• Report (original)
• Predictions
• Predictions (experimental)

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-0000002

gorule-0000005

gorule-0000006

gorule-0000007

gorule-0000008

gorule-0000011

gorule-0000013

gorule-0000015

gorule-0000016

gorule-0000017

gorule-0000018

gorule-0000020

gorule-0000022

gorule-0000026

gorule-0000027

gorule-0000029

gorule-0000030

gorule-0000037

gorule-0000039

gorule-0000042

gorule-0000043

gorule-0000046

gorule-0000050

gorule-0000055

gorule-0000058

gorule-0000061

gorule-0000063

gorule-0000064

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

No report generated.

No report generated.