Entering edit mode
11 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):
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
The
Annotation
field seems to the correspond to theAnnotation Score
, which you would have figured out with a little bit of effort.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.