ensemble transcript ID to gene symbol using pybiomart

Question

[Quak]

I am working with STRING protein interaction data where each nodes are ensembl protein ID as following

ENSP00000272298
ENSP00000253401
ENSP00000401445
ENSP00000418915
ENSP00000327801
ENSP00000466298
ENSP00000232564
ENSP00000393379
ENSP00000371253
ENSP00000373713

I wonder how I can convert them into gene symbol in python ? if you don't recommend, how I can convert my gene symbols into ensembl protein IDs ?

I know I can use the mygene in python

import mygene
mg = mygene.MyGeneInfo()

and convert gene symbols into ensembl genes, but I wonder how can tweak this to have protein id instead

result = mg.query("APOE", scopes='symbol', fields=['ensembl'], species="human")

for hit in result["hits"]:
     if "ensembl" in hit and "gene" in hit["ensembl"]:
          print(hit["ensembl"]["gene"])

I have tried biomart through python

from pybiomart import Server

server = Server(host='http://www.ensembl.org')

dataset = (server.marts['ENSEMBL_MART_ENSEMBL']
                 .datasets['hsapiens_gene_ensembl'])

dataset.query(attributes=['ensembl_gene_id', 'ensembl_transcript_id', 'ensembl_peptide_id'],
              filters={'ensembl_transcript_id': ['ENSP00000371253']})

how ever the error I get is

BiomartException: Unknown filter ensembl_transcript_id, check dataset filters for a list of valid filters.

and there is no other relevant as far as I see. I also couldn't find examples in python, and this is the most relevant one in R

[Ram]

Have you tried other utilities, such as eutils or biomart?

[Quak]

just added to the question !

[Ram]

The ensembl_peptide_id that you have used is a valid filter, so is the ensembl_transcript_id (I checked using biomaRt). Unless the python API is inferior to the R api, I think things should work. You can check using the show_filters() method.

[Quak]

It looks like it is the python API problem !! thanks for the confirmation. I do get the result in R but that filter does not exist in the python API.

Answer 1

[Emily]

The easiest way is the Ensembl REST API, which allows language agnostic access to Ensembl data. There's an online course on using the API in Python, R or Perl.

[Dan]

How would you do this using the Ensembl REST API?

[Ben_Ensembl]

You can do this using the Lookup endpoints, e.g: http://rest.ensembl.org/documentation/info/lookup