Taxon-GO Checks and Commentary - Part 2

From GO Wiki
Jump to: navigation, search

Comments from Susan Tweedie of FlyBase

spindle pole body separation

FlyBase	GO:0000073 "spindle pole body separation" only_in NCBITaxon:4751 "Fungi" :: FB	FBgn0011606	Klp3A		
GO:0000073	FB:FBrf0167864|FB:FBrf0188737|PMID:14528012	IMP		P			gene	   
NCBITaxon:7227	20060803	FlyBase

Looks like a dodgy annotation to me. The paper is about spindle pole separation not spindle pole body separation. I'll take it out and look into whether we need a new term.

12th Jaunary 2010

Susan has looked into this and says that all terms with 'spindle pole body' in the name should be restricted to Fungi, but that other things with the words spindle in them should not.

I have searched for all non-obsolete terms with 'spindle pole body' in the name that are not descendents of 'spindle pole body' and I have added only_in_taxon Fungi rules for all of them. The list is as follows:

GO:0032121	attachment of telomeres to spindle pole body
GO:0034631	microtubule anchoring at spindle pole body
GO:0051417	microtubule nucleation by spindle pole body
GO:0070057	prospore membrane spindle pole body attachment site
GO:0005816	spindle pole body
GO:0070631	spindle pole body localization
GO:0051300	spindle pole body organization

By inheritance this gives restriction to the full set:

GO:0031322	ascospore-type prospore-specific spindle pole body modification
GO:0032121	attachment of telomeres to spindle pole body
GO:0005823	central plaque of spindle pole body
GO:0070632	establishment of spindle pole body localization
GO:0055032	gamma-tubulin large complex, spindle pole body
GO:0000928	gamma-tubulin small complex, spindle pole body
GO:0005825	half bridge of spindle pole body
GO:0005822	inner plaque of spindle pole body
GO:0005821	intermediate layer of spindle pole body
GO:0034631	microtubule anchoring at spindle pole body
GO:0051417	microtubule nucleation by spindle pole body
GO:0010697	negative regulation of spindle pole body separation
GO:0005824	outer plaque of spindle pole body
GO:0010696	positive regulation of spindle pole body separation
GO:0070057	prospore membrane spindle pole body attachment site
GO:0010695	regulation of spindle pole body separation
GO:0005816	spindle pole body
GO:0030474	spindle pole body duplication
GO:0031046	spindle pole body duplication in cytoplasm
GO:0007103	spindle pole body duplication in nuclear envelope
GO:0070631	spindle pole body localization
GO:0051426	spindle pole body maturation
GO:0051300	spindle pole body organization
GO:0000073	spindle pole body separation

Domain matching problems

Summary: Susan has explained how the errors below came about. Some of their IEAs are made using InterPro mappings. For the errors below, the mappings are correct. However the sequence matching programme that reported that the InerPro domain had been found in the gene products was being over-optimistic. In fact, these gene products do not match the InterPro domains, and so transfer of the GO terms via the mappings was not warranted. Apparently it will take a while to change the pipeline and so it would be best for FlyBase if part of the taxon checking script protocol would be to delete these lines before the files are published.

FlyBase	GO:0009288 "bacterial-type flagellum" only_in NCBITaxon:2 "Bacteria" :: FB	FBgn0045038	Proct		
GO:0009288	FB:FBrf0174215	IEA	InterPro:IPR019776	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0009288 "bacterial-type flagellum" only_in NCBITaxon:2 "Bacteria" :: FB	FBgn0033027	TpnC4		
GO:0009288	FB:FBrf0174215	IEA	InterPro:IPR003299	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0009288 "bacterial-type flagellum" only_in NCBITaxon:2 "Bacteria" :: FB	FBgn0010423	TpnC47D		
GO:0009288	FB:FBrf0174215	IEA	InterPro:IPR003299	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0009288 "bacterial-type flagellum" only_in NCBITaxon:2 "Bacteria" :: FB	FBgn0010424	TpnC73F		
GO:0009288	FB:FBrf0174215	IEA	InterPro:IPR003299	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0009288 "bacterial-type flagellum" only_in NCBITaxon:2 "Bacteria" :: FB	FBgn0031692	TpnC25D		
GO:0009288	FB:FBrf0174215	IEA	InterPro:IPR003299	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0009288 "bacterial-type flagellum" only_in NCBITaxon:2 "Bacteria" :: FB	FBgn0005630	lola		
GO:0009288	FB:FBrf0174215	IEA	InterPro:IPR019776	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0019028 "viral capsid" only_in NCBITaxon:10239 "Viruses" :: FB	FBgn0029799	CG15772		
GO:0019028	FB:FBrf0174215	IEA	InterPro:IPR001337	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0019028 "viral capsid" only_in NCBITaxon:10239 "Viruses" :: FB	FBgn0029749	CG15786		
GO:0019028	FB:FBrf0174215	IEA	InterPro:IPR004302	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0019028 "viral capsid" only_in NCBITaxon:10239 "Viruses" :: FB	FBgn0032260	CG13144		
GO:0019028	FB:FBrf0174215	IEA	InterPro:IPR001337	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0019028 "viral capsid" only_in NCBITaxon:10239 "Viruses" :: FB	FBgn0038783	CG4367		
GO:0019028	FB:FBrf0174215	IEA	InterPro:IPR004302	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0019028 "viral capsid" only_in NCBITaxon:10239 "Viruses" :: FB	FBgn0038784	CG4362		
GO:0019028	FB:FBrf0174215	IEA	InterPro:IPR004302	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0019028 "viral capsid" only_in NCBITaxon:10239 "Viruses" :: FB	FBgn0058386	CG40386		
GO:0019028	FB:FBrf0174215	IEA	InterPro:IPR004302	C			gene	NCBITaxon:7227	20090719	
FlyBase

FlyBase	GO:0019684 "photosynthesis, light reaction" only_in ID:0000000 "Viridiplantae or Bacteria" :: FB	
FBgn0002576	lz		GO:0019684	FB:FBrf0174215	IEA	InterPro:IPR002362	P			
gene	NCBITaxon:7227	20090719	FlyBase

FlyBase	GO:0030077 "plasma membrane light-harvesting complex" only_in JD:0000004 "Prokaryota" :: FB	
FBgn0002576	lz		GO:0030077	FB:FBrf0174215	IEA	InterPro:IPR002362	C			
gene	NCBITaxon:7227	20090719	FlyBase

Actin cap

FlyBase	GO:0030478 "actin cap" only_in NCBITaxon:4751 "Fungi" :: FB	FBgn0023172	RhoGEF2		
GO:0030478	FB:FBrf0184065|PMID:15699213	IDA		C			gene	NCBITaxon:7227	20070523	
FlyBase

The def of this one isn't very specific... the fly protein is also found in a "Polarized accumulation of cytoskeletal proteins (including F-actin) and regulatory proteins in a cell." Probably not an equivalent structure but based in the current def I don't think this need to be restricted to fungi.

Fixed: This restriction has been removed.