# Group: paint - Dataset: paint_sgd

## SUMMARY

This report generated on 2024-12-19

  * Associations: 15178
  * Lines in file (incl headers): 15206
  * Lines skipped: 22
## Header From Original Association File

> !gaf-version: 2.2  
> !Created on Thu Nov 21 14:20:18 2024.  
> !generated-by: PANTHER  
> !date-generated: 2024-11-21  
> !PANTHER version: v.19.0.  
> !GO version: 2024-11-03.  

## 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)

[gorule-0000065](#gorule-0000065)

[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: 14
#### Messages
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000003938	BPT1	enables	GO:0015127	GO_REF:0000033	IBA	PANTHER:PTN001200390|SGD:S000003938|SGD:S000002542	F	Bile pigment transporter 1	UniProtKB:P14772|PTN000658408	protein	taxon:559292	20170228	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000000514	STP22	involved_in	GO:0008333	GO_REF:0000033	IBA	PANTHER:PTN000592420|RGD:3909|WB:WBGene00015658	P	Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease	UniProtKB:P25604|PTN000592498	protein	taxon:559292	20211108	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000002542	YCF1	enables	GO:0015127	GO_REF:0000033	IBA	PANTHER:PTN001200390|SGD:S000003938|SGD:S000002542	F	Metal resistance protein YCF1	UniProtKB:P39109|PTN000658409	protein	taxon:559292	20170228	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000000257	YBR053C	involved_in	GO:0019853	GO_REF:0000033	IBA	PANTHER:PTN000097355|MGI:MGI:108024	P	Uncharacterized protein YBR053C	UniProtKB:P38235|PTN001656385	protein	taxon:559292	20170228	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000005420	GPD2	enables	GO:0047952	GO_REF:0000033	IBA	PANTHER:PTN000919759|MGI:MGI:95679|UniProtKB:C8VTT9|SGD:S000005420|SGD:S000002180	F	Glycerol-3-phosphate dehydrogenase [NAD(+)] 2, mitochondrial	UniProtKB:P41911|PTN000198092	protein	taxon:559292	20241120	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000000270	NRG2	part_of	GO:0031519	GO_REF:0000033	IBA	PANTHER:PTN000360827|MGI:MGI:99150|FB:FBgn0002521	C	Probable transcriptional regulator NRG2	UniProtKB:P38082|PTN000360882	protein	taxon:559292	20170602	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000001612	MYO3	is_active_in	GO:0005902	GO_REF:0000033	IBA	PANTHER:PTN001406997|UniProtKB:O00159|MGI:MGI:107732|UniProtKB:Q9UBC5|MGI:MGI:1927091|UniProtKB:P47807	C	Myosin-3	UniProtKB:P36006|PTN000321838	protein	taxon:559292	20240205	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000005072	TEP1	involved_in	GO:0048870	GO_REF:0000033	IBA	PANTHER:PTN000959472|MGI:MGI:109583|dictyBase:DDB_G0286557	P	Probable phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase TEP1	UniProtKB:P53916|PTN000266993	protein	taxon:559292	20200305	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000003930	LMO1	involved_in	GO:0048870	GO_REF:0000033	IBA	PANTHER:PTN000299186|WB:WBGene00000426|FB:FBgn0032409|UniProtKB:Q96JJ3|UniProtKB:Q92556|dictyBase:DDB_G0278051	P	ELMO family protein LMO1	UniProtKB:Q07799|PTN001764799	protein	taxon:559292	20221007	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000002450	NRG1	part_of	GO:0031519	GO_REF:0000033	IBA	PANTHER:PTN000360827|MGI:MGI:99150|FB:FBgn0002521	C	Transcriptional regulator NRG1	UniProtKB:Q03125|PTN000149122	protein	taxon:559292	20170602	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000004460	YPT7	is_active_in	GO:0045335	GO_REF:0000033	IBA	PANTHER:PTN000635769|UniProtKB:P51149|UniProtKB:Q96AH8|WB:WBGene00004271|dictyBase:DDB_G0269236|UniProtKB:Q9NP90|MGI:MGI:2442295|UniProtKB:P51151	C	Ypt_Rab-type GTPase YPT7	UniProtKB:P32939|PTN000635835	protein	taxon:559292	20201002	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000002180	GPD1	enables	GO:0047952	GO_REF:0000033	IBA	PANTHER:PTN000919759|MGI:MGI:95679|UniProtKB:C8VTT9|SGD:S000005420|SGD:S000002180	F	Glycerol-3-phosphate dehydrogenase [NAD(+)] 1	UniProtKB:Q00055|PTN000198091	protein	taxon:559292	20241120	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000004715	MYO5	is_active_in	GO:0005902	GO_REF:0000033	IBA	PANTHER:PTN001406997|UniProtKB:O00159|MGI:MGI:107732|UniProtKB:Q9UBC5|MGI:MGI:1927091|UniProtKB:P47807	C	Myosin-5	UniProtKB:Q04439|PTN000321837	protein	taxon:559292	20240205	GO_Central		
`
* ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- `SGD	S000003034	SGF73	involved_in	GO:0031048	GO_REF:0000033	IBA	PANTHER:PTN001031589|PomBase:SPCC126.04c	P	SAGA-associated factor 73	UniProtKB:P53165|PTN000387891	protein	taxon:559292	20240213	GO_Central		
`
### 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: 19
#### Messages
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0006266) -- `SGD	S000002323	CDC9	involved_in	GO:0006266	GO_REF:0000033	IBA	PANTHER:PTN000048696|RGD:1309875|SGD:S000002323|UniProtKB:P49916	P	DNA ligase 1	UniProtKB:P04819|PTN000048836	protein	taxon:559292	20241121	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0006880) -- `SGD	S000004210	CCC1	involved_in	GO:0006880	GO_REF:0000033	IBA	PANTHER:PTN001275041|TAIR:locus:2090305|UniProtKB:Q6MWE5|UniProtKB:Q6ERE5|TAIR:locus:2199572|TAIR:locus:2030091	P	Protein CCC1	UniProtKB:P47818|PTN000783871	protein	taxon:559292	20230407	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0032508) -- `SGD	S000005929	CHL1	involved_in	GO:0032508	GO_REF:0000033	IBA	PANTHER:PTN000158371|UniProtKB:Q96FC9	P	ATP-dependent DNA helicase CHL1	UniProtKB:P22516|PTN000158421	protein	taxon:559292	20200929	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0032508) -- `SGD	S000005194	RAD50	involved_in	GO:0032508	GO_REF:0000033	IBA	PANTHER:PTN000429848|UniProtKB:Q92878	P	DNA repair protein RAD50	UniProtKB:P12753|PTN000429902	protein	taxon:559292	20170228	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0042989) -- `SGD	S000005648	PFY1	involved_in	GO:0042989	GO_REF:0000033	IBA	PANTHER:PTN000176159|SGD:S000005648|UniProtKB:P35081|UniProtKB:O22655|UniProtKB:Q8I2J4|UniProtKB:Q9FR39	P	Profilin	UniProtKB:P07274|PTN000176200	protein	taxon:559292	20230110	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0042989) -- `SGD	S000003312	TWF1	involved_in	GO:0042989	GO_REF:0000033	IBA	PANTHER:PTN001011683|SGD:S000003312|MGI:MGI:1346078|MGI:MGI:1100520	P	Twinfilin-1	UniProtKB:P53250|PTN000349130	protein	taxon:559292	20170421	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0044806) -- `SGD	S000004526	PIF1	involved_in	GO:0044806	GO_REF:0000033	IBA	PANTHER:PTN001149933|SGD:S000001073|SGD:S000004526|PomBase:SPBC887.14c	P	ATP-dependent DNA helicase PIF1	UniProtKB:P07271|PTN000588800	protein	taxon:559292	20221209	GO_Central		
`
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0044806) -- `SGD	S000001073	RRM3	involved_in	GO:0044806	GO_REF:0000033	IBA	PANTHER:PTN001149933|SGD:S000001073|SGD:S000004526|PomBase:SPBC887.14c	P	ATP-dependent DNA helicase RRM3	UniProtKB:P38766|PTN000588797	protein	taxon:559292	20221209	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0006268) -- `SGD	S000000406	MCM7	involved_in	GO:0006268	GO_REF:0000033	IBA	PANTHER:PTN000180038|MGI:MGI:1298398|UniProtKB:P33993|SGD:S000000406	P	DNA replication licensing factor MCM7	UniProtKB:P38132|PTN000180076	protein	taxon:559292	20211215	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0006268) -- `SGD	S000006223	MCM4	involved_in	GO:0006268	GO_REF:0000033	IBA	PANTHER:PTN000179968|SGD:S000006223|UniProtKB:P33991|MGI:MGI:103199	P	DNA replication licensing factor MCM4	UniProtKB:P30665|PTN000180020	protein	taxon:559292	20211215	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0006268) -- `SGD	S000003169	MCM6	involved_in	GO:0006268	GO_REF:0000033	IBA	PANTHER:PTN000180096|MGI:MGI:1298227|UniProtKB:Q14566|SGD:S000003169	P	DNA replication licensing factor MCM6	UniProtKB:P53091|PTN000180143	protein	taxon:559292	20211215	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0006268) -- `SGD	S000000065	RFA1	involved_in	GO:0006268	GO_REF:0000033	IBA	PANTHER:PTN000588618|SGD:S000000065	P	Replication factor A protein 1	UniProtKB:P22336|PTN000588674	protein	taxon:559292	20210531	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0006268) -- `SGD	S000000119	MCM2	involved_in	GO:0006268	GO_REF:0000033	IBA	PANTHER:PTN000179907|UniProtKB:Q2R482|MGI:MGI:105380|UniProtKB:P49736	P	DNA replication licensing factor MCM2	UniProtKB:P29469|PTN000179950	protein	taxon:559292	20211215	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0006268) -- `SGD	S000004802	SGS1	involved_in	GO:0006268	GO_REF:0000033	IBA	PANTHER:PTN000344874|SGD:S000004802	P	ATP-dependent helicase SGS1	UniProtKB:P35187|PTN000345053	protein	taxon:559292	20190319	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0006268) -- `SGD	S000007222	RIM1	involved_in	GO:0006268	GO_REF:0000033	IBA	PANTHER:PTN000033807|FB:FBgn0010438|UniProtKB:Q04837	P	Single-stranded DNA-binding protein RIM1, mitochondrial	UniProtKB:P32445|PTN000033850	protein	taxon:559292	20240820	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0070413) -- `SGD	S000004566	TSL1	involved_in	GO:0070413	GO_REF:0000033	IBA	PANTHER:PTN000846179|SGD:S000002481|PomBase:SPAC328.03	P	Trehalose synthase complex regulatory subunit TSL1	UniProtKB:P38427|PTN000082187	protein	taxon:559292	20170228	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0070413) -- `SGD	S000002481	TPS2	involved_in	GO:0070413	GO_REF:0000033	IBA	PANTHER:PTN000846179|SGD:S000002481|PomBase:SPAC328.03	P	Trehalose-phosphatase	UniProtKB:P31688|PTN000082226	protein	taxon:559292	20170228	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0070413) -- `SGD	S000000330	TPS1	involved_in	GO:0070413	GO_REF:0000033	IBA	PANTHER:PTN000846179|SGD:S000002481|PomBase:SPAC328.03	P	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] 56 kDa subunit	UniProtKB:Q00764|PTN000082191	protein	taxon:559292	20170228	GO_Central		
`
* WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0070413) -- `SGD	S000004874	TPS3	involved_in	GO:0070413	GO_REF:0000033	IBA	PANTHER:PTN000846179|SGD:S000002481|PomBase:SPAC328.03	P	Trehalose synthase complex regulatory subunit TPS3	UniProtKB:P38426|PTN000082188	protein	taxon:559292	20170228	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: 1
#### Messages
* WARNING - Violates GO Rule: GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms -- `SGD	S000003863	VPS25	enables	GO:0042803	GO_REF:0000033	IBA	PANTHER:PTN000322234|UniProtKB:Q9BRG1	F	Vacuolar protein-sorting-associated protein 25	UniProtKB:P47142|PTN000322275	protein	taxon:559292	20170228	GO_Central		
`
### 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
### gorule-0000065

Annotations to term that are candidates for obsoletion should be removed

* total: 9
#### Messages
* WARNING - Violates GO Rule: GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed -- `SGD	S000000409	KTR3	involved_in	GO:0097502	GO_REF:0000033	IBA	PANTHER:PTN001579360|PomBase:SPBC19C7.12c	P	Probable mannosyltransferase KTR3	UniProtKB:P38130|PTN000779430	protein	taxon:559292	20241120	GO_Central		
`
* WARNING - Violates GO Rule: GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed -- `SGD	S000003675	YUR1	involved_in	GO:0097502	GO_REF:0000033	IBA	PANTHER:PTN001579360|PomBase:SPBC19C7.12c	P	Probable mannosyltransferase YUR1	UniProtKB:P26725|PTN000779425	protein	taxon:559292	20241120	GO_Central		
`
* WARNING - Violates GO Rule: GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed -- `SGD	S000004974	KTR5	involved_in	GO:0097502	GO_REF:0000033	IBA	PANTHER:PTN001579360|PomBase:SPBC19C7.12c	P	Probable mannosyltransferase KTR5	UniProtKB:P53966|PTN000779398	protein	taxon:559292	20241120	GO_Central		
`
* WARNING - Violates GO Rule: GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed -- `SGD	S000001769	KTR2	involved_in	GO:0097502	GO_REF:0000033	IBA	PANTHER:PTN001579360|PomBase:SPBC19C7.12c	P	Probable mannosyltransferase KTR2	UniProtKB:P33550|PTN000779426	protein	taxon:559292	20241120	GO_Central		
`
* WARNING - Violates GO Rule: GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed -- `SGD	S000005974	KTR6	involved_in	GO:0097502	GO_REF:0000033	IBA	PANTHER:PTN001579360|PomBase:SPBC19C7.12c	P	Mannosyltransferase KTR6	UniProtKB:P54070|PTN000779420	protein	taxon:559292	20241120	GO_Central		
`
* WARNING - Violates GO Rule: GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed -- `SGD	S000002891	KRE2	involved_in	GO:0097502	GO_REF:0000033	IBA	PANTHER:PTN001579360|PomBase:SPBC19C7.12c	P	Glycolipid 2-alpha-mannosyltransferase	UniProtKB:P27809|PTN000779421	protein	taxon:559292	20241120	GO_Central		
`
* WARNING - Violates GO Rule: GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed -- `SGD	S000005625	KTR1	involved_in	GO:0097502	GO_REF:0000033	IBA	PANTHER:PTN001579360|PomBase:SPBC19C7.12c	P	Alpha-1,2 mannosyltransferase KTR1	UniProtKB:P27810|PTN000779431	protein	taxon:559292	20241120	GO_Central		
`
* WARNING - Violates GO Rule: GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed -- `SGD	S000000403	KTR4	involved_in	GO:0097502	GO_REF:0000033	IBA	PANTHER:PTN001579360|PomBase:SPBC19C7.12c	P	Probable mannosyltransferase KTR4	UniProtKB:P38131|PTN000779411	protein	taxon:559292	20241120	GO_Central		
`
* WARNING - Violates GO Rule: GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed -- `SGD	S000001347	KTR7	involved_in	GO:0097502	GO_REF:0000033	IBA	PANTHER:PTN001579360|PomBase:SPBC19C7.12c	P	Probable mannosyltransferase KTR7	UniProtKB:P40504|PTN000779397	protein	taxon:559292	20241120	GO_Central		
`
### other

* total: 0