BeeSpace: Analysis Environments for Functional Genomics

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BeeSpace Analysis Environments for Functional
Genomics

• Bruce Schatz
• Neurogenomics and Bioinformatics
• Institute for Genomic Biology
• www.beespace.uiuc.edu
• IGB Fellows Symposium
• February 24, 2007

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• 3rd Workshop, May 21-22

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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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Functional Analysis
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Complex Systems

• Understanding Functional Analysis
• Molecular Mechanisms of Social Behavior
• Can only be Discovered via the
• Interactive Navigations of Distributed Systems
• The Interspace is the next generation of
• of the Net (beyond the Web)
• Where Concept Navigation across
• Distributed Communities is routine

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Post-Genome Informatics

• Classical Organisms have Genetic Descriptions!
• Must use functional genomics to these organisms,
• Via sequence homologies and literature analysis.
• Annotation of genes to standard classifications,
• Such as Gene Ontology via sequence homology.
• 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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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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System Architecture

• BeeSpace

• Concepts

• Concepts

• SEQ

• Expressions

• Expressions

• Databases

• Bees

• Flies

• Documents

• Documents

• SEQ

• Community

• Community

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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

• Concept versus Term
• set of semantically equivalent terms
• Concept switching
• region to region (set to set) match

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Towards the Interspace

• from Objects to Concepts
• from Syntax to Semantics
• Infrastructure is Interaction with Abstraction

Internet is packet transmission across
computers Interspace is concept navigation
across repositories
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LEVELS OF INDEXES
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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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BeeSpace Information Sources

• General for All Spaces
• Scientific Literature
• -Medline, Biosis, Agricola, Agris, CAB Abstracts
• -partitioned by organisms and by functions
• Model Organisms
• -Gene Descriptions (FlyBase, WormBase, MGI, OMIM,
  TAIR, SCD)
• Special Sources for BeeSpace
• -Natural History Books (Cornell Library, Harvard
  Press)

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XSpace Information Sources

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

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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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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)

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Informational Science

• Computational Science is the Third Branch of
  Science (beyond Experimental and Theoretical)
• Genes are Computed, Proteins are Computed,
• Sequence equivalences are Computed.
• Informational Science is coming to be accepted as
  
• The Fourth Branch of Science
• Based on Information Science technologies for
• Functional Mining of Information Sources
• Comparative Analysis within the
• Dry Lab of Biological Knowledge