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?
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.
This post is related somehow.. Lookup A Gene Ontology Definition With Biopython
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).
this ones my favorite http://thomas-cokelaer.info/blog/2014/05/accessing-uniprot-with-python/
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
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?
Is http://wiki.geneontology.org/index.php/Example_Queries#Querying_by_gene_or_protein_symbol what you are asking for ?