[Annotation] Association errors
Mike Cherry
cherry at stanford.edu
Wed Jun 18 09:29:54 PDT 2008
I'm not sure this is the problem. Checking script just looks to see
the abbr is in the xfer file. The loading script will load them all.
It must be a problem that the amigo software is to restrictive. To me
RefSeq is not really a valid prefix, its NCBI.
Cheers, Mike
(from my iPhone)
On Jun 12, 2008, at 4:36 AM, Valerie Wood <val at sanger.ac.uk> wrote:
> pombe fixed
>
> Doesnt Mikes script check the format of the dbxrefs and check they
> have valid prefixes? I though it did. If not can it be added so we
> capture most of these at submission?
>
> Val
>
>
> Amelia Ireland wrote:
>> Hi all,
>>
>> I have been looking at database refs in the GO database and have
>> found a
>> few dodgy xrefs which need fixing. The errors mean that the links
>> from the
>> associations don't work correctly, so it'd be good to get them fixed.
>>
>> I've attached a file with the dodgy refs in it. It's tab delimited
>> so you
>> can open it in excel for your viewing pleasure (or displeasure).
>>
>> Cheers!
>> Amelia
>>
>>
>> ---
>> ---------------------------------------------------------------------
>>
>> gpxref evcode reference with column assigned_by
>>
>> REFERENCE
>> Not sure what TIGR:autoGO is supposed to mean!
>> GeneDB_Tbrucei:Tb10.6k15.3030 ISS TIGR:autoGO
>> UniProt:Q9Y4W6 GeneDB_Tbrucei
>>
>> WITH COLUMN
>> "Should be Interpro, not IUPHAR"
>> dictyBase:DDB0266650 ISS dictyBase_REF:10155
>> IUPHAR:IPR000271 dictyBase
>>
>> Should these be MGI?
>> GeneDB_Spombe:SPBC28E12.06c ISS PMID:17072883 MGD:1096875
>> GeneDB_Spombe
>> SGD:S000005096 ISS SGD_REF:S000125856 MGD:99665 SGD
>> SGD:S000003563 ISS SGD_REF:S000045069 MGD:98181 SGD
>> SGD:S000003241 ISS SGD_REF:S000043550 MGD:74623 SGD
>>
>> Remove the surplus MGD
>> dictyBase:DDB0230136 ISS dictyBase_REF:10155 MGD:MGI:
>> 1914510 dictyBase
>>
>> The MGI IDs for these need to be found
>> SGD:S000005853 ISS SGD_REF:S000043587 MGD:Myo5a SGD
>> SGD:S000000027 ISS SGD_REF:S000043587 MGD:Myo5a SGD
>> SGD:S000003664 ISS SGD_REF:S000046190 MGD:Map2k1 SGD
>>
>> Should be lowercase
>> MGI:MGI:1915651 ISS MGI:MGI:3576961 REFSEQ:NM_138387.2
>> MGI
>>
>> "I think these are supposed to be SGD, not SMD"
>> dictyBase:DDB0230088 ISS dictyBase_REF:10155
>> SMD:S000005654 dictyBase
>> dictyBase:DDB0231094 ISS dictyBase_REF:10155
>> SMD:S000003080 dictyBase
>>
>> TIGR: should these be TIGRFAMS refs instead?
>> TAIR:gene:2050224 RCA TAIR:Communication:501714663
>> TIGR:TIGR00797 TIGR
>> TAIR:gene:2050224 RCA TAIR:Communication:501714663
>> TIGR:TIGR00797 TIGR
>> TIGR_CMR:BA_0175 ISS PMID:12721629 TIGR:TIGR00363 TIGR
>> TIGR_CMR:BA_1378 ISS PMID:12721629 TIGR:TIGR01439 TIGR
>> TIGR_CMR:BA_1378 ISS PMID:12721629 TIGR:TIGR01439 TIGR
>> TIGR_CMR:BA_2818 ISS PMID:12721629 TIGR:TIGR01389 TIGR
>> TIGR_CMR:BA_2818 ISS PMID:12721629 TIGR:TIGR01389 TIGR
>> TIGR_CMR:BA_2818 ISS PMID:12721629 TIGR:TIGR01389 TIGR
>> TIGR_CMR:BA_2818 ISS PMID:12721629 TIGR:TIGR01389 TIGR
>> TIGR_CMR:BA_2818 ISS PMID:12721629 TIGR:TIGR01389 TIGR
>> TIGR_CMR:BA_3635 ISS PMID:12721629 TIGR:annotation TIGR
>> TIGR_CMR:BA_3769 ISS PMID:12721629 TIGR:TIGR01439 TIGR
>> TIGR_CMR:BA_3769 ISS PMID:12721629 TIGR:TIGR01439 TIGR
>> TIGR_CMR:BA_4076 ISS PMID:12721629 TIGR:TIGR01439 TIGR
>> TIGR_CMR:BA_4076 ISS PMID:12721629 TIGR:TIGR01439 TIGR
>> TIGR_CMR:BA_4140 ISS PMID:12721629 TIGR:TIGR00095 TIGR
>> TIGR_CMR:BA_4140 ISS PMID:12721629 TIGR:TIGR00095 TIGR
>> TIGR_CMR:BA_4713 ISS PMID:12721629 TIGR:TIGR00040 TIGR
>> TIGR_CMR:BA_4713 ISS PMID:12721629 TIGR:TIGR00040 TIGR
>> TIGR_CMR:LMOf2365_1146 ISS PMID:15115801 TIGR:TIGR00493
>> TIGR
>> TIGR_CMR:LMOf2365_1146 ISS PMID:15115801 TIGR:TIGR00493
>> TIGR
>> TIGR_CMR:LMOf2365_1146 ISS PMID:15115801 TIGR:TIGR00493
>> TIGR
>> TIGR_CMR:LMOf2365_1733 ISS PMID:15115801 TIGR:TIGR00500
>> TIGR
>> TIGR_CMR:LMOf2365_1733 ISS PMID:15115801 TIGR:TIGR00500
>> TIGR
>> TIGR_CMR:LMOf2365_1888 ISS PMID:15115801 TIGR:TIGR00401
>> TIGR
>> TIGR_CMR:LMOf2365_1888 ISS PMID:15115801 TIGR:TIGR00401
>> TIGR
>> TIGR_CMR:LMOf2365_2483 ISS PMID:15115801 TIGR:TIGR00963
>> TIGR
>> TIGR_CMR:LMOf2365_2483 ISS PMID:15115801 TIGR:TIGR00963
>> TIGR
>>
>> Change Flybase to FB:...
>> GeneDB_Spombe:SPCC550.14 ISS PMID:17072883
>> Flybase:FBgn0027835 GeneDB_Spombe
>> GeneDB_Spombe:SPAC26F1.02 ISS PMID:17072883
>> Flybase:FBgn0037737 GeneDB_Spombe
>>
>> These IDs are wrong - should be FB:FBgn0015477
>> WB:WB:WP:CE30344 ISS WB:WBPaper00004810 FLYBASE:CG8014-
>> PA WB
>> WB:WB:WP:CE30345 ISS WB:WBPaper00004810 FLYBASE:CG8014-
>> PA WB
>> ---
>> ---------------------------------------------------------------------
>>
>> _______________________________________________
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>> Annotation at geneontology.org
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>>
>
>
> --
> ---
> ---
> ---------------------------------------------------------------------
> Valerie Wood Tel: 01223 496909
> S. pombe Genome Project Fax: 01223 494919
> Wellcome Trust Sanger Institute email: val at sanger.ac.uk
> Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe
> Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe
>
>
>
> --
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