1. Pathway/Genome Databases and Software Tools Peter D. Karp, Ph.D. Bioinformatics Research Group SRI International pkarp@ai.sri.com http://ecocyc.DoubleTwist.com/ecocyc/

2. SRI International Bioinformatics Overview Overview of bioinformatics Motivations for the EcoCyc project EcoCyc demo Description of EcoCyc database and Pathway Tools software Underlying technologies l Ocelot object database l GKB Editor l X-windows to WWW translator

3. SRI International Bioinformatics Definition of Bioinformatics Computational techniques for management and analysis of biological data and knowledge l Methods for disseminating, archiving, interpreting, and mining scientific information

4. SRI International Bioinformatics Motivations for Bioinformatics Growth in molecular-biology knowledge Industrialization of biological experimentation High-throughput biology l Genome sequences l Gene and protein expression data l Protein-protein interaction data l Protein 3-D structures l ….

5. SRI International Bioinformatics A E

7. SRI International Bioinformatics Motivations for EcoCyc -- E. coli Encyclopedia Integrate E. coli information dispersed in the literature New paradigm of scientific publishing Model the full metabolic network of an organism Integrate genomic data with functional data Develop algorithms for computing with function Provide a challenging domain for computer- science research

8. SRI International Bioinformatics Definitions A chemical reaction interconverts chemical compounds An enzyme is a protein that accelerates chemical reactions A pathway is a linked set of reactions A conceptual unit of cell’s biochemical machine A + B = C + D A C E

9. SRI International Bioinformatics Organism-Specific Pathway/Genome Databases Layer functional information above the genome Rich ontology to encode biological information with high fidelity l Chromosomes, genes, operons, gene products, reactions, pathways Curated by experts for that organism l Integrate literature and computational predictions

10. SRI International Bioinformatics Pathway Tools Software Pathway/Genome Navigator l WWW publishing of PGDBs l Graphic depictions of pathways, chromosomes, operons l Pathway visualization of gene-expression data Pathway/Genome Editors l Distributed curation of genome annotations l Distributed object database system l Interactive editing tools PathoLogic l Prediction of metabolic network from genome

11. SRI International Bioinformatics EcoCyc = E.coli Dataset + Pathway/Genome Navigator Genes: 4,393 Gene Products: 4,393 Reactions: 1,117 Pathways: 158 Metabolic Network Compounds: 1,887 http://ecocyc.DoubleTwist.com/ecocyc/ Operons: 375

12. SRI International Bioinformatics EcoCyc Collaborative development via internet l Karp -- Bioinformatics architect l Riley -- Metabolic pathways, signal transduction l Saier and Paulsen -- Transport l Collado -- Regulation of gene expression Ontology of 1000 biological classes 14,000 instances Over 2,600 registered users

13. SRI International Bioinformatics Pathway Tools Software Pathway/ Genome Databases Pathway/Genome Navigator PathoLogic Pathway Predictor Pathway/ Genome Editors

14. SRI International Bioinformatics Pathway/Genome Navigator Algorithmic visualization of pathway and genome data Predefined queries for each object type Hypertext navigation X-windows and WWW PathoLogic and Pathway Editors are X-windows only

19. SRI International Bioinformatics Creation of the Overview Graph Run layout algorithms on individual pathway graphs l Automatically determine topology of pathway graph l Apply associated layout algorithm (linear, circular, tidy tree) Use superpathways to create hierarchical layouts l Treat each individual pathway as a single node l Pathway connections are edges l Run appropriate layout algorithm Manually position the resulting pathway clusters

20. SRI International Bioinformatics Inference of Metabolic Pathways Genomic Map Genes Gene Products Reactions Pathway Metabolic Network Compounds Pathway/Genome Database PathoLogic List of Genes/ORFs List of Gene Products ANNOTATED GENOME Structured ASCII Text File DNA Sequence Reports MetaCyc

21. SRI International Bioinformatics Summary of H. pylori Analysis For 121 E. coli pathways, what is the evidence that each pathway occurs in H. pylori? l Strong evidence: 41 l Medium evidence: 29 l Little or no evidence: 51 l 31 reactions catalyzed by H. pylori but not by E. coli H. pylori has partial abilities to synthesize cofactors and amino-acids, extremely limited carbohydrate catabolism, some amino acid utilization, and a reductive citric-acid pathway

22. SRI International Bioinformatics Microbial Pathway/ Genome DBs Literature-based Datasets: MetaCyc Escherichia coli PathoLogic-based Datasets: Bacillus subtilis Mycobacterium tuberculosis Helicobacter pylori Haemophilus influenzae Mycoplasma pneumonia Treponema pallidum Chlamydia trachomatis Saccharomyces cerevisiae

23. SRI International Bioinformatics Pathway Tools Software Architecture Implemented in Common Lisp WWW server runs as a single Unix process with a separate thread to service each query Grasper-CL graph manager Ocelot object database GKB Editor schema-driven editor

24. SRI International Bioinformatics EcoCyc WWW Server

25. SRI International Bioinformatics Pathway Tools Architecture -- Development Configuration Ocelot DBMS GFP API Pathway Genome Navigator WWW Server X-Windows Graphics Object Editor Pathway Editor Reaction Editor Oracle

26. SRI International Bioinformatics Ocelot Database System Object Database Manager Persistence via filesystem or relational DBMS Demand and background faulting of objects from RDBMS Two-level object caching Extensive bioinformatics schema Stored transaction history l Inspect object history

27. SRI International Bioinformatics Ocelot Knowledge Server Architecture Frame data model Persistent storage via l Disk files l Oracle DBMS Optimistic concurrency-control protocol Schema evolution Logging facility

28. SRI International Bioinformatics The Frame Data Model Frames are of two types: classes, instances Frames have slots that define their properties, attributes, relationships A slot has one or more values Each value can be any Lisp datatype Slotunits define metadata about slots: l Domain, range, inverse l Collection type, number of values, value constraints

29. SRI International Bioinformatics Inference Capabilities Inheritance of defaults Slot values computed via attached procedures Maintenance of inverse relationships Constraint system l Deferred evaluation l Tolerant of nonconformant data

30. SRI International Bioinformatics Storage System Architecture Oracle KBs DBMS is submerged within FRS Relational schema is domain independent, supports multiple KBs simultaneously Frames transferred from DBMS to Ocelot l On demand l By background prefetcher l Memory cache l Persistent disk cache to speed performance via Internet

31. SRI International Bioinformatics Frame Faulting (get-slot-value gene ‘map-position) Gene present in in-memory object cache? Gene present in cache on local disk? Query Oracle DBMS

32. SRI International Bioinformatics Logging Oracle DBMS stores: l The latest version of each frame l A history of all OKBC operations applied to KB Reconstruct earlier versions of KB View history of changes to an object Update replicates Concurrency control

33. SRI International Bioinformatics Schema Management FRSs store and process class and instance information similarly Applications can query schema information as easily as they can query instances

34. SRI International Bioinformatics GKB Editor Browser and editor for KBs and ontologies Four editing tools GKB Editor reusable with multiple FRSs l All database queries via OKBC/GFP API l Interoperability achieved with Ocelot, LOOM, Ontolingua All operations are schema driven http://www.ai.sri.com/~gkb/overview.html

35. SRI International Bioinformatics Editors Taxonomy editor Frame editor Relationships editor Spreadsheet editor

38. SRI International Bioinformatics Results Ocelot in use in the EcoCyc project for 5 years Supports collaborative development of EcoCyc by four groups in North America l Distributed architecture l GKB Editor in active use Supports development of 8 Pathway/Genome Databases

39. SRI International Bioinformatics Summary Pathway/Genome Databases Pathway Tools software l Extract pathways from genomes l Distributed curation tools l Query, visualization, WWW publishing l Analysis algorithms

40. SRI International Bioinformatics Computer Science Results Extend scalability and multiuser access for knowledge representation systems Reusable, schema-driven KB editor Hierarchical graph layout algorithms Dynamic translation from X-windows to HTML+GIF Importance of ontologies and of content: Discovery = Algorithm + Database

41. SRI International Bioinformatics Problem Solving Depends on Algorithms and Content Database Size and Quality Solution Quality Algorithm Quality Compute Time

42. SRI International Bioinformatics Bioinformatics Results: Content The EcoCyc database describes the full metabolic map of an organism The MetaCyc database describes over 300 metabolic pathways Ontology spans genome to pathway information

43. SRI International Bioinformatics Bioinformatics Results: Algorithms Software environment for genome and pathway information l Query and visualization l Distributed database development PathoLogic algorithm predicts the metabolic network of an organism from its genome Algorithms under development for qualitative modeling of the cell

44. SRI International Bioinformatics Acknowledgements Funding sources: l NIH National Center for Research Resources Collaborators: l Monica Riley, Marine Biological Laboratory l Milton Saier, UC San Diego l Julio Collado, UNAM l Christos Ouzounis, European Bioinformatics Institute Peter D. Karp, Ph.D. http://www.ai.sri.com/pkarp/ pkarp@ai.sri.com