Question: List of all GO terms
0
gravatar for rororo
4 months ago by
rororo0
rororo0 wrote:

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?

onthology database gene • 358 views
ADD COMMENTlink modified 4 months ago by EagleEye5.3k • written 4 months ago by rororo0
2
gravatar for lieven.sterck
4 months ago by
lieven.sterck1.7k
Belgium, Ghent, VIB
lieven.sterck1.7k wrote:

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

ADD COMMENTlink modified 4 months ago • written 4 months ago by lieven.sterck1.7k

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

ADD REPLYlink written 4 months ago by lieven.sterck1.7k

Glad that you found the solution. Best of luck.

ADD REPLYlink written 4 months ago by Kevin Blighe21k
0
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe21k
University College London Cancer Institute
Kevin Blighe21k wrote:

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

ADD COMMENTlink modified 4 months ago • written 4 months ago by Kevin Blighe21k

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

ADD REPLYlink written 4 months ago by rororo0

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 ?

ADD REPLYlink written 4 months ago by Kevin Blighe21k
0
gravatar for EagleEye
4 months ago by
EagleEye5.3k
Sweden
EagleEye5.3k wrote:

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?

ADD COMMENTlink modified 4 months ago • written 4 months ago by EagleEye5.3k
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