# Group: unknown - Dataset: unknown

## SUMMARY

This report generated on 2024-10-22

  * Associations: 899
  * Lines in file (incl headers): 926
  * Lines skipped: 24
## Header From Original Association File

> !gpa-version: 1.1  
> !collation date: 2024-10-21  
> !collated from production models in https://github.com/geneontology/noctua-models/ where col1 matches xenbase; special rules for MGI (https://github.com/geneontology/pipeline/issues/313)  

## Contents

[gorule-0000001](#gorule-0000001)

[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-0000026](#gorule-0000026)

[gorule-0000027](#gorule-0000027)

[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-0000001

GAF lines are parsed according to GAF 2.2 specifications

* total: 8
#### Messages
* ERROR - Invalid symbol: Problem parsing references (PMID: 28427856) -- `Xenbase	XB-GENE-17336014	acts_upstream_of_or_within_positive_effect	GO:0016477	PMID: 28427856	ECO:0007752			20201119	Xenbase	occurs_in(XAO:0001001)	model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317`
* ERROR - Invalid symbol: Problem parsing references (PMID: 28427856) -- `Xenbase	XB-GENE-1217556	acts_upstream_of_or_within_positive_effect	GO:0016477	PMID: 28427856	ECO:0007752			20201119	Xenbase	occurs_in(XAO:0001001)	model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317`
* ERROR - Invalid symbol: Problem parsing references (PMID: 28427856) -- `Xenbase	XB-GENE-865846	acts_upstream_of_or_within	GO:0016477	PMID: 28427856	ECO:0007752			20201119	Xenbase	occurs_in(XAO:0001001)	model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317`
* ERROR - Invalid symbol: Problem parsing With/From column (XB-six6.S gRNA1: GRNA-29209218) -- `Xenbase	XB-GENE-17337584	acts_upstream_of_or_within	GO:0001654	PMID:28501477	ECO:0000315	XB-six6.S gRNA1: GRNA-29209218		20231208	Xenbase		model-state=production|noctua-model-id=gomodel:65692e7e00001353|contributor=https://orcid.org/0000-0001-5495-4588`
* ERROR - Invalid symbol: Problem parsing With/From column (XB-six6.S gRNA1: XB-GRNA-29209218) -- `Xenbase	XB-GENE-864947	acts_upstream_of_or_within	GO:0001654	PMID:28501477	ECO:0000315	XB-six6.S gRNA1: XB-GRNA-29209218		20231208	Xenbase		model-state=production|noctua-model-id=gomodel:65692e7e00001353|contributor=https://orcid.org/0000-0001-5495-4588`
* ERROR - Invalid symbol: Problem parsing With/From column (XENBASE: XB-GRNA-29209332) -- `Xenbase	XB-GENE-6486473	acts_upstream_of_or_within	GO:0048557	PMID:38152138	ECO:0000315	XENBASE: XB-GRNA-29209332		20240103	Xenbase		model-state=production|noctua-model-id=gomodel:657ba49f00000796|contributor=https://orcid.org/0000-0001-5495-4588`
* ERROR - Invalid symbol: Problem parsing With/From column (XENBASE:XB-MORPHOLINO-22249065; XB-MORPHOLINO-29212937) -- `Xenbase	XB-GENE-17333851	acts_upstream_of_or_within	GO:0055010	PMID:38501224	ECO:0007089	XENBASE:XB-MORPHOLINO-22249065; XB-MORPHOLINO-29212937		20240620	Xenbase	part_of(GO:0007507)	model-state=production|noctua-model-id=gomodel:666b894f00001795|contributor=https://orcid.org/0000-0001-5495-4588`
* ERROR - Invalid symbol: Problem parsing With/From column (XENBASE: XB-MORPHOLINO-29212947; XB-MORPHOLINO-29212948) -- `Xenbase	XB-GENE-17330203	acts_upstream_of_or_within	GO:0120221	PMID:30665704	ECO:0007089	XENBASE: XB-MORPHOLINO-29212947; XB-MORPHOLINO-29212948		20240627	Xenbase	occurs_in(CL:0000064),occurs_in(GO:0005929),occurs_in(XAO:0005179)	model-state=production|noctua-model-id=gomodel:666b894f00002553|contributor=https://orcid.org/0000-0001-5495-4588`
### 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: 5
#### Messages
* WARNING - Violates GO Rule: GORULE:0000008: No annotations should be made to uninformatively high level terms -- `Xenbase	XB-GENE-919827	acts_upstream_of_or_within	GO:0048856	PMID:32196547	ECO:0000315			20220118	Xenbase	results_in_development_of(XAO:0003029)	model-state=production|noctua-model-id=gomodel:61e0e55600000483|contributor=https://orcid.org/0000-0003-1074-8103
`
* WARNING - Violates GO Rule: GORULE:0000008: No annotations should be made to uninformatively high level terms -- `Xenbase	XB-GENE-1012570	acts_upstream_of_positive_effect	GO:0048518	PMID:33999995	ECO:0006063			20220513	Xenbase	positively_regulates(GO:0036032)	noctua-model-id=gomodel:627d95ee00000126|model-state=production|contributor=https://orcid.org/0000-0003-1074-8103
`
* WARNING - Violates GO Rule: GORULE:0000008: No annotations should be made to uninformatively high level terms -- `Xenbase	XB-GENE-1012570	acts_upstream_of_positive_effect	GO:0048518	PMID:33999995	ECO:0006051	Xenbase:XB-MORPHOLINO-23622781		20220513	Xenbase	positively_regulates(GO:0036032)	noctua-model-id=gomodel:627d95ee00000126|model-state=production|contributor=https://orcid.org/0000-0003-1074-8103
`
* WARNING - Violates GO Rule: GORULE:0000008: No annotations should be made to uninformatively high level terms -- `Xenbase	XB-GENE-1012570	acts_upstream_of_positive_effect	GO:0048518	PMID:33999995	ECO:0006051	Xenbase:XB-MORPHOLINO-23622782		20220513	Xenbase	positively_regulates(GO:0036032)	noctua-model-id=gomodel:627d95ee00000126|model-state=production|contributor=https://orcid.org/0000-0003-1074-8103
`
* WARNING - Violates GO Rule: GORULE:0000008: No annotations should be made to uninformatively high level terms -- `Xenbase	XB-GENE-487200	enables	GO:0008134	PMID:32894225	ECO:0006051	Xenbase:XB-MORPHOLINO-17249330		20220613	Xenbase	part_of(GO:1904837)	noctua-model-id=gomodel:62900b6400001096|model-state=production|contributor=https://orcid.org/0000-0003-1074-8103
`
### 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: 1
#### Messages
* ERROR - Obsolete class with no replacement: Violates GORULE:0000020 (GO:1904929) -- `Xenbase	XB-GENE-5846983	enables	GO:1904929	PMID:28427856	ECO:0007752			20230302	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
### gorule-0000022

Check for, and filter, annotations made to retracted publications

* total: 0
### gorule-0000026

IBA annotations must have been sourced from the PAINT inference pipeline

* total: 0
### gorule-0000027

Each identifier in GAF is valid

* total: 3
#### Messages
* ERROR - Invalid identifier: GORULE:0000027: contains non letter, non number character, or spaces (Xenbase:XB-MORPHOLINO-18375548;) -- `Xenbase	XB-GENE-6254887	involved_in	GO:0001843	PMID:38388461	ECO:0007089	Xenbase:XB-MORPHOLINO-18375548; 		20240322	Xenbase		model-state=production|noctua-model-id=gomodel:65f3ae5c00000062|contributor=https://orcid.org/0000-0001-5495-4588
`
* ERROR - Invalid identifier: GORULE:0000027: contains non letter, non number character, or spaces (Xenbase:XB-MORPHOLINO-18375548;) -- `Xenbase	XB-GENE-6254887	enables	GO:0141147	PMID:38388461	ECO:0007089	Xenbase:XB-MORPHOLINO-18375548; 		20240322	Xenbase	part_of(GO:0001843),part_of(GO:0021505)	model-state=production|noctua-model-id=gomodel:65f3ae5c00000062|contributor=https://orcid.org/0000-0001-5495-4588
`
* ERROR - Invalid identifier: GORULE:0000027: contains non letter, non number character, or spaces (Xenbase:XB-MORPHOLINO-18375548;) -- `Xenbase	XB-GENE-6254887	involved_in	GO:0021505	PMID:38388461	ECO:0007089	Xenbase:XB-MORPHOLINO-18375548; 		20240322	Xenbase	part_of(GO:0001843)	model-state=production|noctua-model-id=gomodel:65f3ae5c00000062|contributor=https://orcid.org/0000-0001-5495-4588
`
### 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: 12
#### Messages
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-6251681	enables	GO:0001968	GO_REF:0000050	ECO:0000318	UniProtKB:P34901		20201118	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-1217556	enables	GO:0004705	GO_REF:0000024	ECO:0000318	PANTHER:PTN001171982		20201119	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-865846	enables	GO:0019901	GO_REF:0000024	ECO:0000318	PANTHER:PTN001530052		20201118	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-865024	enables	GO:0005109	PMID:21873635	ECO:0000318	PANTHER:PTN000093831		20201118	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-483735	enables	GO:0042813	PMID:21873635	ECO:0000318	PANTHER:PTN000139394		20201118	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-483735	enables	GO:0017147	PMID:21873635	ECO:0000318	PANTHER:PTN000139394		20201118	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-17331693	enables	GO:0003723	PMID:21873635	ECO:0000318	PANTHER:PTN000259535		20201116	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-865070	enables	GO:0042813	PMID:21873635	ECO:0000318	PANTHER:PTN000139394		20201116	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-17331921	enables	GO:0005109	PMID:21873635	ECO:0000318	PANTHER:PTN000246517		20201118	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-489012	enables	GO:0003924	PMID:21873635	ECO:0000318	PANTHER:PTN000632671		20201118	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-852934	enables	GO:0005096	GO_REF:0000024	ECO:0000318	PANTHER:PTN001141948		20201119	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
* ERROR - Violates GO Rule: GORULE:0000037: IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference -- `Xenbase	XB-GENE-17336014	enables	GO:0072518	GO_REF:0000024	ECO:0000318	PANTHER:PTN000542090		20201119	Xenbase		model-state=production|contributor=https://orcid.org/0000-0003-1074-8103|noctua-model-id=gomodel:5fadbcf000000317
`
### 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: 7
#### Messages
* WARNING - Violates GO Rule: GORULE:0000061: Found violation of: `Only certain gene product to term relations are allowed for a given GO term` but was repaired: BFO:0000050 should be one of RO:0002432, RO:0002325, RO:0001025. Repaired to RO:0001025 -- `Xenbase	XB-GENE-22169574	part_of	GO:0005886	PMID:31644900	ECO:0005804			20200415	Xenbase		noctua-model-id=gomodel:5e72450500001671|model-state=production|contributor=https://orcid.org/0000-0003-1074-8103
`
* WARNING - Violates GO Rule: GORULE:0000061: Found violation of: `Only certain gene product to term relations are allowed for a given GO term` but was repaired: BFO:0000050 should be one of RO:0002432, RO:0002325, RO:0001025. Repaired to RO:0001025 -- `Xenbase	XB-GENE-22169574	part_of	GO:0005886	PMID:31644900	ECO:0001175			20200415	Xenbase		noctua-model-id=gomodel:5e72450500001671|model-state=production|contributor=https://orcid.org/0000-0003-1074-8103
`
* WARNING - Violates GO Rule: GORULE:0000061: Found violation of: `Only certain gene product to term relations are allowed for a given GO term` but was repaired: BFO:0000050 should be one of RO:0002432, RO:0002325, RO:0001025. Repaired to RO:0001025 -- `Xenbase	XB-GENE-982709	part_of	GO:0005770	PMID:30612743	ECO:0007719			20200619	Xenbase		model-state=production|noctua-model-id=gomodel:5ed1aab700000170|contributor=https://orcid.org/0000-0003-1074-8103
`
* WARNING - Violates GO Rule: GORULE:0000061: Found violation of: `Only certain gene product to term relations are allowed for a given GO term` but was repaired: BFO:0000050 should be one of RO:0002432, RO:0002325, RO:0001025. Repaired to RO:0001025 -- `Xenbase	XB-GENE-6486172	part_of	GO:0036064	PMID:32482850	ECO:0005804			20200618	Xenbase	part_of(XAO:0005179)	model-state=production|contributor=https://orcid.org/0000-0001-5495-4588|noctua-model-id=gomodel:5ee8120100000340
`
* WARNING - Violates GO Rule: GORULE:0000061: Found violation of: `Only certain gene product to term relations are allowed for a given GO term` but was repaired: RO:0002327 should be one of RO:0002263, RO:0002331, RO:0004035, RO:0004033, RO:0004034, RO:0004032, RO:0002264. Repaired to RO:0002264 -- `Xenbase	XB-GENE-17337757	enables	GO:0060725	PMID:20858598	ECO:0006063			20231219	Xenbase		noctua-model-id=gomodel:62b4ffe300003420|model-state=production|contributor=https://orcid.org/0000-0003-1074-8103
`
* WARNING - Violates GO Rule: GORULE:0000061: Found violation of: `Only certain gene product to term relations are allowed for a given GO term` but was repaired: RO:0002432 should be one of BFO:0000050. Repaired to BFO:0000050 -- `Xenbase	XB-GENE-6251797	is_active_in	GO:0098797	PMID:34806749	ECO:0007719			20230509	Xenbase		noctua-model-id=gomodel:6446bfcb00001289|model-state=production|contributor=https://orcid.org/0000-0003-1074-8103
`
* WARNING - Violates GO Rule: GORULE:0000061: Found violation of: `Only certain gene product to term relations are allowed for a given GO term` but was repaired: RO:0002432 should be one of BFO:0000050. Repaired to BFO:0000050 -- `Xenbase	XB-GENE-940037	is_active_in	GO:0098797	PMID:34806749	ECO:0001163			20230509	Xenbase		noctua-model-id=gomodel:6446bfcb00001289|model-state=production|contributor=https://orcid.org/0000-0003-1074-8103
`
### gorule-0000063

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

* total: 4
#### Messages
* WARNING - Violates GO Rule: GORULE:0000063: Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column) -- `Xenbase	XB-GENE-17339046	enables	GO:0004521	PMID:24683410	ECO:0000266			20200727	Xenbase	part_of(GO:0031016),part_of(GO:0048557),occurs_in(GO:0005737),has_input(Xenbase:XB-GENE-487128)	model-state=production|noctua-model-id=gomodel:5ee8120100002365|contributor=https://orcid.org/0000-0001-5495-4588
`
* WARNING - Violates GO Rule: GORULE:0000063: Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column) -- `Xenbase	XB-GENE-996950	acts_upstream_of_or_within	GO:0000380	PMID:33230114	ECO:0000266			20210112	Xenbase	part_of(GO:0001843),occurs_in(GO:0005634),has_input(Xenbase:XB-GENE-6041676)	model-state=production|noctua-model-id=gomodel:5fce9b7300000409|contributor=https://orcid.org/0000-0001-5495-4588
`
* WARNING - Violates GO Rule: GORULE:0000063: Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column) -- `Xenbase	XB-GENE-5782073	enables	GO:0003682	PMID:31936777	ECO:0000266			20210909	Xenbase	occurs_in(GO:0000785)	noctua-model-id=gomodel:61283a3000000756|model-state=production|contributor=https://orcid.org/0000-0001-5495-4588
`
* WARNING - Violates GO Rule: GORULE:0000063: Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column) -- `Xenbase	XB-GENE-5782073	is_active_in	GO:0000785	PMID:31936777	ECO:0000266			20210909	Xenbase		noctua-model-id=gomodel:61283a3000000756|model-state=production|contributor=https://orcid.org/0000-0001-5495-4588
`
### gorule-0000064

TreeGrafter IEAs should be filtered for GO reference species

* total: 0
### other

* total: 0