[ensembl-dev] perl API: how to avoid deprecated identifiers?
Michael Yourshaw
myourshaw at g.ucla.edu
Fri Oct 17 19:23:55 BST 2014
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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