Building Analysis Environments Beyond the Genome and the Web

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Building Analysis Environments Beyond the Genome
and the Web
Bruce R. Schatz CANIS LaboratorySchool of
Library Information ScienceSchool of
Biomedical Health Information
Sciences University of Illinois at
Urbana-Champaign schatz_at_uiuc.edu ,
www.canis.uiuc.edu
Michigan Life Sciences Corridor Bioinformatics,
University of Michigan March 14, 2001
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Technological Progress

• In the past decade, technology has created
• the Genome and the Web
• In 1991, these ideas were only plans
• In 2001, they have already progressed
• from research systems to commercial products
• In the next decade, the revolution will actually
• begin and the world will be completely different!

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Paradigm Shift (Pre)

• Towards Dry-Lab Biology, Walter Gilbert (Jan
  1991)
• The new paradigm, now emerging, is that all the
  'genes' will be known (in the sense of being
  resident in databases available electronically),
  and that the starting point of a biological
  investigation will be theoretical. An
  individual scientist will begin with a
  theoretical conjecture, only then turning to
  experiment to follow or test that hypothesis.
  ...
• To use this flood of knowledge the total
  sequence of the human and model organisms, which
  will pour across the computer networks of the
  world, biologists not only must become
  computer-literate, but also change their approach
  to the problem of understanding life. ...
• The Coming of Informational Science
• Correlation of Information across Sources

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Paradigm Shift (Post)

• Dissecting Human Disease, Victor McKusick (Feb
  2001)
• Structural genomics Functional genomics
• Genomics Proteomics
• Map-based gene discovery Sequence-based gene
  discovery
• Monogenic disorders Multifactorial disorders
• Specific DNA diagnosis Monitoring susceptibility
• Analysis of one gene Analysis of multi-gene
  pathways
• Gene action Gene regulation
• Etiology (mutation) Pathogenesis (mechanism)
• One species Several species

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Analysis Environments I

• The Present -- Year 2001
• Search Central Archives
• Locating a Generic (average) solution
• mining sequences from the Genome
• diagnosing diseases from the Clinical Trial
• some Problems may have point Solutions
• find the cystic fibrosis gene
• find the diabetes treatment

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Analysis Environments II

• The Future -- Year 2011
• Navigate Distributed Repositories
• Locating a Specific (situational) solution
• correlating sequences, genes, expressions
• correlating diagnoses, treatments, lifestyles
• most Problems have cluster Solutions
• find genes for Heart Disease
• find treatments for Arthritis

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Testbeds of the Future

• WCS -- a testbed for the world of 2001
• community repositories before the Web
• in 1991, a distributed analysis environment
• MCS -- a testbed for the world of 2011
• concept navigation before the Interspace
• in 2001, a biomedical analysis environment
• to enable Michigan Corridor faculty and students
  
• to live in the world of the future (information
  space)

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Community Systems
results
data
(database management)
(electronic mail)
knowledge
(hypertext annotations)
literature
news
(information retrieval)
(bulletin boards)
Formal
Informal
browse and share all the knowledge of a community
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Worm Community System

• WCS Information
• Literature BIOSIS, MEDLINE, newsletters,
  meetings
• Data Genes, Maps, Sequences, strains, cells
• WCS Functionality
• Browsing search, navigation
• Filtering selection, analysis
• Sharing linking, publishing
• WCS 250 users at 50 labs across Internet (1991)

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WCS Molecular
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WCS Cellular
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WCS Publishing
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WCS Linking
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WCS invokes gm
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WCS vis-à-vis acedb
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WCS PPCS demo
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A Model Community

• 1984-1988 Telesophy (Bellcore)
• prototype to federate objects
• 1989-1994 WCS (Arizona)
• testbed in molecular biology
• National Model for Biomedical Informatics
• NAS National Collaboratories report
• NIH Human Brain project
• Translational Results
• NCSA Mosaic into Web browsers
• acedb (worm) into Genome databases
• Biology Workbench, 10K users across Web

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THE THIRD WAVE OF NET EVOLUTION
CONCEPTS
OBJECTS
PACKETS
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Towards the Interspace

• from Objects to Concepts
• from Syntax to Semantics
• Infrastructure is Interaction with Abstraction

Internet is packet transmission across
computers Interspace is concept navigation
across repositories
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COMPUTING CONCEPTS
92 4,000 (molecular biology) 93 40,000
(molecular biology) 95 400,000 (electrical
engineering) 96 4,000,000 (engineering) 98
40,000,000 (medicine)
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Simulating a New World

• 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
• concept spaces 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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Concept Navigation

• Semantic Indexes for Community Repositories
• Navigating Abstractions within Repository
• concept space
• category map
• Interactive browsing by Community experts

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Interspace Remote Access Client
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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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Navigate Document
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Retrieve Document
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Concept Switching

• In the Interspace
• each Community maintains its own repository
• Switching is navigating Across repositories
• use your specialty vocabulary to search another
  specialty

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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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Towards A Model Discipline

• 1995-1999 Interspace (Illinois, Urbana)
• prototype to federate concepts
• 2000-2004 MEDSPACE (Illinois, Chicago)
• testbed in clinical medicine (plan, demo)
• National Model for Biomedical Informatics
• lead news in Science on MEDLINE dry-run
• Best Paper at AMIA (Medical Informatics)
• 2001-2005 MCS (Michigan)
• testbed in biomedical research

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Michigan Interspace

• Gather the Information Sources
• Michigan Corridor System (MCS)
• each (department, institute, lab) has repository
• Generate the Community Repositories
• text documents with articles and annotations
• specialty datatypes databases and motifs
• Construct the Analysis Environment
• federated concept navigation across repositories
• type-dependent parsing for text/data interlinks

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MCS Sources

• Literature
• Journals MEDLINE, BIOSIS, full-text
• Specialty Conferences (e.g. Neuroscience)
• Community Newsletters, Lab Annotations
• Databases
• Sequences GENBANK, Celera
• Genes and Maps from Model Organisms
• Microarray Expressions, Protein Structures
• Gene Pathways, Cellular Anatomy

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Ten Steps from Here to There

• Determine Users (range of needs)
• Develop Hardware (networks)
• Determine Collections (range of types)
• Develop Software (databases)
• Interlinks Automatic (name recognition)
• Interlinks Manual (distributed annotation)
• Community Literature (journals, conferences)
• Concept Navigation (indexing, switching)
• Custom Databases (community datasets)
• Custom Software (specialized analysis)

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Bioinformatics Center

• Institute for Biological Information Systems
• develop new information systems
• deploy to study biological systems
• integrated analysis for biological information
• analysis environment for community repositories
• Interspace technologies support Communities
• Basic Science Individual Genomes
• Clinical Practice Individual Patients

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IBIS New Glory

• Institute for Biological Information Systems
• unique facility for all Michigan laboratories
• interactive systems training for all levels
• IBIS reborne
• Thoth, sacred ibis who hatched the world
• inventor of writing, keeper of divine archives
• inventor of arts sciences, medicine surgery
• First of the magicians, he was called the Elder
• His disciples claimed access to the crypt where
  he kept his books of magic, so they undertook to
  decipher and learn these formulas which
  commanded all the forces of nature and subdued
  the very gods themselves.