This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Retrieving homologues of human proteins using Ensembl REST API?

I have a question regarding the retrieval of gene homologues using the REST API of Ensembl Genomes. In particular, I am interested in the retrieval of homologues of human genes/proteins from the pan-taxonomic compara of Ensembl Genomes. However, if I supply a Homo sapiens gene/protein ID to the API of Ensembl Genomes, then the API crashes? I can however retrieve some vertebrate homologues of human proteins using the API for the regular Ensembl database, although the taxonomic range of the homologues is too narrow for the analysis that I need to perform.

The only 'solution' so far I have found is to obtain D. melanogaster homologues from the regular Ensembl API as an output, and then to use this ID as an input to the Ensembl Genomes REST API, which will retrieve for me the pan-taxonomic homologues of the Drosophila homologue.

I am just wondering if it would at all be possible for me to retrieve directly the pan-taxonomic homologues for a human ID using Ensembl/EnsemblGenomes services?

ensembl orthologs
• 2,421 views • link
updated by Biostar Biostar • written by db534 • db534

However, if I supply a Homo sapiens gene/protein ID to the API of Ensembl Genomes, then the API crashes?

what was the URL ?

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre,

This is the line of code for a D. melanogaster ID (FBgn0263237), which returns a result: 

wget -q --header='Content-type:application/json' 'http://rest.ensemblgenomes.org/homology/id/FBgn0263237?format=condensed;type=orthologues;compara=pan_homology'  -O test.txt

If I replace the D. melanogaster ID with a human one though (e.g. 'ENSG00000123374'), no result is returned.

Human IDs work for REST API queries of the regular Ensembl database though:

wget -q --header='Content-type:application/json' 'http://rest.ensembl.org/homology/symbol/human/ENSG00000123374?format=condensed;type=orthologues;compara=pan_homology'  -O test.txt

This query however only yields vertebrate homologues (plus yeast and fruit fly), which is too narrow for my required analysis

• 0 views • link
written by db534 • db534

0 answers

No answers yet.

Log in to answer this question.

More posts like this