Question: Gene Ontology - Go Id To Terms, Term Definitions, Name, Etc
2
gravatar for Palani Kannan
8.7 years ago by
Cologne, Germany
Palani Kannan60 wrote:

Hi,

I have bunch of GO ids, I wish to get term, term definitions, term type, name etc.

I wish to get through automated ruby script.

Any possible way to get these information through bioruby or soap service or some other way through ruby script.

I saw documentation of Bio::GO::Ontology. But, it is not clear and I can't get required information using GO Id using this module.

Kindly, give me some idea to get the required information as mentioned above. Thanks advance :)

gene • 8.2k views
ADD COMMENTlink written 8.7 years ago by Palani Kannan60
4
gravatar for Pierre Lindenbaum
8.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

You can use a SQL driver for ruby to query a mysql database for GO; E.g:

$ mysql -D go_latest -u go_select -P 4085 -h mysql.ebi.ac.uk --password=amigo -A \
   -e ' select * from term,term_synonym where term.id=term_synonym.term_id limit 2\G'

*************************** 1. row ***************************
                 id: 20
               name: mitochondrion inheritance
          term_type: biological_process
                acc: GO:0000001
        is_obsolete: 0
            is_root: 0
        is_relation: 0
            term_id: 20
       term_synonym: mitochondrial inheritance
        acc_synonym: NULL
    synonym_type_id: 21
synonym_category_id: NULL
*************************** 2. row ***************************
                 id: 23
               name: reproduction
          term_type: biological_process
                acc: GO:0000003
        is_obsolete: 0
            is_root: 0
        is_relation: 0
            term_id: 23
       term_synonym: reproductive physiological process
        acc_synonym: NULL
    synonym_type_id: 21
synonym_category_id: NULL
ADD COMMENTlink modified 11 months ago by RamRS30k • written 8.7 years ago by Pierre Lindenbaum131k

This is great. Do you know mysql remote servers, uname, pwd, database name (eg. above case) for other databases like KEGG, UNIPROT, and some more biological databases?

ADD REPLYlink written 8.7 years ago by Palani Kannan60

see http://biostar.stackexchange.com/questions/474

ADD REPLYlink written 8.7 years ago by Pierre Lindenbaum131k

Fantastic... Thanks lot :)

ADD REPLYlink written 8.7 years ago by Palani Kannan60
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