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 FIBR Program Review June 1, 2006 BeeSpace Meetings Spring 2007 -- Jan 17, 2007
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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.
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BeeSpace: An Interactive Environment for Analyzing
Nature and Nurture in Societal Roles
BeeSpace: An Interactive Environment for Analyzing
Nature and Nurture in Societal Roles
Bruce SchatzInstitute for Genomic Biology
University of Illinois at Urbana-Champaignwww.beespace.uiuc.edu
FIBR Program Review June 1, 2006BeeSpace Meetings Spring 2007 -- Jan 17, 2007
BeeSpace GoalsBeeSpace Goals
Analyze the relative contributions of Analyze the relative contributions of Nature and Nurture in Nature and Nurture in
Societal Roles in Honey BeesSocietal 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
Power of Social EvolutionPower of Social Evolution Language Agriculture Warfare
Humans do These, So do Social Insects
For Bees, we will carefully study ForagingForaging and DefenseDefense
Nature/Nurture Dissection INature/Nurture Dissection I
DefenseDefense
Roles: Guard and Soldier
Nature: Types of Bees (European, African)
Nurture: Levels of Threats (Alarm pheromones)
Nature/Nurture Dissection IINature/Nurture Dissection II
Hereditary Differences affecting: onset age of onset age of ForagingForaging
Subspecies: European (German, Italian) and Africanized Honey Bees
High/Low Pollen Hoarding Lines
Nature/Nurture Dissection IIINature/Nurture Dissection III
Social Manipulations affecting: onset age of Foragingonset age of Foraging
Precocious vs Normal ForagerNormal vs Overage NurseReverted NurseSocially Isolated
Nature/Nurture Dissection IVNature/Nurture Dissection IV
Physiological Manipulations affecting: onset age of Foragingonset age of Foraging
BeeSpace Analysis EnvironmentBeeSpace Analysis Environment Build 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
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 BehaviorsBehaviors to GenesConcepts to ConceptsClusters to ClustersNavigation across Sources
BeeSpace AnalysisBeeSpace Analysis
Space Navigation-OLD Regions-NEW Regions-Sources towards Semantic Switching
Functional Analysis-MAPS Text-GENES Data-Sources towards Pathway Matching
Single Summarization e.g. FlyBase Genes Related Set Meta-Analysis
e.g. Behavior Maturation with EST array Multiple Sets Intersection
e.g. Nature plus Nurture with Genome array
XSpace Information SourcesXSpace Information SourcesOrganize Genome Databases (XBase)Compute Gene Descriptions from Model OrganismsPartition Scientific Literature for Organism XCompute XSpace using Semantic Indexing
Boost the Functional Analysis from Special SourcesCollecting Useful Data about Natural Historiese.g. PigSpace Leverage in USDA Databases