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
cGMP manganeseNPF vitellogenin JH (Juvenile Hormone) octopamine TOFA (Fatty Acid inhibitor)Brood Pheromone, Queen Pheromone
Goals of Functional AnalysisGoals of Functional Analysis
Identify Genes regulated by heredity and environment
Discover Candidate Genes (Gene Clusters, Gene Pathways) for Behavioral Regulation
System ArchitectureSystem Architecture
Concept Navigation in BeeSpaceConcept Navigation in BeeSpace
NeuroscienceLiterature
MolecularBiology
Literature
BeeLiterature
Flybase,WormBase
BeeGenome
Brain RegionLocalization
Brain GeneExpression
Profiles
BehavioralBiologist
MolecularBiologist
Neuro-scientist
BeeSpace Information SourcesBeeSpace 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)
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
Biological Concept SpacesBiological Concept Spaces
Compute concept spaces for All of BiologyBioSpace across entire biomedical literature
50M abstracts across 50K repositories
Use Gene Ontology to partition literature into biological communities for functional analysis
GO same scale as MeSH but adequate coverage?GO light on social behavior (biological process)
BeeSpace Community CollectionsBeeSpace 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
CONCEPT SWITCHINGCONCEPT SWITCHING
“Concept” versus “Term” set of “semantically” equivalent terms
Concept switching region to region (set to set) match
term
Semantic region
Concept SpaceConcept Space
Interactive Functional AnalysisInteractive 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 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
Space NavigationSpace Navigation
OLD Regions in Concept Space
Custom insect behavior Ontology Gene, Behavior Classification MeSH, Biosis User Themes, Collections
Space NavigationSpace Navigation
NEW Regions in Concept Space
Search text query Search Switch set of terms Region Switch set of documents Spread follow to related
Functional AnalysisFunctional Analysis
MAPS categories of text
Documents Relevance Ranked Intrinsic Natural Bottom-Up Extrinsic Artificial Top-Down
Functional AnalysisFunctional Analysis
GENES concepts to data
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
Towards the InterspaceTowards the Interspace
The Analysis Environment technology is GENERAL!
BirdSpace? BeeSpace?PigSpace? CowSpace? BehaviorSpace? BrainSpace?
BioSpace… Interspace