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Using Ensembl API to get a Gene ID from a protein ID

I am using a Homology adaptor:

my $homology_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi', 'compara', 'Homology');
my $homologies = $homology_adaptor->fetch_all_by_Member($gene_member);

which in when I loop through:

foreach my $homology (@{$homologies}) {
   my $member=${$homology->get_all_Members}[1];​

Does not always return a member description:

$member->description​

But does return an protein ID. I am wondering what is the best way to get the gene id from the protein id using the Ensembl API.

ensembl api
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updated by Ram Ram • written by Joseph Hughes Joseph Hughes

I was trying to do something similar, convert GeneID to Gene Symbol. I was doing this for a large amount of genes and found it to be quite slow using the api. I had much more success downloading a TSV file from the UCSC Genome Browser, provided what your looking for is in there.

If you select the selected fields from primary and related tables option in the output format, you should be able to get the information you want in a text file, which you can either read into memory or store in mysql or something.

Hope this helps!

-Kyle

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updated by Ram Ram • written by mbio.kyle mbio.kyle

4 answers

This is one line of code with gget info which also returns the parent gene:

pip install gget, then simply:

# Command-line
gget info ENSP00000354687

# Python
import gget
gget.info(["ENSP00000354687"])
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written by Laura Luebbert • Laura Luebbert

You could use the protein ID to get a translation object, then use $translation->transcript->gene->stable_id $translation->transcript->getGene->stable_id to get the gene stable ID.

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updated by Ram Ram • written by Emily Emily

Hi Emily, that would actually be good if I could get it to work. I am running API version 81 and get the following error:

Can't locate object method "gene" via package "Bio::EnsEMBL::Transcript"
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updated by Ram Ram • written by Joseph Hughes Joseph Hughes

Sorry, it's Get_gene, not gene. This is what happens when I write stuff from memory rather than check it.

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updated by Ram Ram • written by Emily Emily

For the translation adaptor, is there a way I can specify the genome. In the examples I have seen it is usually the common name, e.g.:

my $translation_adaptor = $reg->get_adaptor('human', 'Core', 'Translation');

But it would be easier if I could use the genome name (e.g. homo_sapiens). Or is there an easy way to get from common name to species name?

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updated by Ram Ram • written by Joseph Hughes Joseph Hughes

Either work.

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updated by Ram Ram • written by Emily Emily

Hi Emily,

I'm still getting:

Can't locate object method "Get_gene" via package "Bio::EnsEMBL::Transcript"
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updated by Ram Ram • written by Joseph Hughes Joseph Hughes

The capitalisation is wrong. It should be get_Gene.

Works a treat now.

Thanks

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updated by Ram Ram • written by Joseph Hughes Joseph Hughes

Following Emily's suggestion I used the following to get the gene id:

my @members = @{$homology->get_all_Members()};
foreach my $this_member (@members) {
   my $translation_adaptor = $reg->get_adaptor($this_member->genome_db->name,'Core','Translation');
   my $translation = $translation_adaptor->fetch_by_stable_id($this_member->stable_id);
   print $translation->transcript->get_Gene->stable_id,"\n";
}
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updated by Ram Ram • written by Joseph Hughes Joseph Hughes

I'm not sure if I understand your question, but I would skip BioPerl and use Ensembl BioMart.

(Also see the BioMaRt Bioconductor package to perform queries programmatically with R.)

Ensembl Gene ID      Ensembl Protein ID
ENSG00000198888      ENSP00000354687
ENSG00000198763      ENSP00000355046
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updated by Ram Ram • written by Kamil Kamil

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