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

Mon Nov 3 16:51:22 GMT 2014

Hi Michael,

Your example gene, ENSMUSG00000091609, is not deprecated in release 75
http://e75.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000091609;r=4:86930691-86934820;t=ENSMUST00000164590

If you are using the API version 75, you will need to check those 
results on the archive website, not the live site.

The fetch_all method will return all the current identifiers, as of the 
release specified by your version of the API.
This means you might get identifiers which have been deprecated in later 
releases.

Hope that helps,
Magali

On 03/11/2014 16:45, Michael Yourshaw wrote:
> Thanks, Andy.
>
> I was using version 75 when I did the check. For now we are stuck on 
> GRCh37 for humans, so we have been keeping everything at v75.
>
> The mouse data was created at another lab, and I'm not sure what 
> version they used.
>
>
> ?
>
> 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>
>
> 970.691.8299
>
> This message (including any attachments) is intended only for the use 
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>
>> On 3Nov, 2014, at 04:32, Andy Yates <ayates at ebi.ac.uk 
>> <mailto:ayates at ebi.ac.uk>> wrote:
>>
>> Hi there,
>>
>> Sorry that your email got lost. Anyway we're on it now. With respect 
>> to your 1st problem I've been unable to replicate the issue. I took 
>> your list of IDs, converted it into an IN statement and queried the 
>> 77 mouse core database and was unable to retrieve the whole list. I 
>> went from 176 identifiers to 115 identifiers. What version of the API 
>> are you using & which database are you connecting to?
>>
>> Even after that though there are 25 MGI symbols attached to multiple 
>> Ensembl identifiers from your list. We're having a look into some of 
>> those cases now and should be back in touch soon.
>>
>> Andy
>>
>> ------------
>> Andrew Yates - Ensembl Support Coordinator
>> European Molecular Biology Laboratory
>> European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge
>> CB10 1SD, United Kingdom
>> Tel: +44-(0)1223-492538
>> Fax: +44-(0)1223-494468
>> Skype: andrewyatz
>> http://www.ensembl.org/
>>
>> On 17 Oct 2014, at 19:23, 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.
>>>
>>> ENSMUSG000000947891700040F15Rik
>>> ENSMUSG000000951411700040F15Rik
>>> ENSMUSG000000541654922502B01Rik
>>> ENSMUSG000000573874922502B01Rik
>>> ENSMUSG000000508834930523C07Rik
>>> ENSMUSG000000903944930523C07Rik
>>> ENSMUSG000000329855730522E02Rik
>>> ENSMUSG000000731015730522E02Rik
>>> ENSMUSG00000057715A830018L16Rik
>>> ENSMUSG00000095719A830018L16Rik
>>> ENSMUSG00000038007Acer2
>>> ENSMUSG00000091609Acer2
>>> ENSMUSG00000041748Ackr4
>>> ENSMUSG00000079355Ackr4
>>> ENSMUSG00000000562Adora3
>>> ENSMUSG00000074344Adora3
>>> ENSMUSG00000047383Als2cr11
>>> ENSMUSG00000072295Als2cr11
>>> ENSMUSG00000031731Ap1g1
>>> ENSMUSG00000096262Ap1g1
>>> ENSMUSG00000052414Atf7
>>> ENSMUSG00000071584Atf7
>>> ENSMUSG00000030213Atf7ip
>>> ENSMUSG00000053935Atf7ip
>>> ENSMUSG00000055936AU015836
>>> ENSMUSG00000081044AU015836
>>> ENSMUSG00000029673Auts2
>>> ENSMUSG00000098133Auts2
>>> ENSMUSG00000036948BC037034
>>> ENSMUSG00000091964BC037034
>>> ENSMUSG00000079537C030048H21Rik
>>> ENSMUSG00000090340C030048H21Rik
>>> ENSMUSG00000094121Ccl21c
>>> ENSMUSG00000096271Ccl21c
>>> ENSMUSG00000096873Ccl21c
>>> ENSMUSG00000023235Ccl25
>>> ENSMUSG00000055951Ccl25
>>> ENSMUSG00000026361Cdc73
>>> ENSMUSG00000078284Cdc73
>>> ENSMUSG00000026616Cr2
>>> ENSMUSG00000094924Cr2
>>> ENSMUSG00000022150Dab2
>>> ENSMUSG00000079102Dab2
>>> ENSMUSG00000048915Efna5
>>> ENSMUSG00000090425Efna5
>>> ENSMUSG00000048910Fam220a
>>> ENSMUSG00000083012Fam220a
>>> ENSMUSG00000069808Fam57a
>>> ENSMUSG00000096115Fam57a
>>> ENSMUSG00000051379Flrt3
>>> ENSMUSG00000079021Flrt3
>>> ENSMUSG00000070733Fryl
>>> ENSMUSG00000090491Fryl
>>> ENSMUSG00000061864Galntl6
>>> ENSMUSG00000096914Galntl6
>>> ENSMUSG00000092021Gbp11
>>> ENSMUSG00000098049Gbp11
>>> ENSMUSG00000052942Glis3
>>> ENSMUSG00000091294Glis3
>>> ENSMUSG00000095611Gm10597
>>> ENSMUSG00000096892Gm10597
>>> ENSMUSG00000091594Gm17067
>>> ENSMUSG00000095144Gm17067
>>> ENSMUSG00000072917Gm1965
>>> ENSMUSG00000090254Gm1965
>>> ENSMUSG00000074812Gm355
>>> ENSMUSG00000096886Gm355
>>> ENSMUSG00000090897Gm5494
>>> ENSMUSG00000092043Gm5494
>>> ENSMUSG00000091779Gm6763
>>> ENSMUSG00000097427Gm6763
>>> ENSMUSG00000094474Gm7792
>>> ENSMUSG00000094722Gm7792
>>> ENSMUSG00000095523Gm7792
>>> ENSMUSG00000050347Gm9844
>>> ENSMUSG00000091955Gm9844
>>> ENSMUSG00000034243Golgb1
>>> ENSMUSG00000078096Golgb1
>>> ENSMUSG00000041907Gpr45
>>> ENSMUSG00000096364Gpr45
>>> ENSMUSG00000026313Hdac4
>>> ENSMUSG00000073617Hdac4
>>> ENSMUSG00000028634Hivep3
>>> ENSMUSG00000078582Hivep3
>>> ENSMUSG00000051396Hspa14
>>> ENSMUSG00000079615Hspa14
>>> ENSMUSG00000090498Kcnb2
>>> ENSMUSG00000092083Kcnb2
>>> ENSMUSG00000025762Larp1b
>>> ENSMUSG00000037814Larp1b
>>> ENSMUSG00000004613Lim2
>>> ENSMUSG00000093639Lim2
>>> ENSMUSG00000097437Lim2
>>> ENSMUSG00000040003Magi2
>>> ENSMUSG00000067798Magi2
>>> ENSMUSG00000073174Magi2
>>> ENSMUSG00000014426Map3k4
>>> ENSMUSG00000079716Map3k4
>>> ENSMUSG00000034912Mdga2
>>> ENSMUSG00000079510Mdga2
>>> ENSMUSG00000003178Mical3
>>> ENSMUSG00000051586Mical3
>>> ENSMUSG00000042570Mier2
>>> ENSMUSG00000091854Mier2
>>> ENSMUSG00000031200Mtcp1
>>> ENSMUSG00000090110Mtcp1
>>> ENSMUSG00000025515Muc2
>>> ENSMUSG00000094393Muc2
>>> ENSMUSG00000095400Muc2
>>> ENSMUSG00000009418Nav1
>>> ENSMUSG00000090399Nav1
>>> ENSMUSG00000069670Nkain2
>>> ENSMUSG00000069671Nkain2
>>> ENSMUSG00000028706Nsun4
>>> ENSMUSG00000090697Nsun4
>>> ENSMUSG00000050836Ntng1
>>> ENSMUSG00000059857Ntng1
>>> ENSMUSG00000023826Park2
>>> ENSMUSG00000073465Park2
>>> ENSMUSG00000095795Park2
>>> ENSMUSG00000021699Pde4d
>>> ENSMUSG00000074661Pde4d
>>> ENSMUSG00000032203Pigb
>>> ENSMUSG00000079469Pigb
>>> ENSMUSG00000030228Pik3c2g
>>> ENSMUSG00000096062Pik3c2g
>>> ENSMUSG00000044407Qk
>>> ENSMUSG00000062078Qk
>>> ENSMUSG00000039717Ralyl
>>> ENSMUSG00000096025Ralyl
>>> ENSMUSG00000030259Rassf8
>>> ENSMUSG00000045110Rassf8
>>> ENSMUSG00000045365Rbm15b
>>> ENSMUSG00000074102Rbm15b
>>> ENSMUSG00000023156Rpp14
>>> ENSMUSG00000094130Rpp14
>>> ENSMUSG00000092572Serpinb10
>>> ENSMUSG00000098034Serpinb10
>>> ENSMUSG00000021852Slc35f4
>>> ENSMUSG00000079246Slc35f4
>>> ENSMUSG00000053877Srcap
>>> ENSMUSG00000090663Srcap
>>> ENSMUSG00000027751Supt20
>>> ENSMUSG00000095832Supt20
>>> ENSMUSG00000019769Syne1
>>> ENSMUSG00000096054Syne1
>>> ENSMUSG00000052293Taf9
>>> ENSMUSG00000078941Taf9
>>> ENSMUSG00000079733Tmem181b-ps
>>> ENSMUSG00000096780Tmem181b-ps
>>> ENSMUSG00000041353Tmem29
>>> ENSMUSG00000090483Tmem29
>>> ENSMUSG00000062210Tnfaip8
>>> ENSMUSG00000094040Tnfaip8
>>> ENSMUSG00000010751Tnfrsf22
>>> ENSMUSG00000090852Tnfrsf22
>>> ENSMUSG00000048546Tob2
>>> ENSMUSG00000078960Tob2
>>> ENSMUSG00000021711Trappc13
>>> ENSMUSG00000078936Trappc13
>>> ENSMUSG00000052749Trim30b
>>> ENSMUSG00000091576Trim30b
>>> ENSMUSG00000026558Uck2
>>> ENSMUSG00000053664Uck2
>>> ENSMUSG00000020220Vps13d
>>> ENSMUSG00000073719Vps13d
>>> ENSMUSG00000026115Vwa3b
>>> ENSMUSG00000050122Vwa3b
>>> ENSMUSG00000039951Wfdc3
>>> ENSMUSG00000076434Wfdc3
>>> ENSMUSG00000022708Zbtb20
>>> ENSMUSG00000036279Zbtb20
>>> ENSMUSG00000046556Zfp319
>>> ENSMUSG00000074140Zfp319
>>> ENSMUSG00000074608Zfp850
>>> ENSMUSG00000096916Zfp850
>>>
>>>
>>> ?
>>>
>>>
>>> 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
>>>
>>> This message (including any attachments) is intended only for the 
>>> use of the addressee(s) and may contain information that is 
>>> PRIVILEGED and CONFIDENTIAL, and/or may constitute ATTORNEY WORK 
>>> PRODUCT. If you are not an intended recipient, you are hereby 
>>> notified that any dissemination of this communication is strictly 
>>> prohibited. If you have received this message in error, please do 
>>> not read, copy, or forward this message or any attachments. Please 
>>> permanently delete all copies of the message and any attachments and 
>>> notify the sender immediately by sending an email to 
>>> myourshaw at yourshaw.org. Thank you. As part of our commitment to the 
>>> environment, this message was manufactured with 100% recycled electrons.
>>>
>>>
>>>
>>>
>>>
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