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  • Semantic Web Application Framework

    Pedro Lopes & Jos Lus Oliveirahello@pedrolopes.net

    http://bioinformatics.ua.pt

    SWAT4LS 2011, December 9th, London, UK

    mailto:hello@pedrolopes.netmailto:hello@pedrolopes.nethttp://bioinformatics.ua.pthttp://bioinformatics.ua.pt

  • What?

    Why?

    How?

    Setting it up...

    Where?

    Closing

  • What?

    http://bioinformatics.ua.pt/

    http://bioinformatics.ua.pt/coeushttp://bioinformatics.ua.pt/coeus

  • Next Generation Semantic Web Application Framework

    Rapid Application Deployment

    Data Integration Platform

    Advanced Data Exploration Framework

    SEMANTIC WEB IN A BOX FOR BIOINFORMATICS

  • Why?

    http://bioinformatics.ua.pt/

    http://bioinformatics.ua.pt/coeushttp://bioinformatics.ua.pt/coeus

  • IMPROVE BIOMEDICAL APPLICATIONS DOMAIN

    (Among others)

  • SEMANTIC WEB + LIFE SCIENCES

    perfect benchmarkawareness from bioinformatics developers

    common intertwined graph relationship structure

    BUT...

    Semantic Web is still underused in the life sciences domain

    transition/migration is very difficultcomplex application deployment

    learn a whole new batch of technologies (again!)

    You are notable exceptions!

  • How?

    http://bioinformatics.ua.pt/

    http://bioinformatics.ua.pt/coeushttp://bioinformatics.ua.pt/coeus

  • KNOWLEDGE

    SEEDis a single app, an instance

    API

    Connectors

    MySQL

    SQL XMLCSV SPARQL

    Jena

    REST Java SPARQL LinkedDataPubbyJoseki

  • KNOWLEDGE

    SEEDis a single app, an instance

    KNOWLEDGE

    GARDENlinks multiple seeds

    FederationGarden

    API

    Connectors

    MySQL

    SQL XMLCSV SPARQL

    Jena

    REST Java SPARQL LinkedDataPubbyJoseki

    API

    Connectors

    MySQL

    SQL XMLCSV SPARQL

    Jena

    REST Java SPARQL LinkedDataPubbyJoseki

    API

    Connectors

    MySQL

    SQL XMLCSV SPARQL

    Jena

    REST Java SPARQL LinkedDataPubbyJoseki

  • INTEGRATIONData in = Connectors

  • CONNECTORS = CSV + XML + SQL + SPARQL

    any predicate matches data from selectors

    csv columns

    xml XPath results

    SQL table columns

    SPARQL query variables

    load everythingflexible format support

    map external data into a seeds model

  • EXPLORATIONData out = APIs

  • API = SPARQL + REST + Java + LinkedData

    one seed, multiple apps and/or multiple seeds, one app

    federate to existing appsaccess with REST or SPARQL

    distributed knowledge network

    code your own appsin any programming language available

    for desktop, web or mobile

  • Setting it up...

    http://bioinformatics.ua.pt/

    http://bioinformatics.ua.pt/coeushttp://bioinformatics.ua.pt/coeus

  • CONFIGURATIONWheres everybody?

  • CONFIGURATION = JS FILE + (ONTOLOGY * SETUP)

    de!ne seed ontology then setup resources

    local app con!gurationJSON object in JavaScript file

    defines application properties (name, version, environment)

    seed ontologybased on COEUS ontology

    your app data model

    resource setupresource connectors configuration

    ontology mappings

  • BUILDINGGetting data together...

  • SEMANTIC WEB TRANSLATION

    subject - predicate - object

    triplify dataapp setup + data = triples

    subject

    created at runtimenew Item individual

    predicate

    configured in app setupfoaf:name

    dc:title

    rdfs:label

    owl:versionInfo

    swat4ls:link

    ...

    object

    resource dataCSV column

    SQL table column

    XML XPath

    SPARQL variable

    Plugin

  • EXPLORINGPutting the Web in Semantic Web

  • INTEROPERABILITY

    /sparql

    perform SPARQL queries

    get data in multiple formats

    GET requests for all data

    /api/_ for relationships

    /api/sub/pred/obj/ for specific content

    abstracted from Jenas methods

    SPARQL

    REST

    Java

    LinkedData /resource/_

  • Where?

    http://bioinformatics.ua.pt/

    http://bioinformatics.ua.pt/coeushttp://bioinformatics.ua.pt/coeus

  • Drugs

    AppHere!

    Whatever

    AppHere!

    Knowledge Here!

    Knowledge Here! Knowledge Here!Knowledge Here!

    Knowledge Here!Knowledge Here!

    FederationGarden

    API

    Connectors

    MySQL

    SQL XMLCSV SPARQL

    Jena

    REST Java SPARQL LinkedDataPubbyJoseki

    API

    Connectors

    MySQL

    SQL XMLCSV SPARQL

    Jena

    REST Java SPARQL LinkedDataPubbyJoseki

    API

    Connectors

    MySQL

    SQL XMLCSV SPARQL

    Jena

    REST Java SPARQL LinkedDataPubbyJoseki

    http://bioinformatics.ua.pt/dc4

    http://bioinformatics.ua.pt/coeus/http://bioinformatics.ua.pt/coeus/

  • Closing

    http://bioinformatics.ua.pt/

    http://bioinformatics.ua.pt/coeushttp://bioinformatics.ua.pt/coeus

  • INTEGRATION

    +EXPLORATION

    = SEMANTIC WEB IN A BOX

    Connectors CSV, SQL, XML, SPARQL

    API Java, REST, SPARQL, LinkedData

    http://bioinformatics.ua.pt/coeus

    WE

    ARE

    LOO

    KIN

    G F

    OR R

    ESEA

    RCH

    CO

    LLA

    BO

    RATI

    ON

    S!

    http://bioinformatics.ua.pt/coeus/http://bioinformatics.ua.pt/coeus/

  • THANK YOU!Questions and Feedback are (very) welcome!

    http://bioinformatics.ua.pt/

    http://bioinformatics.ua.pt/coeushttp://bioinformatics.ua.pt/coeus