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Hello,
I am trying to find GOs for a set of genes. So, not performing an enrichment, but only collecting the GOs where a certain gene is involved. Since I have a great amount of genes to look for, I would like to either performing the search via a REST API or mapping it via a downloadable file. So far I have found Ensemble sufficient for providing me GOs for single genes and species. But when looking into the REST API pages I basically cannot find the apprpriate entry point, there are multiple links for different request types (https://rest.ensembl.org/). Have someone performed a similar task to get the GOs and knows where to enter?
Which species are you using? Are you aware of the BiomaRt package to use the API to retrieve this kind of data?
Human, mouse, chok1 (chinese hamster). I am programming with python. I have found biomart for python, and here is also a reference on it https://www.biostars.org/p/9537255/. You say that will provide me also GOs for each gene i look for?
This site is for Bioconductor package support. For more general question, there are other sites (Biostars, StackExchange,...) as you have found. Biomart has all the data that ENSEMBL has, and I think for these organism it will have the GO annotation too.
Okay, I tested these two implementations of biomart search for python. Both are discontinued. For the one tool, search does not give any result, query is not clear. And the other tool has also bad documentation and output processing is unclear.
Thank you, I will change to Biostar for further questions.