GORULE violations assigned by pombase

Contents

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

gorule-0000013 Taxon-appropriate annotation check

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

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

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_gene taxon:4896 20230710 PomBase has_input(PomBase:SPSNRNA.06),part_of(GO:0016180) `

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_coding_gene 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_coding_gene taxon:4896 20161012 PomBase `

gorule-0000016

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

• total: 6

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 SPAC25B8.06c dia4 involved_in GO:0070127 GO_REF:0000024 IC P mitochondrial serine-tRNA ligase protein_coding_gene taxon:4896 20250312 PomBase `
• 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 SPAC328.09 odc1 enables GO:0000515 GO_REF:0000111 IC GO:0000515 F mitochondrial carrier, 2-oxoadipate/2-oxoglutarate protein_coding_gene taxon:4896 20250318 PomBase `
• 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 SPCC736.06 dar2 involved_in GO:0043038 GO_REF:0000111 IC P mitochondrial aspartate-tRNA ligase Dar2 protein_coding_gene taxon:4896 20250414 PomBase `
• 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_gene taxon:4896 20150206 PomBase `
• 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 SPBTRNATYR.02 SPBTRNATYR.02 enables GO:0033410 GO_REF:0000111 IC GO:0033410 F tRNA Tyrosine tRNA_gene taxon:4896 20150206 PomBase `
• 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 SPBTRNATYR.03 SPBTRNATYR.03 enables GO:0033410 GO_REF:0000111 IC GO:0033410 F tRNA Tyrosine tRNA_gene taxon:4896 20150206 PomBase `

gorule-0000020

Automatic repair of annotations to merged or obsoleted terms

• total: 17

messages

• ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`PomBase SPAC1D4.06c csk1 enables GO:0019912 PMID:16428435 IDA F cyclin-dependent kinase activating kinase Csk1 protein_coding_gene taxon:4896 20240322 PomBase has_input(PomBase:SPBC32H8.10) `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPACUNK12.02c cmk1 involved_in GO:0010621 PMID:25081204 IMP P calcium/calmodulin-dependent protein kinase Cmk1 CaMK-I protein_coding_gene taxon:4896 20150218 PomBase has_input(PomBase:SPAC4G8.13c) `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPAC4D7.04c rer2 involved_in GO:0019408 PMID:25066056 IDA P cis-prenyltransferase protein_coding_gene taxon:4896 20140730 PomBase `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPAC7D4.09c dfg10 involved_in GO:0019408 GO_REF:0000024 ISO UniProtKB:Q9H8P0 P ER polyprenol reductase Dfg10 protein_coding_gene taxon:4896 20240606 PomBase `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPBC2A9.06c nus1 involved_in GO:0019408 PMID:25066056 IDA P di-trans,poly-cis-decaprenylcistransferase Nus1 protein_coding_gene taxon:4896 20140730 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_coding_gene 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_coding_gene 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_coding_gene 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_coding_gene taxon:4896 20240724 PomBase `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPBP4H10.17c SPBP4H10.17c involved_in GO:0030091 GO_REF:0000111 IC GO:0051722 P protein repair carboxyl methyl esterase, Pme1 protein_coding_gene taxon:4896 20180213 PomBase `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPBP4H10.17c SPBP4H10.17c involved_in GO:1990748 GO_REF:0000111 IC GO:0051722 P protein repair carboxyl methyl esterase, Pme1 protein_coding_gene taxon:4896 20180213 PomBase `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPAC22H10.04 ppa3 involved_in GO:0061509 PMID:22119525 IMP P serine/threonine protein phosphatase PP2A catalytic subunit Ppa3 ppg1 protein_coding_gene taxon:4896 20130321 PomBase `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPAC2C4.10c csc4 involved_in GO:0061509 PMID:22119525 IMP P SIP/FAR complex subunit Csc4 protein_coding_gene taxon:4896 20130321 PomBase `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPAP8A3.09c paa1 involved_in GO:0061509 PMID:22119525 IMP P serine/threonine protein phosphatase PP2A scaffold subunit Paa1 protein_coding_gene taxon:4896 20130321 PomBase `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPBC1773.01 csc3 involved_in GO:0061509 PMID:22119525 IMP P SIP/FAR complex WD repeat (scaffold) subunit, striatin Csc3 far8 protein_coding_gene taxon:4896 20130321 PomBase `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPBC27B12.04c csc2 involved_in GO:0061509 PMID:22119525 IMP P SIP/FAR complex subunit Csc2 far11 protein_coding_gene taxon:4896 20130321 PomBase `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`PomBase SPBC3H7.13 csc1 involved_in GO:0061509 PMID:22119525 IMP P SIP/FAR complex FHA domain subunit Csc1 far10 protein_coding_gene taxon:4896 20130321 PomBase `