Closure of the NCBI SRA and implications for the long-term future of genomics data storage.

TLDR: The views of various interested people are asked on what the short-term implications of this announcement will be, and also how they envisaged the future of data storage in the long term.

Abstract: (NCBI) in the US recently announced that, as a result of budgetary constraints, it would no longer be accepting submissions to its Sequence Read Archive (SRA) and that over the course of the next year or so it would slowly phase out support for this database (http://www.ncbi. nlm.nih.gov/sra). There seems to be a certain amount of confusion in the community about what effect this decision will have. At Genome Biology we feel that the free availability of data is an important concept for science, so we asked the views of various interested people on what the short-term implications of this announcement will be, and also how they envisaged the future of data storage in the long term. These people include those involved in the running of the databases (David Lipman (DL) from the NCBI and Paul Flicek (PF) from the European Bio-informatics Institute (EBI)) and users of the data stored in the database as well as data producers (1. Why did the SRA close? How widely used by the community was it? DL: NCBI was facing budgetary constraints and presented a range of options to the National Institutes of Health (NIH) leadership, who chose to phase out the SRA along with other resources. One factor in making the determination was the understanding that because the raw sequence data within the SRA are processed into derived forms in order to answer the underlying biological questions, as methods mature, the SRA was seen as a transitional resource. The SRA primarily has been used by a relatively small community of project analysts and researchers working on methods develop ment in genome scale research projects. PF: The SRA isn't closing. It started as a joint venture between the NCBI and the EBI, so the NCBI ceasing to accept submissions doesn't meant that the SRA is closing, merely changing and the European Nucleotide Archive (ENA) at EMBL-EBI will remain. The NCBI's decision was based on budgetary constraints. It should be noted that most people don't realize that storage space is only a minor fraction of the budget of the database; the bulk of the cost is associated with the staff who maintain the database, process the submissions, develop the software and so on. SS: From the outside, it appears that the SRA is closing because of NIH budgetary considerations. One problem is that the amount of sequence being generated is growing at an extraordinary rate, …