Patient Empowerment for Chronic Diseases System Sifat Islam Graduate Student, Center for Systems...

Patient Empowerment for Chronic Diseases System

Sifat Islam

Graduate Student, Center for Systems Integration, FAU, [email protected]

Copyright © 2011 Center for Systems Integration, Florida Atlantic University

Outline

1. User creates a profile

2. Search with user’s criteria

3. Prepare presentation data

4. Display results


User Creates a Profile •Create an ontology & rules to collect his profile (metadata) using OWL API

•Create GUI using WindowBuilder plug-in for Eclipse

•Create domain ontology – search, correct, add to profile, show results using Protégé 4.1 and OWL API

•Help improve his profile (only on the app side) using OWL API

•Validate with reasoner using Protégé 4.1 and OWL API



GUI – User’s Profile and Search Keywords

• Protege 4.x uses the open source, Java-based OWL API that is proving popular with many developers around the world.

• OWL files are accessible via the OWL API, which was developed at the University Of Manchester (not the Protege-OWL API, which was used in the 3.x series).

• This is a very clean API that closely follows the OWL specification and the parser is optimized to be faster and use less memory.

Reference:

http://protegewiki.stanford.edu/wiki/Protege4Migration

http://owlapi.sourceforge.net/documentation.html

Protégé 4.x and OWL API

WindowBuilder• WindowBuilder is built as a plug-in to Eclipse

• A powerful and easy to use bi-directional Java GUI designer

• WindowBuilder is composed of SWT (Standard Widget Toolkit) Designer and Swing Designer and makes it very easy to create Java GUI applications without spending a lot of time writing code.

Reference:

http://www.eclipse.org/windowbuilder/

Search with User’s Criteria• Build an URL list• App picks a few seed URLs based on metadata• Web search using Lucene Web Crawler

• Crawl the Web• Save sorted/ranked URL list + files

• DB search using EBI’s CiteXplore Web Service• Seed medical databases from a long list• Access medical databases via Web services

• Save files• Merge and re-rank• Incremental updates• Purge old/irrelevant data based on browsing history


• Crawling refers to the process of gathering the documents on which we want to enable the search functionality.

• Parsing is necessary for transforming the documents (XML , HTML, Word, PDF ) into a common structure that will represent the fields of indexing in a purely textual form.

• The NaiveBayes classifier can provide a measure of how likely it is that user A wants to see URL X provided that she submitted query Q.

• We’ll only use its capacity to produce a measure of relevance, which exactly fits our purposes.

• Reference: Chapter 2 from “Algorithms of the Intelligent Web” by Haralambos Marmanis and Dmitry Babenko

Lucene Web Crawler

.

• To request relevance medical information, we utilized the European Bioinformatics Institute’s (EBI) CiteXplore Web Service, a Simple Object Access Protocol (SOAP) based service, to fetch data from the Citation database.

• The CiteXplore literature database offers integrated databases of literature information from a range of resources and contains references to biological databases, text mining findings and links to locations of the abstract or full text version of the citation.

Reference:

http://www.ebi.ac.uk/citexplore/jaxws_help.jsp

European Bioinformatics Institute's (EBI) CiteXplore Web Service

• Scoring patient search -> GUI

• Scoring additional search data -> GUI

• Search criteria

Prepare Presentation Data


Display results

•Two lists of links – web service and web crawl results

•Search Terms

•Presentation format – highlight keywords

•First results

•Periodic alerts


GUI – Results and Search Terms


GUI – Highlighted Links


Tools●Protégé: http://protege.stanford.edu/

●Eclipse for Java Developer: http://www.eclipse.org/downloads/

●European Bioinformatics Institute:

http://www.ebi.ac.uk/citexplore/jaxws_help.jsp

●Lucene: http://www.manning.com/marmanis/

●OWL API: http://owlapi.sourceforge.net/index.html


Patient Empowerment for Chronic Diseases System Sifat Islam Graduate Student, Center for Systems...

Documents

Transcript of Patient Empowerment for Chronic Diseases System Sifat Islam Graduate Student, Center for Systems...