BeeSpace: An Interactive Environment for Analyzing Nature and Nurture in Societal Roles

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