Entering edit mode
5.4 years ago
Adrian Pelin
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2.6k
Hello, there is a very old post (Retrieve All Genes Associated With A Go Term) that shows you can download data from quickGO using bash by using something like this:
curl -s "http://www.ebi.ac.uk/QuickGO/GAnnotation?tax=9606&relType=IP&goid=%20GO:0009615%20&format=tsv"
For some reason there is no output when that is issued. Is it because the API changed in the last 6 years? I can't seem to find a more recent post about this.
There is definitely output in a web page (just try the URL standalone
http://www.ebi.ac.uk/QuickGO/GAnnotation?tax=9606&relType=IP&goid=%20GO:0009615%20&format=tsv) with an "export" button to download 500K+ entries.See the QuickGO API examples here for modifying your query as needed.
Yeah I noticed that. The problem is that it's not supposed to open as a webpage but rather as a tab delimited file and it's supposed to give me only taxid 9606 and not other organisms... It would defeat the point of doing this in bash if I were to manually download entries every time, was hoping to automate this.