Question: Anotations Score of uniprot. ws
0
gravatar for cerikahp
4.0 years ago by
cerikahp0
cerikahp0 wrote:

For many reasons I'm interested in retrieving the annotation score used in UNIPROT. However when using the connection to the specie Rattus norvegicus I cant get any annotation score.

 select(up, 24379,c("REVIEWED","PATHWAY","SCORE", "RGD","ID"), "ENTREZ_GENE" ,na.rm=T)

If I check the website (http://www.uniprot.org/uniprot/P18088), the annotation score is available. Am I missing something? Or it's just the version of uniprot I'm querying.

sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=es_MX.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=es_MX.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=es_MX.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=es_MX.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] UniProt.ws_2.10.0   BiocGenerics_0.16.1 RCurl_1.95-4.7      bitops_1.0-6        RSQLite_1.0.0      
[6] DBI_0.3.1          

loaded via a namespace (and not attached):
[1] IRanges_2.4.4        tools_3.2.2          Biobase_2.30.0       AnnotationDbi_1.32.0 S4Vectors_0.8.3     
[6] stats4_3.2.2

 

uniprot.ws uniprot • 600 views
ADD COMMENTlink modified 4.0 years ago by James W. MacDonald52k • written 4.0 years ago by cerikahp0
Answer: Anotations Score of uniprot. ws
0
gravatar for James W. MacDonald
4.0 years ago by
United States
James W. MacDonald52k wrote:
> select(up, "24379", c("REVIEWED","PATHWAY","EXISTENCE", "RGD","ID"), "ENTREZ_GENE" )
Getting mapping data for 24379 ... and ACC
Getting mapping data for C9E895 ... and RGD_ID
Getting extra data for C9E895 P18088 NA etc
'select()' returned 1:many mapping between keys and columns
  ENTREZ_GENE   REVIEWED PATHWAY                    EXISTENCE  RGD     ID
1       24379 unreviewed    <NA> Evidence at transcript level 2652 C9E895
2       24379   reviewed    <NA> Evidence at transcript level 2652 P18088
>
ADD COMMENTlink written 4.0 years ago by James W. MacDonald52k

Never mind - I misread the page you sent.

ADD REPLYlink written 4.0 years ago by James W. MacDonald52k
Answer: Anotations Score of uniprot. ws
0
gravatar for James W. MacDonald
4.0 years ago by
United States
James W. MacDonald52k wrote:

I have patched UniProt.ws to correctly get the score:

> up <- UniProt.ws(taxId=10116)
> select(up, keys(up, "UNIPROTKB")[1:5], "SCORE","UNIPROTKB")
Getting extra data for P35213 P62260 P68511 etc
'select()' returned 1:1 mapping between keys and columns
  UNIPROTKB      SCORE
1    P35213 5 out of 5
2    P62260 5 out of 5
3    P68511 3 out of 5
4    P61983 5 out of 5
5    P68255 4 out of 5
## try your example
> select(up, "24379", c("REVIEWED","PATHWAY","SCORE", "RGD","ID"), "ENTREZ_GENE" )
Getting mapping data for 24379 ... and ACC
Getting mapping data for C9E895 ... and RGD_ID
Getting extra data for C9E895 P18088 NA etc
'select()' returned 1:many mapping between keys and columns
  ENTREZ_GENE   REVIEWED PATHWAY      SCORE  RGD     ID
1       24379 unreviewed    <NA> 3 out of 5 2652 C9E895
2       24379   reviewed    <NA> 5 out of 5 2652 P18088

## try human
> up <- UniProt.ws()
> select(up, keys(up, "UNIPROTKB")[1:5], c("SCORE","ENTREZ_GENE"),"UNIPROTKB")
Getting mapping data for P31946 ... and P_ENTREZGENEID
Getting extra data for P31946 P62258 Q04917 etc
'select()' returned 1:1 mapping between keys and columns
  UNIPROTKB      SCORE ENTREZ_GENE
1    P31946 5 out of 5        7529
2    P62258 5 out of 5        7531
3    Q04917 5 out of 5        7533
4    P61981 5 out of 5        7532
5    P31947 5 out of 5        2810

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] UniProt.ws_2.10.1   BiocGenerics_0.16.1 RCurl_1.95-4.7     
[4] bitops_1.0-6        RSQLite_1.0.0       DBI_0.3.1          

loaded via a namespace (and not attached):
[1] compiler_3.2.2       IRanges_2.4.4        tools_3.2.2         
[4] Biobase_2.30.0       AnnotationDbi_1.32.1 S4Vectors_0.8.3     
[7] stats4_3.2.2       

This should be available for the release version of Bioconductor in a day or so - you are looking for version 2.10.1

ADD COMMENTlink written 4.0 years ago by James W. MacDonald52k
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