Taxon-GO Checks and Commentary - Part 2
From GO Public
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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.
