Hi Jay,
the best thing is to probably get the data via the ftp site then:
ftp://ftp.ensembl.org/pub/current_mart/data/mysql/ensembl_mart_45/hsapiens_go_biol_process__go_biol_process__main.txt.table.gz
ftp://ftp.ensembl.org/pub/current_mart/data/mysql/ensembl_mart_45/hsapiens_go_mol_function__go_mol_function__main.txt.table.gz
ftp://ftp.ensembl.org/pub/current_mart/data/mysql/ensembl_mart_45/hsapiens_go_cell_location__go_cell_location__main.txt.table.gz
the order of cols is:
gene_id,ensembl gene id, transcript_id, ensembl transcript id,
translation_id, ensembl translation id, GO ID, GO ID, GO term, evidence
code
let me know how you get on
Damian
On Tue, 10 Jul 2007, Jay an wrote:
hello Damian,
because of my computer environment, I can not issue
SQL command. could you please help me to download all
GO in a table like:
GO_id term
parent_GO_id gene_symbol
GO:0009314 biological process
GO:0009628 SNN
....
regards
Jay
--- Damian Smedley <[EMAIL PROTECTED]> wrote:
Hi,
At the moment the table delivering the attibutes
stores the most specific,
low-level term. We do have some separate tables that
store all the higher
-level terms as well but we just use these for
filtering at the moment as
some people seemed to prefer this arrangement. We
can review this of
course. If you are interested in just SQL querying
the tables in question
are:
hsapiens_go_cell_location__go_cell_location__main
hsapiens_go_biol_process__go_biol_process__main
hsapiens_go_mol_function__go_mol_function__main
let me know how you get on,
Damian
On Mon, 9 Jul 2007, Jay an wrote:
hello,
I am looking for GO-terms that are related gene
ENSG00000123570.
I got 7 rows for that gene as below. but I found
these genes all belong to under-level 6.
how can I get high level GO-terms. for example
GO0007852 (level 2) is a GO term related to
gene ENSG00000123570.
Ensembl Gene ID GO ID
External Gene ID
ENSG00000123570 GO:0000166 RAB9B
ENSG00000123570 GO:0005525 RAB9B
ENSG00000123570 GO:0005575 RAB9B
ENSG00000123570 GO:0006895 RAB9B
ENSG00000123570 GO:0007264 RAB9B
ENSG00000123570 GO:0015031 RAB9B
ENSG00000123570 GO:0016020 RAB9B
---------------------------------
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