Saturday, February 19, 2011

as feared: NCBI To Discontinue Sequence Read Archive and Peptidome

For once I put my feelings here, some should be happy as they complained that I was only reproducing others text ;-)

What will happen to paper submissions where data needs to be shared?
How can authors take the load and responsibility to provide access to their millions of reads / annotations?
This is weird and is going against the principles of reproducibility
Too many places to submit complementary data - it all needs to be analyzed together and is now dispersed in dozen of places - NO GO
what next?
If someone know of an action (petition) to support the continuation of SRA (and its evolution) , please share with me and I will post the info here
NCBI To Discontinue Sequence Read Archive and Peptidome:
NCBI To Discontinue Sequence Read Archive and Peptidome

About SRA

Due to budget constraints, NCBI will be discontinuing its Sequence Read Archive (SRA) and Trace Archive repositories for high-throughput sequence data. Closure of the databases will occur in phases. SRA and Trace will stop accepting some types of submissions in the coming weeks, and all submissions within the next 12 months. Over the next several months, NCBI will be working with staff from NIH Institutes that fund large-scale sequencing efforts to develop an approach for future access to and storage of the existing data. NCBI will continue to support and develop information resources for biological data derived from next-generation sequencing such as genotypes, common variations, rare variations, sequence assemblies and gene expression data. We therefore encourage the research community to continue submissions of these data to the applicable databases, including:

RNA-Seq and epigenomic data to GEO
Variants, genotypes, phased haplotypes, and polymorphisms to dbVar, dbGaP and dbSNP
Genomic assemblies to GenBank/WGS
Transcript assemblies to GenBank/TSA
16S ribosomal RNA and other targeted locus survey assemblies to GenBank
NCBI expects new applications will continue to emerge for next generation technology. We are excited to work with the community to develop strategies for archiving other summary experimental measures that are informative, efficient, and valuable to the biomedical research community.

For further information about submissions, contact NCBI's Help Desk.

About Peptidome

Due to budgetary constraints NCBI will be discontinuing the Peptidome Repository. Over the next few weeks, we will phase out the online browser, query, and display interfaces.

All existing data and metadata files will continue to be made available from our ftp server ( indefinitely. Those files are named according to their Peptidome accession numbers, allowing cited data to still be identified and downloaded. Furthermore, we will endeavor to deposit all Peptidome data in a different public mass spectrometry repository; information about this effort will follow soon.

For those datasets that have been accessioned, but have not yet been made public, submitters have the option of withdrawing the data now and moving it to another repository. If we retain the data, it will move to the Peptidome FTP site on the date at which it is currently designated to go public.

If you have any specific questions, please feel free to contact us at