Title: BeeSpace: An Interactive Environment for Analyzing Nature and Nurture in Societal Roles
1BeeSpace 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
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3BeeSpace 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
4BeeSpace is
- A Big Interdisciplinary Project
- The First and the Biggest at IGB
- NSF FIBR 5M 2004-2009
- General Biotechnology (Dry Lab)
- Interactive Environment for Functional Analysis
(Bioinformatics) - Important Science (Wet Lab)
- Model Dissection of Nature-Nurture (Genomics of
Behavioral Plasticity)
5BeeSpace FIBR Project
- BeeSpace project is NSF FIBR flagship
- Frontiers 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
- Bee Biology gene expressions
- Space Informatics concept navigations
6Project Investigators
- Biology
- Gene Robinson, Integrative Biology (genomics)
- Susan Fahrbach, Biology at Wake Forest (anatomy)
- Sandra Rodriguez-Zas, Animal Sciences (data
analysis) - Informatics
- Bruce Schatz, Medical Information Science
(systems) ChengXiang Zhai, Computer Science (text
analysis) - Chip Bruce, Library Information Science
(users) - Collaborators
- FlyBase, BeeBase, Bee Genome Community
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8BeeSpace Goals
- Analyze the relative contributions of
- Nature and Nurture in
- Societal 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
9 for Social Beehavior
10Complex 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
11for Functional Analysis
12Complex Systems II
- Understanding Functional Analysis
- Integrating many sources to explain behavior
- Across organisms and functions
- Most of functional explanations are in text
- Text Mining and Gene Summarizing
- Intersecting Multiple Viewpoints to
- Discover Emergent Properties
13 14Post-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!
15Informatics From Bases to Spaces
- data Bases support genome data
- e.g. FlyBase has sequences and maps
- Insect genes typically re-use Drosophila names.
- BeeBase (Christine Elsik, Texas AM)
- Uses computed orthologs to annotate genes
- information Spaces support biological literature
- BeeSpace uses automatically generated
- conceptual relationships to navigate functions
16System Architecture
17Concept Navigation in BeeSpace
18BeeSpace General Biotechnology
- Bioinformatics of Genes and Behavior
- Using 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
19BeeSpace 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
20Analysis Environment Model
- Explicitly capture SCIENCE in SYSTEM!
- Wet Lab
- Locate Candidate Genes
- Classify Differential Genes
- Dry Lab
- Locate Candidate Texts
- Classify Differential Texts
21Analysis 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
22Analysis 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
-
23CONCEPT SWITCHING
- Concept versus Term
- set of semantically equivalent terms
- Concept switching
- region to region (set to set) match
24BeeSpace 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)
25XSpace Information Sources
- Organize Genome Databases (XBase)
- Compute Gene Descriptions from Model Organisms
- Partition Scientific Literature for Organism X
- Compute XSpace using Semantic Indexing
- Boost the Functional Analysis from Special
Sources - Collecting Useful Data about Natural Histories
- e.g. PigSpace Leverage in USDA Databases
26Towards the Interspace
- The Analysis Environment technology is
GENERAL! BirdSpace? BeeSpace? - PigSpace? CowSpace?
- SoySpace? CornSpace?
- InsectSpace? PlantSpace?
- BioSpace? MedSpace?
27 28Biology The Model Organism
- Western Honey Bee, Apis mellifera
- A model for social behavior
- Coordinated Publication
- 50 papers Oct 2006
- Nature, Science, PNAS
- Genome Research
- Insect Molecular Biology
29Emergent 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
30Nature and Nurture both act on the genome
31Power 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
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33Experimental 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
34 35Education 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
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