[Go] Alert: proposal to obsolete several molecular function terms that impacts existing annotation

[Tanya Berardini]

Dear GO,

The proposal has been made to obsolete

 thrombin activator activity ; GO:0030567
 angiotensin-converting enzyme inhibitor activity ; GO:0042031
 calpain inhibitor activity ; GO:0030161
 carboxypeptidase A inhibitor activity ; GO:0030415
 chymotrypsin inhibitor activity ; GO:0030569
 plasmin inhibitor activity ; GO:0030568
 proprotein convertase 2 activator activity ;GO:0016484
 protein kinase CK2 regulator activity ; GO:0008605
 trypsin inhibitor activity ; GO:0030304
 wide-spectrum protease inhibitor activity ; GO:0017114

These terms have been identified as part of the quality control work done as
part of the addition of regulates links within the molecular function
ontology and between molecular function and biological process terms. They
will be made obsolete because they represent regulators of obsolete
functions (e.g. GO:0030567, GO:0030415) or non-existent functions (e.g.
GO:0017114).

Annotations to these terms exist as listed below:

gene-associations/gene_association.cgd.gz
GO ID   IEA     non-IEA total
GO:0008605      0       4       4

gene-associations/gene_association.dictyBase.gz
GO ID   IEA     non-IEA total
GO:0008605      0       1       1

gene-associations/gene_association.fb.gz
GO ID   IEA     non-IEA total
GO:0008605      2       35      37
GO:0016484      0       1       1

gene-associations/gene_association.GeneDB_Lmajor.gz
GO ID   IEA     non-IEA total
GO:0008605      1       0       1

gene-associations/gene_association.GeneDB_Pfalciparum.gz
GO ID   IEA     non-IEA total

gene-associations/gene_association.GeneDB_Spombe.gz
GO ID   IEA     non-IEA total
GO:0008605      0       2       2

gene_association.goa_chicken.gz
GO ID   IEA     non-IEA total
GO:0008605      2       0       2
GO:0030161      2       0       2

gene_association.goa_cow.gz
GO ID   IEA     non-IEA total
GO:0008605      2       0       2
GO:0030161      8       0       8
GO:0030304      0       1       1
GO:0030568      0       1       1
GO:0030569      0       1       1

gene_association.goa_human.gz
GO ID   IEA     non-IEA total
GO:0008605      0       3       3
GO:0030161      1       0       1
GO:0030304      0       3       3
GO:0030568      0       1       1
GO:0030569      0       1       1

gene_association.goa_uniprot.gz
GO ID   IEA     non-IEA total
GO:0008605      814     0       814
GO:0030161      33      1       34
GO:0030304      0       14      14
GO:0030567      18      0       18
GO:0030568      0       5       5
GO:0030569      0       6       6
GO:0042031      0       2       2

gene_association.mgi.gz
GO ID   IEA     non-IEA total
GO:0008605      1       0       1
GO:0030161      0       1       1
GO:0030304      0       3       3
GO:0030569      0       1       1

gene_association.rgd.gz
GO ID   IEA     non-IEA total
GO:0008605      1       2       3
GO:0030161      1       2       3
GO:0030304      0       4       4
GO:0030568      0       1       1

gene-associations/gene_association.sgd.gz
GO ID   IEA     non-IEA total
GO:0008605      2       4       6

go/gene-associations/gene_association.tair.gz
GO ID   IEA     non-IEA total
GO:0008605      0       7       7

go/gene-associations/gene_association.wb.gz
GO ID   IEA     non-IEA total
GO:0008605      3       0       3


gene_association.zfin.gz
GO ID   IEA     non-IEA total
GO:0008605      3       1       4
GO:0030161      1       1       2

Annotations should be transferred to a parent term or to a biological
process term, as will be indicated for each term in consider or replaced_by
tags.

GO:0030304 and GO:0030567 are the prokaryote subset; none of the other terms
are in subsets or slims maintained in the GO OBO file.

Three terms are used in external mappings:

GO:0030161
interpro2go:InterPro:IPR001259 Proteinase inhibitor I27, calpastatin >
GO:calpain inhibitor activity ; GO:0030161
pfam2go:Pfam:PF00748 Calpain_inhib > GO:calpain inhibitor activity ;
GO:0030161

GO:0030567
spkw2go:SP_KW:KW-0655 Prothrombin activator > GO:thrombin activator activity
; GO:0030567

GO:0008605
interpro2go:InterPro:IPR000704 Casein kinase II, regulatory subunit >
GO:protein kinase CK2 regulator activity ; GO:0008605

interpro2go:InterPro:IPR016149 Casein kinase II, regulatory subunit,
alpha-helical > GO:protein kinase CK2 regulator activity ; GO:0008605

interpro2go:InterPro:IPR016150 Casein kinase II, regulatory subunit,
beta-sheet > GO:protein kinase CK2 regulator activity ; GO:0008605

pfam2go:Pfam:PF01214 CK_II_beta > GO:protein kinase CK2 regulator activity ;
GO:0008605

prints2go:PRINTS:PR00472 CASNKINASEII > GO:protein kinase CK2 regulator
activity ; GO:0008605

prosite2go:PROSITE:PS01101 CK2_BETA > GO:protein kinase CK2 regulator
activity ; GO:0008605



SourceForge links:

https://sourceforge.net/tracker/index.php?func=detail&aid=2665472&group_id=36855&atid=440764

and

http://sourceforge.net/tracker/index.php?func=detail&aid=2613734&group_id=36855&atid=440764


Comment period ends on March 27, 2009.

*** Unless objections are received by March 27,
    we will assume that you agree to this change. ***

Thanks,
Midori, David & Tanya

-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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