Ensembl, Fetch "Phenotypes" information

Question

[hmende.z]

Hi,

Is there a way to retrieve all "Phenotypes" information from a given gene using Perl API or BiomaRt? Like for example: https://useast.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000143549;r=1:154155304-154194648

Thanks, Hector

Answer 1

[Ben_Ensembl]

Hi hmende.z,

You can do this my using the web or R version of BioMart with the Attributes available under the Gene>Phenotype Attributes in the 'Features' section.

You can also use the Ensembl REST API phenotype endpoints. Documentation for the GET phenotype/gene/:species/:gene endpoint can be found below: http://rest.ensembl.org/documentation/info/phenotype_gene

You can also do this using the Ensembl Perl API, and there is a tutorial available here: https://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype

[hmende.z]

Hi Ben, Thank you so much for your feedback, I am going to try your suggestions.