Taxon-GO Checks and Commentary - Part 7

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Comments from WormBase, Ranjana Kishore and Kimberly Van Auken

Taxon inconsistent terms coming from electronic annotation through the InterPro2GO pipeline

GO:0042601 endospore-forming forespore 
GO:0009772 photosynthetic electron transport in photosystem II 
GO:0019684 photosynthesis, light reaction 					
GO:0030077 plasma membrane light-harvesting complex 		
GO:0015979 photosynthesis 		
GO:0015995 chlorophyll biosynthetic process
GO:0008316 structural constituent of vitelline membrane 		
GO:0016032 viral reproduction

For the above terms, should we communicate with InterPro2GO curators, that these mappings do not work for all species, or do we have to block these on our end?

Taxon inconsistent terms used in our annotation

GO:0001703 gastrulation with mouth forming first	

It is generally agreed that C. elegans belongs to the Protostomia, so annotations to this term should remain. Kimberly feels that the term itself might need some work.

Possible changes:

With respect to possible changes in the gastrulation branch of the ontology, one possibility would be to remove the protostome (GO:0001703, gastulation with mouth forming first) and deuterostome (GO:0001702, mouth forming second) terms and just have the current children of those terms be children of the more general gastrulation term, removing the reference to mouth forming first or second in those children.

There is evidence now that there are mechanistic similarities between gastrulation in worms, flies, and vertebrates, so perhaps it'd be more helpful to users to be able to find gastrulation annotations together, where applicable, rather than under specific protostome/deuterostome terms.

A recent review that touches on this is:

Dev Dyn. 2009 Apr;238(4):789-96

Polarity and cell fate specification in the control of Caenorhabditis elegans gastrulation.

Rohrschneider MR, Nance J.

Developmental Genetics Program, Skirball Institute of Biomolecular Medicine and Helen and Martin Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, New York 10016, USA.

Gastrulation is a time during development when cells destined to produce internal tissues and organs move from the surface of the embryo into the interior. It is critical that the cell movements of gastrulation be precisely controlled, and coordinated with cell specification, in order for the embryo to develop normally. Caenorhabditis elegans gastrulation is relatively simple, can be observed easily in the transparent embryo, and can be manipulated genetically to uncover important regulatory mechanisms. Many of these cellular and molecular mechanisms, including cell shape, cytoskeletal, and cell cycle changes, appear to be conserved from flies to vertebrates. Here we review gastrulation in C. elegans, with an emphasis on recent data linking contact-induced cell polarity, PAR proteins, and cell fate specification to gastrulation control. Copyright 2009 Wiley-Liss, Inc.

PMID: 19253398 [PubMed - indexed for MEDLINE]

GO:0001542 ovulation from ovarian follicle

We agree that the assignment of this term is inappropriate for C.elegans. It has been removed in our manual annotation database and replaced with the term 'ovulation'. This change will be reflected in our next upload to the GO consortium.


Photosynthesis

I have written to ask about these flagged errors:


GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"
 :: WB	WBGene00003154	mcm-2		GO:0015979	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"
 :: WB	WBGene00003155	mcm-3		GO:0015979	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" 
:: WB	WBGene00003156	mcm-4		GO:0015979	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" 
:: WB	WBGene00003159	mcm-7		GO:0015979	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" 
:: WB	WBGene00004503	rpt-3		GO:0015979	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" 
:: WB	WBGene00004505	rpt-5		GO:0015979	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"
 :: WB	WBGene00007352	cdc-48.1		GO:0015979	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" 
:: WB	WBGene00008053	cdc-48.2		GO:0015979	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"
 :: WB	WBGene00010842	ymel-1		GO:0015979	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" 
:: WB	WBGene00003154	mcm-2		GO:0015995	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" 
:: WB	WBGene00003155	mcm-3		GO:0015995	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" 
:: WB	WBGene00003156	mcm-4		GO:0015995	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa"
 :: WB	WBGene00003159	mcm-7		GO:0015995	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" 
:: WB	WBGene00004503	rpt-3		GO:0015995	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" 
:: WB	WBGene00004505	rpt-5		GO:0015995	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" 
:: WB	WBGene00007352	cdc-48.1		GO:0015995	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa"
 :: WB	WBGene00008053	cdc-48.2		GO:0015995	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa"
 :: WB	WBGene00010842	ymel-1		GO:0015995	PMID:12520011|PMID:12654719	IEA	INTERPRO:IPR000523
	P			gene	NCBITaxon:6239	20091126	WB		

Ranjana wrote back to say that these should be sent on to Emily at GOA as it is the InterPro2GO mapping that needs modified.