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

[刘鹏飞]

Hi,
Magali
Sorry, the way you suggested above did not work.
using following,
# 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' );
my $goada = $ontology_dba->get_adaptor('OntologyTerm');
I still got the output before:
Can't locate object method "new" via package
"Bio::EnsEMBL::DBSQL::OntologyDBAdaptor" at /home/liupf/hz254_2.pl line 21.

change the OntologyDBAdaptor to DBAdaptor
my $ontology_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(

output:
Can't call method "fetch_by_accession" on an undefined value at /home/liupf/
hz254_2.pl line 38.;

>>>>>>>>>>>>>>>>>my full list of code>>>>>>>>>>>>
# methanocella_conradii_hz254
#!/usr/bin/perl
use strict;
use warnings;
use Bio::EnsEMBL::LookUp;
# 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'
)};
my $genes = $dba->get_GeneAdaptor()->fetch_all(); # where is the
get_GeneAdaptor() documentation
# test
print "Found ".scalar @$genes." genes for ".$dba->species()."\n";
# get adaptor for ontology
my $ontology_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
 -HOST => 'mysql.ebi.ac.uk',
 -USER => 'anonymous',
 -PORT => '4157',
 -group   => 'ontology',
 -dbname => 'ensemblgenomes_ontology_21_74',
 -species => 'multi' );
my $goada = $ontology_dba->get_adaptor('OntologyTerm');
# get go infomation
foreach my $gene (@$genes){
foreach my $link (@{ $gene->get_all_DBLinks } ){
if ($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";
}
  }
 }
}
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Is there something else wrong in it cause the output above?
Thanks!


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

> Hi Pengfei,
>
> Replies above
>
> > 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 ?
>
> I used the information provided in the ensembl bacteria documentation
>
> http://bacteria.ensembl.org/info/data/accessing_ensembl_bacteria.html#advanced-use
> The default host for ensembl genomes databases is mysql.ebi.ac.uk with the
> connection details as mentioned.
> For the database name, an ontology database would normally be called
> ensemblgenomes_ontology_egrelease_erelease
> where egrelease refers to the ensembl genomes release version (here 21)
> and erelease corresponds to the ensembl release version (here 74)
> In ensembl, the corresponding database is called ensembl_ontology_74
> If you have a mysql server installed, you can log directly onto the
> ensembl genomes server to find the exact name of the database you are
> looking for
>
> >
> > # 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?
>
> Sorry about the confusion.
> We normally use registry objects to connect to databases, but it does not
> cope well with multi-species databases like the bacterial ones, hence the
> use of the lookup and direct DBadaptors.
> The correct syntax should have been:
> 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 = $ontology_dba->get_adaptor('OntologyTerm');
>
> Hopefully, this should also solve the issue below.
>
> >
> > 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?
>
> That is correct.
>
> > 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?
>
> The bacterial database contains the genes and all related information.
> It thus contains ontology terms attached to translations and genes.
> It does not however contain the definition for each ontology term, nor its
> relationships with other terms, like descendants and ancestors.
> This additional information is stored separately in the ontology database.
>
> > Hope those not bothering you too much!
> > ###
> > Thank you very much!
>
>
> Hope this helps,
> Magali
>
> >
> >
> >
> > 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!
> >
>
>


-- 
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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