BIOINFORMATICS RESOURCES

PEDRO LOPES pedrolopes@ua.pt

I NPS3Bio - Torremolinos, Spain

October 26th, 2010

TAGGING

David Campos, José Luís Oliveira

‣ BACKGROUND

‣ CHALLENGE

‣ SOLUTION

‣ STRATEGY

‣ PROTOTYPE

‣ HIGHLIGHTS

‣ FUTURE PERSPECTIVES

OUTLINE

BIOINFORMATICS RESOURCES

BIOINFORMATICS RESOURCES

CHALLENGE

‣ ENRICH

• Context & meaning

‣ More than sentences

‣ More than paragraphs

‣ CONNECT

• New relations

‣ Amongst documents

‣ Between documents and resources

‣ From documents to applications

‣ ENHANCE

• User experience

‣ New user interactions

‣ Rich web applications

• Improve research workflow

CHALLENGE

‣ ENRICH

• Context & meaning

‣ More than sentences

‣ More than paragraphs

‣ CONNECT

• New relations

‣ Amongst documents

‣ Between documents and resources

‣ From documents to applications

‣ ENHANCE

• User experience

‣ New user interactions

‣ Rich web applications

• Improve research workflow

CHALLENGE

Improve user experience through the establishment of new connections to enrich existing bioinformatics resources?

SOLUTION

‣ ANNOTATION

• Read/parse resource

• Cross information with huge dataset

‣ Lexicon

• Identify relevant tokens

‣ TAGGING

• Edit annotated content

• Add HTML tags

• Show contextual layer

SOLUTION

‣ ANNOTATION

• Read/parse resource

• Cross information with huge dataset

‣ Lexicon

• Identify relevant tokens

‣ TAGGING

• Edit annotated content

• Add HTML tags

• Show contextual layer

SOLUTION

(LEXICON + TEXT MINING) x AUGMENTED BROWSING!

STRATEGY

STRATEGY

Web Application

Augmented Browsing

Web ServiceLexicon

Annotator Web Service

STRATEGY

Web Application

Augmented Browsing

Web ServiceLexicon

Annotator Web Service

1

STRATEGY

Web Application

Augmented Browsing

Web ServiceLexicon

Annotator Web Service

1

2

STRATEGY

Web Application

Augmented Browsing

Web ServiceLexicon

Annotator Web Service

1

3

2

STRATEGY

Web Application

Augmented Browsing

Web ServiceLexicon

Annotator Web Service

1

3

4 2

PROTOTYPE

‣ 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

HIGHLIGHTS

‣ DEPLOY

• Include in all UA.PT Bioinformatics & Computational Biology applications

‣ PUBLISH

• Offer standalone plugin

‣ Available for any web application

• Offer browser plugin

‣ Firefox + Chrome + Safari

FUTURE PERSPECTIVES

http://bioinformatics.ua.pt

‣ DEPLOY

• Include in all UA.PT Bioinformatics & Computational Biology applications

‣ PUBLISH

• Offer standalone plugin

‣ Available for any web application

• Offer browser plugin

‣ Firefox + Chrome + Safari

FUTURE PERSPECTIVES

ARE YOU INTERESTED?

http://bioinformatics.ua.pt

THANK YOU!

QUESTIONS?