How to get list of all GO terms in each ontology
1
2
Entering edit mode
8.9 years ago
sayonidas03 ▴ 100

Hi,

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 (http://geneontology.org/ontology/go-basic.obo) 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 - http://www.geneontology.org/doc/GO.terms_alt_ids

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 • 9.1k views
ADD COMMENT
0
Entering edit mode

Hi,

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: http://amigo.geneontology.org/goose

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:

http://amigo.geneontology.org/goose?query=SELECT+*+FROM+term+WHERE+term_type%3D%27cellular_component%27%3B&mirror=ebi&limit=0

ADD REPLY
0
Entering edit mode

thanks, very helpful

ADD REPLY
1
Entering edit mode
8.9 years ago

Use the GO.db package.

The term function:

library(GO.db)
Term("GO:0016021")

will return the corresponding ontology

ADD COMMENT
0
Entering edit mode

Great package! Saved me a lot of hassle

ADD REPLY

Login before adding your answer.

Traffic: 2496 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6