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
- FIBR Program Review June 1, 2006
- BeeSpace Meetings Spring 2007 -- Jan 17, 2007
2- 2nd Annual Workshop
- May 21-22, 2007
3BeeSpace Goals
- Analyze the relative contributions of
- Nature and Nurture in
- Societal 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
4Power of Social Evolution
- Language
- Agriculture
- Warfare
- Humans do These, So do Social Insects
- For Bees, we will carefully study
- Foraging and Defense
5Nature/Nurture Dissection I
- Defense
- Roles Guard and Soldier
- Nature Types of Bees (European, African)
- Nurture Levels of Threats (Alarm pheromones)
6Nature/Nurture Dissection II
- Hereditary Differences affecting
- onset age of Foraging
- Subspecies European (German, Italian) and
Africanized Honey Bees - High/Low Pollen Hoarding Lines
-
7Nature/Nurture Dissection III
- Social Manipulations affecting
- onset age of Foraging
- Precocious vs Normal Forager
- Normal vs Overage Nurse
- Reverted Nurse
- Socially Isolated
8Nature/Nurture Dissection IV
- Physiological Manipulations affecting
- onset age of Foraging
- cGMP manganese
- NPF vitellogenin
- JH (Juvenile Hormone) octopamine
- TOFA (Fatty Acid inhibitor)
- Brood Pheromone, Queen Pheromone
9Goals of Functional Analysis
- Identify Genes regulated by heredity and
environment - Discover Candidate Genes (Gene
Clusters, Gene Pathways) for Behavioral Regulation
10System Architecture
11Concept Navigation in BeeSpace
12BeeSpace 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)
13BeeSpace 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
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15Biological Concept Spaces
- Compute concept spaces for All of Biology
- BioSpace 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)
16BeeSpace 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
17CONCEPT SWITCHING
- Concept versus Term
- set of semantically equivalent terms
- Concept switching
- region to region (set to set) match
18Interactive 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 Behaviors
- Behaviors to Genes
- Concepts to Concepts
- Clusters to Clusters
- Navigation across Sources
19BeeSpace Analysis
- Space Navigation
- -OLD Regions
- -NEW Regions
- -Sources towards Semantic Switching
- Functional Analysis
- -MAPS Text
- -GENES Data
- -Sources towards Pathway Matching
20Space Navigation
- OLD Regions in Concept Space
- Custom insect behavior
- Ontology Gene, Behavior
- Classification MeSH, Biosis
- User Themes, Collections
21Space Navigation
- NEW Regions in Concept Space
- Search text query
- Search Switch set of terms
- Region Switch set of documents
- Spread follow to related
22Functional Analysis
- MAPS categories of text
- Documents Relevance Ranked
- Intrinsic Natural Bottom-Up
- Extrinsic Artificial Top-Down
23Functional 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
24XSpace 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
25Towards the Interspace
- The Analysis Environment technology is
GENERAL! BirdSpace? BeeSpace? - PigSpace? CowSpace?
- BehaviorSpace? BrainSpace?
- BioSpace
- Interspace