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

Michael Yourshaw myourshaw at g.ucla.edu
Mon Nov 3 02:09:09 GMT 2014

Apologies for sending this again, but the only ‘reply’ I got was a strange email from 'jv tra jurvin at gmail.com ‘ consisting solely of the text 'Hgpdna guanina tymine cysine adine ribose mitiohandrija skqi’. Looked like spam, or an accident.

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


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 <mailto:myourshaw at ucla.edu>

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