Ensembl down???
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bas_work ▴ 30
Last seen 9 weeks ago

Is the Ensemble server down? Using biomaRt, I get back internal server errors and the suggestion that I use other mirrors, at no avail. The BioMart service was actually down for a while today, i noticed, but I believe all should now be fine as it is up again. However, biomaRt is not able to access it.

sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.1.1

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] C

time zone: Europe/Amsterdam tzcode source: internal

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages: [1] biomaRt_2.58.0 DESeq2_1.42.0
[3] SummarizedExperiment_1.32.0 Biobase_2.62.0
[5] MatrixGenerics_1.14.0 matrixStats_1.1.0
[7] GenomicRanges_1.54.1 GenomeInfoDb_1.38.1
[9] IRanges_2.36.0 S4Vectors_0.40.2
[11] BiocGenerics_0.48.1

loaded via a namespace (and not attached): [1] KEGGREST_1.42.0 gtable_0.3.4 ggplot2_3.4.4
[4] lattice_0.22-5 vctrs_0.6.4 tools_4.3.2
[7] bitops_1.0-7 generics_0.1.3 curl_5.1.0
[10] parallel_4.3.2 tibble_3.2.1 fansi_1.0.5
[13] AnnotationDbi_1.64.1 RSQLite_2.3.3 blob_1.2.4
[16] pkgconfig_2.0.3 Matrix_1.6-3 dbplyr_2.4.0
[19] lifecycle_1.0.4 GenomeInfoDbData_1.2.11 stringr_1.5.1
[22] compiler_4.3.2 progress_1.2.2 Biostrings_2.70.1
[25] munsell_0.5.0 codetools_0.2-19 RCurl_1.98-1.13
[28] pillar_1.9.0 crayon_1.5.2 BiocParallel_1.36.0
[31] DelayedArray_0.28.0 cachem_1.0.8 abind_1.4-5
[34] digest_0.6.33 tidyselect_1.2.0 locfit_1.5-9.8
[37] stringi_1.8.2 purrr_1.0.2 dplyr_1.1.4
[40] fastmap_1.1.1 grid_4.3.2 colorspace_2.1-0
[43] cli_3.6.1 SparseArray_1.2.2 magrittr_2.0.3
[46] S4Arrays_1.2.0 XML_3.99-0.15 utf8_1.2.4
[49] withr_2.5.2 rappdirs_0.3.3 filelock_1.0.2
[52] prettyunits_1.2.0 scales_1.2.1 bit64_4.0.5
[55] XVector_0.42.0 httr_1.4.7 bit_4.0.5
[58] hms_1.1.3 png_0.1-8 memoise_2.0.1
[61] BiocFileCache_2.10.1 rlang_1.1.2 Rcpp_1.0.11
[64] glue_1.6.2 DBI_1.1.3 xml2_1.3.5
[67] R6_2.5.1 zlibbioc_1.48.0

biomaRt • 677 views
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Last seen 11 hours ago
United States

Seems fine now. I'd try again.

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It was down around that time - I know because I was also using it. As per James, just re-try to make the connection with the server.

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Well, I keep getting messages that servers are unresponsive. None of the mirrors work, and messages suggest its on their end, not mine ('Ensembl site unresponsive,[...]').

Entering edit mode

Yup, they seem to be down. What exactly are you trying to do? There may be other options.

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I want to link 'external_gene_names' (mouse, multiple lists) with the ensembl gene IDs and HGNC symbols of human orthologues using getLDS(). I see that getBM() in biomaRt now works (wasn't the case this afternoon), so there's hope!

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I'm beginning to think it is an issue with getLDS(). getBM() just works like a charm, but linking datasets (mouse <-> man) still throws up 'internal sever errors'. I have confirmation from Ensembl that there are problems on their end that they hope to resolve them as soon as possible.

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What are the mouse IDs? There is an Orthology.eg.db package that can be used to map mouse NCBI Gene IDs to human, and you can use the human and mouse OrgDb packages to get the symbols. It might be simpler to take that route, particularly if you don't already have Ensembl IDs.

Entering edit mode

Thanks, I'm now exploring these. I want to map external gene names (long lists, actually) to human HGNC symbols and Ensembl gene IDs...

Entering edit mode

Yes, you have already said that. The length of the lists isn't material to this discussion, but the nature of the IDs is. I have no idea what an 'external gene name' might be, and unless you want to provide that information I am afraid nobody will be able to give you any more help.

Entering edit mode

"external_gene_name" is a biomaRt attribute for mouse gene names, equivalent but (obviously) not identical to human HGNC symbols.

Entering edit mode

I normally caution against mapping between annotation sources (NCBI and Ensembl), as it usually doesn't work well. However, it is possible.

mapIt <- function(x) {
    require("Orthology.eg.db", character.only = TRUE)
    require("org.Mm.eg.db", character.only = TRUE)
    require("org.Hs.eg.db", character.only = TRUE)
    mouse <- mapIds(org.Mm.eg.db, x, "ENTREZID", "ALIAS")
    mapped <- select(Orthology.eg.db, mouse, "Homo.sapiens","Mus.musculus")
    human <- mapIds(org.Hs.eg.db, as.character(mapped[,2]), "SYMBOL","ENTREZID")
    mensembl <- mapIds(org.Mm.eg.db, mouse, "ENSEMBL", "ENTREZID")
    hensembl <- mapIds(org.Hs.eg.db, as.character(mapped[,2]), "ENSEMBL","ENTREZID")
## control for any NULL values
    if(any(is.na(mapped[,2]))) {
        human[sapply(human, is.null)] <- NA
        human <- do.call(c, human)
        hensembl[sapply(hensembl, is.null)] <- NA
        hensembl <- do.call(c, hensembl)
    out <- data.frame(Mouse.symbol = x, Mouse.ensembl = mensembl, mapped,
                      Human.ensembl = hensembl, Human.symbol = human)

> z <- head(keys(org.Mm.eg.db, "SYMBOL"), 20)
> mapIt(z)
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
      Mouse.symbol      Mouse.ensembl Mus.musculus Homo.sapiens   Human.ensembl Human.symbol
11287          Pzp ENSMUSG00000030359        11287           NA            <NA>         <NA>
11298        Aanat ENSMUSG00000020804        11298           15 ENSG00000129673        AANAT
11302         Aatk ENSMUSG00000025375        11302         9625 ENSG00000181409         AATK
11303        Abca1 ENSMUSG00000015243        11303           19 ENSG00000165029        ABCA1
11304        Abca4 ENSMUSG00000028125        11304           24 ENSG00000198691        ABCA4
11305        Abca2 ENSMUSG00000026944        11305           20 ENSG00000107331        ABCA2
11306        Abcb7 ENSMUSG00000031333        11306           22 ENSG00000131269        ABCB7
11307        Abcg1 ENSMUSG00000024030        11307         9619 ENSG00000160179        ABCG1
11308         Abi1 ENSMUSG00000058835        11308        10006 ENSG00000136754         ABI1
11350         Abl1 ENSMUSG00000026842        11350           25 ENSG00000097007         ABL1
11352         Abl2 ENSMUSG00000026596        11352           27 ENSG00000143322         ABL2
11354     Scgb1b27 ENSMUSG00000066583        11354           NA            <NA>         <NA>
11358           ac               <NA>        11358           NA            <NA>         <NA>
11363        Acadl ENSMUSG00000026003        11363           33 ENSG00000115361        ACADL
11364        Acadm ENSMUSG00000062908        11364           34 ENSG00000117054        ACADM
11370       Acadvl ENSMUSG00000018574        11370           37 ENSG00000072778       ACADVL
11409        Acads ENSMUSG00000029545        11409           35 ENSG00000122971        ACADS
11416      Slc33a1 ENSMUSG00000027822        11416         9197 ENSG00000169359      SLC33A1
11418        Asic2 ENSMUSG00000020704        11418           40 ENSG00000108684        ASIC2
11419        Asic1 ENSMUSG00000023017        11419           41 ENSG00000110881        ASIC1
Entering edit mode

Thank you James, very useful!!!


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