Question: How to get list of all GO terms in each ontology
gravatar for sayonidas03
3.5 years ago by
London, U.K
sayonidas03100 wrote:


I want to get lists of all GO terms in each ontology for the a GO release. The GO consortium releases .obo file for the latest GO versions ( containing all the information. However, I would like to get a flat file which is easier to parse for applications in other scripts such as this file which the GO do not release anymore  -

Is there any R Bioconductor package which can help me generate the list or any other tool? Any suggestions are welcome. Thanks

gene ontology R • 4.3k views
ADD COMMENTlink modified 7 weeks ago by samuel.revolinski0 • written 3.5 years ago by sayonidas03100


Thank you for the replies. That is helpful for the next steps in my analysis.

I found a solution for generating the GO term lists for each ontology using GOOSE to query the GO database from the AmiGo 2 webserver:

using the following SQL query:

SELECT * FROM term WHERE term_type='cellular_component'; 

It generates results in a table which can also be downloaded in text format. Similarly lists can be generated for other ontologies.

One can view the results of the above query here:*+FROM+term+WHERE+term_type%3D%27cellular_component%27%3B&mirror=ebi&limit=0

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by sayonidas03100

Thank you for posting that. I was about to office space my computer. It works gloriously. Referring to library(GO.db)

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by samuel.revolinski0
gravatar for informatics bot
3.5 years ago by
United States
informatics bot570 wrote:

Use the GO.db package.

The term function:


will return the corresponding ontology


ADD COMMENTlink written 3.5 years ago by informatics bot570

Great package! Saved me a lot of hassle

ADD REPLYlink written 2.1 years ago by gil.hornung70
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 834 users visited in the last hour