TAGGING BIOINFORMATICS RESOURCES
PEDRO LOPES pedrolopes@ua.pt David Campos, José Luís Oliveira I NPS3Bio - Torremolinos, Spain October 26th, 2010
OUTLINE ‣ BACKGROUND ‣ CHALLENGE ‣ SOLUTION ‣ STRATEGY ‣ PROTOTYPE ‣ HIGHLIGHTS ‣ FUTURE PERSPECTIVES
BIOINFORMATICS RESOURCES
BIOINFORMATICS RESOURCES
CHALLENGE
CHALLENGE ‣ ENRICH • Context & meaning
‣ ENHANCE • User experience
‣ More than sentences
‣ New user interactions
‣ More than paragraphs
‣ Rich web applications
‣ CONNECT • New relations ‣ Amongst documents ‣ Between documents and resources ‣ From documents to applications
• Improve research workflow
CHALLENGE ‣ ENRICH
‣ ENHANCE
• Context & meaning
• User experience
‣ More than sentences
‣ New user interactions
‣ More than paragraphs
‣ Rich web applications
‣ CONNECT
• Improve research workflow
• New relations ‣ Amongst documents ‣ Between documents and resources ‣ From documents to applications
?
Improve user experience through the establishment of new connections to enrich existing bioinformatics resources
SOLUTION
SOLUTION ‣ ANNOTATION
‣ TAGGING
• Read/parse resource
• Edit annotated content
• Cross information with huge dataset
• Add HTML tags
‣ Lexicon • Identify relevant tokens
• Show contextual layer
SOLUTION ‣ ANNOTATION
‣ TAGGING
• Read/parse resource
• Edit annotated content
• Cross information with huge dataset
• Add HTML tags
‣ Lexicon
• Show contextual layer
• Identify relevant tokens
!
(LEXICON + TEXT MINING) x AUGMENTED BROWSING
STRATEGY
STRATEGY
Web Application
Annotator Web Service
Augmented Browsing Web Service
Lexicon
STRATEGY
1 Web Application
Annotator Web Service
Augmented Browsing Web Service
Lexicon
STRATEGY
1 Web Application
Annotator Web Service
2 Augmented Browsing Web Service
Lexicon
STRATEGY
1 Web Application
Annotator Web Service
3 2 Augmented Browsing Web Service
Lexicon
STRATEGY
1 Web Application
Annotator Web Service
3 4 Augmented Browsing Web Service
2 Lexicon
PROTOTYPE
HIGHLIGHTS ‣ SCALABLE • Lexicon ‣ Changed/updated any time • Service Deployment ‣ Local ‣ Remote
‣ DYNAMIC • Augmented browsing ‣ Real time ‣ XML settings file • Resources ‣ As long as it is online...
‣ AGILE • User Experience ‣ Lightweight ‣ Integrated in any web app • Augmented browsing ‣ On-the-fly modal box
FUTURE PERSPECTIVES ‣ DEPLOY • Include in all UA.PT Bioinformatics & Computational Biology applications http://bioinformatics.ua.pt
‣ PUBLISH • Offer standalone plugin ‣ Available for any web application • Offer browser plugin ‣ Firefox + Chrome + Safari
FUTURE PERSPECTIVES ‣ DEPLOY • Include in all UA.PT Bioinformatics & Computational Biology applications http://bioinformatics.ua.pt
‣ PUBLISH • Offer standalone plugin ‣ Available for any web application • Offer browser plugin ‣ Firefox + Chrome + Safari
ARE YOU INTERESTED?
QUESTIONS? THANK YOU!