1. Creating a … Community Database Organism-Specific Database Model-Organism Database

2. SRI International Bioinformatics Why Create a PGDB? Perform pathway analyses as part of a genome project Analyze omics data Create a central information resource for the organism Create an FBA model Perform comparative analyses

3. SRI International Bioinformatics Model Organism Databases DBs that describe the genome and other information about an organism Curated by experts for that organism l No one group can curate all the world’s genomes l Distribute workload across a community of experts to create a community resource Every sequenced organism with an active experimental community requires a MOD l Integrate genome data with information about the biochemical and genetic network of the organism l Integrate literature-based information with computational predictions

4. SRI International Bioinformatics Rationale for MODs Each “complete” genome is incomplete in several respects: l 40%-60% of genes have no assigned function l Roughly 7% of those assigned functions are incorrect l Many assigned functions are non-specific MODs are platforms for global analyses of an organism l Interpret omics data in a pathway context l In silico prediction of essential genes l Characterize systems properties of metabolic and genetic networks

5. SRI International Bioinformatics What is Curation? Ongoing updating and refinement of a PGDB Correct false-positive and false-negative predictions Incorporate information from experimental literature l Update genome sequence l Update gene functions, gene positions, gene names l Author comments and citations l Add new pathways, modify existing pathways l Enter information about regulatory networks

6. SRI International Bioinformatics Issues in Creating Public MODs Obtaining funding Scoping the project Identify user community Obtain buy-in and help from scientific community IT: Set up database server, Web server Hire and train curators

7. SRI International Bioinformatics Questions Do you intend to make your PGDB public and to update it on an ongoing basis? To create a Model Organism Database?

8. Administering Pathway Tools

9. SRI International Bioinformatics Obtaining Pathway Tools Free to non-commercial organizations To obtain license agreement go to BioCyc.org and click on Software/Database Download Follow Installation Guide ptools-local directory l Locate in common directory l PGDBs created by all users who use this ptools installation l PGDBs downloaded via the registry l ptools-init.dat for this ptools installation

10. SRI International Bioinformatics New Pathway Tools Releases Major releases = External software releases l Twice per year l Announced on ptools-users mailing list Minor releases twice per year affect only our BioCyc.org Web site and flatfile distributions We support one prior release only Releases announced on ptools-users@ai.sri.com Read release notes at l http://brg.ai.sri.com/ptools/release-notes.html http://brg.ai.sri.com/ptools/release-notes.html Install process: l Upgrade schema of your DB (software assisted)

11. SRI International Bioinformatics PGDB Storage: File or Relational Database File storage: l Advantages: u No RDBMS installation and configuration l Disadvantages: u Must be loaded and saved in its entirety u No transaction history u No concurrent access for multiple users Oracle/MySQL storage: l Advantages: u Faster read access, faster saves u Concurrent update access for multiple users u Stores history of all PGDB updates l Disadvantages: u RDBMS must be installed and configured

12. SRI International Bioinformatics Multiuser Access to PGDBs PGDB stored within one Oracle or MySQL server Each curator installs PTools on their workstation Different curators can use different software platforms Workstations query RDBMS server via internet Local disk cache speeds access For each frame access, PTools queries l In-memory cache, disk cache, RDBMS server After curator saves changes, all changes made by other users are loaded into curator’s session

13. SRI International Bioinformatics How to Release a PGDB? Decide on release frequency and schedule l Don’t wait until it’s perfect to release it! Freeze curation for 1 week Quality assurrance l Run consistency checker u Tools -> Consistency Checker u Also updates organism-summary statistics Update publications, authors in organism frame l Update via Organism editor Create new version of PGDB l ptools-local/pgdbs/yeastcyc/1.0/kb/yeastbase.ocelot l Edit against the new version, release the old version Author release notes Register PGDB in SRI PGDB registry l Will allow SRI to include it in BioCyc

14. SRI International Bioinformatics Pathway Tools Data Import/Export File->Export File->Import Export/import to/from tab-delimited files Export to Genbank, SBML, BioPAX Export to attribute-value files Attribute-value files can be imported into BioWarehouse l Relational database system for bioinformatics database integration

15. SRI International Bioinformatics Napster Comes to Bioinformatics Public sharing of Pathway/Genome Databases l PGDB registry maintained by SRI at URL http://biocyc.org/registry.html http://biocyc.org/registry.html Registry operations l List contents of registry l Download PGDBs listed in the registry l Register PGDBs you have created

16. SRI International Bioinformatics Registry Details Why register your PGDB? l Declare existence of your PGDB in a central location l Facilitate its download by other scientists l Facilitate its inclusion in BioCyc.org Why download a PGDB? l Desktop Navigator provides more functionality than Web l Comparative operations l Programmatic querying and processing of PGDB Registration process l Registered PGDBs have open availability by default l Authors can provide their own license agreements l Registered PGDBs reside in authors’ FTP site or HTTP server

17. SRI International Bioinformatics Pathway Tools Workshop Planned for October 25-29, 2010 in Menlo Park Presentations by users on results they have attained, suggested enhancements, software developments SRI presentations on new developments, programming examples Talks of general scientific interest in genomics, genome annotation, pathway bioinformatics

18. SRI International Bioinformatics Desktop versus Web Mode Pathway Tools runs in two different modes: l Desktop mode l Web mode (e.g., BioCyc.org) Desktop vs Web functionality in Pathway Tools http://biocyc.org/desktop-vs-web-mode.shtml You can run both desktop and web modes at your site Your PTools web server need not be open to the public