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DBMS system for NCBI/Genbank data?

Hi,

I'm looking for a good solution to store NCBI/GenBank/RefSeq data locally. I thought about a custom (simple) SQLite schema to avoid a server-client system and write parsers and importers myself to get the annotations/qualifiers/sequences I want.

Any thoughts on that? I also read about BioSQL. Does anyone have experience with that?

dbms biosql sqlite
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updated by Satyajeet Khare Satyajeet Khare • written by TimK • TimK

I hope you have taken into account how much data that is going to be and a need to keep it refreshed daily. You should be able to get most everything you need by using eutils (unless you expect to do very large scale queries all the time).

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written by GenoMax GenoMax

I'm aware of the amount of data and the problem of keeping it updated. That's why I'm trying to figure out what the best options are. As this project is more going in the direction of institute wide bioinf resource eutils is not an option.

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written by TimK • TimK

1 answer

I used MySQL RDBMS with PHP (PHPmyAdmin) for a metadabase. A Python script was used to parse XML files downloaded from UniprotKb to create a small, curated, meta-database. There were separate tables for genes, mRNA isoforms and proteins. Also, some added tables for disease information etc. It was a single species database.

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written by Satyajeet Khare Satyajeet Khare

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