GORULE violations assigned by pombase

Contents

gorule-0000001 GAF lines are parsed according to GAF 2.2 specifications

gorule-0000008 No annotations should be made to uninformative high level terms

gorule-0000011 ND evidence code should be to root nodes only, and no terms other than root nodes can have the evidence code ND

gorule-0000013 Taxon-appropriate annotation check

gorule-0000016 With/From: IC annotations require a With/From GO ID

gorule-0000018 IPI annotations require a With/From entry

gorule-0000020 Automatic repair of annotations to merged or obsoleted terms

gorule-0000027 Each identifier in GAF is valid

gorule-0000063 Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column)

gorule-0000065 Annotations to term that are candidates for obsoletion should be removed

MESSAGES

gorule-0000001

GAF lines are parsed according to GAF 2.2 specifications

• total: 2

messages

• ERROR - Syntax error in annotation extension field:extensions should be relation(curie) and relation should have corresponding URI--`PomBase SPBC106.19 ppr10 enables GO:0140517 PMID:28334955 EXP F mitochondrial translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.05.1),occurs_in(GO:0005759),part_of(GO:0070124) `
• WARNING - Invalid subject type:defaulting to 'gene_product'--`PomBase SPNCRNA.530 sno530 enables GO:0030563 PMID:37403782 EXP F small nucleolar RNA sno530 sncRNA taxon:4896 20230710 PomBase has_input(PomBase:SPSNRNA.06),part_of(GO:0016180) `

gorule-0000008

No annotations should be made to uninformative high level terms

• total: 4

messages

• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`PomBase SPAC27F1.02c cdc8 involved_in GO:1904530 PMID:17452625 IDA P tropomyosin fus4 protein taxon:4896 20170811 PomBase `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`PomBase SPAC27F1.02c cdc8 enables GO:0098772 PMID:12796476 IDA F tropomyosin fus4 protein taxon:4896 20200317 PomBase has_input(PomBase:SPAC1F5.04c) `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`PomBase SPAC637.12c mst1 enables GO:0034212 PMID:19915592 EXP F histone acetyltransferase, KAT5 family Mst1 kat5 protein taxon:4896 20240402 PomBase has_input(PomBase:SPBC11B10.10c) `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`PomBase SPBC1778.06c fim1 involved_in GO:1904530 PMID:20705466 IDA P fimbrin protein taxon:4896 20170630 PomBase has_input(PomBase:SPAC27F1.02c) `

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: 1

messages

• ERROR - Violates GO Rule:GORULE:0000011: ND annotations to root nodes only--`PomBase SPAC1F7.14c dmo2 enables GO:0003674 PMID:39932033 TAS F mitochondrial inner membrane protein chaperone/ protein-disulfide reductase, Dmo2 tam6 protein taxon:4896 20250212 PomBase has_input(PomBase:SPMIT.11) `

gorule-0000013

Taxon-appropriate annotation check

• total: 2

messages

• ERROR - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`PomBase SPAC1805.10 ccz1 part_of GO:0035658 GO_REF:0000024 ISO SGD:S000000335 C Mon1-Ccz1 GEF complex subunit Ccz1 protein taxon:4896 20240810 PomBase `
• ERROR - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`PomBase SPAC27D7.08c mtl16 enables GO:0052907 GO_REF:0000024 ISO UniProtKB:P75782 F 23S rRNA/U6 snRNA (adenine-N(6))-methyltransferase Mtl16 protein taxon:4896 20161012 PomBase `

gorule-0000016

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

• total: 1

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 SPATRNATYR.01 SPATRNATYR.01 enables GO:0033410 GO_REF:0000111 IC GO:0033410 F tRNA Tyrosine tRNA taxon:4896 20150206 PomBase `

gorule-0000018

IPI annotations require a With/From entry

• total: 1

messages

• WARNING - Violates GO Rule:GORULE:0000018: IPI annotations require a With/From entry--`PomBase SPAC1565.08 cdc48 enables GO:0031625 PMID:22086920 IPI F AAA family ATPase involved in ubiquitin-mediated protein degradation Cdc48 SPAC6F12.01|dsc6 protein taxon:4896 20120712 PomBase `

gorule-0000020

Automatic repair of annotations to merged or obsoleted terms

• total: 5

messages

• ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`PomBase SPMTR.01 mat2-Pc is_active_in GO:0005634 GO_REF:0000036 IC GO:0003677,GO:0036003 C silenced P-specific transcription factor Pc mat-Pc|mat2Pc|matPc protein taxon:4896 20150121 PomBase `
• 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 taxon:4896 20240724 PomBase `
• 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 taxon:4896 20240724 PomBase `
• 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 taxon:4896 20240724 PomBase `
• 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 taxon:4896 20240724 PomBase `

gorule-0000027

Each identifier in GAF is valid

• total: 1

messages

• WARNING - Invalid identifier:GORULE:0000027: PBQ not found in list of database names in dbxrefs--`PomBase SPBC3B8.10c nem1 is_active_in GO:0005634 PMID:30116786 IDA C serine/threonine protein phosphatase (Nem1-Spo7 complex) catalytic subunit Nem1 protein taxon:4896 20180828 PomBase existence_overlaps(PBQ:0000003) `

gorule-0000063

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

• total: 2

messages

• WARNING - Violates GO Rule:GORULE:0000063: Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column)--`PomBase SPAC4G9.11c cmb1 involved_in GO:0090139 GO_REF:0000024 ISO P mitochondrial transcription factor A, and genome packaging protein (TFAM ortholog) protein taxon:4896 20250112 PomBase `
• WARNING - Violates GO Rule:GORULE:0000063: Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column)--`PomBase SPBC115.02c afg1 involved_in GO:0141164 GO_REF:0000024 ISO P mitochondrial AFG1 family ATPase/chaperone Afg1 protein taxon:4896 20241103 PomBase `

gorule-0000065

Annotations to term that are candidates for obsoletion should be removed

• total: 1

messages

• WARNING - Violates GO Rule:GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed--`PomBase SPBC17A3.09c aim22 involved_in GO:0009249 GO_REF:0000111 IC GO:0016979 P mitochondrial lipoate-protein ligase A protein taxon:4896 20250212 PomBase `