BeeSpace: An Interactive Environment for Functional Analysis of Social Behavior

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BeeSpace An Interactive Environment for
Functional Analysis of Social Behavior

• Bruce Schatz, Principal Investigator
• Graduate School of Library Information Science
  (GSLIS)
• Department of Computer Science, Program in
  Neuroscience
• schatz_at_uiuc.edu, www.canis.uiuc.edu
• Theme for Genomics of Neural and Behavioral
  Plasticity
• www.beespace.uiuc.edu
• IGB Thematic Research Seminar, November 2, 2004

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Bee Counted Vote Today!
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BeeSpace FIBR Project

• BeeSpace project is NSF FIBR flagship
• Frontiers Integrative Biological Research,
• 5M for 5 years at University of Illinois
• Nature-Nurture using honey bee as model
• Genome technologies in wet lab and dry lab
  biology
• Localized Gene Expression for Normal Social
  Behavior
• Gene Robinson, Entomology (behavioral
  expressions)
• Susan Fahrbach, Entomology (anatomical
  localization)
• Sandra Rodriguez-Zas, Animal Sciences (data
  analysis)
• Interactive Information System for Functional
  Analysis
• Bruce Schatz, Library Information Science
  (info systems)
• ChengXiang Zhai, Computer Science (text
  analysis)
• Chip Bruce, Library Information Science (user
  support)

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Post-Genome Informatics

• Classical Organisms have extensive Genetic
  Descriptions
• There will be NO more classical organisms beyond
• Mice and Men other than Worms and Flies, Yeasts
  and Weeds.
• So must use comparative genomics to classical
  organisms,
• Via sequence homologies and literature analysis.
• Automatic annotation of genes to standard
  classifications,
• Such as Gene Ontology via sequence homology.
• Automatic analysis of functions to scientific
  literature,
• Such as concept spaces via text mining.
• Descriptions in Literature MUST be used for
  future
• interactive environments for functional analysis!

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Informational Science

• Computational Science is widely accepted as the
• Third Branch of Science (beyond Experimental and
  Theoretical)
• Genes are Computed, Proteins are Computed,
• Sequence equivalences are Computed.
• Informational Science is coming to be accepted as
  the
• Fourth Branch of Science
• Based on Information Science technologies for
• Functional Mining of Information Sources
• Comparative Analysis within the
• Dry Lab of Biological Knowledge

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Conceptual Navigation in BeeSpace
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Biology The Model Organism

• The Western Honey Bee, Apis mellifera
• has become a primary model for social behavior
• Complex social behavior in controllable urban
  environment
• Normal Behavior honey bees live in the wild
• Controllable Environment hives can be modified
• Small size manageable with current genomic
  technology
• Capture bees on-the-fly during normal behavior
• Record gene expressions for whole-brain or
  brain-region

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Informatics From Bases to Spaces

• data Bases support genome data
• e.g. FlyBase has sequences and maps
• Genes annotated by GeneOntology and linked to
  literature
• BeeBase (Christine Elsik, Texas AM)
• Uses computed homologies to annotate genes
• information Spaces support biomedical literature
• e.g. BeeSpace uses automatically generated
• conceptual relationships to navigate functions

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BeeSpace Software Environment

• Will build a 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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BeeSpace Software Implementation

• Natural Language Processing
• Identify noun phrases
• Recognize biological entities
• Statistical Information Retrieval
• Compute statistical contexts
• Support conceptual navigation
• Network Information System
• Concept switch across community collections
• Semantic Links into biological databases

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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)

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Worm Community System (1991)

• WCS Information Sources
• Literature Biosis, Medline, newsletters,
  meetings
• Data Genes, Maps, Sequences, strains, cells
• WCS Interactive Environment
• Browsing search, navigation
• Filtering selection, analysis
• Sharing linking, publishing
• WCS 250 users at 50 labs across Internet (1991)
• Flagship in NSF National Collaboratory program

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WCS Molecular
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WCS Cellular
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WCS PPCS demo
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Medical Concept Spaces (1998)

• Obtain discipline-scale collection
• Medline from NLM, 10M bibliographic abstracts
• human classification Medical Subject Headings
• Partition discipline into Community Repositories
• 4 core terms per abstract for MeSH classification
• 32K nodes with core terms (classification tree)
• Community is all abstracts classified by core
  term
• 40M abstracts containing 280M concepts
• computation took 2 days on NCSA Origin 2000
• Simulating World of Medical Communities
• 10K repositories with gt 1K abstracts (1K w/ gt
  10K)

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Navigation in MedSpace

• For a patient with Rheumatoid Arthritis
• Find a drug that reduces the pain (analgesic)
• but does not cause stomach (gastrointestinal)
  bleeding

Choose Domain
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Concept Search
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Concept Navigation
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Retrieve Document
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Biomedical Session
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Categories and Concepts
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Concept Switching
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Document Retrieval
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Biological Concept Spaces (2005)

• 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)

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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

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BeeSpace 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, SCD,
  TAIR)
• Special Sources for BeeSpace
• -Natural History Books (Cornell Library, Harvard
  Press)

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XSpace Information Sources

• Organize Genome Databases (XBase)
• Compute Gene Descriptions from Model Organisms
• Partition Scientific Literature for Organism X
• Compute XSpace using Semantic Indexing Technology
  
• Boost the Functional Analysis from Special
  Sources
• Collecting Useful Data about Natural Histories
• e.g. CowSpace Leverage in AIPL Databases

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Beyond BeeSpace

• The Analysis Environment technology is
  GENERAL! BirdSpace? BehaviorSpace? BrainSpace?
  SoySpace? CowSpace? IGBSpace?
• BioSpace
• Internet will evolve into Interspace