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