Hi JJ and mailing list,
I think it was John who mailed earlier about implementing an SQLite datatype for
proteomics. I sort of like this, since I find myself using SQLite all the time for my own
command line tool to do filtering, protein grouping, and relating quant output to ID data.
— I basically wrote this to combine percolator,
mzidentml, and openMS intermediate formats. It’s currently a bit of a mixture of different
databases and tables for different operations, but maybe it would be a good idea to have
one large proteomics experiment SQLite database. Note that this is nothing I want to push
onto people like it would be the next PSI standard, more like a very convenient and fast
I believe that the proteome discoverer msf files are also based on sqlite. While I’m not
sure if it’s a good fit for a server environment since it can get locking/access problems
when accessed by too many processes, it’s a very nice fit for a bioinformatic cli tool.
Are you guys currently working on any standardized SQLite thing?
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden