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    <br>
    Hi Nathalie,<br>
    <br>
    There are duplicates because all variant associations are reported.
    If you look at the table given by the
    <meta http-equiv="content-type" content="text/html; charset=utf-8">
    'Show' option on 'ALL variants with a phenotype annotation' on the
    web page you will see multiple variants sometimes have reported
    associations to the same trait. In one case multiple associations
    are reported at different levels of significance between a variant
    and a trait.<br>
    <br>
    Full HGMD data is only available to registered users, so Ensembl can
    only report the presence of a variant location in the HGMD database.
    ClinVar accepts submissions with different levels of information, so
    it is sometimes only reported that a variant is pathogenic but no
    phenotype is available.<br>
    <br>
    If you are not interested in significance levels and undescribed
    phenotypes, they should be simple to filter out.<br>
    <br>
    Best wishes,<br>
    <br>
    Sarah<br>
    <br>
    <div class="moz-cite-prefix">On 26/02/2016 16:42, nconte wrote:<br>
    </div>
    <blockquote cite="mid:08c138437a1ad7df85193dbc998426e7@ebi.ac.uk"
      type="cite">Hi Sarah,
      <br>
      Another question when the script show phenotypes there will be
      some duplicate (see below), why is this ?
      <br>
      and why some have  phenotype is not specified (clinvar) or not
      avalaible (like with HMGD)? and how to remove these like in the
      website ?
      <br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000115963;r=2:150468195-150539011">http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000115963;r=2:150468195-150539011</a>
      <br>
      <br>
      many thanks
      <br>
      <br>
      <br>
       my $gene = $ga->fetch_by_stable_id('ENSG00000115963');
      <br>
      this is an example with
      <br>
      human Orthologue: RND3    ENSG00000115963    2    150468195   
      150539011    -1
      <br>
      gene is RND3ENSG00000115963
      <br>
      Assoc    ClinVar    ClinVar: phenotype not specified
      <br>
      Assoc    ClinVar    ClinVar: phenotype not specified
      <br>
      Assoc    ClinVar    ClinVar: phenotype not specified
      <br>
      Assoc    ClinVar    ClinVar: phenotype not specified
      <br>
      Assoc    ClinVar    ClinVar: phenotype not specified
      <br>
      Assoc    ClinVar    ClinVar: phenotype not specified
      <br>
      Assoc    dbGaP    Blood pressure
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    Body Height
      <br>
      Assoc    dbGaP    BODY MASS INDEX
      <br>
      Assoc    dbGaP    BODY MASS INDEX
      <br>
      Assoc    dbGaP    BODY MASS INDEX
      <br>
      Assoc    dbGaP    BODY MASS INDEX
      <br>
      Assoc    dbGaP    Calcium
      <br>
      Assoc    dbGaP    Calcium
      <br>
      Assoc    dbGaP    Cholesterol, HDL
      <br>
      Assoc    dbGaP    Glucose
      <br>
      Assoc    dbGaP    Respiration Disorders
      <br>
      Assoc    dbGaP    Sleep
      <br>
      Assoc    dbGaP    Stroke
      <br>
      Assoc    NHGRI-EBI GWAS catalog    Endometriosis
      <br>
      Assoc    NHGRI-EBI GWAS catalog    Type 2 diabetes
      <br>
      <br>
      <br>
      <br>
      <br>
       > Hi Nathalie,
      <br>
      <blockquote type="cite">
        <br>
         You are extracting phenotype features for the input mouse gene,
        not
        <br>
        the human gene, which is why you are not seeing the human
        phenotype
        <br>
        feature. If you change the print statement to:
        <br>
        <br>
         print 'gene is    '.$gene->external_name() ."  ".
        $gene->stable_id();
        <br>
        <br>
         You will see the 'ENSMUS' prefix on the gene name:
        <br>
        <br>
         human Orthologue: LEP    ENSG00000174697    7    128241284   
        <br>
        128257628    1   
        <br>
         gene is    Lep  ENSMUSG00000059201    scalar  0
        <br>
         no PHE
        <br>
        <br>
         We store associations as reported, so querying by both gene and
        <br>
        variant will return the most complete set of results
        <br>
        <br>
         fetch_all_by_Gene takes a gene object and returns associations
        <br>
        reported to the gene
        <br>
         fetch_all_by_associated_gene() takes a gene name and returns
        variant
        <br>
        associations in which it is mentioned
        <br>
        <br>
         For example:
        <br>
        <br>
         use Bio::EnsEMBL::Registry;
        <br>
        <br>
         Bio::EnsEMBL::Registry->load_registry_from_db(
        <br>
             -host=>  'ensembldb.ensembl.org', -user=>'anonymous',
        <br>
             -port=>'3306', 'db_version' => 83,);
        <br>
         Bio::EnsEMBL::Registry->set_reconnect_when_lost(1);# will
        help with
        <br>
        connection issues
        <br>
        <br>
         my $ga = Bio::EnsEMBL::Registry->get_adaptor("homo_sapiens",
        "core", "gene");
        <br>
         my $pfh_adaptor =
        Bio::EnsEMBL::Registry->get_adaptor('human',
        <br>
        'variation', 'phenotypefeature');
        <br>
        <br>
         my $gene = $ga->fetch_by_stable_id('ENSG00000174697');
        <br>
        <br>
         if ($gene){
        <br>
           print "gene is " .$gene->external_name() ."n";
        <br>
        <br>
           my $pfs = $pfh_adaptor->fetch_all_by_Gene($gene);
        <br>
           foreach my $pm(@{$pfs}){
        <br>
             print
        "Directt",$pm->source_name,"t",$pm->phenotype->description,
        "n";
        <br>
           }
        <br>
          
        <br>
           my $pfsvar =
        <br>
$pfh_adaptor->fetch_all_by_associated_gene($gene->external_name());
        <br>
           foreach my $pmv(@{$pfsvar}){
        <br>
             print
        "Assoct",$pmv->source_name,"t",$pmv->phenotype->description,
        "n";
        <br>
           }
        <br>
         }
        <br>
        <br>
         Outputs:
        <br>
        <br>
         gene is LEP
        <br>
         Direct    Orphanet    Obesity due to congenital leptin
        deficiency
        <br>
         Direct    MIM morbid    LEPTIN DEFICIENCY OR DYSFUNCTION
        <br>
         Assoc    ClinVar    ClinVar: phenotype not specified
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    HGMD-PUBLIC    Annotated by HGMD but no phenotype
        <br>
        description is publicly available
        <br>
         Assoc    Uniprot    Leptin deficiency
        <br>
         Assoc    OMIM    LEPTIN DYSFUNCTION
        <br>
         Assoc    OMIM    Leptin deficiency
        <br>
         Assoc    ClinVar    LEPTIN DYSFUNCTION
        <br>
         Assoc    ClinVar    Obesity, severe, due to leptin deficiency
        <br>
         Assoc    dbGaP    Blood pressure
        <br>
         Assoc    dbGaP    Erythrocyte Count
        <br>
         Assoc    NHGRI-EBI GWAS catalog    Type 2 diabetes
        <br>
         Assoc    dbGaP    Amyotrophic lateral sclerosis
        <br>
         Assoc    ClinVar    ClinVar: phenotype not specified
        <br>
         Assoc    ClinVar    ClinVar: phenotype not specified
        <br>
        <br>
         Best wishes,
        <br>
        <br>
         Sarah
        <br>
        <br>
        On 26/02/2016 12:50, nconte wrote:
        <br>
        <br>
        <blockquote type="cite">Hello
          <br>
          I have an issue with phenotypeFeature fetch_all_by_Gene($gene)
          method. I am trying to retrieve phenotype from gene object and
          the script I have doesn't find any phenotype relating to this
          gene, whereas the ensembl website shows some  phenotype linked
          with gene
          <br>
          <a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000174697;r=7:128241284-128257628;t=ENST00000308868">http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000174697;r=7:128241284-128257628;t=ENST00000308868</a>
          [1]
          <br>
          <br>
          my starting point is a mouse gene from which i retrieve the
          human orthologue, and then query the phenotype related to this
          orthologue.
          <br>
          the script below should work and print no PHE for human LEP
          gene whereas there are phenotype linked to gene according to
          website
          <br>
          output:
          <br>
          human Orthologue: LEP    ENSG00000174697    7    128241284   
          128257628    1
          <br>
          gene is    Lep    scalar  0
          <br>
          no PHE
          <br>
          <br>
          any advise would be great - Also is it better to find
          phenotypes relating to variation of a gene rather than to the
          gene itself in order to get the full picture of phenotype
          related to a specific gene?
          <br>
          thanks
          <br>
          Nathalie
          <br>
          <br>
          script:
          <br>
          #!/usr/local/bin/perl
          <br>
          use strict;
          <br>
          use warnings;
          <br>
          use DBI;
          <br>
          use Bio::EnsEMBL::Registry;
          <br>
          <br>
          Bio::EnsEMBL::Registry->load_registry_from_db(
          <br>
              -host=>  'ensembldb.ensembl.org',
          -user=>'anonymous',
          <br>
              -port=>'3306', 'db_version' => 83,);
          <br>
          Bio::EnsEMBL::Registry->set_reconnect_when_lost(1);# will
          help with connection issues
          <br>
          <br>
          my $gene_member_adaptor=
          Bio::EnsEMBL::Registry->get_adaptor("Multi", "compara",
          "GeneMember");
          <br>
          my $homology_adaptor =
          Bio::EnsEMBL::Registry->get_adaptor("Multi", "compara",
          "Homology");
          <br>
          my $pfh_adaptor =
          Bio::EnsEMBL::Registry->get_adaptor('human', 'variation',
          'phenotypefeature');
          <br>
          <br>
          my $gene_member =
          $gene_member_adaptor->fetch_by_stable_id('ENSMUSG00000059201');
          <br>
          #get the ensembl object correspoding to this mouse stable ID
          <br>
          <br>
                      if ($gene_member){
          <br>
          <br>
          #get orthologues in human
          <br>
                      my $all_homologies =
          $homology_adaptor->fetch_all_by_Member($gene_member,
          -TARGET_SPECIES => 'homo_sapiens',-METHOD_LINK_TYPE =>
          'ENSEMBL_ORTHOLOGUES');
          <br>
                          if (!scalar(@{$all_homologies})){
          <br>
          <br>
                          print   "no orthologue with ensembl orthology
          methodn";  ##1
          <br>
                             } # print a message if there is no
          corresponding mouse orthologue
          <br>
                              else{
          <br>
              #if there is/are orthologue(s) ,find them and print
          annotation about these
          <br>
                              foreach my $this_homology
          (@{$all_homologies}){
          <br>
                              my $homologue_genes =
          $this_homology->gene_list();
          <br>
                              my $homgene;
          <br>
                                  foreach $homgene(@{$homologue_genes}){
          <br>
                                  #get human orthologues only
          <br>
                                      if (defined
          ($homgene->genome_db->name) && 
          $homgene->genome_db->name eq "homo_sapiens") {
          <br>
          <br>
                                      print  join("t", "human
          Orthologue:
          ".$homgene->display_label,$homgene->stable_id,$homgene->dnafrag()->name(),
                                 
          $homgene->dnafrag_start,$homgene->dnafrag_end,$homgene->dnafrag_strand,
          "n" ) ;
          <br>
          <br>
                                      }
          <br>
          <br>
                                  }
          <br>
                              }
          <br>
                          }
          <br>
          <br>
                              my $gene = $gene_member->get_Gene();
          <br>
          <br>
                              if ($gene){
          <br>
                              print 'gene is   
          '.$gene->external_name();
          <br>
                              my $pfs =
          $pfh_adaptor->fetch_all_by_Gene($gene);
          <br>
                              print "t", 'scalar  '.scalar(@$pfs), "n";
          <br>
                                  if ( scalar(@$pfs)== 0 ){print "no
          PHEn";}else{
          <br>
                                  foreach my $pm(@{$pfs}){
          <br>
                                      if ($pm){
          <br>
          <br>
                                      #fill with info about ensembl gene
          phenotype
          <br>
          <br>
                                      print
          "t",$pm->source_name,"t",$pm->phenotype->description,
          "n";
          <br>
                                      }else {next;}
          <br>
                                  }
          <br>
                              }
          <br>
          <br>
                              } else{next;}
          <br>
          <br>
                      }else {print 'no gene member',"n"};
          <br>
          <br>
          __END__
          <br>
          <br>
          _______________________________________________
          <br>
          Dev mailing list    <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
          <br>
          Posting guidelines and subscribe/unsubscribe info:
          <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a> [2]
          <br>
          Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a> [3]
          <br>
        </blockquote>
        <br>
        <br>
        <br>
        Links:
        <br>
        ------
        <br>
        [1]
        <br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000174697;r=7:128241284-128257628;t=ENST00000308868">http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000174697;r=7:128241284-128257628;t=ENST00000308868</a>
        <br>
        [2] <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
        <br>
        [3] <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
        <br>
        <br>
        _______________________________________________
        <br>
        Dev mailing list    <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
        <br>
        Posting guidelines and subscribe/unsubscribe info:
        <br>
        <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
        <br>
        Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
        <br>
      </blockquote>
      <br>
      _______________________________________________
      <br>
      Dev mailing list    <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
      <br>
      Posting guidelines and subscribe/unsubscribe info:
      <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
      <br>
      Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
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