B125 changed the FTP site completely. Could you explain how the dbSNP FTP site is now organized?

The updated ftp directory is organized as follows:

The main ftp directory for dbSNP contains a number of directories, the most useful of which are:

• organisms/
• database/
• specs/

The organization of each of the above directories is explained below:

The FTP “organisms/” directory:

The FTP “organisms/” directory contains a list of the organisms for which we have SNP data, organized by common name, and followed by its NCBI taxonomy id number. For example, the organism “Homo sapiens” is listed as “human_9606”.

Click on the organism of choice to access the ftp report files available for it. For example, if you click on human_9606 from the list of organisms, you will find that the human organism subdirectory contains the following files:

• ASN1_bin/
• ASN1_flat/
• XML/
• chr_rpts/
• rs_fasta/
• submit_format/
• genotype_by_gene/
• genotype/
• haplotypes/
• database/
• misc/

Please note that the “database/” subdirectory within a species directory (see above list) contains the following files or links to files:

View in own window

organism_data This subdirectory contains the species .bcp files for many tables, including: “Batch”, “dn_table_rowcount”, “RsMergeArch”, and “SNPAncestralAllele”. organism_shared_data link This link takes the user to the organism​_shared_data subdirectory, which contains tables of .bcp data shared among organisms. schema

The FTP “database/” directory:

The FTP “database/” directory contains the following subdirectories:

View in own window

organism​_shared_data This subdirectory contains tables of .bcp data shared among Organisms, and includes the “Allele​.bcp” file schema This subdirectory contains the schema of dbSNP_main, which contains tables shared among organisms. Illumina​_top_bot_strand_note This document defines the “top” and “bottom” strands of a sequence in the absence of a reference genome to orient submissions. b124 This subdirectory contains all the old database related files as of build 124.

The FTP “specs/” directory:

The FTP “specs/” directory contains a number of text, .pdf, .asn, and .xsd files on everything from dbSNP submission instructions, and b125 mapping information to genotype resource information and haplotype submission .xsd files. (12/9/05)

Is there a gradual movement toward moving NCBI data output preferentially to XML rather than ASN.1?

No, we have a large user base for both formats, and will likely support both formats in the future.(6/8/06)

Are there any plans to modify the XML Schema for dbSNP?

We will make future modifications to the XML schema as necessary to fit evolving SNP data model. We'll announce any schema changes on the dbSNP homepage and the dbSNP maillist, should you care to subscribe.(6/8/06)

I have looked through dbSNP_main tables.sql.gz, but can’t find SNPAncestralAllele.bcp.gz. Where is it?

The SNPAncestralAllele.bcp.gz for each organism is available on the FTP site in the /organism_data subdirectory of the main database directory. To get human SNPAncestralAllele.bcp.gz, you would go to the dbSNP FTP site, select “database”, then once you are in the database directory, select “organism_data”. Once you are in the organism_data subdirectory, choose “human_9606”. Once in the human subdirectory, choose “SNPAncestralAllele.bcp.gz”, located about a third of the way down the page.(9/19/06)

Naming Convention for SNP FTP Organism Folders

The file docsum_2005.xsd.old has an attribute called "physMapStr". The new docsum_2005.xsd does not have this attribute. Which attribute(s) in the new schema is (are) the equivalent of "physMapStr"?

The "physMapStr" attribute was deprecated (made invalid or obsolete) starting with build 125 due to a location type change. Please see the (old) Column Description for SNPContigLoc and look at the information for “phys_pos”. You may also wish to look at the new location type description. The attributes that correspond to the new location type are 'leftFlankNeighborPos', 'rightFlankNeighborPos', 'leftContigNeighborPos', 'rightContigNeighborPos'.(7/26/06)