Dr. Knowledge Or: I Stopped Worrying and Loved the Semantic Web

Page 1

Dr. Knowledge Or: How I Learned To Stop Worrying And Love The Semantic Web


NO TECH WARS!


A MOVING TRAIN!



Hellenic FBD Hellenic PD

Crime Reports UK Ox Points

NHS (EnAKTing)

Ren. Energy Generators

EEA

Open Election Data Project

EU Institutions

Mortality (EnAKTing)

Ordnance Survey

legislation data.gov.uk UK Postcodes

ESD standards

ISTAT Immigration

Lichfield Spending

Scotland Pupils & Exams

Traffic Scotland

Data Gov.ie

reference data.gov. uk

London Gazette

TWC LOGD

Eurostat

Eurostat (FUB)

CORDIS (FUB)

(RKB Explorer)

Linked EDGAR (Ontology Central)

EURES

(Ontology Central)

GovTrack

FTS

New York Times

Geo Names

World Factbook

Geo Species

UMBEL

Italian public schools

Greek DBpedia

DDC

BibBase

Freebase

DBLP (FU Berlin)

dataopenac-uk

TCM Gene DIT

Daily Med

SIDER

Twarql

EUNIS

PDB

SMC Journals

Ocean Drilling Codices

Turismo de Zaragoza

Janus AMP

Climbing

Linked GeoData

Alpine Ski Austria

AEMET

Metoffice Weather Forecasts

Yahoo! Geo Planet

National Radioactivity JP

ChEMBL Open Data Thesaurus

Sears

DBLP (RKB Explorer)

STW

GESIS

Budapest

Pisa

RESEX

Scholarometer

IRIT

ACM

NVD

IBM DEPLOY

Newcastle

RAE2001

LOCAH Roma

CiteSeer

Courseware

dotAC

ePrints

IEEE RISKS

PROSITE

Affymetrix

SISVU

GEMET

Airports

lobid Organisations

ECS (RKB Explorer)

HGNC

PubMed

ProDom

VIVO Cornell

STITCH

Linked Open Colors

SGD

Gene Ontology

AGROV OC

Product DB

Weather Stations

Swedish Open Cultural Heritage

LAAS

NSF

KISTI JISC

WordNet (RKB Explorer)

EARTh

ECS Southampton EPrints

VIVO Indiana

(Bio2RDF)

LODE WordNet (W3C)

Wiki

ECS Southampton

Pfam

UniProt

Taxono my

Cornetto

NSZL Catalog

P20

Eurécom

LinkedCT UniProt

WordNet (VUA)

lobid Resources

UN/ LOCODE

Drug Bank

Enipedia

Lexvo

DBLP (L3S)

ERA Diseasome

lingvoj

Europeana Deutsche Biographie

OAI

data dcs

Uberblic dbpedia lite

Norwegian MeSH

VIAF

Ulm

data bnf.fr

BNB

Project Gutenberg

Rådata nå!

GND

ndlna UB Mannheim

Calames

OS

YAGO

Open Cyc

riese

GeoWord Net

El Viajero Tourism

IdRef Sudoc

totl.net

US Census (rdfabout)

Piedmont Accomodations

URI Burner

LIBRIS

LCSH

MARC Codes List

PSH

RDF Book Mashup

Open Calais

ntnusc

Thesaurus W

SW Dog Food

Portuguese DBpedia

LEM

RAMEAU SH

LinkedL CCN

Sudoc

iServe

US SEC

Scotland Geography

Finnish Municipalities

Event Media

DBpedia

(rdfabout)

Semantic XBRL

Linked MDB

t4gm info

Open Library (Talis)

theses. fr

my Experiment

flickr wrappr

NDL subjects

Plymouth Reading Lists

Revyu

Fishes of Texas

Linked Sensor Data (Kno.e.sis)

Eurostat

Chronicling America

Telegraphis

Geo Linked Data

CORDIS

Pokedex

NTU Resource Lists

Open Library

SSW Thesaur us

semantic web.org

BBC Music

BBC Wildlife Finder

NASA (Data Incubator)

transport data.gov. uk

Source Code Ecosystem Linked Data

Didactal ia Goodwin Family

St. Andrews Resource Lists

Manchester Reading Lists

gnoss Poképédia

Classical (DB Tune)

Taxon Concept

LOIUS

Jamendo (DBtune)

Last.FM (rdfize)

BBC Program mes

Rechtspraak. nl

Openly Local

data.gov.uk intervals

Music Brainz (DBTune)

Ontos News Portal

Sussex Reading Lists

Bricklink

yovisto

Semantic Tweet

Linked Crunchbase

RDF ohloh

(Data Incubator)

(DBTune)

OpenEI

statistics data.gov. uk

GovWILD

Brazilian Politicians

educatio n.data.g ov.uk

Music Brainz (zitgist)

Discogs

FanHubz

patents data.go v.uk

research data.gov. uk

CO2 Emission (EnAKTing)

Energy (EnAKTing)

Surge Radio

Klappstuhlclub

Lotico

(Data Incubator)

Last.FM artists

Population (EnAKTing)

reegle

(DBTune)

tags2con delicious

Slideshare 2RDF

(DBTune)

Music Brainz

John Peel

EUTC Productions

business data.gov. uk

Crime (EnAKTing)

GTAA

Magnatune

DB Tropes

Moseley Folk

Linked User Feedback

LOV

Audio Scrobbler

OMIM

MGI

InterPro Smart Link

Product Types Ontology

Open Corporates

Italian Museums

Amsterdam Museum

UniParc

UniRef

UniSTS

GeneID

Linked Open Numbers

Reactome

OGOLOD

KEGG Pathway

Medi Care

Google Art wrapper

meducator

KEGG Drug

Pub Chem

UniPath way

Chem2 Bio2RDF

Homolo Gene

VIVO UF

ECCOTCP bible ontology

KEGG Enzyme

PBAC

KEGG Reaction

KEGG Compound

KEGG Glycan

Media Geographic Publications

User-generated content Government Cross-domain Life sciences As of September 2011


What is the Semantic Web? Semantic Web is the Web of Knowledge

It is about standards for publishing, sharing and querying knowledge drawn from distributed and heterogeneous resources

It enables the answering of sophisticated questions

OK‌ BUT WHAT DO WE NEED TO DO?


Free Text

The Eiffel Tower (French: La Tour Eiffel, [tuʁ ɛfɛl], nickname La dame de fer, the iron lady) is an 1889 iron lattice tower located on the Champ de Mars in Paris that has become both a global icon of France and one of the most recognizable structures in the world. The tallest building in Paris,[10] it is the most-visited paid monument i the world; millions of people ascend it every year. Named for its designer, engineer Gustave Eiffel, the tower was built as the entrance arch t the 1889 World's Fair. The tower stands 324 metres (1,063 ft) tall, abo the same height as an 81-storey building. It was the tallest man-made structure in the world from its completion until the Chrysler Building in New York City was built in 1930. Not including broadcast antennas, it is the second-tallest structure in France after the 2004 Millau Viaduc The tower has three levels for visitors. Tickets can be purchased to ascend, by stairs or lift, to the first and second levels. The walk to the first level is over 300 steps, as is the walk from the first to the second level. The third and highest level is accessible only by elevator. Both the firs and second levels feature restaurants.


Structured Text

Name: Eiffel Tower, La Tour Eiffel Location: Paris, France, Architect: Stephen Sauvestre Height: 324m ...


Relational Model

NAME

LOCATION

HEIGHT

Eiffel Tower

Paris, France

324m

...

...

...


Semantic Web

324 m

La Tour Eiffel

sameAs

hasHeight

Eiffel Tower isLocatedAt hasArchitect Stephen Sauvestre

Paris, France


EXPRESSING MEANING Triples Everything (really everything!) can be described as a statement based on a triple (or combination of statements)

Examples Beira-Mar is a sport club Ridley Scott directed Alien Protein P05067 is located in Membrane

Subject Predicate Object Building and connecting statements creates knowledge


ENABLING KNOWLEDGE

Amyloid precursor protein

Alzheimer label

uniprot:P05067 is a

Protein

label

involved

omim:104300 is a

Disease


Hellenic FBD Hellenic PD

Crime Reports UK Ox Points

NHS (EnAKTing)

Ren. Energy Generators

EEA

Open Election Data Project

EU Institutions

Mortality (EnAKTing)

Ordnance Survey

legislation data.gov.uk UK Postcodes

ESD standards

ISTAT Immigration

Lichfield Spending

Scotland Pupils & Exams

Traffic Scotland

Data Gov.ie

reference data.gov. uk

London Gazette

TWC LOGD

Eurostat

Eurostat (FUB)

CORDIS (FUB)

(RKB Explorer)

Linked EDGAR (Ontology Central)

EURES

(Ontology Central)

GovTrack

FTS

New York Times

Geo Names

World Factbook

Geo Species

UMBEL

Italian public schools

Greek DBpedia

DDC

BibBase

Freebase

DBLP (FU Berlin)

dataopenac-uk

TCM Gene DIT

Daily Med

SIDER

Twarql

EUNIS

PDB

SMC Journals

Ocean Drilling Codices

Turismo de Zaragoza

Janus AMP

Climbing

Linked GeoData

Alpine Ski Austria

AEMET

Metoffice Weather Forecasts

Yahoo! Geo Planet

National Radioactivity JP

ChEMBL Open Data Thesaurus

Sears

DBLP (RKB Explorer)

STW

GESIS

Budapest

Pisa

RESEX

Scholarometer

IRIT

ACM

NVD

IBM DEPLOY

Newcastle

RAE2001

LOCAH Roma

CiteSeer

Courseware

dotAC

ePrints

IEEE RISKS

PROSITE

Affymetrix

SISVU

GEMET

Airports

lobid Organisations

ECS (RKB Explorer)

HGNC

PubMed

ProDom

VIVO Cornell

STITCH

Linked Open Colors

SGD

Gene Ontology

AGROV OC

Product DB

Weather Stations

Swedish Open Cultural Heritage

LAAS

NSF

KISTI JISC

WordNet (RKB Explorer)

EARTh

ECS Southampton EPrints

VIVO Indiana

(Bio2RDF)

LODE WordNet (W3C)

Wiki

ECS Southampton

Pfam

UniProt

Taxono my

Cornetto

NSZL Catalog

P20

Eurécom

LinkedCT UniProt

WordNet (VUA)

lobid Resources

UN/ LOCODE

Drug Bank

Enipedia

Lexvo

DBLP (L3S)

ERA Diseasome

lingvoj

Europeana Deutsche Biographie

OAI

data dcs

Uberblic dbpedia lite

Norwegian MeSH

VIAF

Ulm

data bnf.fr

BNB

Project Gutenberg

Rådata nå!

GND

ndlna UB Mannheim

Calames

OS

YAGO

Open Cyc

riese

GeoWord Net

El Viajero Tourism

IdRef Sudoc

totl.net

US Census (rdfabout)

Piedmont Accomodations

URI Burner

LIBRIS

LCSH

MARC Codes List

PSH

RDF Book Mashup

Open Calais

ntnusc

Thesaurus W

SW Dog Food

Portuguese DBpedia

LEM

RAMEAU SH

LinkedL CCN

Sudoc

iServe

US SEC

Scotland Geography

Finnish Municipalities

Event Media

DBpedia

(rdfabout)

Semantic XBRL

Linked MDB

t4gm info

Open Library (Talis)

theses. fr

my Experiment

flickr wrappr

NDL subjects

Plymouth Reading Lists

Revyu

Fishes of Texas

Linked Sensor Data (Kno.e.sis)

Eurostat

Chronicling America

Telegraphis

Geo Linked Data

CORDIS

Pokedex

NTU Resource Lists

Open Library

SSW Thesaur us

semantic web.org

BBC Music

BBC Wildlife Finder

NASA (Data Incubator)

transport data.gov. uk

Source Code Ecosystem Linked Data

Didactal ia Goodwin Family

St. Andrews Resource Lists

Manchester Reading Lists

gnoss Poképédia

Classical (DB Tune)

Taxon Concept

LOIUS

Jamendo (DBtune)

Last.FM (rdfize)

BBC Program mes

Rechtspraak. nl

Openly Local

data.gov.uk intervals

Music Brainz (DBTune)

Ontos News Portal

Sussex Reading Lists

Bricklink

yovisto

Semantic Tweet

Linked Crunchbase

RDF ohloh

(Data Incubator)

(DBTune)

OpenEI

statistics data.gov. uk

GovWILD

Brazilian Politicians

educatio n.data.g ov.uk

Music Brainz (zitgist)

Discogs

FanHubz

patents data.go v.uk

research data.gov. uk

CO2 Emission (EnAKTing)

Energy (EnAKTing)

Surge Radio

Klappstuhlclub

Lotico

(Data Incubator)

Last.FM artists

Population (EnAKTing)

reegle

(DBTune)

tags2con delicious

Slideshare 2RDF

(DBTune)

Music Brainz

John Peel

EUTC Productions

business data.gov. uk

Crime (EnAKTing)

GTAA

Magnatune

DB Tropes

Moseley Folk

Linked User Feedback

LOV

Audio Scrobbler

OMIM

MGI

InterPro Smart Link

Product Types Ontology

Open Corporates

Italian Museums

Amsterdam Museum

UniParc

UniRef

UniSTS

GeneID

Linked Open Numbers

Reactome

OGOLOD

KEGG Pathway

Medi Care

Google Art wrapper

meducator

KEGG Drug

Pub Chem

UniPath way

Chem2 Bio2RDF

Homolo Gene

VIVO UF

ECCOTCP bible ontology

KEGG Enzyme

PBAC

KEGG Reaction

KEGG Compound

KEGG Glycan

Media Geographic Publications

User-generated content Government Cross-domain Life sciences As of September 2011


OWL “Define” Relations Web Ontology Language

Define complex concept environments Individual + Property assertion = Axiom “Object-Oriented” Classes Properties Instances

FOAF Friend-Of-A-Friend


RDF Description and Storage Resource Description Framework Store data as triples File formats Relational database

Quite heavy and not easy to deal with Text files must be read (and parsed) (and cached)


SPARQL Ask Questions SPARQL Protocol and RDF Query Language Query data stored in RDF SQL’s “younger brother” Ambiguous Multiple variables



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What?

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Why?

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How?

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Setting it up...

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Where?

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Closing


BREAK FOR 9GAG!


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Next Generation Semantic Web Application Framework Take advantage of Semantic Web technologies/standards Integrate heterogeneous/distributed resources Provide data-access APIs Open federation layer connecting miscellaneous instances Easy to configure/setup Streamline Semantic Web application development

“Semantic Web in a box� for bioinformatics NO STANDALONE APPS, ENTIRE ECOSYSTEMS


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http://bioinformatics.ua.pt/

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(Among others…)

IMPROVE BIOMEDICAL APPLICATIONS DOMAIN


SEMANTIC WEB + LIFE SCIENCES perfect benchmark awareness from bioinformatics developers common intertwined graph relationship structure

BUT... Semantic Web is underused in the life sciences domain transition/migration is very difficult complex application deployment learn a whole new batch of technologies (again!) no killer apps/frameworks

and

are notable exceptions


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How? ¢

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http://bioinformatics.ua.pt/

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There?

Here


Do you like gardening?


My experience so far‌


KNOWLEDGE

SEED is a single app, an instance Connectors CSV

SQL

SPARQL

MySQL

Jena

REST

XML

Java

API

Joseki

Pubby

SPARQL

LinkedData


KNOWLEDGE

SEED

CSV

XML

SQL

SPARQL

is a single app, an instance SEED ENGINE

API REST

Biomedical Application

SPARQL

12:00 Carrier PM Pagehttp:// Title www.domain. com


KNOWLEDGE

SEED is a single app, an instance

KNOWLEDGE

GARDEN links multiple seeds SEED SEED SPARQL

SPARQL

SEED SEED

SPARQL

SPARQL

FEDERATION

Knowledge Here!

SEED SPARQL


INTEGRATION Data in = Connectors


CONNECTORS = CSV + XML + SQL + SPARQL load everything flexible format support map external data into a seed’s model

any predicate matches data from... csv columns xml XPath results SQL table columns SPARQL query variables


FEDERATION Data out = APIs


API = SPARQL + REST + Java + LinkedData code your own apps in any programming language available for desktop, web or mobile

one seed, multiple apps or multiple seeds, one app federate to existing apps access with REST or SPARQL distributed knowledge network


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Setting it up... ¢ ¢

http://bioinformatics.ua.pt/

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STRATEGY 1, 2, 3 go!


1 CONFIGURE 2 BUILD 3 EXPLORE


CONFIGURATION Where’s everybody?


CONFIGURATION = JS FILE + (ONTOLOGY * SETUP) local app configuration JSON object in JavaScript file defines application properties (name, version, environment‌)

define seed ontology then setup resources seed ontology

resource setup

based on COEUS ontology

resource connectors configuration

your app data model

ontology mappings


Framework Model

Seed Entity

Bridge

Concept

Item

Resource

SPARQL

SQL

CSV

XML


ST2011 Semantics Tweets 2011: our new app

ID

Name

st:hasId

st:Tweet

st:hasAuthor

foaf:name

st:Author Title

st:hasURI

dc:title

st:hasLink

Link

st:hasPublicationDate

Date

URI


... <owl:NamedIndividual rdf:about="http://bioinformatics.ua.pt/coeus/resource_Twitter"> <rdf:type rdf:resource="http://bioinformatics.ua.pt/coeus/Resource"/> <rdfs:label rdf:datatype="&xsd;string">resource_twitter</rdfs:label> <query rdf:datatype="&xsd;string">//entry</query> <order rdf:datatype="&xsd;integer">10</order> <dc:title rdf:datatype="&xsd;string">Twitter</dc:title> <dc:creator rdf:datatype="&xsd;string">Pedro Lopes pedrolopes@ua.pt</dc:creator> <dc:description rdf:datatype="&xsd;string">Resource connecting Twitter information.</dc:description> <method rdf:datatype="&xsd;string">cache</method> <endpoint rdf:datatype="&xsd;string">http://search.twitter.com/search.atom?q=iknow2011</endpoint> <dc:publisher rdf:datatype="&xsd;string">xml</dc:publisher> <isResourceOf rdf:resource="http://bioinformatics.ua.pt/coeus/concept_Twitter"/> <loadsFrom rdf:resource="http://bioinformatics.ua.pt/coeus/xml_Twitter_title"/> <loadsFrom rdf:resource="http://bioinformatics.ua.pt/coeus/xml_Twitter_link"/> ... <loadsFrom rdf:resource="http://bioinformatics.ua.pt/coeus/xml_Twitter_id"/> </owl:NamedIndividual> ... <owl:NamedIndividual rdf:about="http://bioinformatics.ua.pt/coeus/xml_Twitter_title"> <rdf:type rdf:resource="http://bioinformatics.ua.pt/coeus/XML"/> <rdfs:label rdf:datatype="&xsd;string">xml_twitter_title</rdfs:label> <query rdf:datatype="&xsd;string">//title</query> <dc:creator rdf:datatype="&xsd;string">Pedro Lopes pedrolopes@ua.pt</dc:creator> <property rdf:datatype="&xsd;string">dc:title</property> </owl:NamedIndividual> <owl:NamedIndividual rdf:about="http://bioinformatics.ua.pt/coeus/xml_Twitter_link"> <rdf:type rdf:resource="http://bioinformatics.ua.pt/coeus/XML"/> <rdfs:label rdf:datatype="&xsd;string">xml_twitter_link</rdfs:label> <query rdf:datatype="&xsd;string">//link</query> <dc:creator rdf:datatype="&xsd;string">Pedro Lopes pedrolopes@ua.pt</dc:creator> <property rdf:datatype="&xsd;string">st:hasLink</property> </owl:NamedIndividual> <owl:NamedIndividual rdf:about="http://bioinformatics.ua.pt/coeus/xml_Twitter_id"> <rdf:type rdf:resource="http://bioinformatics.ua.pt/coeus/XML"/> <rdfs:label rdf:datatype="&xsd;string">xml_twitter_id</rdfs:label> <query rdf:datatype="&xsd;string">//id</query> <dc:creator rdf:datatype="&xsd;string">Pedro Lopes pedrolopes@ua.pt</dc:creator> <property rdf:datatype="&xsd;string">dc:identifier</property> </owl:NamedIndividual> ...


BUILDING Getting data together...


SEMANTIC WEB TRANSLATION triplify data app setup + data = triples

subject - predicate - object subject created at runtime

predicate configured in app setup

object loaded from resource data


... <owl:NamedIndividual rdf:about="http://bioinformatics.ua.pt/coeus/xml_Twitter_title"> <rdf:type rdf:resource="http://bioinformatics.ua.pt/coeus/XML"/> <rdfs:label rdf:datatype="&xsd;string">xml_twitter_title</rdfs:label> <query rdf:datatype="&xsd;string">//title</query> <dc:creator rdf:datatype="&xsd;string">Pedro Lopes pedrolopes@ua.pt</dc:creator> <property rdf:datatype="&xsd;string">dc:title</property> </owl:NamedIndividual> <owl:NamedIndividual rdf:about="http://bioinformatics.ua.pt/coeus/xml_Twitter_link"> <rdf:type rdf:resource="http://bioinformatics.ua.pt/coeus/XML"/> <rdfs:label rdf:datatype="&xsd;string">xml_twitter_link</rdfs:label> <query rdf:datatype="&xsd;string">//link</query> <dc:creator rdf:datatype="&xsd;string">Pedro Lopes pedrolopes@ua.pt</dc:creator> <property rdf:datatype="&xsd;string">st:hasLink</property> </owl:NamedIndividual> <owl:NamedIndividual rdf:about="http://bioinformatics.ua.pt/coeus/xml_Twitter_id"> <rdf:type rdf:resource="http://bioinformatics.ua.pt/coeus/XML"/> <rdfs:label rdf:datatype="&xsd;string">xml_twitter_id</rdfs:label> <query rdf:datatype="&xsd;string">//id</query> <dc:creator rdf:datatype="&xsd;string">Pedro Lopes pedrolopes@ua.pt</dc:creator> <property rdf:datatype="&xsd;string">dc:identifier</property> </owl:NamedIndividual> ...

... <entry> <id>tag:search.twitter.com,2005:111391828925890561</id> <published>2011-09-07T10:54:16Z</published> <link type="text/html" href="..." rel="alternate"/> <title>die twitterwall auf der #iknow2011 http://t.co/LsxFLDk #visibletweets</title> <content type="html">die twitterwall auf ‌</content> <updated>2011-09-07T10:54:16Z</updated> <link type="image/png" href="..." rel="image"/> <twitter:source><a href="http://www.tweetdeck.com" ‌ /a></twitter:source> <twitter:lang>en</twitter:lang> <author> <name>issi (Isabel Anger)</name> <uri>http://twitter.com/issi</uri> </author> </entry> ...


EXPLORING Also getting data together...


INTEROPERABILITY …/sparql

SPARQL

perform SPARQL queries get data in multiple formats

GET request for all data

REST

…/api/<key>:<value> for relationships …/api/sub/pred/obj/<format> for specific content

Java LinkedData

abstracted from Jena’s methods

…/resource/<concept>_<id>



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http://bioinformatics.ua.pt/

Where? ¢ ¢


Drug

Protein

Locus HGNC

CSV

Disease OMIM

DrugBank

UniProt

XML

Protein

CSV

PDB Locus Entrez

Literature SQL

PubMed

SPARQL

XML

XML


SPARQL

Proteins

Drugs

Symptoms

App

App

App

Here!

Here!

Here!

SPARQL

SPARQL

SPARQL

SPARQL

FEDERATION

Knowledge Here!

Knowledge Here!

Knowledge Here!

Knowledge Here! Knowledge Here! Knowledge Here!

Knowledge Here!

Knowledge Here!


Distributed Hospital Information EHR System Repository SPARQL

SPARQL

Distributed

Distributed

Repository

Repository

Clinical Radiology Reports

SPARQL

SPARQL

SPARQL

Genetics EHR

FEDERATION

Knowledge Here!

Knowledge Here!

Knowledge Here!

Knowledge Here! Knowledge Here! Knowledge Here!

Knowledge Here!

Knowledge Here!


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http://bioinformatics.ua.pt/

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Closing ¢


http://bioinformatics.ua.pt/coeus





‣ Architecture

Wrapping it all up... ‣ Specification


INTEGRATION + EXPLORATION

CONNECTORS

API

csv, sql, xml, sparql

java, rest, sparql, linkeddata

=FEDERATION

KNOWLEDGE NETWORK

http://bioinformatics.ua.pt/coeus

I’M REALLY REALLY LOOKING FOR TESTERS!!

“Semantic Web in a box”


FUTURE

work in progress ~ 2 months

get some more prototypes running test federation

Writing a couple more papers thesis!!


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

http://bioinformatics.ua.pt/


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