Phasing out support for non-human genome organism data in dbSNP and dbVar

This blog post is directed toward people who use dbSNP and dbVar, particularly those who submit non-human data to the two databases.

dbSNP and dbVar archive, process, display and report information related to germline and somatic variations from multiple species. These two databases have grown rapidly as sequencing and other discovery technologies have evolved, and now contain nearly two billion variants from over 360 species.

Based on projected growth and the resources required to archive and distribute the data, continued support for all organisms will become unsustainable for NCBI in the near future. Therefore, NCBI will phase out support for all non-human organisms in dbSNP and dbVar, and will support only human variation.

NCBI will phase out support for non-human organisms in dbSNP and dbVar following this timeline:

  • September 1, 2017 – dbSNP and dbVar stop accepting non-human variant data submissions
  • November 1, 2017 – dbSNP and dbVar interactive websites and related NCBI services stop presenting non-human variant data. The data will, however, continue to be available for download on the dbSNP and dbVar FTP sites.

Any non-human data that is already in the databases or that is submitted before September 1, 2017 will continue to be available via the dbSNP and dbVar FTP download sites.

If you want to submit non-human variation data now or after September 1, 2017, European Bioinformatics Institute (EBI) – one of our partners in the International Nucleotide Sequence Database (INSDC) – is accepting these data in the European Variation Archive.

Finally, we would like to thank all the submitters and users who have supported dbSNP and dbVar throughout the years.

28 thoughts on “Phasing out support for non-human genome organism data in dbSNP and dbVar

  1. I have been accessing canine (dog) SNP data via this website. Any idea where this will end up now??

    1. As the post above states, any non-human data that is already in the databases or that is submitted before September 1, 2017 will continue to be available via the dbSNP and dbVar FTP download sites. Please write to info@ncbi.nlm.nih.gov if you have further questions.

      1. Any non-human data submitted to us after September 1 will not be accepted.

        Any non-human data that is already in the databases or that is submitted before September 1, 2017 will continue to be available via the dbSNP and dbVar FTP download sites.

    1. Yes, as stated in the post: If you want to submit non-human variation data now or after September 1, 2017, European Bioinformatics Institute (EBI) – one of our partners in the International Nucleotide Sequence Database (INSDC) – is accepting these data in the European Variation Archive.

  2. Though I understand the reasoning, speaking as someone who collaborates with a number of researchers whose primary research is non-model organisms, I think this is fairly horrible news (particularly if no other alternatives or suggestions are given).

    1. Ah, after coming back I see that (as pointed out) EBI submission is still possible; so, still disappointing news but at least there is an option.

      1. Indeed, the European Variation Archive will continue to accept, archive, and accession variation data from non-human species.

  3. Greetings NCBI Support Team Members

    I am a veterinary student and currently work with animal SNPs.

    Can you recommend another database where you can find SNPs in pigs?

    Believe me, it is a real shame that in a short time we can not go to pbSNP.

    Anyway, thank you very much for your effort. Your page helped me on many occasions.

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