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Get Go Terms From Python
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5.9 years ago
TitoPullo • 150
United Kingdom

Given a gene set (IDs) is there a tool to access Gene Ontology dataset from Python? For example I need to get GO terms associated to each gene and find their distance from GO root terms. Is there something available to implement this?

go python • 7.9k views
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5.7 years ago
France

You can query the database via python and sql commands ( See gene ontology website ). Just import your favorite msql db interface python module and connect. Then query. See also this wiki.

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Correct me please if I'm wrong (I'm very new to bioinformatic) but in this way I can explore the dataset only if I know the desired GO term ID, what if I only have gene IDs? Is there a way to directly query the GO dataset using them?

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12 months ago
Leandro Lima • 920
San Francisco, CA

https://github.com/tanghaibao/goatools

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This post is related somehow.. http://www.biostars.org/p/1169/

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4.3 years ago
Konrad • 690
Germany

You can write something using this REST API. If you need some inspiration look at this very basic library (and this GO XML parser lib).

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