Converting between Ensembl Versions

Question

[jwhidd]

Hi All,

I have a list of Ensembl gene IDs from version 87. I would like to convert these IDs to the current Ensembl gene IDs (version 89). I have downloaded biomaRt, which I think should allow me to download archived versions of Ensembl databases. Is biomaRt the correct package/approach to solving my problem?

Furthermore, when I use listMarts(archive=TRUE) to ask biomaRt for which archived versions are available, I see versions 43-51 listed, but nothing more recent. Is this correct? Can I really not access Version 87 via biomaRt?

Thanks! Jenn

> listMarts(archive=TRUE)
                       biomart                     version
1              ensembl_mart_51                  Ensembl 51
2                  snp_mart_51                      SNP 51
3                 vega_mart_51                     Vega 32
4              ensembl_mart_50                  Ensembl 50
5                  snp_mart_50                      SNP 50
6                 vega_mart_50                     Vega 32
7              ensembl_mart_49   ENSEMBL GENES 49 (SANGER)
8     genomic_features_mart_49            Genomic Features
9                  snp_mart_49                         SNP
10                vega_mart_49                        Vega
11             ensembl_mart_48   ENSEMBL GENES 48 (SANGER)
12    genomic_features_mart_48            Genomic Features
13                 snp_mart_48                         SNP
14                vega_mart_48                        Vega
15             ensembl_mart_47   ENSEMBL GENES 47 (SANGER)
16    genomic_features_mart_47            Genomic Features
17                 snp_mart_47                         SNP
18                vega_mart_47                        Vega
19    compara_mart_homology_47            Compara homology
20 compara_mart_multiple_ga_47 Compara multiple alignments
21 compara_mart_pairwise_ga_47 Compara pairwise alignments
22             ensembl_mart_46   ENSEMBL GENES 46 (SANGER)
23    genomic_features_mart_46            Genomic Features
24                 snp_mart_46                         SNP
25                vega_mart_46                        Vega
26    compara_mart_homology_46            Compara homology
27 compara_mart_multiple_ga_46 Compara multiple alignments
28 compara_mart_pairwise_ga_46 Compara pairwise alignments
29             ensembl_mart_45   ENSEMBL GENES 45 (SANGER)
30                 snp_mart_45                         SNP
31                vega_mart_45                        Vega
32    compara_mart_homology_45            Compara homology
33 compara_mart_multiple_ga_45 Compara multiple alignments
34 compara_mart_pairwise_ga_45 Compara pairwise alignments
35             ensembl_mart_44   ENSEMBL GENES 44 (SANGER)
36                 snp_mart_44                         SNP
37                vega_mart_44                        Vega
38    compara_mart_homology_44            Compara homology
39 compara_mart_pairwise_ga_44 Compara pairwise alignments
40             ensembl_mart_43   ENSEMBL GENES 43 (SANGER)
41                 snp_mart_43                         SNP
42                vega_mart_43                        Vega
43    compara_mart_homology_43            Compara homology
44 compara_mart_pairwise_ga_43 Compara pairwise alignments

[cpad0112]

> listMarts()
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 89
2   ENSEMBL_MART_MOUSE      Mouse strains 89
3     ENSEMBL_MART_SNP  Ensembl Variation 89
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 89

Answer 1

[Emily]

The way to update old IDs is using the ID history converter.

Answer 2

[Mike Smith]

To answer your other question about the Ensembl archives with biomaRt, I think the archive = TRUE arguments are now long out of date. You can access mirrors using the appropriate URL to host and just ignoring the archive argument entirely e.g. for Ensembl 87

> listMarts(host = "http://dec2016.archive.ensembl.org/")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 87
2   ENSEMBL_MART_MOUSE      Mouse strains 87
3     ENSEMBL_MART_SNP  Ensembl Variation 87
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 87
5    ENSEMBL_MART_VEGA                  Vega

I'll update the vignette and manual pages to reflect this.

[Mike Smith]

Version 2.33.4 of biomaRt now contains the function listEnsemblArchives() which will display all the available archives and the URL used to access them:

> listEnsemblArchives()
      version          date       url                                 
 [1,] "Ensembl GRCh37" "Feb 2014" "http://grch37.ensembl.org"         
 [2,] "Ensembl 89"     "May 2017" "http://May2017.archive.ensembl.org"
 [3,] "Ensembl 88"     "Mar 2017" "http://Mar2017.archive.ensembl.org"
 [4,] "Ensembl 87"     "Dec 2016" "http://Dec2016.archive.ensembl.org"
 [5,] "Ensembl 86"     "Oct 2016" "http://Oct2016.archive.ensembl.org"
 [6,] "Ensembl 85"     "Jul 2016" "http://Jul2016.archive.ensembl.org"
 [7,] "Ensembl 84"     "Mar 2016" "http://Mar2016.archive.ensembl.org"
 [8,] "Ensembl 83"     "Dec 2015" "http://Dec2015.archive.ensembl.org"
 [9,] "Ensembl 82"     "Sep 2015" "http://Sep2015.archive.ensembl.org"
[10,] "Ensembl 81"     "Jul 2015" "http://Jul2015.archive.ensembl.org"
[11,] "Ensembl 80"     "May 2015" "http://May2015.archive.ensembl.org"
[12,] "Ensembl 79"     "Mar 2015" "http://Mar2015.archive.ensembl.org"
[13,] "Ensembl 78"     "Dec 2014" "http://Dec2014.archive.ensembl.org"
[14,] "Ensembl 77"     "Oct 2014" "http://Oct2014.archive.ensembl.org"
[15,] "Ensembl 76"     "Aug 2014" "http://Aug2014.archive.ensembl.org"
[16,] "Ensembl 75"     "Feb 2014" "http://Feb2014.archive.ensembl.org"
[17,] "Ensembl 74"     "Dec 2013" "http://Dec2013.archive.ensembl.org"
[18,] "Ensembl 67"     "May 2012" "http://May2012.archive.ensembl.org"
[19,] "Ensembl 54"     "May 2009" "http://May2009.archive.ensembl.org"