List of all GO terms

Question

[rororo]

I am desperately looking for a gene onthology database file, that contains the GO Number and the corresponding category (molecular function/biological process/cellular component). How do I retrieve such a list?

Answer 1

[lieven.sterck]

All that info is contained in the GO.obo file available from here: GO download page It's not a tabular file, so processing is a bit cumbersome

[lieven.sterck]

'category' is denoted as 'namespace' in that file btw.

[Kevin Blighe]

Glad that you found the solution. Best of luck.

Answer 2

[EagleEye]

GeneSCF will be simple to extract all the terms and corresponding genes as plain text (table format).

A: How to look up GO terms associated to a certain organism?

Answer 3

[Kevin Blighe]

I'm just wondering if you checked your search engine first before coming to Biostars?

I just went to google.co.uk, typed download gene ontology, and the second hit was this: Where can I view or download the complete sets of GO annotations?, i.e., a FAQ page hosted on the Gene Ontology itself.

Best of luck

Kevin

[rororo]

exactly. But there is not a single file that has the information about the category...

[Kevin Blighe]

Yes, they do have the categories.

Take a look here (linked from the page to which I linked in my post, above): Download GO annotations.

In the Filtered Annotation File Downloads section, download the 5 megabyte file for Homo sapiens that has GO terms annotated for 19 473 genes. In this file, Column 8 has 3 possible values:

• C, Celllular Component
• F, Molecular Function
• P, Biological Process

Also take a look here to better understand the GO Evidence Codes: A: Go annotation reliability ?