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Question: Get Go Terms From Python
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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?

ADD COMMENTlink 7.0 years ago TitoPullo • 150 • updated 3.5 years ago O.rka • 110
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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.

ADD COMMENTlink 7.0 years ago quentin.delettre • 430
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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?

ADD REPLYlink 7.0 years ago
TitoPullo
• 150
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https://github.com/tanghaibao/goatools

ADD COMMENTlink 7.0 years ago Leandro Lima • 920
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This post is related somehow.. http://www.biostars.org/p/1169/

ADD REPLYlink 7.0 years ago
Leandro Lima
• 920
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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).

ADD COMMENTlink 7.0 years ago Konrad • 690
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ADD COMMENTlink 4.4 years ago Endre Bakken Stovner • 880
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ADD COMMENTlink 3.5 years ago O.rka • 110

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