BeeSpace: An Interactive Environment for Analyzing Nature and Nurture in Societal Roles

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BeeSpace An Interactive Environment for
Analyzing Nature and Nurture in Societal Roles

• Bruce Schatz
• Institute for Genomic Biology
• University of Illinois at Urbana-Champaign
• www.beespace.uiuc.edu
• Social Insects Bee Workshop
• Washington DC July 27, 2006

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BeeSpace Goals

• Analyze the relative contributions of
• Nature and Nurture in
• Societal Roles in Honey Bees
• Experimentally measure brain gene expression for
  important societal roles during normal behavior
• varying heredity (nature) and environment
  (nurture)
• Interactively annotate gene functions for
  important gene clusters using concept navigation
  across biological literature representing
  community knowledge

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Post-Genome Informatics

• Classical Organisms have extensive Genetic
  Descriptions!
• There will be NO more classical organisms beyond
• Mice and Men other than Worms and Flies, Yeasts
  and Weeds.
• So must use comparative genomics to classical
  organisms,
• Via sequence homologies and literature analysis.
• Automatic annotation of genes to standard
  classifications,
• Such as Gene Ontology via sequence homology.
• Automatic analysis of functions to scientific
  literature,
• Such as concept spaces via text mining.
• Descriptions in Literature MUST be used for
  future
• interactive environments for functional analysis!

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BeeSpace Conceptual Navigation
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BeeSpace Information Sources

• 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)

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BeeSpace Functional Analysis

• Genes-gt Concepts
• Concept Annotation using Literature postGO
• Concepts -gt Concepts (Conceptual Navigation)
• Concept Switching across Collections (Terms)
• Category Browsing for Search (Documents)
• Category Browsing for Collection (Documents)
• Collaboration Saving across Users (Sets)
• Concepts -gt Genes
• Gene Summary from Collection Automatic

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BeeSpace Functional Analysis

• Genes-gt Concepts
• 3 Concept Annotation using Literature postGO
• Conceptual Navigation
• 2 Concept Switching across Collections (Terms)
• 2 Category Browsing for Search (Documents)
• 1 Category Browsing for Collection (Documents)
• 1 Collaboration Saving across Users (Sets)
• Concepts -gt Genes
• 1 Gene Summarization auto from Collection
• 1 v2May 2 v2Sep 3 v2Dec 2006

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Gene Summarization, BeeSpace v2
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Collaboration across Users
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Category Browse (Collection)
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Category Browse (Search)
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BeeSpace Community Collections

• Organism
• Honey Bee / Fruit Fly
• Song Bird / Soy Bean
• Behavior
• Social / Territorial
• Foraging / Nesting
• Development
• Behavioral Maturation
• Insect Development
• Insect Communication
•  Structure
• Fly Genetics / Fly Biochemistry
• Fly Physiology / Insect Neurophysiology

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Concept Switching, BeeSpace v1
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Credits

• BeeSpace at Institute for Genomic Biology
• University of Illinois at Urbana-Champaign
• Biology
• Gene Robinson, Entomology (behavioral
  expression)
• Susan Fahrbach, Wake Forest (anatomical
  localization)
• Sandra Rodriguez-Zas, Animal Sciences (data
  analysis)
• Informatics
• Bruce Schatz, Medical Information Science
  (systems) ChengXiang Zhai, Computer Science (text
  analysis)
• Chip Bruce, Library Information Science (users)