BeeSpace: An Interactive Environment for Analyzing Nature and Nurture in Societal Roles - PowerPoint PPT Presentation

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

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Title: THE INTERSPACE PROTOTYPE An Analysis Environment for Semantic Interoperability Author: canis Last modified by: Bruce Schatz Created Date: 3/2/1999 3:46:30 PM – PowerPoint PPT presentation

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


1
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
  • FIBR Program Review June 1, 2006
  • BeeSpace Meetings Spring 2007 -- Jan 17, 2007

2
  • 2nd Annual Workshop
  • May 21-22, 2007

3
BeeSpace 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

4
Power of Social Evolution
  • Language
  • Agriculture
  • Warfare
  • Humans do These, So do Social Insects
  • For Bees, we will carefully study
  • Foraging and Defense

5
Nature/Nurture Dissection I
  • Defense
  • Roles Guard and Soldier
  • Nature Types of Bees (European, African)
  • Nurture Levels of Threats (Alarm pheromones)

6
Nature/Nurture Dissection II
  • Hereditary Differences affecting
  • onset age of Foraging
  • Subspecies European (German, Italian) and
    Africanized Honey Bees
  • High/Low Pollen Hoarding Lines

7
Nature/Nurture Dissection III
  • Social Manipulations affecting
  • onset age of Foraging
  • Precocious vs Normal Forager
  • Normal vs Overage Nurse
  • Reverted Nurse
  • Socially Isolated

8
Nature/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

9
Goals of Functional Analysis
  • Identify Genes regulated by heredity and
    environment
  • Discover Candidate Genes (Gene
    Clusters, Gene Pathways) for Behavioral Regulation

10
System Architecture
  • BeeSpace
  • Concepts
  • Concepts
  • SEQ
  • Expressions
  • Expressions
  • Databases
  • Bees
  • Flies
  • Documents
  • Documents
  • SEQ
  • Community
  • Community

11
Concept Navigation in BeeSpace
12
BeeSpace 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)

13
BeeSpace 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

14
(No Transcript)
15
Biological 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)

16
BeeSpace 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

17
CONCEPT SWITCHING
  • Concept versus Term
  • set of semantically equivalent terms
  • Concept switching
  • region to region (set to set) match

18
Interactive 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

19
BeeSpace Analysis
  • Space Navigation
  • -OLD Regions
  • -NEW Regions
  • -Sources towards Semantic Switching
  • Functional Analysis
  • -MAPS Text
  • -GENES Data
  • -Sources towards Pathway Matching

20
Space Navigation
  • OLD Regions in Concept Space
  • Custom insect behavior
  • Ontology Gene, Behavior
  • Classification MeSH, Biosis
  • User Themes, Collections

21
Space Navigation
  • NEW Regions in Concept Space
  • Search text query
  • Search Switch set of terms
  • Region Switch set of documents
  • Spread follow to related

22
Functional Analysis
  • MAPS categories of text
  • Documents Relevance Ranked
  • Intrinsic Natural Bottom-Up
  • Extrinsic Artificial Top-Down

23
Functional 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

24
XSpace 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

25
Towards the Interspace
  • The Analysis Environment technology is
    GENERAL! BirdSpace? BeeSpace?
  • PigSpace? CowSpace?
  • BehaviorSpace? BrainSpace?
  • BioSpace
  • Interspace
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