[Annotation] Association errors

[Valerie Wood]

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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>   


-- 
---------------------------------------------------------------------------
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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