Question: Converting between Ensembl Versions
0
gravatar for jwhidd
16 months ago by
jwhidd0
jwhidd0 wrote:

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
biomart ensembl • 730 views
ADD COMMENTlink modified 16 months ago by Mike Smith950 • written 16 months ago by jwhidd0
> 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
ADD REPLYlink written 16 months ago by cpad011210k
3
gravatar for Emily_Ensembl
16 months ago by
Emily_Ensembl16k
EMBL-EBI
Emily_Ensembl16k wrote:

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

ADD COMMENTlink written 16 months ago by Emily_Ensembl16k
2
gravatar for Mike Smith
16 months ago by
Mike Smith950
EMBL Heidelberg / de.NBI
Mike Smith950 wrote:

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.

ADD COMMENTlink written 16 months ago by Mike Smith950

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"
ADD REPLYlink written 16 months ago by Mike Smith950
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