1. Michigan Life Sciences Corridor Bioinformatics, University of Michigan March 14, 2001 Building Analysis Environments Beyond the Genome and the Web Bruce R. Schatz CANIS Laboratory School of Library & Information Science School of Biomedical & Health Information Sciences University of Illinois at Urbana-Champaign schatz@uiuc.edu, www.canis.uiuc.edu

2. 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!

3. 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

4. Paradigm Shift (Post) Dissecting Human Disease, Victor McKusick (Feb 2001) Structural genomicsFunctional genomics GenomicsProteomics Map-based gene discoverySequence-based gene discovery Monogenic disordersMultifactorial disorders Specific DNA diagnosisMonitoring susceptibility Analysis of one geneAnalysis of multi-gene pathways Gene actionGene regulation Etiology (mutation)Pathogenesis (mechanism) One speciesSeveral species

5. 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

6. 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

7. 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 Future

8. Community 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

9. Worm Community System WCS Information: Literature BIOSIS, MEDLINE, newsletters, meetings Data Genes, Maps, Sequences, strains, cells WCS Functionality Browsingsearch, navigation Filteringselection, analysis Sharinglinking, publishing WCS: 250 users at 50 labs across Internet (1991)

10. WCS Molecular

11. WCS Cellular

12. WCS Publishing

13. WCS Linking

14. WCS invokes gm

15. WCS vis-à-vis acedb

16. WCS PPCS demo

17. 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

18. THE THIRD WAVE OF NET EVOLUTION PACKETS OBJECTS CONCEPTS

19. 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 Interspace

20. 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)

21. 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 > 1K abstracts (1K w/ > 10K)

22. Concept Navigation Semantic Indexes for Community Repositories Navigating Abstractions within Repository concept space category map Interactive browsing by Community experts

23. Interspace Remote Access Client

24. 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

25. Concept Search

26. Concept Navigation

27. Retrieve Document

28. Navigate Document

29. Retrieve Document

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

31. Biomedical Session

32. Categories and Concepts

33. Concept Switching

34. Document Retrieval

35. 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

36. 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

37. 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

38. 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)

39. 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

40. 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”.