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

2. Why Create a PGDB?
Perform pathway analyses as part of a genome project
Analyze omics data
Create a central public information resource for the organism, update on ongoing basis
Create a metabolic model
Perform comparative analyses

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

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

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

6. Issues in Creating Public MODs
Scope/prioritize the project
Identify user community
Obtain buy-in and help from scientific community
Obtain funding
IT: Set up database server, Web server
Hire and train curators

7. Administering Pathway Tools

8. New Pathway Tools Releases
Major releases = External software releases
Twice per year
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
Read release notes at
Install process:
Upgrade schema of your DB (software assisted)

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

10. Multiuser Access to PGDBs
PGDB stored within one MySQL server
Each curator installs PTools on their computer
Curator computers query RDBMS server via internet
For each frame access, PTools queries
In-memory cache, disk cache, RDBMS server
After curator saves changes, all changes made by other users are loaded into curator’s session

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

12. Pathway Tools Data Import/Export
File->Export
File->Import
Export/import to/from tab-delimited files
Export to Genbank, GFF3 (soon), SBML, BioPAX
Export to attribute-value files
Attribute-value files can be imported into BioWarehouse
Relational database system for bioinformatics database integration

13. Registry: Public PGDB Sharing
PGDB registry maintained by SRI at URL
Registry operations
List contents of registry
Download PGDBs listed in the registry
Register PGDBs you have created

14. Registry Details Why register your PGDB?
Facilitate its download by other scientists
Facilitate its inclusion in BioCyc.org
Why download a PGDB?
Desktop Navigator provides faster/more functionality than Web
Comparative operations
Programmatic querying and processing of PGDB

15. Changes Planned for BioCyc.org
BioCyc will be starting a subscription model
July 1

16. Why? Government funding for databases shrinking
BioCyc funding cut 27% as number of genomes climbed 5X in 5 years
No other foreseeable sources of funding for "Big Knowledge" in life sciences
Goals:
Create high-quality curated EcoCyc-like DBs for many organisms
Couple with extensive user-friendly bioinformatics tools

17. How? Subscription access to BioCyc.org by institutions, individuals
Subscription rates will depend on usage levels from previous year
EcoCyc and MetaCyc will remain free
Pathway Tools will remain free