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-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)

MESSAGES

gorule-0000001

GAF lines are parsed according to GAF 2.2 specifications

• total: 1

messages

• 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: 8

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 SPBC1778.06c fim1 involved_in GO:1904530 PMID:20705466 IDA P fimbrin protein taxon:4896 20170630 PomBase has_input(PomBase:SPAC27F1.02c) `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`PomBase SPCC16A11.07 coq10 enables GO:0140104 GO_REF:0000024 ISO SGD:S000005368 F mitochondrial ubiquinone binding protein Coq10 protein taxon:4896 20240505 PomBase has_input(CHEBI:46245) `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`JaponicusDB SJAG_03088 fim1 involved_in GO:1904530 GO_REF:0000107 IEA PomBase:SPBC1778.06c P fimbrin protein taxon:4897 20241118 PomBase `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`JaponicusDB SJAG_04223 coq10 enables GO:0140104 GO_REF:0000107 IEA PomBase:SPCC16A11.07 F mitochondrial ubiquinone binding protein Coq10 protein taxon:4897 20241118 PomBase `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`JaponicusDB SJAG_04887 cdc8 involved_in GO:1904530 GO_REF:0000107 IEA PomBase:SPAC27F1.02c P tropomyosin protein taxon:4897 20241118 PomBase `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`JaponicusDB SJAG_04887 cdc8 enables GO:0098772 GO_REF:0000107 IEA PomBase:SPAC27F1.02c F tropomyosin protein taxon:4897 20241118 PomBase `

gorule-0000013

Taxon-appropriate annotation check

• total: 4

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 `
• ERROR - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`PomBase SPCC1223.03c gut2 part_of GO:0009331 GO_REF:0000024 ISO SGD:S000001417 C glycerol-3-phosphate dehydrogenase Gut2 protein taxon:4896 20040618 PomBase `
• ERROR - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`JaponicusDB SJAG_01958 mtl16 enables GO:0052907 GO_REF:0000107 IEA PomBase:SPAC27D7.08c F 23S rRNA/U6 snRNA (adenine-N(6))-methyltransferase Mtl16 protein taxon:4897 20241118 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: 1

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 `

gorule-0000027

Each identifier in GAF is valid

• total: 9

messages

• WARNING - Invalid identifier:GORULE:0000027: CBS not found in list of database names in dbxrefs--`PomBase SPBC3B8.07c dsd1 is_active_in GO:0016020 GO_REF:0000050 ISM CBS:TMHMM C dihydroceramide delta-4 desaturase protein taxon:4896 20060411 PomBase `
• WARNING - Invalid identifier:GORULE:0000027: ECOGENE not found in list of database names in dbxrefs--`PomBase SPAC12B10.08c til1 enables GO:0032267 GO_REF:0000024 ISO ECOGENE:EG13357 F mitochondrial tRNA(Ile)-lysidine synthetase Til1 protein taxon:4896 20060922 PomBase `
• WARNING - Invalid identifier:GORULE:0000027: 1298204 does not match any id_syntax patterns for MGI in dbxrefs--`PomBase SPBC530.12c pdf1 enables GO:0008474 PMID:15075260 ISO MGI:MGI:1298204 F palmitoyl protein thioesterase/ dolichol pyrophosphate phosphatase fusion protein Pdf1 protein taxon:4896 20040414 PomBase `
• WARNING - Invalid identifier:GORULE:0000027: 1316717 does not match any id_syntax patterns for MGI in dbxrefs--`PomBase SPBC20F10.03 SPBC20F10.03 is_active_in GO:0005634 GO_REF:0000024 ISS MGI:MGI:1316717 C armadillo-type fold protein, human IFRD1 ortholog, implicated in transcription or signaling protein taxon:4896 20170830 PomBase `
• WARNING - Invalid identifier:GORULE:0000027: 1346084 does not match any id_syntax patterns for MGI in dbxrefs--`PomBase SPAC6C3.09 rpp40 part_of GO:0005655 GO_REF:0000024 ISS MGI:MGI:1346084 C RNase P and RNase MRP subunit Rpp40 protein taxon:4896 20061017 PomBase `
• WARNING - Invalid identifier:GORULE:0000027: 1919005 does not match any id_syntax patterns for MGI in dbxrefs--`PomBase SPAC513.06c dhd1 involved_in GO:0042843 GO_REF:0000024 ISS MGI:MGI:1919005 P D-xylose 1-dehydrogenase (NADP+) protein taxon:4896 20150502 PomBase `
• WARNING - Invalid identifier:GORULE:0000027: 1919005 does not match any id_syntax patterns for MGI in dbxrefs--`PomBase SPAC513.06c dhd1 enables GO:0047837 GO_REF:0000024 ISS MGI:MGI:1919005 F D-xylose 1-dehydrogenase (NADP+) protein taxon:4896 20150502 PomBase `
• 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) `
• WARNING - Invalid identifier:GORULE:0000027: UniprotKB not found in list of database names in dbxrefs--`PomBase SPCPB1C11.02 SPCPB1C11.02 is_active_in GO:0005886 GO_REF:0000024 ISS PomBase:SPAC869.11,SGD:S000000272,SGD:S000005875,UniprotKB:P30825 C plasma membrane amino acid transmembrane transporter protein taxon:4896 20240815 PomBase `

gorule-0000063

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

• total: 1

messages

• 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 AFG1 family mitochondrial ATPase/chaperone Afg1 protein taxon:4896 20241103 PomBase `