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
MESSAGES
gorule-0000001
GAF lines are parsed according to GAF 2.2 specifications
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
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--`JaponicusDB SJAG_03088 fim1 involved_in GO:1904530 GO_REF:0000107 IEA PomBase:SPBC1778.06c P fimbrin protein taxon:4897 20240721 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 20240721 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 20240721 PomBase
`
gorule-0000013
Taxon-appropriate annotation check
messages
- ERROR - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`PomBase SPCC1840.09 coq11 involved_in GO:1901006 GO_REF:0000024 ISO SGD:S000004281 P ubiquinone biosynthesis protein Coq11 protein taxon:4896 20150218 PomBase
`
- ERROR - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`JaponicusDB SJAG_01820 coq11 involved_in GO:1901006 GO_REF:0000107 IEA PomBase:SPCC1840.09 P ubiquinone biosynthesis protein Coq11 protein taxon:4897 20240721 PomBase
`
gorule-0000016
With/From: IC annotations require a With/From GO ID
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
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
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
`
- ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`PomBase SPAC14C4.12c laf1 involved_in GO:0045815 GO_REF:0000111 IC GO:1990483 P Clr6 associated factor 1 Laf1 protein taxon:4896 20230310 PomBase
`
- ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`PomBase SPAC25B8.02 sds3 involved_in GO:0045815 GO_REF:0000111 IC GO:1990483 P Clr6 and Rpd3L histone deacetylase complex subunit Sds3 protein taxon:4896 20230310 PomBase
`
- ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`PomBase SPBC12C2.10c pst1 involved_in GO:0045815 GO_REF:0000111 IC GO:1990483 P Clr6 I prime and Rpd3L histone deacetylase complex subunit Pst1 SPBC21D10.01c protein taxon:4896 20230310 PomBase
`
- ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`PomBase SPBC428.06c rxt2 involved_in GO:0045815 GO_REF:0000111 IC GO:1990483 P Clr6 and Rpd3L histone deacetylase complex subunit Rxt2 protein taxon:4896 20230310 PomBase
`
- ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`PomBase SPCC1682.13 laf2 involved_in GO:0045815 GO_REF:0000111 IC GO:1990483 P Clr6 associated factor 2, Laf2 protein taxon:4896 20230310 PomBase
`
- WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPAC5H10.06c adh4 enables GO:0004024 GO_REF:0000024 ISO SGD:S000003225 F alcohol dehydrogenase Adh4 protein taxon:4896 20050412 PomBase
`
- WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`JaponicusDB SJAG_00240 SJAG_00240 enables GO:0004024 GO_REF:0000107 IEA PomBase:SPAC5H10.06c F alcohol dehydrogenase Adh4-like protein taxon:4897 20240721 PomBase
`
- WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`JaponicusDB SJAG_03822 SJAG_03822 enables GO:0004024 GO_REF:0000107 IEA PomBase:SPAC5H10.06c F alcohol dehydrogenase Adh4-like protein taxon:4897 20240721 PomBase
`
- WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPCC1442.08c cox12 involved_in GO:0006123 GO_REF:0000111 IC GO:0005751 P cytochrome c oxidase protein VIb protein taxon:4896 20200609 PomBase
`