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<H1>[dbsnp-announce] dbSNP Build 137: Database updates, corrections, and upcoming changes</H1>
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<B>Public announcements regarding dbSNP</B>
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<A HREF="mailto:dbsnp-announce%40ncbi.nlm.nih.gov?Subject=Re%3A%20%5Bdbsnp-announce%5D%20dbSNP%20Build%20137%3A%20%20Database%20updates%2C%20corrections%2C%0A%20and%20upcoming%20changes&In-Reply-To=%3Cmailman.41082.1340910908.20059.dbsnp-announce%40ncbi.nlm.nih.gov%3E"
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TITLE="[dbsnp-announce] dbSNP Build 137: Database updates, corrections, and upcoming changes">dbsnp-announce at ncbi.nlm.nih.gov
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</A><BR>
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<I>Thu Jun 28 15:13:40 EDT 2012</I>
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<LI>Previous message: <A HREF="000123.html">[dbsnp-announce] Announcement Corrections: NCBI dbSNP Build 137 for Human
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<PRE>dbSNP Build 137: Database schema updates and upcoming changes
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1. UPDATE: The assembly version will no longer be included in the names of build specific tables. For instance, in build 135 the build table ContigInfo was "b135_ContigInfo_37_3", but in build 137 the corresponding table is b137_ContigInfo without the version prefix ("_37_3"). Because an organism can have multiple assemblies (reference and alternative) and versions in a single build, it was more appropriate to use official accession and version from NCBI Genome database (<A HREF="http://www.ncbi.nlm.nih.gov/genome">http://www.ncbi.nlm.nih.gov/genome</A>) to track assembly version in ContigInfo table (i.e. b137_ContigInfo).
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Sample query to get assembly accession and version:
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select distinct asm_acc, asm_version from human_9606..b137_ContigInfo
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asm_acc asm_version
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GCF_000001405 17
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GCF_000002125 1
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GCF_000002135 2
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The accession and version can be queried to get details about the assembly from NCBI Genome.
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Example: <A HREF="http://www.ncbi.nlm.nih.gov/genome/?term=GCF_000001405.17">http://www.ncbi.nlm.nih.gov/genome/?term=GCF_000001405.17</A>
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2. CORRECTION: The human SQL schema was updated (06/28/2012) to correct the table b137_ContigInfo definition.
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<A HREF="ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_schema/human_9606/human_9606_table.sql.gz">ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_schema/human_9606/human_9606_table.sql.gz</A>
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3.CORRECTION: The BED file schema was updated (06/28/2012) to correct column #7 (refNCBI) and column #25 (validation) definitions.
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<A HREF="ftp://ftp.ncbi.nih.gov/snp/specs/BED_rsDocsum_Mapping.README.txt">ftp://ftp.ncbi.nih.gov/snp/specs/BED_rsDocsum_Mapping.README.txt</A>
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4. NOTICE: SNPContigProtein.bcp and SNPMapLinkProtein.bcp will be deprecated in future builds since dbSNP protein annotation has been streamlined and these transition tables are no longer need. All protein data will be in available in SNPContigLocusId. SNPContigProtein.bcp and SNPMapLinkProtein.bcp will be removed in future builds, they're only made available for now, albeit empty, until all other organisms schema are updated.
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5. NOTICE: There is a slight decrease in human b137_SNPContigLoc.bcp.gz as newer rs are no longer propagated to alt assemblies (i.e. HuRef and Celera). However, let us know if you need the alt assembly mapping and we can provide it in a separate table. You can also use NCBI remap service (<A HREF="http://1.usa.gov/MCv96Q">http://1.usa.gov/MCv96Q</A>) to get positions on the alt-assembly.
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6. NOTICE: dbSNP human genotype data will be mostly static in upcoming releases except with some occasional incremental increases from small submissions. This is due to the large volume genotype data from large sequencing projects such as 1000 Genomes that no longer fit or scale well in dbSNP SQL tables. NCBI is currently developing an alternative genotype database to store and serve genotype and frequency data which should be available later this year. For now, we advise users to get the genotype directly from 1000 Genomes FTP site (<A HREF="ftp://ftp.ncbi.nlm.nih.gov/1000genomes/">ftp://ftp.ncbi.nlm.nih.gov/1000genomes/</A>).
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Thank you to all the users that provided feedbacks.
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Please contact us (<A HREF="http://www.ncbi.nlm.nih.gov/mailman/listinfo/dbsnp-announce">snp-admin at ncbi.nlm.nih.gov</A><mailto:<A HREF="http://www.ncbi.nlm.nih.gov/mailman/listinfo/dbsnp-announce">snp-admin at ncbi.nlm.nih.gov</A>>) if you have questions or concerns.
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The dbSNP Production Team
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June 28, 2012
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