A Semantic Web Application Framework for Health Systems Interoperability

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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How? ¢ ¢

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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/