[ensembl-dev] perl API: how to avoid deprecated identifiers?

Fri Oct 17 20:05:50 BST 2014

Hgpdna guanina tymine cysine adine ribose mitiohandrija skqi
On Oct 17, 2014 9:24 PM, "Michael Yourshaw" <myourshaw at g.ucla.edu> wrote:

> At least with regard to mouse, GeneAdapter ->fetch_all() returns some
> genes with deprecated identifiers. For example, the mouse Acer2 gene has
> both ENSMUSG00000038007 and ENSMUSG00000091609.
>
> Ensembl gene ENSMUSG00000091609 is no longer in the database but it has
> been mapped to 1 deprecated identifier . Not a Primary Assembly Gene.
>
> Both the current and the deprecated genes have an is_current value of 1.
>
> Although I have not checked them all manually, there appear to be 85 mouse
> genes with one or two such deprecated stable ids.
>
> Is there a perl API way to fetch all genes and get only non-deprecated
> stable ids, or a method to detect and avoid them after fetching?
>
> List of multiple Ensembl mouse stable ids associated with a single MGI
> gene symbol.
>
> ENSMUSG00000094789 1700040F15Rik
> ENSMUSG00000095141 1700040F15Rik
> ENSMUSG00000054165 4922502B01Rik
> ENSMUSG00000057387 4922502B01Rik
> ENSMUSG00000050883 4930523C07Rik
> ENSMUSG00000090394 4930523C07Rik
> ENSMUSG00000032985 5730522E02Rik
> ENSMUSG00000073101 5730522E02Rik
> ENSMUSG00000057715 A830018L16Rik
> ENSMUSG00000095719 A830018L16Rik
> ENSMUSG00000038007 Acer2
> ENSMUSG00000091609 Acer2
> ENSMUSG00000041748 Ackr4
> ENSMUSG00000079355 Ackr4
> ENSMUSG00000000562 Adora3
> ENSMUSG00000074344 Adora3
> ENSMUSG00000047383 Als2cr11
> ENSMUSG00000072295 Als2cr11
> ENSMUSG00000031731 Ap1g1
> ENSMUSG00000096262 Ap1g1
> ENSMUSG00000052414 Atf7
> ENSMUSG00000071584 Atf7
> ENSMUSG00000030213 Atf7ip
> ENSMUSG00000053935 Atf7ip
> ENSMUSG00000055936 AU015836
> ENSMUSG00000081044 AU015836
> ENSMUSG00000029673 Auts2
> ENSMUSG00000098133 Auts2
> ENSMUSG00000036948 BC037034
> ENSMUSG00000091964 BC037034
> ENSMUSG00000079537 C030048H21Rik
> ENSMUSG00000090340 C030048H21Rik
> ENSMUSG00000094121 Ccl21c
> ENSMUSG00000096271 Ccl21c
> ENSMUSG00000096873 Ccl21c
> ENSMUSG00000023235 Ccl25
> ENSMUSG00000055951 Ccl25
> ENSMUSG00000026361 Cdc73
> ENSMUSG00000078284 Cdc73
> ENSMUSG00000026616 Cr2
> ENSMUSG00000094924 Cr2
> ENSMUSG00000022150 Dab2
> ENSMUSG00000079102 Dab2
> ENSMUSG00000048915 Efna5
> ENSMUSG00000090425 Efna5
> ENSMUSG00000048910 Fam220a
> ENSMUSG00000083012 Fam220a
> ENSMUSG00000069808 Fam57a
> ENSMUSG00000096115 Fam57a
> ENSMUSG00000051379 Flrt3
> ENSMUSG00000079021 Flrt3
> ENSMUSG00000070733 Fryl
> ENSMUSG00000090491 Fryl
> ENSMUSG00000061864 Galntl6
> ENSMUSG00000096914 Galntl6
> ENSMUSG00000092021 Gbp11
> ENSMUSG00000098049 Gbp11
> ENSMUSG00000052942 Glis3
> ENSMUSG00000091294 Glis3
> ENSMUSG00000095611 Gm10597
> ENSMUSG00000096892 Gm10597
> ENSMUSG00000091594 Gm17067
> ENSMUSG00000095144 Gm17067
> ENSMUSG00000072917 Gm1965
> ENSMUSG00000090254 Gm1965
> ENSMUSG00000074812 Gm355
> ENSMUSG00000096886 Gm355
> ENSMUSG00000090897 Gm5494
> ENSMUSG00000092043 Gm5494
> ENSMUSG00000091779 Gm6763
> ENSMUSG00000097427 Gm6763
> ENSMUSG00000094474 Gm7792
> ENSMUSG00000094722 Gm7792
> ENSMUSG00000095523 Gm7792
> ENSMUSG00000050347 Gm9844
> ENSMUSG00000091955 Gm9844
> ENSMUSG00000034243 Golgb1
> ENSMUSG00000078096 Golgb1
> ENSMUSG00000041907 Gpr45
> ENSMUSG00000096364 Gpr45
> ENSMUSG00000026313 Hdac4
> ENSMUSG00000073617 Hdac4
> ENSMUSG00000028634 Hivep3
> ENSMUSG00000078582 Hivep3
> ENSMUSG00000051396 Hspa14
> ENSMUSG00000079615 Hspa14
> ENSMUSG00000090498 Kcnb2
> ENSMUSG00000092083 Kcnb2
> ENSMUSG00000025762 Larp1b
> ENSMUSG00000037814 Larp1b
> ENSMUSG00000004613 Lim2
> ENSMUSG00000093639 Lim2
> ENSMUSG00000097437 Lim2
> ENSMUSG00000040003 Magi2
> ENSMUSG00000067798 Magi2
> ENSMUSG00000073174 Magi2
> ENSMUSG00000014426 Map3k4
> ENSMUSG00000079716 Map3k4
> ENSMUSG00000034912 Mdga2
> ENSMUSG00000079510 Mdga2
> ENSMUSG00000003178 Mical3
> ENSMUSG00000051586 Mical3
> ENSMUSG00000042570 Mier2
> ENSMUSG00000091854 Mier2
> ENSMUSG00000031200 Mtcp1
> ENSMUSG00000090110 Mtcp1
> ENSMUSG00000025515 Muc2
> ENSMUSG00000094393 Muc2
> ENSMUSG00000095400 Muc2
> ENSMUSG00000009418 Nav1
> ENSMUSG00000090399 Nav1
> ENSMUSG00000069670 Nkain2
> ENSMUSG00000069671 Nkain2
> ENSMUSG00000028706 Nsun4
> ENSMUSG00000090697 Nsun4
> ENSMUSG00000050836 Ntng1
> ENSMUSG00000059857 Ntng1
> ENSMUSG00000023826 Park2
> ENSMUSG00000073465 Park2
> ENSMUSG00000095795 Park2
> ENSMUSG00000021699 Pde4d
> ENSMUSG00000074661 Pde4d
> ENSMUSG00000032203 Pigb
> ENSMUSG00000079469 Pigb
> ENSMUSG00000030228 Pik3c2g
> ENSMUSG00000096062 Pik3c2g
> ENSMUSG00000044407 Qk
> ENSMUSG00000062078 Qk
> ENSMUSG00000039717 Ralyl
> ENSMUSG00000096025 Ralyl
> ENSMUSG00000030259 Rassf8
> ENSMUSG00000045110 Rassf8
> ENSMUSG00000045365 Rbm15b
> ENSMUSG00000074102 Rbm15b
> ENSMUSG00000023156 Rpp14
> ENSMUSG00000094130 Rpp14
> ENSMUSG00000092572 Serpinb10
> ENSMUSG00000098034 Serpinb10
> ENSMUSG00000021852 Slc35f4
> ENSMUSG00000079246 Slc35f4
> ENSMUSG00000053877 Srcap
> ENSMUSG00000090663 Srcap
> ENSMUSG00000027751 Supt20
> ENSMUSG00000095832 Supt20
> ENSMUSG00000019769 Syne1
> ENSMUSG00000096054 Syne1
> ENSMUSG00000052293 Taf9
> ENSMUSG00000078941 Taf9
> ENSMUSG00000079733 Tmem181b-ps
> ENSMUSG00000096780 Tmem181b-ps
> ENSMUSG00000041353 Tmem29
> ENSMUSG00000090483 Tmem29
> ENSMUSG00000062210 Tnfaip8
> ENSMUSG00000094040 Tnfaip8
> ENSMUSG00000010751 Tnfrsf22
> ENSMUSG00000090852 Tnfrsf22
> ENSMUSG00000048546 Tob2
> ENSMUSG00000078960 Tob2
> ENSMUSG00000021711 Trappc13
> ENSMUSG00000078936 Trappc13
> ENSMUSG00000052749 Trim30b
> ENSMUSG00000091576 Trim30b
> ENSMUSG00000026558 Uck2
> ENSMUSG00000053664 Uck2
> ENSMUSG00000020220 Vps13d
> ENSMUSG00000073719 Vps13d
> ENSMUSG00000026115 Vwa3b
> ENSMUSG00000050122 Vwa3b
> ENSMUSG00000039951 Wfdc3
> ENSMUSG00000076434 Wfdc3
> ENSMUSG00000022708 Zbtb20
> ENSMUSG00000036279 Zbtb20
> ENSMUSG00000046556 Zfp319
> ENSMUSG00000074140 Zfp319
> ENSMUSG00000074608 Zfp850
> ENSMUSG00000096916 Zfp850
>
>
> ॐ
>
> Michael Yourshaw, PhD
> UCLA Geffen School of Medicine
> Department of Pediatrics
> 695 Charles E Young Drive S
> Gonda 5554
>
> Los Angeles CA 90095-8348 USA
>
> myourshaw at ucla.edu
>
> 970.691.8299
>
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