# Group: paint - Dataset: paint_ecocyc

## SUMMARY

This report generated on 2024-10-22

  * Associations: 6051
  * Lines in file (incl headers): 6064
  * Lines skipped: 7
## Header From Original Association File

> !gaf-version: 2.2  
> !Created on Mon Sep 23 12:29:03 2024.  
> !generated-by: PANTHER  
> !date-generated: 2024-09-23  
> !PANTHER version: v.19.0.  
> !GO version: 2024-06-17.  

## Contents

[gorule-0000002](#gorule-0000002)

[gorule-0000005](#gorule-0000005)

[gorule-0000006](#gorule-0000006)

[gorule-0000007](#gorule-0000007)

[gorule-0000008](#gorule-0000008)

[gorule-0000011](#gorule-0000011)

[gorule-0000013](#gorule-0000013)

[gorule-0000015](#gorule-0000015)

[gorule-0000016](#gorule-0000016)

[gorule-0000017](#gorule-0000017)

[gorule-0000018](#gorule-0000018)

[gorule-0000020](#gorule-0000020)

[gorule-0000022](#gorule-0000022)

[gorule-0000028](#gorule-0000028)

[gorule-0000029](#gorule-0000029)

[gorule-0000030](#gorule-0000030)

[gorule-0000037](#gorule-0000037)

[gorule-0000039](#gorule-0000039)

[gorule-0000042](#gorule-0000042)

[gorule-0000043](#gorule-0000043)

[gorule-0000046](#gorule-0000046)

[gorule-0000050](#gorule-0000050)

[gorule-0000055](#gorule-0000055)

[gorule-0000058](#gorule-0000058)

[gorule-0000061](#gorule-0000061)

[gorule-0000063](#gorule-0000063)

[gorule-0000064](#gorule-0000064)

[other](#other)


## MESSAGES

### gorule-0000002

No 'NOT' annotations to binding ; GO:0005488 or 'protein binding ; GO:0005515'

* total: 0
### gorule-0000005

IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae not allowed for direct annotations to to 'protein binding ; GO:0005515 or GO:0005488 binding''

* total: 0
### gorule-0000006

IEP and HEP usage is restricted to terms from the Biological Process ontology, except when assigned by GOC

* total: 0
### gorule-0000007

IPI should not be used with GO:0003824 catalytic activity or descendents

* total: 0
### gorule-0000008

No annotations should be made to uninformative high level terms

* total: 0
### gorule-0000011

ND evidence code should be to root nodes only, and no terms other than root nodes can have the evidence code ND

* total: 0
### gorule-0000013

Taxon-appropriate annotation check

* total: 0
### gorule-0000015

Dual species taxon check

* total: 0
### gorule-0000016

With/From: IC annotations require a With/From GO ID

* total: 0
### gorule-0000017

IDA annotations must not have a With/From entry

* total: 0
### gorule-0000018

IPI annotations require a With/From entry

* total: 0
### gorule-0000020

Automatic repair of annotations to merged or obsoleted terms

* total: 15
#### Messages
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0003867) -- `UniProtKB	P50457	puuE	enables	GO:0003867	GO_REF:0000033	IBA	PANTHER:PTN000944876|UniProtKB:P94427|UniProtKB:P80404|PomBase:SPAC19D5.07|UniProtKB:P22256|UniProtKB:P50457|SGD:S000003251	F	4-aminobutyrate aminotransferase PuuE	UniProtKB:P50457|PTN000944968	protein	taxon:83333	20240919	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0003867) -- `UniProtKB	P22256	gabT	enables	GO:0003867	GO_REF:0000033	IBA	PANTHER:PTN000944876|UniProtKB:P94427|UniProtKB:P80404|PomBase:SPAC19D5.07|UniProtKB:P22256|UniProtKB:P50457|SGD:S000003251	F	4-aminobutyrate aminotransferase GabT	UniProtKB:P22256|PTN000944969	protein	taxon:83333	20240919	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0019391) -- `UniProtKB	P05804	uidA	involved_in	GO:0019391	GO_REF:0000033	IBA	PANTHER:PTN004122708|MGI:MGI:95872|UniProtKB:P05804	P	Beta-glucuronidase	UniProtKB:P05804|PTN001296252	protein	taxon:83333	20190815	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0052665) -- `UniProtKB	P0AE01	trmJ	enables	GO:0052665	GO_REF:0000033	IBA	PANTHER:PTN000247326|UniProtKB:P0AE01	F	tRNA (cytidine_uridine-2'-O-)-methyltransferase TrmJ	UniProtKB:P0AE01|PTN000947742	protein	taxon:83333	20170228	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0052665) -- `UniProtKB	P37005	lasT	enables	GO:0052665	GO_REF:0000033	IBA	PANTHER:PTN000247326|UniProtKB:P0AE01	F	Uncharacterized tRNA_rRNA methyltransferase LasT	UniProtKB:P37005|PTN000247338	protein	taxon:83333	20170228	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0052665) -- `UniProtKB	P0AGJ7	trmL	enables	GO:0052665	GO_REF:0000033	IBA	PANTHER:PTN000247318|UniProtKB:P0AGJ7	F	tRNA (cytidine(34)-2'-O)-methyltransferase	UniProtKB:P0AGJ7|PTN000947666	protein	taxon:83333	20230720	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0097304) -- `UniProtKB	P00804	lspA	involved_in	GO:0097304	GO_REF:0000033	IBA	PANTHER:PTN002134743|UniProtKB:P00804	P	Lipoprotein signal peptidase	UniProtKB:P00804|PTN002134787	protein	taxon:83333	20240827	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0004024) -- `UniProtKB	P25437	frmA	enables	GO:0004024	GO_REF:0000033	IBA	PANTHER:PTN000191653|UniProtKB:P08319|UniProtKB:P00325|MGI:MGI:1349472|UniProtKB:P25437|UniProtKB:P40394|UniProtKB:P07327	F	S-(hydroxymethyl)glutathione dehydrogenase	UniProtKB:P25437|PTN000914946	protein	taxon:83333	20181004	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0008272) -- `UniProtKB	P16676	cysA	involved_in	GO:0008272	GO_REF:0000033	IBA	PANTHER:PTN000655803|UniProtKB:P9WQM1	P	Sulfate_thiosulfate import ATP-binding protein CysA	UniProtKB:P16676|PTN000655820	protein	taxon:83333	20170420	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0019516) -- `UniProtKB	P06149	dld	involved_in	GO:0019516	GO_REF:0000033	IBA	PANTHER:PTN000202405|UniProtKB:P06149	P	Quinone-dependent D-lactate dehydrogenase	UniProtKB:P06149|PTN001367983	protein	taxon:83333	20170228	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0044255) -- `UniProtKB	P45524	yheT	involved_in	GO:0044255	GO_REF:0000033	IBA	PANTHER:PTN000082644|UniProtKB:P08910|SGD:S000004823|MGI:MGI:2147183|SGD:S000006016|UniProtKB:Q8WU67|SGD:S000000381	P	Putative esterase YheT	UniProtKB:P45524|PTN000082836	protein	taxon:83333	20200807	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0045226) -- `UniProtKB	P37760	rfbD	involved_in	GO:0045226	GO_REF:0000033	IBA	PANTHER:PTN000051855|UniProtKB:P9WH09|UniProtKB:P26392	P	dTDP-4-dehydrorhamnose reductase	UniProtKB:P37760|PTN001313665	protein	taxon:83333	20180619	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0045226) -- `UniProtKB	P37745	rfbC	involved_in	GO:0045226	GO_REF:0000033	IBA	PANTHER:PTN000471594|UniProtKB:P26394|UniProtKB:P9WH11	P	dTDP-4-dehydrorhamnose 3,5-epimerase	UniProtKB:P37745|PTN001464550	protein	taxon:83333	20210305	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0045226) -- `UniProtKB	P37751	wbbK	involved_in	GO:0045226	GO_REF:0000033	IBA	PANTHER:PTN000749272|UniProtKB:Q9I1N0	P	Putative glycosyltransferase WbbK	UniProtKB:P37751|PTN000283102	protein	taxon:83333	20240229	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0052857) -- `UniProtKB	P31806	nnr	enables	GO:0052857	GO_REF:0000033	IBA	PANTHER:PTN000287613|UniProtKB:P31806	F	Bifunctional NAD(P)H-hydrate repair enzyme Nnr	UniProtKB:P31806|PTN000287628	protein	taxon:83333	20191128	GO_Central		
`
### gorule-0000022

Check for, and filter, annotations made to retracted publications

* total: 0
### gorule-0000028

GO aspect should match the term's namespace; otherwise it is repaired to the appropriate aspect

* total: 0
### gorule-0000029

IEAs should be less than one year old.

* total: 0
### gorule-0000030

Obsolete GO_REFs are not allowed

* total: 0
### gorule-0000037

IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference

* total: 0
### gorule-0000039

Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants

* total: 0
### gorule-0000042

Qualifier: IKR evidence code requires a NOT qualifier

* total: 0
### gorule-0000043

Check for valid combination of evidence code and GO_REF

* total: 0
### gorule-0000046

The ‘with’ field (GAF column 8) must be the same as the gene product (GAF column 2) when annotating to ‘self-binding’ terms.

* total: 0
### gorule-0000050

Annotations to ISS, ISA and ISO should not be self-referential

* total: 0
### gorule-0000055

References should have only one ID per ID space

* total: 0
### gorule-0000058

Object extensions should conform to the extensions-patterns.yaml file in metadata

* total: 0
### gorule-0000061

Allowed gene product to term relations (gp2term)

* total: 0
### gorule-0000063

Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column)

* total: 0
### gorule-0000064

TreeGrafter IEAs should be filtered for GO reference species

* total: 0
### other

* total: 0