Transcript The Registry - SRI International

The PGDB Registry
Markus Krummenacker
Bioinformatics Research Group
SRI, International
Q3 2012
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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outdated.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
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The PGDB Registry
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The Registry – Schema Upgrades
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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.
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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.
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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
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