dbSNP is a 'hub-and-spoke' design with dbSNP_main as the hub storing all the ‘lookup’ tables that are shared by each organism specific databases. Each spoke is an organism-specific database, named by organism_taxid(ex.: human_9606) that contains the latest data from submission, mapping, clustering, genotypes, haplotypes, validation etc.
2. Files needed to create a local copy of dbSNP:
To create a local copy of dbSNP, go to the following ftp directory:
ftp://ftp.ncbi.nih.gov/snp/database/
There are 4 subdirectories:
/organism_data: Data for each organism specific database.
/organism_schema: Schema DDL(Data Definition Language) for organism specific database.
/shared_data: Data in dbSNP_main that is shared by all organism database.
/shared_schema: Schema DDL for dbSNP_main.
3. Data File Format:
The entire data of dbSNP tables are dumped table-wise into files named as "tablename.bcp" under “shared_data” and “organism_data” subdirectories. Fields of data within each file are tab delimited. (Note, this is an update to file on 11/22/99. The delimiter used to be '|'. ) ´
4. General Steps to create local dbSNP:
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First create dbSNP_main with schema files in /shared_schema and data in
/shared_data. After dbSNP_main is created, create the organism
specific database using files in /organism_schema and /organism_data.
For example, to create human_9606 database:
In ftp://ftp.ncbi.nih.gov/snp/database/shared_schema/:
Use dbSNP_main_table.sql.gz to create tables for dbSNP_main.
Use dbSNP_main_view.sql.gz to create views for dbSNP_main.
Use dbSNP_main_index_contraint.sql.gz to create indexes for dbSNP_main.
In ftp://ftp.ncbi.nih.gov/snp/database/shared_data/:
Use the <table>.bcp file to load into the tables.
Create database human_9606 with files in
ftp://ftp.ncbi.nih.gov/snp/database/organism_schema/human_9606,
human_9606_table.sql.gz
human_9606_view.sql.gz
human_9606_index_constraint.sql.gz
human_9606_foreign_key.sql.gz
Then load human_9606 table data with *.bcp files in
ftp://ftp.ncbi.nih.gov/snp/database/organism_data/human_9606.
Local dbSNP database should be re-created with each build, using the
latest schema file to ensure that all tables will be correctly loaded.
GUIDE
A sample Unix C shell script cmd.create_local_dbSNP has been provided
in ftp site: ftp://ftp.ncbi.nih.gov/snp/database/loadscript.
cmd.create_local_dbSNP.txt shows how to use dbSNP_table.sql and *.bcp
to create a local sql database. Users of other database platform can
use the same method with modifications of platform specific commands.
cmd.create_local_dbSNP first creates all tables without indexes. This
allows fast load of bcp data. It then loads table data using a second
script cmd.bulkinsert.txt and compares lines in the data file with
table row counts as error checking.
