Question: (Closed) UniProt.ws version 2.10.2
0
gravatar for DHS
3.8 years ago by
DHS0
USA/Stanford
DHS0 wrote:

Dear BioConductor Community, I am using the UniProt.ws version 2.10.2 to retrieve features for my protein hitlists. I am particularly interested in the SUBCELLULAR LOCATION information.

While the info is available on uniprot.org (e.g.: http://www.uniprot.org/uniprot/P35579#subcellular_location) I seem to be unable to retrieve any SUBCELLULAR LOCATION information via the UniProt.ws package, I only get NA as results while other cols return the correct infos:

res <- select(up, "P35579", "REACTOME", "UNIPROTKB")
Getting mapping data for P35579 ... and REACTOME_ID
'select()' returned 1:many mapping between keys and columns
> res
  UNIPROTKB      REACTOME
1    P35579 R-HSA-5627117
2    P35579 R-HSA-5625900
3    P35579 R-HSA-5625740
4    P35579 R-HSA-5627123
5    P35579  R-HSA-416572
6    P35579 R-HSA-3928663
7    P35579 R-HSA-2029482

but

res <- select(up, "P35579", "SUBCELLULAR-LOCATIONS", "UNIPROTKB")
Getting extra data for P35579 NA NA etc
'select()' returned 1:1 mapping between keys and columns
> res
  UNIPROTKB SUBCELLULAR-LOCATIONS
1    P35579                  <NA>

So I wonder whether the SUBCELLULAR LOCATION info is actually updated in the package or whether this supporting data can be accessed in any other way?

Best,
D

 

 

 

 

ADD COMMENTlink written 3.8 years ago by DHS0

Hello d.siepe!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 3.8 years ago by James W. MacDonald52k
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