[ensembl-dev] mapping between ensembl and other databases

Andrea Edwards edwardsa at cs.man.ac.uk
Sun Dec 5 20:44:47 GMT 2010


Hello

I am confused as to why sometimes i can retrieve records from ensembl 
via an entrezgene id and other times not.

Take this entrezgene id: 441521
The entry for this record says it is related to 2 ensembl genes

===========================================
    taken from entrezgene record
===========================================
See related
    Ensembl:ENSG00000228836; <http://www.ensembl.org/id/ENSG00000228836>
    Ensembl:ENSG00000242284; <http://www.ensembl.org/id/ENSG00000242284>
    HPRD:17573; <http://www.hprd.org/protein/17573> MIM:300796
    <http://www.ncbi.nlm.nih.gov/omim/300796>

==========================================

but this code returns nothing

my @genes = @{$gene_adaptor->fetch_all_by_external_name(441521, 
"EntrezGene")};
foreach my $gene  (@genes){
     print "gene name: ", $gene->stable_id(), "\n";
}


the same code for another gene, 280753, with related ensembl records

===========================================
    taken from entrezgene record
===========================================
See related
    Ensembl:ENSBTAG00000016514
    <http://www.ensembl.org/id/ENSBTAG00000016514>

===========================================

does return the ensembl gene. I don't know the mappings which determine 
the whether i can get a gene from ensembl by its entrez gene id

thanks a lot




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