How to get GO terms to specific to perticular biological process
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29 days ago
BISEP • 0

Hello, I have list of GO terms I wanted to get GO terms specific to BP like development can any one suggest me.

Thank You

GO Enrichment RNA-seq • 276 views
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29 days ago
geneticatt ▴ 120

You can use the GO database (http://current.geneontology.org/ontology/go.obo). The namespace field for each term indicates the parent category of the term (molecular function, cellular component or biological process). Download it with wget:

wget "http://current.geneontology.org/ontology/go.obo"

To make a list of all biological process GO terms, you can use the following command:

grep -B 2 "namespace: biological_process" go.obo | grep "id:" | cut -d" " -f 2 > bp_terms.txt

If you have a text file (my_go.txt) with your query GO terms, you can compare that list with bp_terms,txt using the command below:

comm -12 <( sort my_go.txt ) <( sort bp_terms.txt )

The output will be a list of your GO terms within the biological process category.

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geneticatt I can get all bioloical process category not able to get to specific biological process like development I want to select only development related GO terms is there any tool or method I can use

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28 days ago
geneticatt ▴ 120

See the 'is_a' field in the go.obo file. If you're looking for all subcategories of GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds, you can tell awk to split the file into records by blanklines and then search for that GO term in the 'is_a' field of each record. If you need to go further, you can implement this recursively by then taking all IDs matched by the first query and using those to run a new query using the same command.

awk -v RS= '$0 ~ /is_a: GO:0004553/ {print $0"\n"}' go.obo
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