GO ontology
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13 days ago
martta95 • 0

Hi, I have GO number, eg. GO:0003676 GO:0015074 GO:0005515 GO:0006996 GO:0003677 GO:0005634 GO:0006355 GO:0003700 GO:0003824 GO:0030154 GO:0043565 GO:0044212 GO:0005198 GO:0006886 GO:0016192 GO:0030117 GO:0006873 GO:0008308 GO:0016021 GO:0055085

I would like to get descriptions of the list go numbers
eg. GO:0000811 GINS complex What tool could I use?

Hordeum GO • 291 views
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Entering edit mode
13 days ago
 join -t $'\t' -1 1 -2 1 <(wget -q -O - "http://purl.obolibrary.org/obo/go.obo" | awk '$1=="id:" || $1=="name:"' | cut -d ':' -f2- | sed 's/ //' | paste - -  | grep ^GO | sort -t $'\t' -k1,1 ) <(sort input.txt) 2> /dev/null 

Redirecting output to ‘wget-log.5’.
GO:0003676  nucleic acid binding
GO:0003677  DNA binding
GO:0003700  DNA-binding transcription factor activity
GO:0003824  catalytic activity
GO:0005198  structural molecule activity
GO:0005515  protein binding
GO:0005634  nucleus
GO:0006355  regulation of DNA-templated transcription
GO:0006873  intracellular monoatomic ion homeostasis
GO:0006886  intracellular protein transport
GO:0006996  organelle organization
GO:0008308  voltage-gated monoatomic anion channel activity
GO:0015074  DNA integration
GO:0016192  vesicle-mediated transport
GO:0030117  membrane coat
GO:0030154  cell differentiation
GO:0043565  sequence-specific DNA binding
GO:0055085  transmembrane transport
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Entering edit mode
13 days ago

Use the search bar on the footer of Intermine (Which InterMine is for you?) and then select the most appropriate specific tool.

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13 days ago
barslmn ★ 1.2k

Ontologies are mostly shared in obo format. There are different libraries which lets you explore this data. You can probably find a library in your preferred language. Here is an example in python with obonet to parse the file and networkx to explore.

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