpedia.org%2Fresource%2FPropranolol&PARSE=Parse+URI%3A+&TRIPLES_AND_GRAPH=PRINT_TRIPLES&FORMAT=PNG_EMBED

• N3 and Turtle: Developer-friendly serializations :subject :property “value” .– e.g. http://dbpedia.org/data/Propranolol.n3

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http://dbpedia.org/data/Propranolol.rdf

http://www.w3.org/RDF/Validator/


RDF in a nutshellSerializing RDF in Turtle - namespaces

URI terms can be abbreviated using namespaces@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .@prefix dbpedia: <http://dbpedia.org/resource/> .@prefix dbpedia-owl: <http://dbpedia.org/ontology/> .

dbpedia:Propranolol rdf:type dbpedia-owl:Drug .

<http://www.w3.org/1999/ 02/22-rdf-syntax-ns#type> = 'a'

dbpedia:Propranolol a dbpedia-owl:Drug .

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RDF in a nutshellSerializing RDF in Turtle - Literals Literals: "Propranolol"

• Literals with language tags: " プロプラノロール "@jp

@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .

dbpedia:Propranolol rdfs:label "Propranolol"@en . dbpedia:Propranolol rdfs:label "Propranololo"@it . dbpedia:Propranolol rdfs:label "プロプラノロール "@jp .

• Typed literals: "3.14"^^xsd:floatdbpedia:Propranolol dbpprop:molecularWeight "259.34"^^xsd:float .

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RDF in a nutshellSerializing RDF in Turtle - Convenience Syntax Abbreviating repeated subjects:

dbpedia:Propranolol rdfs:label "Propranololo"@it . dbpedia:Propranolol dbpprop:molecularWeight "259.34"^^xsd:float .

... is the same as ...dbpedia:Propranolol rdfs:label "Propranololo"@it ; dbpprop:molecularWeight "259.34"^^xsd:float .

Abbreviating repeated subject/predicate pairs:dbpedia:Propranolol rdfs:label "Propranolol"@en . dbpedia:Propranolol rdfs:label "Propranololo"@it . dbpedia:Propranolol rdfs:label " プロプラノロール "@cn .

... is the same as ...dbpedia:Propranolol rdfs:label "Propranolol"@en , "Propranololo"@it , "プロプラノロール "@cn .

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RDF in a nutshellAre you following? Let's check!

[source http://origin-www.yoursingapore.com/content/traveller/zh/browse/see-and-do/hands-on/_jcr_content/flash/image.img.png ]


RDF in a nutshellAre you following? Let's check! Represent in the graphical syntax presented at slide 6 the

following database

Is this only a pedantic application of slide 6? Serialize it in turtle syntax

• using rdf:type to say "is a" and rdfs:label to say "name"• Using "@prefix : <http://www.ex.org/>" for all other terms,

e.g., :Doctor, :treats, etc. Shorted down the serialization using the convenience syntax Check correctness at http://www.easyrdf.org/converter Results are published on the course Web site

DID Name

D1 Alice

D2 Bob

Doctor treatsPID Name

P1 Carl

P2 David

PatientDID PID

D1 P2

D1 P1

D2 P1


What if I cannot thing about a good URI?• When no go URI exists, you can use blank nodes ( ) • The following relational data …

• … can be translated in RDF, in the BIO vocabulary [1], as follows

[1] http://vocab.org/bio/0.1.html


Person Bio Event Date

Sofia Birth 1974-02-28

Sofia Marriage 1995-08-04

1974-02-28

http://www.sofia.org/#me

http://purl.org/vocab/bio/0.1/Birth

http://purl.org/vocab/bio/0.1/Marriage

1995-08-04

http://purl.org/vocab/bio/0.1/event



http://purl.org/vocab/bio/0.1/date

http://www.w3.org/1999/02/22-rdf-syntax-ns#typehttp://purl.org/vocab/bio/0.1/date

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RDF in a nutshellSerializing RDF in Turtle – black nodes The following RDF model (see previous slide), including two

blank nodes, can be serialized as shown hereafter

@prefix bio: <http://purl.org/vocab/bio/0.1/> .

http://www.sofia.org/#me bio:event _:1, _:2 ._:1 a bio:Birth; bio:date "1974-02-28"^^xsd:date ._:2 a bio:Mariage; bio:date "1995-08-04"^^xsd:date .

1974-02-28




1995-08-04







Blank node identifiers

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RDF in a nutshellSerializing RDF in Turtle – black nodes The following RDF model (see previous slide), including two

blank nodes, can be serialized as shown hereafter

@prefix bio: <http://purl.org/vocab/bio/0.1/> .

http://www.sofia.org/#me bio:event [ a bio:Birth; bio:date "1974-02-28"^^xsd:date ] , [ a bio:Mariage; bio:date "1995-08-04"^^xsd:date ].

1974-02-28




1995-08-04







Blank node Convenience syntax

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RDF in a nutshellXML vs. RDF w.r.t. Evolving Data Scenario: Describe printer capabilities V1 has several features

XML RDF

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RDF in a nutshellXML vs. RDF w.r.t. Evolving Data V1.1 adds two features

• What effect on existing client software? – Regenerate stubs?– Recompile?– Did any queries break?– (Depends how they're written. Best programmers?)

XML RDF

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RDF in a nutshellXML vs. RDF w.r.t. Evolving Data V1.2 adds three more features

• What effect on existing client software?

XML RDF

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RDF in a nutshellXML vs. RDF w.r.t. Evolving Data V2 adds colors

• What effect on existing client software?

XML RDF

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RDF in a nutshellXML vs. RDF w.r.t. Evolving Data Version n combines printer, scanner, fax:

Problem: How to combine trees?• Printer and fax both have output paper settings (red)• Scanner and fax both have input image settings (blue)

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RDF in a nutshellXML vs. RDF w.r.t. Evolving Data Flexibility is important

• Products are always changing(competitive environment)

• People are always adding more features• Graceful evolution is important• Relational data is remarkably flexible

XML syntax is important• Lots of application, which use XML, are already available• Lots of tools for XML are already available• Trees alows for simple parsing without loading the entire

model (i.e., XML parsing using SAX)

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RDF in a nutshellSerializing RDF in XML - basics W3C standardized an RDF/XML syntax [1] The basic idea is to insert an XML element for each node

(sobject and value) and arc (predicate) Es.

<rdf:RDF xmlns:rdf=”http://www.w3.org/1999/02/22-rdf-syntax-ns#” xmlns:ex=”http://www.example.org/” xmlns:sid=“URN:org:example:staffid:” xmlns:dc=”http://purl.org/dc/elements/1.1/”> <rdf:Description rdf:about="http://www.example.org/index.html ">

<dc:creator> <rdf:Description rdf:about="URN:org:example:staffid:85740"/>

</dc:creator ></rdf:Description>

</rdf:RDF>[1] RDF/XML Syntax Specification available at http://www.w3.org/TR/rdf-syntax-grammar/

ex:index.html sid:85740

dc:creator

propertyelement

Root tag

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RDF in a nutshellSerializing RDF in XML - abbreviation A possible abbreviation is using rdf:resource in the

property elements Es.

<rdf:RDF xmlns:rdf=”http://www.w3.org/1999/02/22-rdf-syntax-ns#” xmlns:ex=”http://www.example.org/” xmlns:sid=“URN:org:example:staffid:” xmlns:dc=”http://purl.org/dc/elements/1.1/”> <rdf:Description rdf:about="http://www.example.org/index.html ">

<dc:creator rdf:resource="URN:org:example:staffid:85740"/> </rdf:Description></rdf:RDF>

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RDF in a nutshellSerializing RDF in XML – more statements Other statements

• Es.

can be added • afterwords

<rdf:Description rdf:about="http://www.example.org/index.html"> <dc:creator rdf:resource="URN:org:example:staffid:85740"/>

</rdf:Description><rdf:Description rdf:about="URN:org:example:staffid:85740">

<foaf:email rdf:resource="mailto:[email protected]"/></rdf:Description>

• or inline if they share the same subject <rdf:Description rdf:about="http://www.example.org/index.html ">

<dc:creator> <rdf:Description rdf:about="URN:org:example:staffid:85740">

<foaf:email rdf:resource="mailto:[email protected]"/> </rdf:Description> </dc:creator ></rdf:Description>


dc:creator

mailto:[email protected]:email

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RDF in a nutshellSerializing RDF in XML – rdf:type abbreviation It’s possible to abbreviate rdf:type

• Es.

• Long form

<rdf:Description rdf:about="http://www.example.org/index.html"><rdf:type rdf:resource="http://www.example.org/pagina_web">

</rdf:Description>

• Abbreviated form

<ex:pagina_web rdf:about="http://www.example.org/index.html" />

ex:index.html

ex:pagina_web

rdf:type

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RDF in a nutshellSerializing RDF in XML – a larger example A compact XML serialization of

is<ex:pagina_web rdf:about="http://www.example.org/index.html"> <dc:creator> <ex:employee rdf:about="sid:55740" foaf:email="mailto:[email protected]"/> <dc:creator> </ex:pagina_web>


dc:creator

mailto:[email protected]:email

ex:pagina_web ex:impiegato

rdf:type rdf:type

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RDF in a nutshellMerging XML files 1/2 Suppose you have to merge the two following XML

Merging the XML trees is difficult, but being RDF …

<Park rdf:about="Yosemite"> <conteins> <Camp rdf:about="North-Pines"/> </conteins> <crossedBy> <Path rdf:about="S11"/> </crossedBy></Park>

<Camp rdf:about="North-Pines" locatedIn="Yosemite"> <accessibleBy> <Path rdf:about="S11"/> </accessibleBy> </Camp>

Yosemite

North-Pines

Park

rdf:type

rdf:type

conteins

Camp

S11rdf:type

Path

crossedBy

Yosemite

North-Pinesrdf:type

Camp

S11

rdf:typePath

accessibleBylocatedIn

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RDF in a nutshellMerging XML files 2/2 It’s (just) a matter to merge the two RDF graphs

NOTE: It works out nicely because both RDF/XML documents refer to the same resources and use the same vocabularies.

U

Yosemite

North-Pines

Park

rdf:type

rdf:type

conteins

Camp

S11

Path

accessibleBy

crossedBylocatedIn

rdf:type

Yosemite

North-Pines

Park

rdf: type

rdf: type

conteins

Camp

S11rdf: type

Path

crossedBy

Yosemite

North-Pinesrdf:type

Camp

S11

rdf:typePath

accessibleBylocatedIn

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RDF in a nutshellRDFa Resource Description Framework in Attributes (RDFa)

• First proposed in 2004• W3C recommendation since October 14, 2008:

http://www.w3.org/TR/rdfa-syntax/ The essence

• it provides a set of markup attributes to augment the visual information on the Web with machine-readable hints

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RDF in a nutshellRDFa – An example Consider the HTML snippet hereafter

• The microformats.org site was launched on 2005-06-20 at the Supernova Conference in San Francisco, CA, USA.

Let’s annotate it using hCalendar • 

 The microformats.org site was launched on 2005-06-20 at the Supernova Conference in San Francisco, CA, USA . 

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RDF in a nutshellRDFa – the attributes about – a URI specifying the resource the metadata is

about rel and rev – specifying a relationship and reverse-

relationship with another resource, respectively src, href and resource – specifying the partner resource property – specifying a property for the content of an

element or the partner resource content – optional attribute that overrides the content of

the element when using the property attribute datatype – optional attribute that specifies the datatype of

text specified for use with the property attribute typeof – optional attribute that specifies the RDF type(s) of

the subject or the partner resource37


RDF in a nutshellRDFa – resources For more information

• http://www.slideshare.net/ivan_herman/introduction-to-rdfa/ Validation tool

• http://validator.w3.org/nu/

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Publishing RDF as Linked DataPrinciples

1. Things must be identified with dereferenceable HTTP URIs.2. If such a URI is dereferenced asking for the MIME-type

application/rdf+xml, a data source must return an RDF/XML description of the identified resource.

3. Besides RDF links to resources within the same data source, RDF descriptions should also contain RDF links to resources provided by other data sources

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Publishing RDF as Linked Data Example based on dbpedia Approach

E.g. • Resource identifier

– http://dbpedia.org/resource/Propranolol • RDF representation describing Propranolol

– http://dbpedia.org/data/Propranolol • HTML representation describing Propranolol

– http://dbpedia.org/page/Propranolol Test it! http://idi.fundacionctic.org/vapour

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RDF in a nutshellRDF Resources RDF at the W3C - primer and specifications

• http://www.w3.org/RDF/ Semantic Web tools - community maintained list; includes

triple store, programming environments, tool sets, and more• http://esw.w3.org/topic/SemanticWebTools

302 Semantic Web Videos and Podcasts - includes a section specifically on RDF videos• http://www.semanticfocus.com/blog/entry/title/302-semantic-

web-videos-and-podcasts/

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credits Some slides are derived from

• “How to Publish Linked Data on the Web” by Chris Bizer, Richard Cyganiak and Tom Heath http://sites.wiwiss.fu-berlin.de/suhl/bizer/pub/LinkedDataTutorial/

• “Bio2RDF and Beyond!” by Michel Dumontier http://www.slideshare.net/micheldumontier/bio2rdf-and-beyond

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Ist16-04 An introduction to RDF