Ensembl ID conversion - other than Uniprot

Question

[NS]

Hi all,

I have a list of ensembl IDs, and I normally use Uniprot ID conversion to convert them. The Uniprot server seems to be down and this is not the first time I have encountered this problem. Could you suggest any other alternative for ID conversion of Ensembl IDs to Uniprot IDs. I have zero knowledge on programming, hence could you suggest any website that could alternatively do the conversion.

Thanks a lot!

[finswimmer]

Hello NS ,

you could try Biomart.

fin swimmer

[NS]

Hi, I am unable to reply to the above response and hence writing it here. Thank you fin swimmer for your suggestion. However, why are the IDs being replicated on that? Also, I tried using DAVID gene ID conversion for the same - on DAVID, there are several uniprot IDs for a single ensemble ID; therefore how do we identify which is the first hit of the ID on DAVID?

Thank you.

[GenoMax]

Post examples of ID's that are exhibiting this problem so we can evaluate the issue.

As an aside, if you are posting from china using chrome browser apparently allows one to use ADD REPLY button.

[NS]

Hi all, Thank you for your support. Incidentally I had also written to Uniprot as query. The response indicates that there is a connectivity problem with job management between mirror sites. I am hoping they rectify it.

Noted on the functionality of the Add Reply button. Thank you.

On DAVID for e.g., ENSG00000179388 returns three Uniprot accession - E5RIM5, B4DH80, Q06889. Is it possible to identify the first hit here?

Kind regards

[Emily]

Mapping between databases is not always 1:1, as they have different philosophies of annotation. In the case of ENSG00000179388, different transcripts of the gene map to different UniProt identifiers.

[NS]

Hi Emily, Thanks for explaining. Kind regards

Answer 1

[Alex Reynolds]

Here's a way to use mygene.info to script queries. Say you have this script called mapEnsemblGeneToUniprot.py:

#!/usr/bin/env python

import sys
import mygene

mg = mygene.MyGeneInfo()

genes = []
for line in sys.stdin:
    genes.append(line.strip())

results = mg.querymany(genes, scopes='ensembl.gene', fields=['uniprot'], species='human', verbose=False)

header_written = False
for r in results:
    if 'uniprot' in r:
        if not header_written:
            sys.stdout.write('{}\t{}\t{}\n'.format('Ensembl', 'Swiss-Prot', 'TrEMBL'))
            header_written = True
        q = r['query']
        try:
            sp = r['uniprot']['Swiss-Prot']
            te = r['uniprot']['TrEMBL']
        except KeyError as ke:
            pass
        sys.stdout.write('{}\t{}\t{}\n'.format(q, sp, te))

Given the text file records.txt, e.g.:

ENSG00000225235
ENSG00000165359
ENSG00000150676
ENSG00000099308
ENSG00000142676
ENSG00000180776
ENSG00000236953
ENSG00000108848
ENSG00000277370
ENSG00000103811
ENSG00000101473

You could run the script like so:

$ ./mapEnsemblGeneToUniprot.py < records.txt
Ensembl Swiss-Prot  TrEMBL
ENSG00000165359 Q5JSJ4  A0A1W2PPI5
ENSG00000150676 Q8IWF9  H0YDV3
ENSG00000099308 O60307  V9GYV0
ENSG00000142676 P62913  ['Q5VVC8', 'Q5VVD0', 'A0A2R8Y447']
ENSG00000180776 Q5W0Z9  ['A0A0D9SEN4', 'B4DRN8']
ENSG00000108848 O95232  ['Q86Y74', 'J3KPP4', 'A8K3C5', 'C9JL41', 'H0YA81', 'U3KQT3', 'H7C5U7', 'D6RHH0', 'E7EN55', 'H0YAX1', 'H0YBV7', 'H0YAR4', 'H0YAY6', 'D6RDI2']
ENSG00000103811 P09668  ['E9PN60', 'A0A0B4J217', 'E9PKT6', 'A0A087X0D5', 'E9PN84']
ENSG00000101473 O14734  ['F6VBM3', 'E9PRD4', 'E9PIS4', 'H7C5A7', 'Q9BR14', 'E9PJN0', 'H0Y698', 'E9PMC4']

[NS]

Hi Alex, Thank you for the suggestion. I have no knowledge on programming, but shall try this as instructed. Thanks again.