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The Gene Ontology Helpdesk
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How to make a list of mitochondrial genes and one of ribosomal genes? #280

Closed Munfred closed 3 years ago

Munfred commented 3 years ago

Hello, I’m trying to compile two lists: one of C elegans mithochondrial genes, and one of ribosomal genes.

For ribosomal genes I know there are rpl and rps gene families for large and small subunits, and similarly for mitochondrial genes there are mrpl and mrps gene families, but there are many more.

How could I use GO to create these lists programmatically?

Thanks!

suzialeksander commented 3 years ago

Hi @Munfred,

You might want to try using Amigo. Here's a link to all worm entities under GO:0005840 ribosome: http://amigo.geneontology.org/amigo/search/bioentity?q=*:*&fq=regulates_closure:%22GO:0005840%22&fq=taxon_subset_closure_label:%22Caenorhabditis%20elegans%22&sfq=document_category:%22bioentity%22

If this isn't what you were looking for, we also have an API at http://api.geneontology.org, where you can get back to http://api.geneontology.org/api/bioentity/function/GO%3A0005840/genes. If you'd like to get more info on the API, or ontobio for Python (https://github.com/biolink/ontobio), let me know.

Munfred commented 3 years ago

Thanks, that answers my questions!