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I have a list of GO ids and I want to find out a unique term description such that if I provide say 200 GO IDs I will give 200 specific GO terms. The code snippet I am using is given below. Although it kind of works, for one given GO ID I get several terms like for my 200 GO ids I get 2577 terms whereas I am interested in a specific GO term. The output that I want is like this GO:0007254 = JNK cascade. I will like to mention that I have also cross-posted the query in biostars and got no reply for the last 2 days and hence I am posting the query on Stack exchange bioinformatics. Any help will be useful.

library(biomaRT)
mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "drerio_gene_ensembl", host = "asia.ensembl.org")  
v1 <-c(target)   # The list of GO ids that I want to pass as a list.
go_list <- getBM(attributes=c("go_id", "name_1006", "namespace_1003"),
              filters = "go",
              values = c("v1"),
              mart=mart, uniqueRows = TRUE)
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  • $\begingroup$ Thank you for mentioning the cross-post. It would help if you also added a link to that post here and a link to this post there so anyone starting at one post would be able to reach the other. $\endgroup$
    – Ram RS
    Aug 27, 2021 at 14:57
  • $\begingroup$ Here goes the link to the cross-post as requested. biostars.org/p/9486373/#9486827 $\endgroup$ Aug 27, 2021 at 15:59
  • $\begingroup$ You mean biostars.org/p/9486373 - your link is to a specific comment on that post. Also, edit your post and add the link, then edit your biostars post and add the link to this post there. $\endgroup$
    – Ram RS
    Aug 27, 2021 at 17:23

1 Answer 1

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library(biomaRt)
mart <- biomaRt:::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "drerio_gene_ensembl", host = "asia.ensembl.org")  

v1 <- c("GO::0009055","GO:0016020","GO:0016491","GO:0006122","GO:0008121")

go_list <- biomaRt:::getBM(attributes=c("go_id", "name_1006", "namespace_1003"),
              filters = "go",
              values = v1,
              mart=mart, uniqueRows = TRUE)

so it is likely the "v1" that should not be in quotes

head(go_list)
        go_id                                                   name_1006
1 GO:0016020                                                    membrane
2 GO:0005739                                               mitochondrion
3 GO:0005743                                mitochondrial inner membrane
4 GO:0070469                                                 respirasome
5 GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c
6 GO:0001525                                                angiogenesis
      namespace_1003
1 cellular_component
2 cellular_component
3 cellular_component
4 cellular_component
5 biological_process
6 biological_process
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  • $\begingroup$ when search filters option is used searchFilters(ensembl, pattern = "GO") . We get the above filters (ensembl, pattern = "GO") name description 12 with_go With GO ID(s) 13 with_goslim_goa With GOSlim GOA ID(s) 58 go GO ID(s) [e.g. GO:0000003] 59 goslim_goa GOSlim GOA ID(s) [e.g. GO:0000003] 183 go_evidence_code GO Evidence code. NO go_id filter exists. $\endgroup$ Aug 27, 2021 at 17:36

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