Question: Get Go Terms From Python
2
gravatar for TitoPullo
6.2 years ago by
TitoPullo150
United Kingdom
TitoPullo150 wrote:

Given a gene set (IDs) is there a tool to access Gene Ontology dataset from Python? For example I need to get GO terms associated to each gene and find their distance from GO root terms. Is there something available to implement this?

python go • 7.8k views
ADD COMMENTlink modified 2.8 years ago by O.rka90 • written 6.2 years ago by TitoPullo150
1
gravatar for quentin.delettre
6.2 years ago by
France
quentin.delettre430 wrote:

You can query the database via python and sql commands ( See gene ontology website ). Just import your favorite msql db interface python module and connect. Then query. See also this wiki.

ADD COMMENTlink written 6.2 years ago by quentin.delettre430

Correct me please if I'm wrong (I'm very new to bioinformatic) but in this way I can explore the dataset only if I know the desired GO term ID, what if I only have gene IDs? Is there a way to directly query the GO dataset using them?

ADD REPLYlink written 6.2 years ago by TitoPullo150
1

Is http://wiki.geneontology.org/index.php/Example_Queries#Querying_by_gene_or_protein_symbol what you are asking for ?

ADD REPLYlink written 6.2 years ago by quentin.delettre430
1
gravatar for Leandro Lima
6.2 years ago by
Leandro Lima920
San Francisco, CA
Leandro Lima920 wrote:

https://github.com/tanghaibao/goatools

ADD COMMENTlink written 6.2 years ago by Leandro Lima920
1

This post is related somehow.. Lookup A Gene Ontology Definition With Biopython

ADD REPLYlink written 6.2 years ago by Leandro Lima920
0
gravatar for Konrad
6.2 years ago by
Konrad690
Germany
Konrad690 wrote:

You can write something using this REST API. If you need some inspiration look at this very basic library (and this GO XML parser lib).

ADD COMMENTlink written 6.2 years ago by Konrad690
0
gravatar for Endre Bakken Stovner
3.7 years ago by
Norway
Endre Bakken Stovner880 wrote:

https://github.com/endrebak/godb

ADD COMMENTlink written 3.7 years ago by Endre Bakken Stovner880
0
gravatar for O.rka
2.8 years ago by
O.rka90
O.rka90 wrote:

this ones my favorite http://thomas-cokelaer.info/blog/2014/05/accessing-uniprot-with-python/

ADD COMMENTlink written 2.8 years ago by O.rka90
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