BeeSpace: Functional Analysis of Social Behavior

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BeeSpace Functional Analysis of Social Behavior

• Bruce Schatz
• Genomics of Neural Behavioral Plasticity
• Bioinformatics Laboratory
• Institute for Genomic Biology
• schatz_at_uiuc.edu, www.beespace.uiuc.edu
• IGB Fellows Symposium
• April 5, 2008

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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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Conceptual Navigation in BeeSpace
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Informatics From Bases to Spaces

• data Bases support genome data
• e.g. FlyBase has sequences and maps
• Genes annotated by GeneOntology and
• linked to biological literature
• information Spaces support biological literature
• e.g. BeeSpace uses automatically generated
• conceptual relationships to navigate functions

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BeeSpace General Bioinformatics

• Bioinformatics of Genes and Behavior
• Using scalable semantics technology
• Using General Expressions and Literatures
• Annotation Pipelines from Sequence and Text
• Creating and Merging multiple SPACES
• Where REGIONS are semantically created
• And useful regions become shared spaces

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System Architecture

• BeeSpace

• Concepts

• Concepts

• SEQ

• Expressions

• Expressions

• Databases

• Bees

• Flies

• Documents

• Documents

• SEQ

• Community

• Community

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BeeSpace v3 Sample

• Refining and Merging Space Regions
• Cross bee species differential gene expression
  for behavioral maturation into adult forager
• Functional Analysis for Similar Situation!
• Behavioral Maturation merge
• Cross-Species Comparisons merge
• Different Taxa (insect,fish,bird,rodent)

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Interactive Functional Analysis

• BeeSpace will enable users to navigate a uniform
  space of diverse databases and literature sources
  for hypothesis development and testing, with a
  software system that goes beyond a searchable
  database, using statistical literature analyses
  to discover functional relationships between
  genes and behavior.
• Genes to Behaviors
• Behaviors to Genes
• Concepts to Concepts
• Clusters to Clusters
• Navigation across Sources

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New Interface v4

• Single Window, Multiple Panes
• Email Model Folders, Lists, Messages
• Coordinated Levels of Resolution
• SPACES merge, switch
• MAPS topic, custom, ontology
• DOCUMENTS summarize, annotate

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Towards the Interspace

• The Analysis Environment technology is
  GENERAL! BirdSpace? BeeSpace?
• PigSpace? CowSpace?
• BrainSpace? BehaviorSpace?
• BioSpace
• Interspace

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Faculty Investigators

• 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)

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Informatics Researchers I

• Bruce Schatz (faculty), systems
• ChengXiang Zhai (faculty), algorithms
• David Arcoleo (staff), research programmer
• Moushumi Sen Sarma (postdoc), biology usage
• Jim Buell (staff), user support
• Faculty Collaborators
• Saurabh Sinha (CS), Sheng Zhong (BIOENG)
• Jiawei Han (CS), Roxana Girju (LING)

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Informatics Researchers II

• Bioinformatics students
• Xu Ling gene summarizer (cf. FlyBase)
• Xin He gene annotator (meta-analysis)
• Yanen Li gene classification (ontology)
• Computer Science students
• Yue Lu entity recognizer (relations)
• Peixiang Zhao concept switching (subgraphs)
• Yuanhua Lv user personalization (spaces)
• Informatics students
• Brant Chee semantic clusterer (smallworlds)