infer top level go category from GO:ID
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3.6 years ago
Carambakaracho ★ 2.9k

Hi folks,

I integrate proteome annotation from the eggnog emapper into a structured database. I'm getting annotations in the form described on the github emapper page. The GO terms look in practice like this:

GO:0005575,GO:0005623,GO:0005886,GO:0016020,GO:0044464,GO:0071944

for the integration I need to map it to one of the principal categories

  • P (biological process)
  • F (molecular function)
  • C (cellular component)

Which ranges of GO categories are part of which of these group? Is there some explanation to this? What I found is the GAF 2.1 format definition which requires the definition of the Aspect . Is there some resource available that can map GO category to it's toplevel?

Thanks!

gene ontology GO eggnog-mapper • 2.0k views
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3.6 years ago

Hi Carambakaracho

API's to the rescue! ;)

I suppose this project being part of a large software development. Integrating REST API's should work. Never used one but have a look at this GO API. Might be of some help.

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Hi Vijay Lakhujani, great idea! Thanks for the link, I didn't know their API - I'll try to give it a go

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3.6 years ago
Tm ★ 1.0k

From the emapper.annotations file, you can take 1st (query name) and 6th (GO terms) column in tab delimited format and can upload the same in WEGO. It will assign main category to these GO terms and will also plot graph.

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Hi Toralmanvar, thanks for your solution but I'm looking for something for easier general programmatic access without manual upload steps - it's supposed to become part of a more general pipeline for genome integration into a database.

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