# GORULE violations assigned by pombase

## SUMMARY

This report generated on 2026-05-21

## Contents

[gorule-0000016](#gorule-0000016)[With/From: IC annotations require a With/From GO ID]{}

[gorule-0000020](#gorule-0000020)[Automatic repair of annotations to merged or obsoleted terms]{}

[gorule-0000027](#gorule-0000027)[Each identifier in GAF is valid]{}

## MESSAGES

###gorule-0000016

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

* total: 4
#### Messages
* WARNING - Violates GO Rule:GORULE:0000016: All IC annotations should include a GO ID in the "With/From" column that is also different from the entry in the "GO ID" column--`PomBase	SPAC11H11.04	mam2	enables	GO:0005085	GO_REF:0000111	IC		F	pheromone p-factor receptor Mam2		protein	NCBITaxon:4896	20260415	PomBase		PomBase:SPAC11H11.04
`
* WARNING - Violates GO Rule:GORULE:0000016: All IC annotations should include a GO ID in the "With/From" column that is also different from the entry in the "GO ID" column--`PomBase	SPAC18G6.04c	shm2	is_active_in	GO:0005759	GO_REF:0000111	IC		C	serine hydroxymethyltransferase Shm2		protein	NCBITaxon:4896	20260202	PomBase		PomBase:SPAC18G6.04c
`
* WARNING - Violates GO Rule:GORULE:0000016: All IC annotations should include a GO ID in the "With/From" column that is also different from the entry in the "GO ID" column--`PomBase	SPAC328.09	odc1	enables	GO:0000515	GO_REF:0000111	IC	GO:0000515	F	mitochondrial carrier, 2-oxoadipate/2-oxoglutarate		protein	NCBITaxon:4896	20250318	PomBase		PomBase:SPAC328.09
`
* WARNING - Violates GO Rule:GORULE:0000016: All IC annotations should include a GO ID in the "With/From" column that is also different from the entry in the "GO ID" column--`PomBase	SPBC31F10.07	lsb5	enables	GO:0030674	GO_REF:0000111	IC		F	actin cortical patch component Lsb5		protein	NCBITaxon:4896	20260422	PomBase		PomBase:SPBC31F10.07
`

###gorule-0000020

Automatic repair of annotations to merged or obsoleted terms

* total: 13
#### Messages
* ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`PomBase	SPAC1D4.06c	csk1	involved_in	GO:0007165	PMID:10226032	IC	GO:0019912	P	cyclin-dependent kinase activating kinase Csk1		protein	NCBITaxon:4896	20090506	PomBase		PomBase:SPAC1D4.06c
`
* ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`PomBase	SPAC3H5.09c	hob2	enables	GO:0043495	PMID:34415038	TAS		F	ER-PM contact site phospholipid-binding protein Hob2		protein	NCBITaxon:4896	20210823	PomBase	part_of(GO:0061817)	PomBase:SPAC3H5.09c
`
* ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`PomBase	SPCC320.04c	gem1	involved_in	GO:1990456	GO_REF:0000111	IC	GO:0032865	P	ERMES complex GTPase subunit Gem1		protein	NCBITaxon:4896	20170628	PomBase		PomBase:SPCC320.04c
`
* WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase	SPAC7D4.07c	trx1	involved_in	GO:0019379	PMID:18758731	IMP		P	cytosolic thioredoxin Trx1		protein	NCBITaxon:4896	20150126	PomBase		PomBase:SPAC7D4.07c
`
* WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase	SPAC222.12c	atp2	is_active_in	GO:0099617	GO_REF:0000111	IC	GO:0045269	C	F1-FO ATP synthase beta subunit (central stalk) Atp2		protein	NCBITaxon:4896	20240724	PomBase		PomBase:SPAC222.12c
`
* WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase	SPBC13E7.04	atp16	is_active_in	GO:0099617	GO_REF:0000111	IC	GO:0045269	C	F1-FO ATP synthase delta subunit (central stalk) Atp16		protein	NCBITaxon:4896	20240724	PomBase		PomBase:SPBC13E7.04
`
* WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase	SPBC1734.13	atp3	is_active_in	GO:0099617	GO_REF:0000111	IC	GO:0045269	C	F1-FO ATP synthase gamma subunit		protein	NCBITaxon:4896	20240724	PomBase		PomBase:SPBC1734.13
`
* WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase	SPBC31F10.15c	atp15	is_active_in	GO:0099617	GO_REF:0000111	IC	GO:0045269	C	F1-FO ATP synthase epsilon subunit (central stalk) Atp15		protein	NCBITaxon:4896	20240724	PomBase		PomBase:SPBC31F10.15c
`
* WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase	SPBP4H10.17c	SPBP4H10.17c	involved_in	GO:0030091	GO_REF:0000111	IC	GO:0051722	P	protein repair carboxyl methyl esterase, Pme1		protein	NCBITaxon:4896	20180213	PomBase		PomBase:SPBP4H10.17c
`
* WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase	SPBP4H10.17c	SPBP4H10.17c	involved_in	GO:1990748	GO_REF:0000111	IC	GO:0051722	P	protein repair carboxyl methyl esterase, Pme1		protein	NCBITaxon:4896	20180213	PomBase		PomBase:SPBP4H10.17c
`
* WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase	SPAC13F5.03c	gld1	involved_in	GO:0061610	PMID:20396879	IMP		P	mitochondrial glycerol dehydrogenase Gld1		protein	NCBITaxon:4896	20120227	PomBase	part_of(GO:0042149)	PomBase:SPAC13F5.03c
`
* WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase	SPAC22A12.11	dak1	involved_in	GO:0061610	PMID:10091325	IDA		P	dihydroxyacetone kinase Dak1		protein	NCBITaxon:4896	20130211	PomBase		PomBase:SPAC22A12.11
`
* WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase	SPAC977.16c	dak2	involved_in	GO:0061610	GO_REF:0000111	IC	GO:0004371,GO:0019563	P	dihydroxyacetone kinase Dak2		protein	NCBITaxon:4896	20260422	PomBase		PomBase:SPAC977.16c
`

###gorule-0000027

Each identifier in GAF is valid

* total: 1
#### Messages
* WARNING - Unknown identifier:Class ID GO:0004265 is not present in the ontology--`PomBase	SPAC1F12.09	gpi17	is_active_in	GO:0098553	GO_REF:0000111	IC	GO:0004265	C	GPI-anchor transamidase complex subunit Pig-S, Gpi17		protein	NCBITaxon:4896	20260312	PomBase		PomBase:SPAC1F12.09
`