Ist16-04 An introduction to RDF

E. Della Valle – http://emanueledellavalle.org - @manudellavalle
Interoperability and Semantic Technologies 2015-16
An Introduction RDF
Emanuele Della Valle
DEIB - Politecnico di Milano
http://emanueledellavalle.org - @manudellavalle

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2

Data Interchange: RDF

RDF in a nutshell
Looking 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
4

RDF in a nutshell
Resource 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
5

RDF in a nutshell
Representing relational data in RDF (almost)
 E.g., drug data
 Represented in RDF (almost)
ID Category Formula
BB.2 Anxiolytics C16H21NO2
ID Name Lang
BB.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
Category
Formula
Is a Drug
Legend
resource
literal
Name
6
Drug Drug Names

RDF in a nutshell
Representing 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
C16H21NO
2
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
7

 Which URI should we use?
• Popular ones! Data merge will take place automatically!
RDF in a nutshell
Representing 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
8

 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/ )
– …
RDF in a nutshell
9

 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 Web
e.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
RDF in a nutshell
BRCA
BRCA
+ = ?
10

RDF in a nutshell
Other data structure in RDF
 Trees can be represented in RDF
 Anything can be represented in RDF
11

RDF in a nutshell
Multi Source Data Integration with RDF
Gene
Ontology
rdf:type
iRef
Index
uniprot:P05067 Uniprot:P05067
Interacts with
uniprot:P05067 Go:Membrane
locatedIn
uniprot:Proteinrdf:type
Uniprot:P05067
Interacts with
Go:Membrane
locatedIn
uniprot:P05067
uniprot:P05067 uniprot:Protein
RDF

RDF in a nutshell
Serializing 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
13

RDF in a nutshell
Serializing 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 .
14

RDF in a nutshell
Serializing 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:float
dbpedia:Propranolol dbpprop:molecularWeight "259.34"^^xsd:float .
15

RDF in a nutshell
Serializing RDF in Turtle - Convenience Syntax
 Abbreviating repeated subjects:
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 " 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 .
16

RDF in a nutshell
Are 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 nutshell
Are 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 treats
PID Name
P1 Carl
P2 David
Patient
DID 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
RDF in a nutshell
Person Bio Event Date
Sofia Birth 1974-02-28
Sofia Marriage 1995-08-04
1974-02-28
http://www.sofia.org/#m
e
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
19

RDF in a nutshell
Serializing 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
e
1995-08-04
Blank node
identifiers
20

RDF in a nutshell
Serializing 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
e
1995-08-04
Blank node
Convenience syntax
21

RDF in a nutshell
XML vs. RDF w.r.t. Evolving Data
 Scenario: Describe printer capabilities
 V1 has several features
XML RDF
22

RDF in a nutshell
 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
23

RDF in a nutshell
 V1.2 adds three more features
XML RDF
24

RDF in a nutshell
 V2 adds colors
XML RDF
25

RDF in a nutshell
 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)
26

RDF in a nutshell
 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)
27

RDF in a nutshell
Serializing 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
property
element
Root tag
28

RDF in a nutshell
Serializing 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/”>
<dc:creator rdf:resource="URN:org:example:staffid:85740"/>
</rdf:Description>
</rdf:RDF>
29

RDF in a nutshell
Serializing 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:mrossi@example.org"/>
</rdf:Description>
• or inline if they share the same subject
<dc:creator>
<rdf:Description rdf:about="URN:org:example:staffid:85740">
<foaf:email rdf:resource="mailto:mrossi@example.org"/>
</rdf:Description>
</dc:creator >
</rdf:Description>
dc:creator
mailto:mrossi@example.org
foaf:email
30

RDF in a nutshell
Serializing 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
31

RDF in a nutshell
Serializing 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:mrossi@example.org"/>
<dc:creator>
</ex:pagina_web>
dc:creator
mailto:mrossi@example.org
foaf:email
ex:pagina_web ex:impiegato
rdf:type rdf:type
32

RDF in a nutshell
Merging 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
S11
rdf:type
Path
crossedBy
Yosemite
North-Pines
rdf:type
Camp
S11
rdf:type
Path
accessibleBy
locatedIn
33

RDF in a nutshell
Merging 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
crossedBy
locatedIn
rdf:type
Yosemite
North-Pines
Park
rdf:type
rdf:type
conteins
Camp
S11
rdf:type
Path
crossedBy
Yosemite
North-Pines
rdf:type
Camp
S11
rdf:type
Path
accessibleBy
locatedIn
34

RDF in a nutshell
RDFa
 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
35

RDF in a nutshell
RDFa – 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

.


36

RDF in a nutshell
RDFa – 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 resource
37

RDF in a nutshell
RDFa – resources
 For more information
• http://www.slideshare.net/ivan_herman/introduction-to-rdfa/
 Validation tool
• http://validator.w3.org/nu/
38

Publishing RDF as Linked Data
Principles
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.
1. Besides RDF links to resources within the same data
source, RDF descriptions should also contain RDF links to
resources provided by other data sources
39

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
40

RDF in a nutshell
RDF 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/
41

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
42

Ist16-04 An introduction to RDF

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