Interactive Functional Analysis from the Biomedical Literature

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Interactive Functional Analysis from the
Biomedical Literature
Bruce Schatz BeeSpace ProjectInstitute for
Genomic BiologyUniversity of Illinois at
Urbana-Champaign schatz_at_uiuc.edu ,
www.beespace.uiuc.edu
Gene Ontology (GO) Users Meeting Chicago, October
14, 2004
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BeeSpace Environment

• BeeSpace project is NSF FIBR flagship,
• 5M for 5 years at University of Illinois
• Frontiers Integrative Biological Research
• Nature-Nurture using honey bee as the model
• Gene expression for normal Social Behavior
• based on Bee Genome (Gene Robinson)
• Interactive system for Functional Analysis
• based on Interspace Prototype (Bruce
  Schatz)

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From Bases to Spaces

• data Bases support genome data
• e.g. FlyBase has sequences and maps
• Genes annotated by GO 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 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 Information Sources

• Biomedical Literature
• Medline (medicine)
• Biosis (biology)
• Agricola, Agris (agriculture)
• Model Organisms (heredity)
• -Gene Descriptions (FlyBase, WormBase)
• Natural Histories (environment)
• -BeeKeeping Books (Cornell, Harvard)

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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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Biological Concept Spaces (2005)

• Compute concept spaces for All of Biology
• BioSpace across 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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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