I'm failing to retrieve Cosmic variations for some human genes using Ensembl API.
Using a web browser with this link:
illustrates that Cosmic variations are available for gene TP53 (ensembl id=ENSG00000141510); in the above URL, I actually retrieved variations for one on the many TP53 transcripts, ENST00000617185.
Ok, now, if I use one of these URLs (Ensembl API based) :
- using TP53 gene ID: curl -H 'Content-type:text/xml' -o variations.xml 'http://rest.ensembl.org/overlap/id/ENSG00000141510?feature=variation;variant_set=ph_variants'
- using TP53 transcript ID: curl -H 'Content-type:text/xml' -o variations.xml 'http://rest.ensembl.org/overlap/id/ENST00000617185?feature=variation;variant_set=ph_variants'
I can retrieve Clinvar, PhenCode, etc. mutations but no Cosmic ones.
Any idea of what I did wrong?
An optional question: to which kind of Ensembl objects (gene, transcript, protein) are attached the many variation features available from Ensembl? I could not find a documentation about that.