1. Applications of the Interspace Analysis for Community Repositories
Bruce Schatz
CANIS Laboratory Graduate School of Library and Information Science University of Illinois at Urbana-Champaign
Graduate School of Informatics
Kyoto University, November 28, 2001

2. THE THIRD WAVE OF NET EVOLUTION
CONCEPTS
OBJECTS
PACKETS

3. 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!

4. Paradigm Shift (Pre) The Coming of Informational Science
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

5. 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

6. 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

7. 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

8. 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)

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

10. 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)

11. WCS
Molecular

12. WCS
Cellular

13. WCS Publishing

14. WCS
Linking

15. WCS
invokes gm

16. WCS
vis-à-vis acedb

17. A Model Community 1984-1988 Telesophy (Bellcore)
prototype to federate objects
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

18. Towards A Model Discipline
Interspace (Illinois, Urbana)
prototype to federate concepts
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)
MCS (Michigan)
testbed in biomedical research

19. 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

20. MCS Sources Literature Databases 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

21. 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)

22. THE NET OF THE 21st CENTURY
Beyond Objects to Concepts
Beyond Search to Analysis
Problem Solving via Cross-Correlating Multimedia Information across the Net
Every community has its own special library
Every community does semantic indexing
The Interspace is true Cyberspace

23. Healthcare Infrastructure
For Amateurs rather than Professionals
packaged Interspace with inferred navigation
Internet Health Monitors for ordinary persons
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