Question

Gene Ontology Database

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3.7 years ago

jason.taotaotan ▴ 10

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 Gene Ontology Database • 1.5k views

ADD COMMENT • link updated 3.7 years ago by Shalu Jhanwar ▴ 520 • written 3.7 years ago by jason.taotaotan ▴ 10

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

ADD REPLY • link 3.7 years ago by Chirag Parsania ★ 2.0k

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

ADD REPLY • link 3.7 years ago by jason.taotaotan ▴ 10

score 2 · Answer 1 · 2020-08-18

2

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3.7 years ago

Shalu Jhanwar ▴ 520

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

ADD COMMENT • link 3.7 years ago by Shalu Jhanwar ▴ 520