Gene Ontology - Go Id To Terms, Term Definitions, Name, Etc

Question

[Palani Kannan]

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 :)

Answer 1

[Pierre Lindenbaum]

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

[Palani Kannan]

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?

[Pierre Lindenbaum]

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

[Palani Kannan]

Fantastic... Thanks lot :)