Question: Gene Ontology mining from IDs
0
gravatar for aj123
3.1 years ago by
aj12380
United States
aj12380 wrote:

Hi, I have a list of GO IDs and would like to know how I can get their associated term?

gene ontology gene • 1.5k views
ADD COMMENTlink modified 3.1 years ago by LLTommy1.2k • written 3.1 years ago by aj12380

If you've got a list of GO IDs and want to know their associated terms, use BioMart, available as a web interface, in R or through its Perl API and RESTful services. Which species are you interested in?

ADD REPLYlink written 3.1 years ago by Denise - Open Targets5.0k

Hi Denise-interested in Human and Mouse. thank you.

ADD REPLYlink written 3.1 years ago by aj12380

Good. And for 'associated terms'. What do you mean by those? GO IDs associated with gene IDs? Or associated GO descriptions? Have a look at this GO FAQ to get to a previous post in BioStars.

ADD REPLYlink written 3.1 years ago by Denise - Open Targets5.0k

I just don't see where there's anything ambiguous here. The Gene Ontology has terms which have IDs. The OP has a list of IDs from GO for which they want to find the corresponding terms. Nowhere is there any mention of genes or p-values or anything else. For once we have a clearly stated question, why do we want to make things confusing ?

ADD REPLYlink written 3.1 years ago by Jean-Karim Heriche19k
1
gravatar for jackfrost2199
3.1 years ago by
Washington D.C.
jackfrost219970 wrote:

If you're going to do a bunch of them in batch, probably downloading the GO ontology release (http://geneontology.org/page/download-ontology) and then extracting out the information you want through a small script would be the best way.

If you have few enough you can do them by hand, I would say just go through AmiGO 2 (http://amigo.geneontology.org/amigo).

ADD COMMENTlink written 3.1 years ago by jackfrost219970
1

Another option if you need to do this a lot is to use the MySQL database. A dump is available on the download page. For this, you only need the term table.

ADD REPLYlink written 3.1 years ago by Jean-Karim Heriche19k
0
gravatar for ivivek_ngs
3.1 years ago by
ivivek_ngs4.8k
Seattle,WA, USA
ivivek_ngs4.8k wrote:

Do you mean you have GO terms, and are they associated with p-values? Then you can do a summarisation or lets say over-representation analysis of GO terms with ReviGo or GO term mapper

I would still ask you to be a bit more descriptive with your question and tell us what you intend to perform and what have you tried till now. It would be easier for others to help you out.

Note: Search Google with GO Term association. A lot of hits will turn with Biostars.

ADD COMMENTlink written 3.1 years ago by ivivek_ngs4.8k
0
gravatar for EagleEye
3.1 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

Easy way by simple commandline tool GeneSCF,

A: focus on specific pathway

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by EagleEye6.4k
0
gravatar for LLTommy
3.1 years ago by
LLTommy1.2k
LLTommy1.2k wrote:

I agree with vchris. It would help if you are more specific.

I mean, of course there are many places where you can find the related term for a Go id, for example the GO website...? So what is the actual problem here?

ADD COMMENTlink written 3.1 years ago by LLTommy1.2k
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