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

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
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Palani Kannan • Palani Kannan

1 answer

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
• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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?

• 0 views • link
written by Palani Kannan • Palani Kannan

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