Semantic Web for Life Sciences: vision, aims, tools, platforms

Semantic Web for Life Sciences

Visions, Aims, Tools, PlatformsAndrea Splendiani

Nettab, 16th October 2013, Venice Andrea Splendiani @AndSplendandrea.splendiani@[deri.org,intellileaf.com]

Semantic Web for Life Sciences: Visions, Aims, Tools, Platforms

mercoledì 16 ottobre 13

Index




An Introduction to Semantic Web Technologies




A new form of Web content that is meaningful to computers will unleash a revolution of new possibilities

Web + Semantics

What




• RDF: Resource Description Framework

• A language to represent concepts and their relations

• Simple statements:

Subject Predicate Object

• Conceptually a graph

Quick Intro to RDF




• RDF: Resource Description Framework

• A language to represent concepts and their relations

• Simple statements:

Subject Predicate Object

• Conceptually a graph

Quick Intro to RDF

subjectpredicate

object




• How does this work in practice ?

• We identify each node and edge by a URI

• (we only need to identify, not define things!)

• URIs could be Web-resolvable

Quick Intro to RDF

subjectpredicate

object

http://nettab.org/biology/Chromosome http://nettab.org/properties/contains http://nettab.org/biology/DNANettab, 16th October 2013, Venice Andrea Splendiani @AndSplend

andrea.splendiani@[deri.org,intellileaf.com]Semantic Web for Life Sciences: Visions, Aims, Tools, Platforms


http://anatomy.org/Chromosome


Quick Intro to RDF

http://nettab.org/biology/Chromosome http://nettab.org/properties/contains http://nettab.org/biology/DNA






Quick Intro to RDF

http://nettab.org/biology/Chromosome http://nettab.org/properties/contains http://nettab.org/biology/DNA






RDF:

• No data-types

• No cardinalities

• Importance of identification

http://milicicvuk.com/blog/2011/08/10/fixing-the-rdf-model/

Quick Intro to RDF: RDF vs other modeling






The Semantic Web is easy(a bit like html)

Quick Intro to RDF: RDF vs other modeling




Technology details

• URIs

• The technology stack

• Serializations

• Blank nodes

• Named graphs

• Semantics

• Computational representation of meaning

• RDFS

• OWL

• SKOSNettab, 16th October 2013, Venice Andrea Splendiani @AndSplend



• URIs are global identifiers

• Supported by a widely adopted infrastructure (the Web)

• Simple but implicit authority mechanism (namespace)

http://nettab.org/biology/Chromosome

Technology details: URIs




http://anatomy.org/ontology/DNA


http://www.ncbi.nlm.nih.gov/pubmed/20605693http://dbpedia.org/resource/Berlinhttp://biocyc.org/biopax/biopax#smallMolecule84998http://www.reactome.org/biopax#H2O__ChEBI_15377_http://bio2rdf.org/go:0032283


• Not a consistent “scheme” to define URIs

• Good practices: e.g.: no parameters

• Decision points: semantically opaque or not




http://www.ncbi.nlm.nih.gov/pubmed/20605693

http://www.ncbi.nlm.nih.gov/pubmed/20605693

http://dbpedia.org/resource/Berlin

http://dbpedia.org/resource/Berlin

http://biocyc.org/biopax/biopax#smallMolecule84998

http://biocyc.org/biopax/biopax#smallMolecule84998

http://purl.org/obo/owl/NCBITaxon#




• What is necessary:

• Unambiguous identification

• Persistence (versions)


http://nettab.org/Venice






What should URIs resolve to ?

Nothing

http://wifo5-03.informatik.uni-mannheim.de/bizer/pub/LinkedDataTutorial/







Not a coherent monolithic technology!

Technology details: the technology stack




http://purl.org/go/owl#GO_0006915


110020

programmed cell death

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

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

http://www.example.com/hasdbaccession

http://www.example.com/instance1

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

English

Integer

Technology details: serializations

RDF can be represented in many syntaxes

• N-Triples

• Turtle

• XML(s)

• ...

• JSON

• Binary

http://librdf.org/raptor/

Use a tool like Rapper to convert among syntaxes









110020







English

Integer

<http://purl.org/obo/owl/GO#GO_0006915> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.org/obo/owl/GO#GO_0012501> .

<http://purl.org/obo/owl/GO#GO_0012501> <http://www.w3.org/2000/01/rdf-schema#label> "programmed cell death"@en .

<http://www.example.com/instance1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/obo/owl/GO#GO_0006915> .

<http://www.example.com/instance1> <http://www.example.com/hasdbaccession> "110020"^^<http://www.w3.org/2001/XMLSchema#int> .


N-Triples

• Every subset (lines) is valid N-Triples

• Good for large files, streaming,...

• Very simple to produce via scripts




http://purl.org/obo/owl/GO#GO_0006915




















http://www.w3.org/2001/XMLSchema#int




110020







English

Integer






N-Triples































110020







English

Integer






N-Triples






























110020







English

Integer


Turtle

• Easy to read

• Easy to write by hand (keyboard)

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .@prefix GO: <http://purl.org/obo/owl/GO#> .@prefix : <http://www.example.com/> .

go:GO_0006915 rdfs:subClassOf go:GO_0012501 .

go:GO_0012501> rdfs:label "programmed cell death"@en .

:instance1 :hasdbaccession "110020"^^<http://www.w3.org/2001/XMLSchema#int> ; a go:GO_0006915 .

http://prefix.cc/




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



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





http://www.example.com/
















http://prefix.cc

http://prefix.cc


RDFXML<?xml version="1.0" encoding="utf-8"?><rdf:RDF xmlns:go="http://purl.org/obo/owl/GO#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns="http://www.example.com/"> <rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0006915"> <rdfs:subClassOf rdf:resource="http://purl.org/obo/owl/GO#GO_0012501"/> </rdf:Description> <rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0012501"> <rdfs:label xml:lang="en">programmed cell death</rdfs:label> </rdf:Description> <rdf:Description rdf:about="http://www.example.com/instance1"> <rdf:type rdf:resource="http://purl.org/obo/owl/GO#GO_0006915"/> </rdf:Description> <rdf:Description rdf:about="http://www.example.com/instance1"> <hasdbaccession rdf:datatype="http://www.w3.org/2001/XMLSchema#int">110020</hasdbaccession> </rdf:Description></rdf:RDF>

Good for ?

<go:GO_0006915 rdf:about="http://www.example.com/instance1"> <hasdbaccession rdf:datatype="http://www.w3.org/2001/XMLSchema#int">110020 </hasdbaccession> </go:GO_0006915>










<http://dbpedia.org/resource/Venice> foaf:based_near [ geo:lat "45.4375" ; geo:long "12.335833" ; a <http://example/Point> ] .

<http://dbpedia.org/resource/Venice> foaf:based_near _:p1 ._:p1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://example/Point> ._:p1 <http://www.w3.org/2003/01/geo/wgs84_pos#:lat> "45.4375" ._:p1 <http://www.w3.org/2003/01/geo/wgs84_pos#:long> "12.335833" .

<rdf:Description rdf:about="http://dbpedia.org/resource/Venice"> <foaf:based_near> <geo:Point> <geo:lat>45.4375</geo:lat> <geo:long>12.335833</geo:long> </geo:Point> </foaf:based_near> </rdf:Description>

Technology details: blank nodes

• Some entities may not have a global identifier

• Could we always provide one ?




http://dbpedia.org/resource/Venice


http://example/Point












<http://dbpedia.org/resource/Venice> foaf:based_near _:p1 nettabex:1._:p1 rdf:type <http://example/Point> nettabex:1._:p1 geo:lat "45.4375" nettabex:1._:p1 geo:long "12.335833" nettabex:1.

Technology details: named graphs

• An entire (sub)graph can be identified (“named”) by a URI

• Graphs can be subject and object of predicates

• Good to represent context (hence provenance...)

(pseudo N-quads)Nettab, 16th October 2013, Venice Andrea Splendiani @AndSplend







https://www.usenix.org/legacy/event/tapp09/tech/full_papers/pediaditis/pediaditis_html/

Technology details: semantics

Facts Defining reality Computing definitions

Ontology:“A formalization of a conceptualization”






http://www.ifomis.org/bfo

Ontologies:The conceptualization

Technology details: semantics

extract from BFO

extract from RONettab, 16th October 2013, Venice Andrea Splendiani @AndSplend



GO:GO_0006915

GO:GO_0012501apoptosis


rdfs:subClassOf

rdfs:label

rdfs:label

GO:GO_0008585

rdfs:subClassOf

virus-infected cell

apoptosis

rdfs:label

GO:GO_0006915



rdfs:subClassOf

rdfs:label

rdfs:label

GO:GO_0008585

rdfs:subClassOf

virus-infected cell

apoptosis

rdfs:label

(?x rdfs:subClassOf ?y)(?y rdfs:subClassOf ?z) -> (?x rdfs:subClassOf ?z)

Technology details: representation of meaning

Computational representation of meaning: transitive property




• Inconsistency• Classification• Consistency• Subsumption


Some possible computations




• Emergent Semantics• First order logic• Inference rules• RDFS• OWL (-2, DL, RL, QL...)• SKOS





RDF-S: • type • subClassOf• subPropertyOf• ...

GO:GO_0006915



rdfs:subClassOf

rdfs:label

rdfs:label

GO:GO_0008585

rdfs:subClassOf

virus-infected cell

apoptosis

rdfs:label

Inconsistence ?

Technology details: RDFS




OWL: • Class Union/Intersection• Universal/Existential restriction• Property Domain/Range• Transitive/Reflexive/Functional properties• ...

• OWL provides a set of properties and resources to characterize classes.

• OWL supports inference of the class structure of an ontology

• OWL has several variants addressing different trade-offs in computability/expressivity

• Many ontologies “use OWL”, but they really only use a few axioms (almost like RDFS)

• OWL is not a schema language! (Classes and properties have a different meaning than OO)

Inconsistence !

Technology details: OWL




Example: cell motility part of localization of cell

<owl:Class rdf:about="GO#GO_0006928"> <rdfs:label xml:lang="en">cell motility</rdfs:label> <rdfs:subClassOf> <owl:Restriction> <owl:onProperty rdf:resource="obo#part_of"/> <owl:someValuesFrom rdf:resource="GO#GO_0051674"/> </owl:Restriction> </rdfs:subClassOf>...</owl:Class>





OWL Inference is not validation!

Person hasFather exactly 1

George a PersonGeorge hasFather MarkGeorge hasFather John

John sameAs Mark

•RDF Validation: Syntax•(OWL) Reasoning: Consistency•SPIN Rules (later)





Two things to possibly avoid when working with OWL/RDF:

• use RDF/XML

• use OO tools





Technology details: SKOS

• SKOS: Simple Knowledge Organization System

• Not a formal system (can be mapped to OWL)

• Weak semantic connotation, but useful in many classification tasks

You don’t improve the ontological commitment of a classification system by representing it in OWL (if the conceptualization doesn’t improve!)




Why Life Sciences ?

Why Semantic Web ?Nettab, 16th October 2013, Venice Andrea Splendiani @AndSplend



Why ? Heterogeneous information




• The DNA model has around 60 years (’53)

• “basic principles” changed in a timescale of about 10 years

The textbook tale

Missing: epigenetics, miRNA

Why ? Mutability of information (schema)




The meaning of “Gene”

Why ? Complex Semantics




Why ? The Semantic Web can Help How ?

• Makes data integration easier

• Makes semantic problems explicit





• Makes data integration easier

• Makes semantic problems explicit




Easy data integration: what if we used a relational model

CityID population CityName

INT INT VARHCHAR(45)

1 40885 Venezia

UniversityID students established CityID CityName

INT INT Date INT TEXT

1 20000 1868 2 Venice







1 40885 Venezia



1 20000 1868 2 Venice



Implicit foreign key

In the Semantic Web “keys” are explicit by definitionNettab, 16th October 2013, Venice Andrea Splendiani @AndSplend





1 40885 Venezia



1 20000 1868 2 Venice



Local identifiers, mappings required






1 40885 Venezia



1 20000 1868 2 Venice



What is the type of a CityName ?How many names can a city have ? Is the city name a key ?

Perhaps we can assume that in the same country, two cities with the same name are the same city.We could just declare rdfs:property as functional to deduce such equivalences.

Does the University of Venice only exists in Venice ? Nettab, 16th October 2013, Venice Andrea Splendiani @AndSplend



The broader view




The broader view




• All predicates are global (no implicit contexts)

• Declarative vs imperative processing of information

• Immutability: once information is out, you cannot control it

• Monotonicity: you only add information

• There may be more that what you know: Open World Assumption

The broader view: Not only NoSQL

The Semantic Web is not only a technology to handle data. Being “Semantic” and “Web” has some implication on the way information is thought




HOWTO publish information on the Semantic Web





Simply link an RDF filePossibly via a good URI





Programmatic access via a SPARQL endpoint(can be resource intensive)




<div xmlns:dc="http://purl.org/dc/elements/1.1/"> <div about="/alice/posts/trouble_with_bob"> <h2 property="dc:title">The trouble with Bob</h2> <h3 property="dc:creator">Alice</h3> ... </div>

<div about="/alice/posts/jos_barbecue"> <h2 property="dc:title">Jo's Barbecue</h2> <h3 property="dc:creator">Eve</h3> ... </div>

</div>


Embed RDF in html (e.g.: RDFa)




http://purl.org/dc/elements/1.1/


Linked Data APIs (ELDA), Linked Data Platform, Linked Data JSON ...

http://www4.wiwiss.fu-berlin.de/bizer/pub/LinkedDataTutorial/


Publish information as Linked-Data

• Linked Data is a set of good practices to publish RDF

• Use only HTTP resolvable URIs

• Dereferencing URIs (202 information resources 303 see other)

• Content negotiation




http://en.wikipedia.org/wiki/Linked_data

http://en.wikipedia.org/wiki/Linked_data

LAT pp Grb2LAT pp PI3K_p85-alphaLAT pp PLC-gammaLAT pp GrapLAT pp GadsSLP-76 pp VavSLP-76 pp NckSLP-76 pp SLAP-130SLP-76 pp GadsSLP-76 pp ShcSLP-76 pp CblSLP-76 pp LynSLP-76 pp PLC-gamma2CD28 pp Grb2CD28 pp PI3K_p85-betaCD28 pp CD80



1 40885 Venice

Table SIFhttp://ns/ID#1 http://ns/prop#population 40885http://ns/ID#1 http://ns/prop#CityName Venice

<http://ns/ID#$1 http://ns/prop#$2 http://ns/ID#$3>

HOWTO: simple conversions to RDF




http://ns/ID#

http://ns/ID#

http://ns/ID#

http://ns/ID#

http://ns/ID#

http://ns/ID#

http://d2rq.org

http://www.w3.org/TR/2012/PR-rdb-direct-mapping-20120814/http://www.w3.org/TR/2012/REC-r2rml-20120927/

HOWTO: relational to RDF mapping

D2RQ

• Relational to RDF conversion

• Dynamic rendering (SPARQL)

• Linked data frontend (Pubby)




http://d2rq.org

http://d2rq.org

http://www.w3.org/TR/2012/PR-rdb-direct-mapping-20120814/




Automated mapping:

D2RQ (like other tools) by default only generates a structural mapping (this can then be tuned).It cannot generate a dc:creator property between Paper and Author


ID (key)

Name

Email

AuthorID (fkey)

PaperID (fkey)

...

ID (key)

PubmedID

Title

Author Paper

Author2Paper




# Table Authormap:author a d2rq:ClassMap; d2rq:dataStorage map:database; d2rq:uriPattern "author/@@Author.ID@@"; d2rq:class foaf:person; d2rq:classDefinitionLabel "author"; .map:author_name a d2rq:PropertyBridge; d2rq:belongsToClassMap map:author; d2rq:property foaf:name; d2rq:propertyDefinitionLabel "Author_name"; d2rq:column "Author.Name"; .


Example edited mapping:

ID (key)

Name

Email

AuthorID (fkey)

PaperID (fkey)

...

ID (key)

PubmedID

Title

Author Paper

Author2Paper




map:hasAuthor a d2rq:PropertyBridge; d2rq:belongsToClassMap map:Paper; d2rq:property :hasAuthorEmail; d2rq:column "Author.Email"; d2rq:join "Paper.ID <= Author2Paper.PaperID"; d2rq:join "Author2Paper.PersonID => Person.ID"; d2rq:datatype xsd:string; d2rq:propertyDefinitionLabel "email"@en; d2rq:propertyDefinitionComment "Author email"@en; .


ID (key)

Name

Email

AuthorID (fkey)

PaperID (fkey)

...

ID (key)

PubmedID

Title

Author Paper

Author2Paper

map:Paper a d2rq:ClassMap; d2rq:class :Paper; d2rq:uriPattern "http://togows.dbcls.jp/entry/pubmed/@@Paper.PubmedID@@.ttl d2rq:condition "Papers.PubmedID != \”\”"; d2rq:dataStorage map:Database1.




http://togows.dbcls.jp/entry/pubmed/@[email protected]

http://togows.dbcls.jp/entry/pubmed/@[email protected]

Discussion + Jena

http://www.apache.org/dist/jena/binaries/

HOWTO setup your own triplestore

Just run: fuseki --loc=path --update /Nettab, 16th October 2013, Venice Andrea Splendiani @AndSplend





http://protege.stanford.edu

Ontologies and Protege

Practical suggestions:

• Produce RDF (simple scripts or mapper)

• Translate among syntaxes via Rapper

• Build ontologies (for your RDF) in Protege

Ontology editor




Protege to edit and visualize the ontology. Rely on the triplestore for inference.


Two typical scenarios of interoperability between RDF and Ontologies

Ontologies are large taxonomies or DAGs, only transitive inference is used.(E.g.: SKOS-like)

Ontologies are complex terminology that rely on axioms for consistency and inference

Edit in Protege, classify the ontology via reasoner, then use the results in combination with other RDF statements.

Third scenario....Nettab, 16th October 2013, Venice Andrea Splendiani @AndSplend




You can specify URIs as to match your RDF



• Relations are first class objects

• Specifying domain, range and annotation can go a long way in

• “documenting” the ontology




rdf.myexperiment.org/void.rdfhttp://www.w3.org/TR/void/

VOID and metadata

VOID: Metadata about a dataset.

• Provenance• License• Vocabularies• Statistics




http://www.w3.org/TR/void/




curl -H "Accept: application/rdf+xml" http://beta.sparql.uniprot.org/sparql

VOID and metadata

SPARQL service descriptor

• Query language supported

• Formats returned• Entailment regime• ...




http://beta.sparql.uniprot.org/sparql


VOID and metadata

Consider registering your data in a data registerNettab, 16th October 2013, Venice Andrea Splendiani @AndSplend



HOWTO use information from the Semantic Web




# NAME : Get psoriasis proteins# PARAMETER: psoriasis: the disease name# FUNCTION : returns all the proteins that have 'psoriasis' in# their Swiss-Prot disease description and their# interacting proteins (if known)

BASE <http://www.semantic-systems-biology.org/>PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>PREFIX ssb:<http://www.semantic-systems-biology.org/SSB#>SELECT distinct ?protein_name ?disease_description ?interacts_with ?encoded_byWHERE { GRAPH <uniprot_sprot> { ?protein_id ssb:disease ?disease_description. ?protein_id ssb:mnemonic ?protein_name. OPTIONAL { ?protein_id ssb:interacts_with ?interactor. ?interactor ssb:mnemonic ?interacts_with. ?interactor ssb:encoded_by ?encoded_by. } } FILTER regex(?disease_description, 'psoriasis').}

http://www.semantic-systems-biology.org/biogateway/endpoint?default-graph-uri=&query=%23+NAME+++++%3A+Get+psoriasis+proteins%0D%0A%23+PARAMETER%3A+psoriasis%3A+the+disease+name%0D%0A%23+FUNCTION+%3A+returns+all+the+proteins+that+have+%27psoriasis%27+in%0D%0A%23++++++++++++their+Swiss-Prot+disease+description+and+their%0D%0A%23++++++++++++interacting+proteins+%28if+known%29%0D%0A%0D%0ABASE+++%3Chttp%3A%2F%2Fwww.semantic-systems-biology.org%2F%3E%0D%0APREFIX+rdfs%3A%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0D%0APREFIX+ssb%3A%3Chttp%3A%2F%2Fwww.semantic-systems-biology.org%2FSSB%23%3E%0D%0ASELECT+distinct+%3Fprotein_name+%3Fdisease_description%0D%0A+++++++%3Finteracts_with+%3Fencoded_by%0D%0AWHERE+%7B%0D%0A++GRAPH+%3Cuniprot_sprot%3E+%7B%0D%0A++++%3Fprotein_id+ssb%3Adisease+%3Fdisease_description.%0D%0A++++%3Fprotein_id+ssb%3Amnemonic+%3Fprotein_name.%0D%0A++++OPTIONAL+%7B%0D%0A++++++%3Fprotein_id+ssb%3Ainteracts_with+%3Finteractor.%0D%0A++++++%3Finteractor+ssb%3Amnemonic+%3Finteracts_with.%0D%0A++++++%3Finteractor+ssb%3Aencoded_by+%3Fencoded_by.%0D%0A++++%7D%0D%0A++%7D%0D%0A++FILTER+regex%28%3Fdisease_description%2C+%27psoriasis%27%29.%0D%0A%7D&format=text%2Fhtml&debug=on

Introduction to SPARQL

SPARQL is REST! (one query is one URL)




http://www.semantic-systems-biology.org/

http://www.semantic-systems-biology.org/





http://www.semantic-systems-biology.org/SSB#












































SELECT ?x ?y...WHERE {GRAPH PATTERN}

CONSTRUCT {?x ?y ?z}WHERE {GRAPH PATTERN}

ASKDESCRIBE


SPARQL supports different kind of queries








PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>PREFIX owl: <http://www.w3.org/2002/07/owl#>PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>PREFIX dc: <http://purl.org/dc/elements/1.1/>PREFIX dcterms: <http://purl.org/dc/terms/>PREFIX foaf: <http://xmlns.com/foaf/0.1/>PREFIX skos: <http://www.w3.org/2004/02/skos/core#>PREFIX biopax3: <http://www.biopax.org/release/biopax-level3.owl#>

SELECT DISTINCT ?pathway ?pathwayname WHERE {?pathway rdf:type biopax3:Pathway . ?pathway biopax3:displayName ?pathwayname .?pathway biopax3:pathwayComponent ?reaction . ?reaction rdf:type biopax3:BiochemicalReaction . ?reaction ?rel ?protein .?protein rdf:type biopax3:Protein . ?protein biopax3:entityReference <http://purl.uniprot.org/uniprot/P01308> } LIMIT 100

<http://identifiers.org/reactome/REACT_15550.4> Insulin Processing<http://identifiers.org/reactome/REACT_18325.4> Regulation of Insulin Secretion


Graph patterns








http://www.w3.org/2002/07/owl#


http://www.w3.org/2001/XMLSchema#




http://purl.org/dc/terms/


http://xmlns.com/foaf/0.1/


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


http://www.biopax.org/release/biopax-level3.owl#


http://purl.uniprot.org/uniprot/P01308


http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fidentifiers.org%2Freactome%2FREACT_15550.4





Graph patterns





How do I know what to query ?





SELECT DISTINCT ?pathway ?pathwayname WHERE {?pathway rdf:type biopax3:Pathway . ?pathway biopax3:displayName ?pathwayname .FILTER regex(?pathwayname, "Insulin", "i")} LIMIT 100


Filters

More operators!






















SELECT DISTINCT ?pathway ?pathwayname WHERE {?pathway rdf:type biopax3:Pathway . ?pathway biopax3:displayName ?pathwayname .?pathway biopax3:pathwayComponent ?reaction . ?reaction rdf:type biopax3:BiochemicalReaction . { {?reaction ?rel ?protein .} UNION { ?reaction ?rel ?complex . ?complex rdf:type biopax3:Complex . ?complex ?comp ?protein . }} ?protein rdf:type biopax3:Protein . ?protein biopax3:entityReference <http://purl.uniprot.org/uniprot/P01308> } LIMIT 100


Combining graph matching: union and diff







SELECT DISTINCT ?pathway ?pathwayname WHERE {?pathway rdf:type biopax3:Pathway . ?pathway biopax3:displayName ?pathwayname .?pathway biopax3:pathwayComponent ?reaction . ?reaction rdf:type biopax3:BiochemicalReaction . { {?reaction ?rel ?protein .} UNION { ?reaction ?rel ?complex . ?complex rdf:type biopax3:Complex . ?complex ?comp ?protein . }} ?protein rdf:type biopax3:Protein . ?protein biopax3:entityReference <http://purl.uniprot.org/uniprot/P01308> } LIMIT 100

Aggregators






<http://www.openlinksw.com/schemas/virtrdf#><http://rdf.ebi.ac.uk/dataset/reactome/45><http://rdf.ebi.ac.uk/dataset/reactome/description>


Named graphs




http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.openlinksw.com%2Fschemas%2Fvirtrdf%23


http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fdataset%2Freactome%2F45


http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fdataset%2Freactome%2Fdescription


select distinct ?g where { graph ?g {?s ?p ?o}}

<http://www.openlinksw.com/schemas/virtrdf#><http://rdf.ebi.ac.uk/dataset/reactome/45><http://rdf.ebi.ac.uk/dataset/reactome/description>

select distinct ?o where { graph <http://rdf.ebi.ac.uk/dataset/reactome/45> {?s a ?o}}

2221044

select count (distinct ?s) where { graph <http://rdf.ebi.ac.uk/dataset/reactome/45> {?s ?p ?o}}

owl:Ontologybiopax3:FragmentFeaturebiopax3:SmallMoleculeReferencebiopax3:TemplateReactionbiopax3:Controlbiopax3:EvidenceCodeVocabularybiopax3:SequenceSitebiopax3:Stoichiometrybiopax3:Catalysisbiopax3:PathwayStepbiopax3:UnificationXrefbiopax3:Proteinbiopax3:PublicationXrefbiopax3:PhysicalEntitybiopax3:CellularLocationVocabularybiopax3:Complexbiopax3:BiochemicalReaction...

select count (distinct ?s) where { ?s ?p ?o} 2221353

Introduction to SPARQLHow do I know what to query ?A “practical example”...










http://rdf.ebi.ac.uk/dataset/reactome/45




http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23Ontology

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23Ontology

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23FragmentFeature

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23FragmentFeature

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23SmallMoleculeReference

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23SmallMoleculeReference

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23TemplateReaction

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23TemplateReaction

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Control

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Control

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23EvidenceCodeVocabulary

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23EvidenceCodeVocabulary

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23SequenceSite

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23SequenceSite

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Stoichiometry

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Stoichiometry

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Catalysis

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Catalysis

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23PathwayStep

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23PathwayStep

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23UnificationXref

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23UnificationXref

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Protein

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Protein

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23PublicationXref

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23PublicationXref

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23PhysicalEntity

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23PhysicalEntity

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23CellularLocationVocabulary

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23CellularLocationVocabulary

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Complex

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Complex

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23BiochemicalReaction

http://www.ebi.ac.uk/rdf/services/reactome/describe?uri=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23BiochemicalReaction


SELECT DISTINCT ?pathway ?pathwayname WHERE {SERVICE<http://beta.sparql.uniprot.org/sparql> {?uniprotID <http://purl.uniprot.org/core/encodedBy> ?o .?o <http://www.w3.org/2004/02/skos/core#prefLabel> "INS"} ?pathway rdf:type biopax3:Pathway . ?pathway biopax3:displayName ?pathwayname .?pathway biopax3:pathwayComponent ?reaction . ?reaction rdf:type biopax3:BiochemicalReaction . ?protein rdf:type biopax3:Protein . ?protein biopax3:entityReference ?uniprotID } LIMIT 100

SPARQL: advanced features

Distributed queries

Don’t change the order!Nettab, 16th October 2013, Venice Andrea Splendiani @AndSplend























http://purl.uniprot.org/core/encodedBy




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

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

http://www.w3.org/TR/sparql11-update/

PREFIX dc: <http://purl.org/dc/elements/1.1/>INSERT DATA{ <http://example/book1> dc:title "A new book" ; dc:creator "A.N.Other" .}

PREFIX dc: <http://purl.org/dc/elements/1.1/>INSERT DATA { GRAPH <http://example/graph>{ <http://example/book1> dc:title "A new book" ; dc:creator "A.N.Other" .} }

PREFIX dc: <http://purl.org/dc/elements/1.1/>PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

INSERT { GRAPH <http://example/bookStore2> { ?book ?p ?v } }WHERE { GRAPH <http://example/bookStore> { ?book dc:date ?date . FILTER ( ?date > "1970-01-01"^^xsd:dateTime ) ?book ?p ?v } }

PREFIX foaf: <http://xmlns.com/foaf/0.1/>DELETE WHERE { ?person foaf:givenName 'Fred'; ?property ?value }


SPARQL update






http://example/graph

http://example/graph

http://spinrdf.org/





http://spinrdf.org/

http://spinrdf.org/

http://spinrdf.org/

Reasoners

• Different varieties: simple transitive reasoning can be embedded in triplestores

• Rule based

• OWL-reasoners (OWL, Fact++): can be stand-alone or embedded in other applications (e.g.: Protege)

http://www.w3.org/2001/sw/wiki/OWL/Implementations

Example of Tools






http://semweb.salzburgresearch.at/apps/rdf-gravity/user_doc.html

Example of Tools

RDF visualization tools (graph based)

Think about reification! (not always intuitive)






Example of Tools

OWL visualization tools (class based)

http://protegewiki.stanford.edu/index.php/OWLViz






http://www.visualdataweb.org/relfinder.php

Example of Tools

Information discovery






Example of ToolsIntegrated environments: mapping, visualization, editing, analysis, exploration

http://io-informatics.com






Example of Tools

Facet browsers




https://code.google.com/p/sgvizler/

<div id="sgvzl_example1" data-sgvizler-endpoint="http://sws.ifi.uio.no/sparql/npd" data-sgvizler-query="SELECT ?class (count(?instance) AS ?noOfInstances) WHERE{ ?instance a ?class } GROUP BY ?class ORDER BY ?class" data-sgvizler-chart="gPieChart" style="width:800px; height:400px;"></div>

Example of Tools

Visualization/mashup libraries






http://biordf.net/cardioSHARE/

Example of Tools

Infrastructures




http://cardioshare.biordf.net/cardioSHARE/query

http://cardioshare.biordf.net/cardioSHARE/query

The Semantic Web Landscape




http://www.uniprot.org

RDF available via:•Content negotiation•Extension•Endpoint

Lot of triples!

http://www.ebi.ac.uk/rdf/documentation/uniprot/

Primary Resources

Uniprot








Primary Resources

EBI RDF Platform




Primary Resources

EBI: indentifiers.org




http://data.nature.com

Pubmed: http://togows.dbcls.jp

Primary Resources

“Some” literature






http://togows.dbcls.jp

http://togows.dbcls.jp

http://beta.geneontology.org/page/download-ontology

Primary Resources

Gene Ontology

getting OWL!Nettab, 16th October 2013, Venice Andrea Splendiani @AndSplend





http://sparql.wikipathways.org

Primary Resources

Wikipathways (OpenPhacts)






freebase...

Primary Resources

DBPedia




http://bioportal.bioontology.org/

Integrated Resources

BioPortal

• Ontologies, mappings and tools• Most of ontologies are large

terminology collections




http://bioportal.bioontology.org

http://bioportal.bioontology.org

To be filled


BioPortal: detail on SPARQL queries and ontology representation





BioPortal: detail on SPARQL queries and ontology representation





Bio2RDF




http://linkedlifedata.com








DistilBio











PathwayCommons integrates pathway information via BioPAX

GO: 39k termsNettab, 16th October 2013, Venice Andrea Splendiani @AndSplend







http://lod-cloud.net/versions/2011-09-19/lod-cloud_colored.html

LOD: Linked Open Data






















Is the Semantic Web good for you ?

• Are resources reliable ? (a business problem)

• Does it solve the Semantic Integration problem ? (No)

• How can I know which resources to use ? (Not easy)

• Is the technology mature ? Part of it.

Conclusions




• Beyond Syntax

• Explicit Semantics

• Web technologies (SPARQL as REST, distributed queries)

• Several interesting resources

• Some technologies are robust (RDF, SPARQL, ...)

Conclusions

Is the Semantic Web good for you ?




Exercise

• Get Jena Fuseki

• Start the server

• Add some triples via the web interface

• Make a distributed query to Uniprot

<http://myHomePage> <http://nettab.org/example/chosenProtein> <uniprotID>




http://nettab.org/example/chosenProperty

http://nettab.org/example/chosenProperty