Important dbSNP updates: New JSON data files, RefSNP report, API

dbSNP is moving to the new design with new products ready for testing including new JSON data files, the RefSNP page, and an API.

New JSON data files

Human Build 151 release is the last build that will provide relational database table dumps on the FTP site. Instead, dbSNP data will be available as a cumulative file of RefSNP objects in the JSON format in future build releases. These JSON files are available now for users to begin migration and testing. Tutorials for parsing JSON are on GitHub.

The RefSNP Report (alpha) page

The new RefSNP Report (alpha) can be accessed by clicking on the banner on the top right of the current dbSNP report page or directly by using the following URL as an example:

https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs268

The link works for any rs known in the current system. The new report page will remain available along with the existing dbSNP RefSNP report. An NCBI Insights post provides more detail about the RefSNP report page.

A new API

The new API is ready for testing and user feedback (example). Details are available on NCBI Insights.

Retired services and non-human data

Entrez search is available only for human. We will retire all Eutils report formats (RS docsum XML and ASN.1, FASTA, and FLAT text) later this year. Only eSummary XML report will be supported.

Batch Query Service for all organisms will be retired October 2018. Users of human dbSNP data should transition to the new API.

We will place non-human FTP data in the archive directory. Please see the phase-out plan announced last year.

Please email your questions, suggestions and comments to snp-admin@ncbi.nlm.nih.gov.

1 thought on “Important dbSNP updates: New JSON data files, RefSNP report, API

  1. Pingback: dbSNP build 152 uses SPDI variant notation | NCBI Insights

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