BeeSpace: An Interactive Environment for Functional Analysis of Social Behavior

1
BeeSpace An Interactive Environment for
Functional Analysis of Social Behavior

• Bruce Schatz, Principal Investigator
• Graduate School of Library Information Science
• Institute for Genomic Biology
• schatz_at_uiuc.edu, www.canis.uiuc.edu
• www.beespace.uiuc.edu
• GSLIS Research Showcase, March 14, 2005

2
Mechanisms for Social Beehavior
3
UIUC BeeSpace FIBR Project

• BeeSpace project is NSF FIBR flagship
• Frontiers Integrative Biological Research,
• 5M for 5 years at University of Illinois
• Nature-Nurture using honey bee as model
• Genome technologies in wet lab and dry lab
  biology
• Localized Gene Expression for Normal Social
  Behavior
• Gene Robinson, Entomology (behavioral
  expressions)
• Susan Fahrbach, Entomology (anatomical
  localization)
• Sandra Rodriguez-Zas, Animal Sciences (data
  analysis)
• Interactive Information System for Functional
  Analysis
• Bruce Schatz, Library Information Science
  (info systems)
• ChengXiang Zhai, Computer Science (text
  analysis)
• Bertram Bruce, Library Information Science
  (user collab)

4
Library Information Science

• Broad-spectrum Bioinformatics project covering
  wide range of research within Library and
  Information Science
• Basic problem is annotating genes for honey bees
  using known genetic models (e.g. fruit flies) and
  scientific literature
• Library Science
• Subject Assignments for Community Collections
• On 50K repositories for 50M articles
• Information Science
• Semantic Indexing for Scientific Literature
• Supporting concept navigation across community
  collections
• Community Informatics
• Collaborative development and Collaboratory
  deployment
• For different users from graduate to middle
  school students

5
Conceptual Navigation in BeeSpace
6
BeeSpace Library Science

• Biomedical Literature
• Medline (medicine)
• Biosis (biology)
• Agricola, CAB Abstracts, Agris (agriculture)
• Model Organisms (heredity)
• -Gene Descriptions (FlyBase, WormBase)
• Natural Histories (environment)
• -BeeKeeping Books (Cornell Library, Harvard
  Press)
• 50M articles in 50K collections
• partition by MeSH and GO

7
WCS Molecular
8
Concept Navigation
9
Retrieve Document
10
BeeSpace Information Science

• Will build a Concept Space of Biomedical
  Literature for Functional Analysis of Bee Genes
• -Partition Literature into Community Collections
• -Extract and Index Concepts within Collections
• -Navigate Concepts within Documents
• -Follow Links from Documents into Databases
• Locate Candidate Genes in Related Literatures
  then
• follow links into Genome Databases

11
BeeSpace Information Science

• Natural Language Processing
• Identify noun phrases
• Recognize biological entities
• Statistical Information Retrieval
• Compute statistical contexts
• Support conceptual navigation
• Network Information System
• Concept switch across community collections
• Semantic Links into biological databases

12
BeeSpace portal using iLabs
13
BeeSpace Community Informatics

• Part of GSLIS Community Informatics Initiative --
  at high-end
• Colloborative Development
• Research users are biology postdocs and graduate
  students
• Via Experimental International Community (5 then
  15 labs)
• Education users are high school and middle school
  students
• Via Uni Hi and Summer Math (university education
  outreach)
• Collaboratory Deployment
• Differential Access and Community Annotation
• A Primary Driver of Community Inquiry Labs
  (iLabs)

14
XSpace Information Sources

• Organize Genome Databases (XBase)
• Compute Gene Descriptions from Model Organisms
• Partition Scientific Literature for Organism X
• Compute XSpace using Semantic Indexing Technology
  
• Boost the Functional Analysis from Special
  Sources
• Collecting Useful Data about Natural Histories
• e.g. CowSpace Leverage in AIPL Databases

15
Beyond BeeSpace

• The Analysis Environment technology is
  GENERAL! BirdSpace? BehaviorSpace? BrainSpace?
  PigSpace? CowSpace? IGBSpace?
• towards the BioSpace!
• Internet will evolve into Interspace