Question: List of all GO terms
0
gravatar for rororo
2.1 years 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 • 4.1k views
ADD COMMENTlink modified 2.1 years ago by EagleEye6.6k • written 2.1 years ago by rororo0
2
gravatar for lieven.sterck
2.1 years ago by
lieven.sterck6.9k
VIB, Ghent, Belgium
lieven.sterck6.9k 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 2.1 years ago • written 2.1 years ago by lieven.sterck6.9k

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

ADD REPLYlink written 2.1 years ago by lieven.sterck6.9k

Glad that you found the solution. Best of luck.

ADD REPLYlink written 2.1 years ago by Kevin Blighe54k
1
gravatar for EagleEye
2.1 years ago by
EagleEye6.6k
Sweden
EagleEye6.6k 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 2.1 years ago • written 2.1 years ago by EagleEye6.6k
0
gravatar for Kevin Blighe
2.1 years ago by
Kevin Blighe54k
Kevin Blighe54k 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 2.1 years ago • written 2.1 years ago by Kevin Blighe54k

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

ADD REPLYlink written 2.1 years 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 2.1 years ago by Kevin Blighe54k
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