How to extract gene location from a list of Ensembl Bacteria IDs?

Question

[biobaker]

I am trying to get obtain genomic coordinates for a list of proteins from different species of bacteria. I obtained the IDs through HMMer, on Ensembl's website. Here are a few of them and what they look like:

AAR34000
OEG73082
EQMM11970

I had previously used the lookup endpoint from Ensembl's REST API without any problems. However, now when I try searching with my code that worked in the past, I get 0 hits. Based on what I've seen online, it looks like the issue may be the fact that these IDs are not in the form of Ensembl stable IDs. However, I haven't found a way to convert these IDs to the Ensembl IDs, and it still doesn't explain why I was able to use the lookup function successfully in the past without the stable IDs.

For context, this is the code I'm running from R, where "accs2" is a vector of the IDs listed above:

library(httr)
library(jsonlite)
library(xml2)

server <- "http://rest.ensembl.org"
ext <- "/lookup/id/"


r <- POST(paste(server, ext, sep = ""), 
          content_type("application/json"), 
          accept("application/json"), body = paste0('{ "ids" :', jsonlite::toJSON(accs2), ' }'))


stop_for_status(r)

dbinfo<-fromJSON(toJSON(content(r)))

dbinfo.df<-data.frame(do.call(rbind, lapply(dbinfo, function(x) x[match(names(dbinfo[[1]]), names(x))])))

Is there something I'm missing here?

[Emily]

I'm looking into this. Two of the IDs you've got are the correct IDs, but something else strange is happening with the endpoints, I tried the get endpoint with the first two IDs like:

http://rest.ensembl.org/lookup/id/AAR34000

And the error is:

--- 
error: Can not find internal name for species 'geobacter_sulfurreducens_pca'

I suspect this is related to how the bacterial species are held in collections, but I need to check with our developers. I will get back to you when I know more.

The third ID EQMM11970 is telling me ID not found. We did a release yesterday and it's possible that this species or identifier is no longer in the database.

[biobaker]

Good to know it's not just me, thank you! Given that I originally obtained these IDs through HMMer on Ensembl's website, I am going to give it a run once more to see if the IDs I get out of HMMer will be consistent with the latest release. I'll post my update shortly.

Answer 1

[Emily]

This was an error in Ensembl and is now fixed.