Looking For Instances Of Database Schema To Store Data Such As Cnvs, Loh, Mutations ...

Question

[Fred Fleche]

When people are looking for inspiration to build a database there is the Library of Free Data Models from DatabaseAnswers.org.

Unfortunatelly there is no instance of biological database that would store and integrate CNVs, LOH or mutations data.

Do you know where it is possible to find such instance. Or would you share your model if you are involved in such kind of project.

Answer 1

[Pierre Lindenbaum]

here is the schema for dbSNP (good luck :-) !) ftp://ftp.ncbi.nih.gov/snp/database/b124/mssql/schema/erd_dbSNP.pdf

most of those data (SNP, CNV...) can be stored in a simple table 'chrom/position/attributes' for example: http://projects.tcag.ca/variation/tableview.asp?table=DGV_Content_Summary.txt , http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.sql etc...

Having a good engine for quickly querying those data is another problem.

As far as I can the mysql indexes used by the UCSC have a good performance ( see the 'bin' field ).

When I need to quickly retrieve this kind of data, I upload it into a berkeleyDB database using a complex sorted key {chrom,position}.

and I'm still trying to find how HDF5 could be used to store+query this kind of data.

[Fred Fleche]

Thanks a lot for sharing your experience.