How to find category names of Gene Ontoloy based on category ID

Question

[Mehmet]

Dear All,

I have a data set that has category IDs as below:

    Category
1  GO:0016021
2  GO:0044425
3  GO:0031224
4  GO:0004872

I want to find what category they belong to (Molecular function, cellular component and biological process)

Any idea about that?

Answer 1

[Leite]

Hey Mehmet,

Look at the links below:

GO:0016021

GO:0044425

GO:0031224

GO:0004872

Best regards,

Leite

[Mehmet]

Hi Leite,

Thanks. but I have a lot of GO Ids, so I need a way to put all Ids and get results.Do you have any idea for this?

[Leite]

Hi Mehmet,

You can use QuickGO

Answer 2

[Pierre Lindenbaum]

using mysql:

$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D go -e 'select acc,term_type,name from term where  acc in ("GO:0016021","GO:0044425","GO:0031224","GO:0004872");'
+------------+--------------------+---------------------------------+
| acc        | term_type          | name                            |
+------------+--------------------+---------------------------------+
| GO:0004872 | molecular_function | receptor activity               |
| GO:0016021 | cellular_component | integral component of membrane  |
| GO:0031224 | cellular_component | intrinsic component of membrane |
| GO:0044425 | cellular_component | membrane part                   |
+------------+--------------------+---------------------------------+

or

cat list_of_acn |\
awk '{printf("select acc,term_type,name from term where  acc=\"%s\";\n",$1);}' | \
mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D go -N
GO:0016021  cellular_component  integral component of membrane
GO:0044425  cellular_component  membrane part
GO:0031224  cellular_component  intrinsic component of membrane
GO:0004872  molecular_function  receptor activity