Transcript Biomedical Informatics DiabetesType2 Power Point

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
Copyright © 2011 Center for Systems Integration, Florida Atlantic University
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
Copyright © 2011 Center for Systems Integration, Florida Atlantic University
GUI – User’s Profile and Search Keywords
Copyright © 2011 Center for Systems Integration, Florida Atlantic University
Protégé 4.x and OWL API
• 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 ProtegeOWL 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
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
Copyright © 2011 Center for Systems Integration, Florida Atlantic University
Lucene Web Crawler
• 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
European Bioinformatics Institute's (EBI)
.
CiteXplore Web Service
• 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
Prepare Presentation Data
• Scoring patient search -> GUI
• Scoring additional search data -> GUI
• Search criteria
Copyright © 2011 Center for Systems Integration, Florida Atlantic University
Display results
• Two lists of links – web service and web
crawl results
• Search Terms
• Presentation format – highlight keywords
• First results
• Periodic alerts
Copyright © 2011 Center for Systems Integration, Florida Atlantic University
GUI – Results and Search Terms
Copyright © 2011 Center for Systems Integration, Florida Atlantic University
GUI – Highlighted Links
Copyright © 2011 Center for Systems Integration, Florida Atlantic University
Tools
Protégé: http://protege.stanford.edu/
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Eclipse for Java Developer:
http://www.eclipse.org/downloads/
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European Bioinformatics Institute:
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http://www.ebi.ac.uk/citexplore/jaxws_help.jsp
Lucene: http://www.manning.com/marmanis/
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OWL API: http://owlapi.sourceforge.net/index.html
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Copyright © 2011 Center for Systems Integration, Florida Atlantic University