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Question: bash & quickGO to download gene symbols of a GO term
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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.

ADD COMMENTlink 15 months ago Adrian Pelin ♦ 2.3k • updated 14 months ago EagleEye 6.4k
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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.

ADD REPLYlink 15 months ago
genomax
68k
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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.

ADD REPLYlink 15 months ago
Adrian Pelin
♦ 2.3k
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Have you tried with GeneSCF ?

ADD COMMENTlink 14 months ago EagleEye 6.4k
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This is pretty sweet! Thanks!

ADD REPLYlink 14 months ago
Adrian Pelin
♦ 2.3k

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