Bioinformatics Director LectureBioinformatics Director LectureUniversity of Michigan Medical SchoolUniversity of Michigan Medical School

February 7, 2000February 7, 2000

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 Urbana-Champaignschatz@uiuc.edu , www.canis.uiuc.edu

Technological ProgressTechnological Progress

In the past decade, technology has created the Genome and the Web

In 1990, these ideas were only plansIn 2000, 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 ShiftParadigm ShiftTowards 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 Knowledge across Sources

Analysis Environments IAnalysis Environments I

The Present -- Year 2000

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 2010

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 2000 community repositories before the Web

in 1991, a distributed analysis environment

MIBI -- a testbed for the world of 2010 concept navigation before the Interspace

in 2001, a biomedical analysis environment

to enable Michigan faculty and students to live

in the world of the future

Testbeds of the FutureTestbeds of the Future

Bioinformatics [basic] Scientific. Biology: genetics, genomics.

Medical Informatics [translational] Clinical. Medicine: literature, records.

Healthcare Informatics [management] Practical. Outcomes: tracking, quality.

The Kinds of InformaticsThe Kinds of Informatics

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 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

Scalable SemanticsScalable Semantics

Automatic indexing Domain-Independent indexing Statistical clustering

Compute Context of

concepts within documents documents within repositories

CROSS-OVERS IN SEMANTIC INDEXINGCROSS-OVERS IN SEMANTIC INDEXING

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 MIBI (Michigan) testbed in biomedical research

Michigan InterspaceMichigan Interspace Gather the Information Sources

Michigan Integrated Biomedical Interspace (MIBI)

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 switching across sites type-dependent parsing for text/data interlinks

MIBI SourcesMIBI Sources Literature

Journals: MEDLINE, BIOSIS, fulltext Specialty Conferences (e.g. Neuroscience) Community Newsletters, Lab Annotations

Databases Sequences: GENBANK, Celera Genes and Maps from Model Organisms Expressions from Microarrays Gene Pathways, Cellular Anatomy

U-M Medical School TestbedU-M Medical School Testbed

Department by Department Propagation

Similar to Illinois Digital Library Testbed

for College of Engineering at UIUC

NSF DLI, 1994-98, then University Library

Federated Search using Document Structure

Full-text Journals used in classes and labs

U-M Health System TestbedU-M Health System Testbed

Central Propagation to Hospital and Clinics

Similar to UIC Medical Center Testbed pilot project for Surgery residents after seed, planned to all Medical Center

Concept Spaces for Community Repositories All Medical Literature (MEDLINE, BIOSIS) All Medical Records (Cerner narratives)

Chronic IllnessChronic Illness Aging Population is Economics of 21st century

2010 -- Interspace is worldwide infrastructure 2010 -- Baby Boomers start retirement age

Process for Health Status Frequency twice a year community clinic twice a month alternative medicine twice a day self-care home monitors

Arthritis versus Modern Medicine 12% of population, 30 million people Tylenol versus NSAIDs chiropractors versus surgery

Healthcare InformaticsHealthcare Informatics Users are Amateurs rather than Professionals

packaged Interspace with inferred navigation Internet Health Monitors for individuals

Generate the Personal Repositories interact with health status questionnaires builds a customized dynamic database

Construct the Analysis Environment similarity matching to locate similar patients

Evolve Community Interspace statistical clustering for lifestyle coaching

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”.