I have a list of A. thaliana proteins and I'd like to know their location in the cell. I've found SUBA but they seem not to share their dataset and only allow queries through their website. It's inconvenient for me, because I need to locate 1.6k of proteins and process the results further. Is there a dataset or an API I could use instead?
Given the fact that it is a simple query, in my opinion, the best approach would be an advanced search on AmigoGO. There is no need to bother with complex methods like programmatic access APIs, as you basically have only two criteria to meet: organism and cellular localization. After you specify those, you can download the file using the appropriate button, or mess a bit with the columns that you are interested in. Once you have the file, you can then manipulate it further to your specific need with any tool of your preference, for example, to retain only proteins of your interest. Hope this helps.