NMPDR Development Blog

I have restored the missing attributes and implemented a logging facility to make it easier to track major changes to the database.

In the background, I am reloading the NMPDR data because it has been lying fallow for so long. My goal when it's done is to get version 18 out the door as quickly as possible, which means major changes will be put off until version 19.

• New Development Site loaded: February 8, 2006
• Latest code and data copied to Staging Site for beta testing: February 14, 2006
• Version 18 published to Public Site: February 16, 2006

• The drug target pages are working again. The drug target database and search capabilities will be put off until version 19.
• The unclassified subsystems have been moved to the bottom of the subsystem tree.
• Links to the attribute server control panel and the documentation directory are now available directly from the sidebar on the development blog.
• The Signature Genes search now displays the match score. In addition, you can ask for the matching genes to be displayed. This will show the genes that were BBHs from the reference gene to the target set genomes.
• The ShowCounts script has been updated to output the genome list control to all_genomes.inc instead of subsystems.inc. The organism summary page was not being updated properly due to the inconsistency of the file names.
• The search word box has been moved to the top on the gene search page.
• If there is only one type of advanced search (which is currently the case), the table of contents is not displayed on the advanced search page.
• The feature loader has been changed so that the functional assignment for non-PEG features are taken from the annotations instead of the alias list.

I am currently reloading the Feature table to insure that the RNAs have the correct assignments. Once that is done, I will run the standard post-load scripts to rebuild the cover pages. My goal is to have the staging site up some time tomorrow and then bring up version 18 on the following Tuesday (February 27). Leslie's serotype data will be lost, but I hope to have this information available on the attribute server next week so it can be made part of the load process in version 19.

Mike's new attributes have been uploaded to the attribute server. The new attributes and their descriptions are given below the fold.

To access these attributes during testing, you need to connect to the main attribute server in your FIG_Config.pm file. The required text is as follows.

$attrURL = "http://anno-3.nmpdr.org/attrib_server/AttribXMLRPC.cgi";

NMPDR version 18 is now available for preview on the Staging Server. A complete comparison of the data differences between version 17 and version 18 is available in the revised difference report.

The current plan is to roll v18 into production on Tuesday, February 27. In the meantime, you can have some fun by typing riboswitch into the search box.