Question: Gene Ontology Database
0
gravatar for jason.taotaotan
5 months ago by
New York
jason.taotaotan0 wrote:

Hi everyone,

I am trying to build a web application. GO term is almost a standard step in the bioinformatic pipeline and I certainly want to include this in my application. I can easily download the GO term file here called go-basic.obo (very small, ~30 Mb). This is a plain text file, but what I really want is a SQL (MySQL, SQLite..) database. I don't want to build a database from scratch and I am sure there are some high-quality pre-built databases around there. Can anyone suggest a link where I can download the GO term database?

Note: It seems quickGO has API, but I really want the whole database...

Much appreciated.

gene ontology database gene • 265 views
ADD COMMENTlink modified 5 months ago by Shalu Jhanwar480 • written 5 months ago by jason.taotaotan0
1

You can have a look into GO.DB r package.

ADD REPLYlink written 5 months ago by Chirag Parsania1.9k

Thanks, that's very helpful. I found a prebuilt nice SQLite database in this R library.

ADD REPLYlink modified 5 months ago • written 5 months ago by jason.taotaotan0
1
gravatar for Shalu Jhanwar
5 months ago by
Shalu Jhanwar480
Switzerland
Shalu Jhanwar480 wrote:

Have a look at the gene ontology site that allows downloading of GO database in several formats.

ADD COMMENTlink written 5 months ago by Shalu Jhanwar480
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