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Michigan Life Sciences CorridorMichigan Life Sciences CorridorBioinformatics, University of MichiganBioinformatics, University of Michigan
March 14, 2001March 14, 2001
Building Analysis EnvironmentsBuilding Analysis Environments Beyond the Genome and the WebBeyond the Genome and the Web
Bruce R. SchatzCANIS Laboratory
School of Library & Information ScienceSchool of Biomedical & Health Information Sciences
University of Illinois at [email protected] , www.canis.uiuc.edu
Technological ProgressTechnological Progress
In the past decade, technology has created the Genome and the Web
In 1991, these ideas were only plansIn 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!
Paradigm Shift (Pre)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 ScienceCorrelation of Information across Sources
Paradigm Shift (Post)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
Analysis Environments IAnalysis 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
Analysis Environments IIAnalysis 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
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)
Testbeds of the FutureTestbeds of the Future
Community SystemsCommunity Systems
browse and share all the knowledge of a community
data results(database management) (electronic mail)
literature news(information retrieval) (bulletin
boards)
knowledge(hypertext annotations)
Formal Informal
Worm Community SystemWorm Community System WCS Information:Literature BIOSIS, MEDLINE, newsletters,
meetings
Data Genes, Maps, Sequences, strains, cells
WCS FunctionalityBrowsing search, navigationFiltering selection, analysisSharing linking, publishing
WCS: 250 users at 50 labs across Internet (1991)
WCSMolecular
WCS Cellular
WCS Publishing
WCS Linking
WCS invokes
gm
WCS vis-à-vis
acedb
WCSPPCS
demo
A Model CommunityA 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
THE THIRD WAVE OF NET EVOLUTIONTHE THIRD WAVE OF NET EVOLUTION
PACKETS
OBJECTS
CONCEPTS
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
Towards the InterspaceTowards the Interspace
1992 1993 1995 1996 1998
COMPUTING CONCEPTSCOMPUTING 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)
Simulating a New WorldSimulating 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 > 1K abstracts (1K w/ > 10K)
Concept NavigationConcept Navigation
Semantic Indexes for Community Repositories
Navigating Abstractions within Repository concept space category map
Interactive browsing by Community experts
Interspace Remote Access ClientInterspace Remote Access Client
Navigation in MEDSPACENavigation in MEDSPACE
For a patient with Rheumatoid Arthritis Find a drug that reduces the pain (analgesic) but does not cause stomach (gastrointestinal) bleeding
Choose DomainChoose Domain
Concept SearchConcept Search
Concept NavigationConcept Navigation
Retrieve DocumentRetrieve Document
Navigate DocumentNavigate Document
Retrieve DocumentRetrieve Document
Concept SwitchingConcept Switching
In the Interspace…
each Community maintains its own repository
Switching is navigating Across repositories
use your specialty vocabulary to search another specialty
Biomedical SessionBiomedical Session
Categories and ConceptsCategories and Concepts
Concept SwitchingConcept Switching
Document RetrievalDocument Retrieval
Towards A Model DisciplineTowards 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
Michigan InterspaceMichigan 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
MCS SourcesMCS 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
Ten Steps from Here to ThereTen 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)
Bioinformatics CenterBioinformatics 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
IBIS New GloryIBIS 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”.