A Semantic Web Application Framework for Health Systems Interoperability Pedro Lopes & José Luís Oliveira {pedrolopes,jlo}@ua.pt http://bioinformatics.ua.pt
MIX-HS’11, October 28th, Glasgow, Scotland
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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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Conclusion
http://bioinformatics.ua.pt/
Why? ¢
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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
“Semantic Web in a box” NO STANDALONE APPS, ENTIRE ECOSYSTEMS
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http://bioinformatics.ua.pt/
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Do you like gardening?
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
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Setting it up... ¢ ¢
http://bioinformatics.ua.pt/
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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
EXPLORING 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
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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Where? ¢ ¢
http://bioinformatics.ua.pt/
Understanding the Human Variome Reading the â&#x20AC;&#x153;Book-of-Lifeâ&#x20AC;?
Collect genetics datasets Enrich them
Hub for Rare Disease Information Link aggregation
Connects diseases with... Genes, Enzymes, Pathways, Literature
Targeted at gene curators
Targeted at clinicians/students
http://bioinformatics.ua.pt/WAVe
http://bioinformatics.ua.pt/dc4
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/
Conclusion ¢
“Semantic Web in a box”
INTEGRATION + EXPLORATION
CONNECTORS
API
csv, sql, xml, sparql
java, rest, sparql, linkeddata
=INTEROPERABILITY
http://bioinformatics.ua.pt/coeus
THANK YOU! Questions and Feedback are welcome!
http://bioinformatics.ua.pt/