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Question: UNIPROT not available in org.EcK12.eg.db
0
gravatar for biodavidjm
13 days ago by
biodavidjm0
biodavidjm0 wrote:

I am trying to map ecoli k12 UNIPROT ids to ENTREZID and GENENAME using the annotation package org.EcK12.eg.db, and while available in most of the annotation packages (to my surprise) the keytype UNIPROT is not available in org.EcK12.eg.db. Questions:

  • Why is not available? any plan to make it available?
  • Any alternative approach to doing this?

Thanks a lot! David

annotation • 38 views
ADD COMMENTlink modified 13 days ago by James W. MacDonald49k • written 13 days ago by biodavidjm0
Answer: UNIPROT not available in org.EcK12.eg.db
0
gravatar for James W. MacDonald
13 days ago by
United States
James W. MacDonald49k wrote:

You could use the UniProt.ws package:

> libraryUniProt.ws)
> up <- UniProt.ws(83333)
> up
"UniProt.ws" object:
An interface object for UniProt web services
Current Taxonomy ID:
83333
Current Species name:
Escherichia coli (strain K12)
To change Species see: help('availableUniprotSpecies')

> select(up, "944958", "UNIPROTKB","ENTREZ_GENE")
Getting mapping data for 944958 ... and ACC
'select()' returned 1:many mapping between keys and columns
  ENTREZ_GENE  UNIPROTKB
1      944958 A0A387CVM5
2      944958     P31663
> 
ADD COMMENTlink written 13 days ago by James W. MacDonald49k
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