BioFacets: Solution Towards Leveraging the Wealth of Online - - PowerPoint PPT Presentation

▶
biofacets solution towards leveraging the wealth of
SMART_READER_LITE
LIVE PREVIEW

BioFacets: Solution Towards Leveraging the Wealth of Online - - PowerPoint PPT Presentation

Nov 30, 2022 184 likes •329 views

DI LS 2006 July 20, 2006 BioFacets: Solution Towards Leveraging the Wealth of Online Biological Databases Malika Mahoui, Zina Ben Miled, Amey Godse, Harshad Kulkarni, Nianhua Li Presented by: Malika Mahoui Biological Domain Data

slide-1
SLIDE 1

BioFacets: Solution Towards Leveraging the Wealth of Online Biological Databases

DI LS 2006

July 20, 2006 Presented by: Malika Mahoui Malika Mahoui, Zina Ben Miled, Amey Godse, Harshad Kulkarni, Nianhua Li

slide-2
SLIDE 2

DI LS 2006 2

Biological Domain

100 200 300 400 500 600 700 800 900 1999 2000 2001 2002 2003 2004 2005 2006 2007 n u m b e r o f b io lo g ic a l d a ta b a s e s

  • Data intensive domain
  • Gene

– GenBank – EMBL

  • Protein

– SwissProt – PI R – PDB

slide-3
SLIDE 3

DI LS 2006 3

Biological Research

  • Characteristics: Biological Databases

– Representational heterogeneity – Diversity of biological data – Large result sets

  • 1. Querying remote databases
  • 2. I ntegrating multiple databases
  • 3. Representing result sets
slide-4
SLIDE 4

DI LS 2006 4

Biofacets Solution

  • features

– Meta-search engine for biological databases – Wrapper-mediator approach for data integration – Dynamic Facetted approach for results classification – Results presentation and query refinement based on faceted classification – Cache management and query optimization to support system performance

slide-5
SLIDE 5

DI LS 2006 5

BioFacets Architecture

slide-6
SLIDE 6

DI LS 2006 6

Faceted Classification

  • Concept largely understood in digital

libraries

  • Assign multiple classifications to a

result record

  • Examples include Flamenco

framework for image search

  • Limitation: assume existence of

data/ metadata a priori

slide-7
SLIDE 7

DI LS 2006 7

Facet & Facet Specification

  • A method of classification
  • Facet name
  • Assignment of value:

– Static

  • Data Type

– Dynamic

  • Protein Length
  • Level:

– Non-hierarchical

  • Gene function

– Hierarchical

  • Organism Lineage

<Facet fName=”data_type” type="static” isHierarchical="false”> </Facet>

slide-8
SLIDE 8

DI LS 2006 8

Classification Rules

Facet Type Rule Type Specification

Static fixed value rule

< Rule> < ruleFacetName> data_type< / ruleFacetName> < ruleMethod> fixed< / ruleMethod> < Value> protein_data< / Value> < / Rule>

Dynamic field value rule

< Rule> < ruleFacetName> organism< / ruleFacetName> < ruleMethod> fieldvalue< / ruleMethod> < Field> scientific_name< / Field> < / Rule>

Dynamic lookup value rule

< Rule> < ruleFacetName> organism< / ruleFacetName> < ruleMethod> lookup< / ruleMethod> < DataSource> newt< / DataSource> < LookupBaseURL> http:/ / www.ebi.ac.uk/ newt/ display? from= au& amp;match= taxonomy+ identifier&amp;search= < / LookupBaseURL> < LookupField> tax_id< / LookupField> < ValueField> scientific_name< / ValueField> < / Rule>

slide-9
SLIDE 9

DI LS 2006 9

Start Page

slide-10
SLIDE 10

DI LS 2006 10

Faceted Browsing

ITEM ITEM COUNT FACET HISTORY FACET SELECTION RESULTS

slide-11
SLIDE 11

DI LS 2006 11

Demonstration

  • Demo
slide-12
SLIDE 12

DI LS 2006 12

Conclusions

  • BioFacets has the potential to

become the “Google” for biologists enhanced with a dynamic faceted classification approach for results presentation

slide-13
SLIDE 13

DI LS 2006 13

Acknowledgments

  • NSF CAREER DBI -DBI -0133946
  • NSF DBI -0110854