Question: How to get list of all GO terms in each ontology
2
gravatar for sayonidas03
4.2 years ago by
sayonidas03100
London, U.K
sayonidas03100 wrote:

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 • 4.9k views
ADD COMMENTlink modified 9 months ago by samuel.revolinski10 • written 4.2 years ago by sayonidas03100

Check A: Retrieve All Genes Associated With A Go Term and A: How Do I Do Simple Go Term Lookup Given A Gene (Or Mrna) Identifier?

Also GO.db package.

ADD REPLYlink modified 11 weeks ago by RamRS26k • written 4.2 years ago by Sukhdeep Singh10.0k

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 REPLYlink modified 11 weeks ago by RamRS26k • written 4.2 years ago by sayonidas03100

thanks, very helpful

ADD REPLYlink modified 7 months ago • written 9 months ago by samuel.revolinski10
1
gravatar for informatics bot
4.2 years ago by
United States
informatics bot610 wrote:

Use the GO.db package.

The term function:

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

will return the corresponding ontology

ADD COMMENTlink modified 11 weeks ago by RamRS26k • written 4.2 years ago by informatics bot610

Great package! Saved me a lot of hassle

ADD REPLYlink written 2.7 years ago by gil.hornung70
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