use bioservices.UniProt (python) to map uniprot accession to [multiple] ensembl ids
1
0
Entering edit mode
8 months ago
mk ▴ 300

I am just trying to get a (one to many) mapping from uniprot accession -> Ensembl ids.

In the spirit of exploration, I have the following code to use bioservices.UniProt pull all possible columns for the selection of uniprot accession ids.

from bioservices import UniProt
u = UniProt()
accession_numbers = ['P30561', 'P53762']
result = u.get_df(accession_numbers)
type(result)
result.columns.tolist()

I know that this mapping exists in UniProt, here is the annotation field on the uniprot website for the first accession (P30561):

enter image description here

However, going through the output columns of result above, the column labeled "Annotation" has the following contents:

0    5.0
1    5.0
2    5.0
3    5.0
4    5.0
5    5.0
6    4.0
7    1.0

This is clearly not a list of Ensembl ids

bioservices ensembl python uniprot • 616 views
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1
Entering edit mode

The Annotation field seems to the correspond to the Annotation Score, which you would have figured out with a little bit of effort.

result[['Entry','Annotation']]
    Entry  Annotation
0  P30561         5.0
1  P53762         5.0
2  O94763         5.0
3  P97481         5.0
4  P79832         5.0
5  Q61221         5.0
6  Q61045         4.0
7  G7ZFL7         1.0

Annotation score for:

Look for a column that can take you to the NCBI/Entrez Gene ID. There is no basis to assume that a column titled Annotation will give you a gene ID.

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2
Entering edit mode
8 months ago
mk ▴ 300

Turns out this works:

from bioservices import UniProt
u = UniProt()
accession_numbers = ['P30561', 'P53762']
u.mapping(fr='UniProtKB_AC-ID',to='Ensembl',query=accession_numbers)
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