1. Bioinformatics Research Group
The PGDB Registry
Markus Krummenacker
Bioinformatics Research Group
SRI, International
Q3 2012 1

2. PGDB Registry Basics
Internet-based mechanism for sharing PGDBs among Pathway Tools
PGDB content is hosted on publisher’s http (or ftp) server
SRI Registry records downloadable PGDBs and their location
The Tier 3 PGDBs of biocyc.org are in the Registry. But many other user-contributed PGDBs are not under SRI’s control
The schema version of a downloaded PGDB may be outdated.  Version upgrade
Conversely, using an old Pathway Tools version may cause trouble with newer PGDBs

3. The Pathway Registry
The PGDB Registry
SRI International 2008

4. The Registry – Schema Upgrades

5. Publishing a PGDB in the Registry
After creating a PGDB by Pathologic and additional curation, it makes sense to share the PGDB with other users.
Ensure that the author list of the PGDB is correct.
Run the Consistency Checker and fix any problems.
Publishing will turn the directories and files for the PGDB into a compressed archive file.
Have a Web server or FTP server available, where the archive file can be hosted.
Fill in Database Sharing preferences dialog.

6. Database Sharing preferences
ToolsPreferencesDatabase Sharing
Initial setup dialog: Can FTP used for uploading the PGDB ? Else, the archive file has to be copied manually.
The URL (could be ftp) from where the PGDB archive can be downloaded.

7. The Registry – Uploading Your PGDB
The process of uploading a PGDB to the Registry is largely automated. See “Publishing PGDBs in the Registry” in the User Guide for details