GO ontology
3
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
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•
link
updated 20 months ago by
barslmn
★
2.3k
•
written 20 months ago by
martta95
▴
10
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
Use the search bar on the footer of Intermine (Which InterMine is for you?) and then select the most appropriate specific tool.
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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