[ensembl-dev] problems on fetching GO terms for all genes of a bacteria using API

[刘鹏飞]

Hi,
Magali
Thanks for your quick reply. I followed your instruction and modified line
as follows:
# get adaptor for ontology
my $ontology_dba=Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
-HOST=>"mysql.ebi.ac.uk",
-USER=>'anonymous',
-PORT=>'4157',
-group =>'ontology',
-dbname=>'ensemblgenomes_ontology_21_74',
-species=>'multi');

#one more question: where could I find those informations like host, user,
and dbname that I needed to get data object or adaptor wanted ?

# now use the DBAdaptor to get_adaptor
my $goada=$ontology_dba->get_adaptor('Multi','Ontology','OntologyTerm');
# in your reply is $goada=$registry, but i think it shoud by
$goada=$ontology_dba, right?

the output:
Can't locate object method "new" via package
"Bio::EnsEMBL::DBSQL::OntologyDBAdaptor" at /home/liupf/hz254_2.pl line 21.

I check the doxygen for OntologyDBAdaptor, the new() methods, but returned
examples were all Bio::EnsEMBL::DBSQL::DBAdaptor::new(), so I think new
method is no longer supported by OntologyDBAdaptor, so I also tried
my $ontology_dba=Bio::EnsEMBL::DBSQL::DBAdaptor->new(.....

unfortunately, output came:
Can't call method "fetch_by_accession" on an undefined value at /home/liupf/
hz254_2.pl line 37.

### confusion on understanding Ensembl API
Use API to fetch data, you need to use the right database and the
corresponding DBAdaptor, and then use the right object adaptor and methods
to do it. Is my understanding right?
I am confused by that:
my genes was in the bacteria database, I could fetch them, but if the gene
ontology terms was in another database, how could the connected and does
that mean I need two DBAdaptor for each of them?
Hope those not bothering you too much!
###
Thank you very much!



2014/1/7 <mr6 at ebi.ac.uk>

> Hi Pengfei,
>
> The get_GeneAdaptor method is equivalent using get_Adaptor('Gene').
> More documentation can be found here:
>
> http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1DBAdaptor.html#a2a1ee81ecb9507fc5ea7bdf39be97bf9
>
> As for the undefined value message you are getting.
> By calling get_adaptor on $dba, you are attempting to get an object
> adaptor defined in the context of your bacteria database.
> Ontologies are stored separately in their own database, ensembl_ontology.
>
> The easiest way to access the ontology database would be as follow:
> my $ontology_dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
> -HOST => 'mysql.ebi.ac.uk',
> -USER => 'anonymous',
> -PORT => '4157',
> -group   => 'ontology',
> -dbname => 'ensemblgenomes_ontology_21_74',
> -species => 'multi' );
>
> my $goada = $registry->get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );
>
> You should then be able to call fetch_by_accession on $goada for a given
> GO accession.
>
>
> Hope that helps,
> Magali
>
> > Hi all
> >   I am new to API. Now I am trying to use it to get all GO terms for each
> > genes of a archaea(Methanocella conradii HZ254), and want to get a table
> > with two columns, on for gene name and the other for GO term correponding
> > to it
> >
> > Following the instruction of API and the modifications to use API for
> > bacteria, I use the following code to do the job:
> > # load the lookup from the main Ensembl Bacteria public server
> > my $lookup = Bio::EnsEMBL::LookUp->new(
> >   -URL => "http://bacteria.ensembl.org/registry.json",
> >   -NO_CACHE => 1
> > );
> > # find the correct database adaptor using a unique name
> > my ($dba) = @{$lookup->get_by_name_exact(
> >   'methanocella_conradii_hz254'
> > )};
> > # get adaptor for ontology
> > my $goada=$dba->get_adaptor('Multi','Ontology','OntologyTerm');
> > my $genes = $dba->get_GeneAdaptor()->fetch_all(); # where is the
> > get_GeneAdaptor() documentation
> > # ###test####
> > print "Found ".scalar @$genes." genes for ".$dba->species()."\n";
> >
> > # get go infomation (modified from kokocinsky.net ensembl coding)
> > foreach my $gene (@$genes){
> > my $links = $gene->get_all_DBLinks();
> > foreach my $link (@$links){
> > if ($link->database eq "GO"){
> > my $term_id=$link->display_id;
> > my $term_name='-';
> > my $term=$goada->fetch_by_accession($term_id);
> > if($term and $term->name){
> > $term_name=$term->name;}
> > print $gene->stable_id.":$term_id ($term_name)\n";
> > # fetch complete GO hierachy
> > foreach my $ancestor_term (@{$term->ancestors()}){
> > print "\t". $ancestor_term->accession." (".$ancestor_term->name.")\n";
> > }
> >   }
> >  }
> > }
> >
> > it works well before "get go information"
> > the output was as following:
> > Can't call method "fetch_by_accession" on an undefined value at
> > /home/liupf/
> > hz254.pl line 27.
> > 1, I do not understand the use of 'get_GeneAdaptor', I could not find
> > documentation on this synthax.
> > 2, please give me some suggestiones on how to fullfill my task.
> >
> > Thank you all!
> >
> > $ perl ~/ApiVersion.pl
> > The API version used is 74
> >
> > --
> > Pengfei Liu, PhD Candidate
> >
> > Lab of Microbial Ecology
> > College of Resources and Environmental Sciences
> > China Agricultural University
> > No.2 Yuanmingyuanxilu, Beijing, 100193
> > P.R. China
> >
> > Tel: +86-10-62731358
> > Fax: +86-10-62731016
> >
> > E-mail: liupfskygre at gmail.com
> > _______________________________________________
> > Dev mailing list    Dev at ensembl.org
> > Posting guidelines and subscribe/unsubscribe info:
> > http://lists.ensembl.org/mailman/listinfo/dev
> > Ensembl Blog: http://www.ensembl.info/
> >
>
>


-- 
Pengfei Liu, PhD Candidate

Lab of Microbial Ecology
College of Resources and Environmental Sciences
China Agricultural University
No.2 Yuanmingyuanxilu, Beijing, 100193
P.R. China

Tel: +86-10-62731358
Fax: +86-10-62731016

E-mail: liupfskygre at gmail.com

If you are afraid of tomorrow, how can you enjoy today!
Keep hungry, Keep foolish!
Moving forward!
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