how to convert a list of MGI to gene names ?

Question

[Bioinfo]

Hello,

Anyone knows how to convert a bunch of MGI to gene names possibly over 25000 , as an example I give a short list here one way is to go here http://www.informatics.jax.org/genes.shtml and one by one search for it but it will take forever!

0610010B08Rik
0610010F05Rik
0610010K14Rik
0610010O12Rik
0610011F06Rik
0610011L14Rik
0610012G03Rik
0610012H03Rik
0610030E20Rik
0610031J06Rik
0610031O16Rik
0610037L13Rik
0610037P05Rik
0610038B21Rik
0610038L08Rik
0610039K10Rik

Answer 1

[GenoMax]

You can download relevant file from the MGI link you posted above to parse locally

$ more id
0610010B08Rik
0610010F05Rik
0610010K14Rik
0610010O12Rik
0610011F06Rik
0610011L14Rik
0610012G03Rik

$ grep -wf id MRK_List1.rpt
NULL    2          N/A              0610010B08Rik   W   withdrawn, = Gm2026 Gene
NULL    11    14.33             0610010F05Rik   W   withdrawn, = Sanbr  Gene
MGI:1915609 11    42.99 70126032    70128740    -   0610010K14Rik   O   RIKEN cDNA 0610010K14 gene  Gene    protein coding gene
NULL    18         N/A              0610010O12Rik   W   withdrawn, = Cystm1 Gene
NULL    17         N/A              0610011F06Rik   W   withdrawn, = Mettl26    Gene
NULL    2          N/A              0610011L14Rik   W   withdrawn, = Aar2   Gene
MGI:1913301 16    22.40 31765868    31767312    -   0610012G03Rik   O   RIKEN cDNA 0610012G03 gene  Gene    protein coding gene
NULL    2          N/A              0610012H03Rik   W   withdrawn, = Them7  Gene
MGI:1915614 6     32.27 72324300    72330131    +   0610030E20Rik   O   RIKEN cDNA 0610030E20 gene  Gene    protein coding gene
NULL    3          N/A              0610031J06Rik   W   withdrawn, = Glmp   Gene
MGI:1915619 3     syntenic  137916478   137945424   -   0610031O16Rik   O   RIKEN cDNA 0610031O16 gene  Gene    lncRNA gene

or do something like this. Using EntrezDirect:

$ for i in `cat id`; do printf ${i}"\t"; esearch -db gene -query ${i} | esummary | xtract -pattern DocumentSummary -element Name; done
0610010B08Rik   Gm2026
0610010B08Rik
0610010F05Rik   Sanbr
0610010K14Rik   Pou5f1
Nanog
Atxn1
0610010K14Rik
0610010K14Rik
0610010K14Rik
0610010O12Rik   Cystm1
0610011F06Rik   Mettl26
0610011L14Rik   Aar2
0610012G03Rik   0610012G03Rik
LOC556589
0610012G03Rik
0610012H03Rik   Them7
0610030E20Rik   0610030E20Rik
0610031J06Rik   Glmp
Glmp
0610031J06Rik
0610031O16Rik   0610031O16Rik
0610037L13Rik   Czib
0610037P05Rik   Cep20
0610038B21Rik   0610038B21Rik
0610038L08Rik   Tbc1d22bos
0610039K10Rik   0610039K10Rik

[Bioinfo]

@GenoMax YOU ROCK!!!!