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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 at Urbana-Champaign www.beespace.uiuc.edu Third Annual Project Workshop IGB, Urbana IL May 21, 2007. BeeSpace Workshop Schedule. - PowerPoint PPT Presentation
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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
Third Annual Project WorkshopIGB, Urbana IL May 21, 2007
BeeSpace Workshop ScheduleBeeSpace Workshop Schedule Introductory Lectures (Bevier Auditorium), 9-12
Informatics, Biology, Education Faculty Investigators across Campus
Working Sessions (IGB Training Rooms), 1-5 System Demo, Biology Usage, User Support Staff Members within IGB
Strategic Planning (IGB Conference Rooms),9-12 Project Members and Visitors
BeeSpace is…BeeSpace is… A Big Interdisciplinary Project A Big Interdisciplinary Project
The First and the Biggest at IGBThe First and the Biggest at IGB NSF FIBR $5M 2004-2009NSF FIBR $5M 2004-2009
General Biotechnology (Dry Lab)General Biotechnology (Dry Lab) Interactive Environment for Interactive Environment for
Functional Analysis (Bioinformatics)Functional Analysis (Bioinformatics) Important Science (Wet Lab)Important Science (Wet Lab)
Model Dissection of Nature-Nurture Model Dissection of Nature-Nurture (Genomics of Behavioral Plasticity) (Genomics of Behavioral Plasticity)
BeeSpace FIBR ProjectBeeSpace FIBR Project
BeeSpace project is NSF FIBR flagshipFrontiers Integrative Biological Research, $5M for 5 years at University of Illinois
Analyzing Nature and Nurture in Societal Roles using honey bee as model
(Functional Analysis of Social Behavior)
Genomic technologies in wet lab and dry lab BeeBee [Biology] gene expressions SpaceSpace [Informatics] concept navigations
Project InvestigatorsProject Investigators
BiologyGene Robinson, Integrative Biology (genomics)Susan Fahrbach, Biology at Wake Forest (anatomy)Sandra Rodriguez-Zas, Animal Sciences (data analysis)
InformaticsBruce Schatz, Medical Information Science (systems) ChengXiang Zhai, Computer Science (text analysis)Chip Bruce, Library & Information Science (users)
CollaboratorsFlyBase, BeeBase, Bee Genome Community
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 gene expression in the brain for important societal roles during normal behavior varying heredity (nature) and environment (nurture)
Interactively annotate functions for differential expression using concept-based navigation of biological literature and gene –centered summarization analysis
for Social Beehavior for Social Beehavior
Complex Systems IComplex Systems I
Understanding Social Behavior
Honey Bees have only 1 million neurons Yet… A Worker Bee exhibits Social Behavior!
She forages when she is not hungry but the Hive is She fights when she is not threatened but the Hive is
for Functional Analysisfor Functional Analysis
Complex Systems IIComplex Systems II
Understanding Functional Analysis
Integrating many sources to explain behaviorAcross organisms and functions
Most of functional explanations are in text
Text Mining and Gene Summarizing Intersecting Multiple Viewpoints to
Discover Emergent Properties
Post-Genome InformaticsPost-Genome Informatics
Comparative Genomics to Classical Models
Sequence-based gene annotation To standard classifications such as Gene Ontology
Literature-based gene annotation To computed classifications via extracted concepts
Descriptions in Literature MUST be used in future interactive environments for functional analysis!
Informatics: From Bases to SpacesInformatics: From Bases to Spaces
data Bases support genome datae.g. FlyBase has sequences and mapsInsect genes typically re-use Drosophila names.
BeeBase (Christine Elsik, Texas A&M)Uses computed orthologs to annotate genes
information Spaces support biological literatureBeeSpace uses automatically generated conceptual relationships to navigate functions
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 General BiotechnologyBeeSpace General Biotechnology
Bioinformatics of Genes and BehaviorBioinformatics of Genes and BehaviorUsing scalable semantics technologyUsing 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
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
Analysis Environment: ModelAnalysis Environment: Model
Explicitly capture SCIENCE in SYSTEM!
Wet Lab:Locate Candidate GenesClassify Differential Genes
Dry Lab:Locate Candidate TextsClassify Differential Texts
Analysis Environment: FeaturesAnalysis Environment: Features
SPACE is a Paradigm not a Metaphor!
Point of View for YOUR Problem
Externally:-Dynamically describe custom Region of Space-Merge Regions to form Hypothesis Space-Differentially express genes against Space
Analysis Environment: SystemAnalysis Environment: System
Concepts and Genes are Universal Entities!
Uniformly Represented Uniformly Manipulated
Internally:-Extract and Index Concepts within Collections-Navigate Concepts within Documents-Follow Genes from Documents into Databases
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
BeeSpace Information SourcesBeeSpace 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)
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? SoySpace? CornSpace?
InsectSpace? PlantSpace?BioSpace? MedSpace?
Biology: The Model OrganismBiology: The Model Organism
Western Honey Bee, Apis melliferaA model for social behavior
Emergent PropertiesEmergent Properties
Complex Behavior from Simple Model Normal Behavior – honey bees live in the wild
Controllable Heredity – Queens and Hormones Controllable Environment – hives can be modified
Small size manageable with genomic technology Differential genes for normal behavior
Nature and Nurture both act on the genome
Heredity Environment
Power of Social EvolutionPower of Social Evolution Agriculture (bee forager) Warfare (bee defender) Language (bee dancer)
Humans do These, So do Social Insects
We are performing Nature-Nurture dissection to locate candidate genes spanning these normal behaviors of honey bees
(Whitfield et al, 2002)
Experimental StatusExperimental Status Genome Complete and Microarray Fabricated Bees collected for Societal Role experiments
Initial Dissections complete on EST array On-going first Genome Array dissection
Sequence Annotation Pipeline being used Literature Annotation Pipeline being tested
Designing Meta-analysis Environment
Education: Scientific InquiryEducation: Scientific Inquiry Graduate
New Research via Functional Analysis 5 early adopter labs, then 15 international labs
Undergraduate New Bioinformatics Course using BeeSpace
High School Integrate into Field Biology course at Uni High