Question: Retrieving homologues of human proteins using Ensembl REST API?
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gravatar for db534
4 months ago by
db5340
United Kingdom
db5340 wrote:

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 • 245 views
ADD COMMENTlink modified 9 weeks ago by Biostar ♦♦ 20 • written 4 months ago by db5340

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

what was the URL ?

ADD REPLYlink written 4 months ago by Pierre Lindenbaum99k

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

ADD REPLYlink modified 4 months ago • written 4 months ago by db5340
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