GORULE Violations Assigned by PomBase

⛔️ GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications

• Total Violations: 18

• Line 17073 – PomBase SPAC5D6.12 mtf2 enables GO:0008494 PMID:38499152 EXP F mitochondrial translational activator Mtf2 ppr12 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 17074 – PomBase SPAC5D6.12 mtf2 contributes_to GO:0008494 PMID:29458562 EXP F mitochondrial translational activator Mtf2 ppr12 protein taxon:4896 20180307 PomBase has_input(SPMIT.01.1)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 17075 – PomBase SPAC5D6.12 mtf2 contributes_to GO:0008494 PMID:34634819 EXP F mitochondrial translational activator Mtf2 ppr12 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 19636 – PomBase SPAC8C9.06c ppr4 enables GO:0008494 PMID:38499152 EXP F mitochondrial PPR repeat protein, translation activator for Cox1 Ppr4 srd2 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 19637 – PomBase SPAC8C9.06c ppr4 contributes_to GO:0008494 PMID:34634819 EXP F mitochondrial PPR repeat protein, translation activator for Cox1 Ppr4 srd2 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 20966 – PomBase SPAP8A3.14c sls1 enables GO:0008494 PMID:38499152 EXP F mitochondrial translational activator Sls1 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 20967 – PomBase SPAP8A3.14c sls1 contributes_to GO:0008494 PMID:34634819 EXP F mitochondrial translational activator Sls1 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 22045 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general 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)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 22046 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.01.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 22047 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.11.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 22048 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.04.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 22049 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.07.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 22050 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.08.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 22051 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.09.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 22052 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.10.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 30520 – PomBase SPBC25D12.06 mrh5 enables GO:0008494 PMID:38499152 EXP F mitochondrial translation ATP-dependent RNA helicase Mrh5 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 30521 – PomBase SPBC25D12.06 mrh5 contributes_to GO:0008494 PMID:34634819 EXP F mitochondrial translation ATP-dependent RNA helicase Mrh5 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1)
  GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications-(see also GORULE:0000058) bad extension syntax
• Line 48162 – 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:0000001-GAF lines are parsed according to GAF 2.2 specifications-bad entity type - sncRNA

✅ GORULE:0000002-No 'NOT' annotations to binding ; GO:0005488 or 'protein binding ; GO:0005515'

• All checks passed - 0 violations

✅ GORULE:0000005-IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations are not allowed for direct annotations to protein binding ; GO:0005515 or GO:0005488 binding

• All checks passed - 0 violations

✅ GORULE:0000006-IEP and HEP usage is restricted to terms from the Biological Process ontology, except when assigned by GOC

• All checks passed - 0 violations

✅ GORULE:0000007-IPI should not be used with GO:0003824 catalytic activity or descendants

• All checks passed - 0 violations

⛔️ GORULE:0000008-No annotations should be made to uninformative high level terms

• Total Violations: 4

• Line 6807 – PomBase SPAC19G12.11 coq9 enables GO:0098772 PMID:38425362 TAS F ubiquinone biosynthesis protein Coq9 protein taxon:4896 20260630 PomBase
  GORULE:0000008-No annotations should be made to uninformative high level terms
• Line 12217 – PomBase SPAC27F1.02c cdc8 involved_in GO:1904530 PMID:17452625 IDA P tropomyosin fus4 protein taxon:4896 20170811 PomBase
  GORULE:0000008-No annotations should be made to uninformative high level terms
• Line 12221 – PomBase SPAC27F1.02c cdc8 enables GO:0098772 PMID:12796476 IDA F tropomyosin fus4 protein taxon:4896 20200317 PomBase has_input(PomBase:SPAC1F5.04c)
  GORULE:0000008-No annotations should be made to uninformative high level terms
• Line 27689 – PomBase SPBC17G9.11c pyr1 involved_in GO:0006090 GO_REF:0000033 IBA PANTHER:PTN001821692,RGD:3262 P pyruvate carboxylase Pyr1 protein taxon:4896 20260408 PomBase
  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

• All checks passed - 0 violations

⚠️ GORULE:0000013-Taxon-appropriate annotation check

• Total Violations: 10

• Line 7723 –
  GORULE:0000013-Taxon-appropriate annotation check-GO:0019628 annotated to taxon:4896 violated never_in_taxon 4896
• Line 12074 –
  GORULE:0000013-Taxon-appropriate annotation check-GO:0052907 annotated to taxon:4896 violated in_taxon_union 4
• Line 19956 –
  GORULE:0000013-Taxon-appropriate annotation check-GO:0050085 annotated to taxon:4896 violated never_in_taxon 4896
• Line 19957 –
  GORULE:0000013-Taxon-appropriate annotation check-GO:0032115 annotated to taxon:4896 violated never_in_taxon 4896
• Line 20406 –
  GORULE:0000013-Taxon-appropriate annotation check-GO:0019654 annotated to taxon:4896 violated never_in_taxon 4895
• Line 21171 –
  GORULE:0000013-Taxon-appropriate annotation check-GO:0070485 annotated to taxon:4896 violated never_in_taxon 4896
• Line 21175 –
  GORULE:0000013-Taxon-appropriate annotation check-GO:0003885 annotated to taxon:4896 violated never_in_taxon 4896
• Line 28430 –
  GORULE:0000013-Taxon-appropriate annotation check-GO:0009008 annotated to taxon:4896 violated never_in_taxon 4896
• Line 43957 –
  GORULE:0000013-Taxon-appropriate annotation check-GO:0019628 annotated to taxon:4896 violated never_in_taxon 4896
• Line 44778 –
  GORULE:0000013-Taxon-appropriate annotation check-GO:0004617 annotated to taxon:4896 violated never_in_taxon 4890

✅ GORULE:0000015-Dual species taxon check

• All checks passed - 0 violations

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

• Total Violations: 5

• Line 1436 – PomBase SPAC11H11.04 mam2 enables GO:0005085 GO_REF:0000111 IC F pheromone p-factor receptor Mam2 protein taxon:4896 20260423 PomBase
  GORULE:0000016-With/From: IC annotations require a With/From GO ID
• Line 5832 – PomBase SPAC18G6.04c shm2 is_active_in GO:0005759 GO_REF:0000111 IC C serine hydroxymethyltransferase Shm2 protein taxon:4896 20260202 PomBase
  GORULE:0000016-With/From: IC annotations require a With/From GO ID
• Line 13988 – PomBase SPAC328.09 odc1 enables GO:0000515 GO_REF:0000111 IC GO:0000515 F mitochondrial carrier, 2-oxoadipate/2-oxoglutarate protein taxon:4896 20250318 PomBase
  GORULE:0000016-With/From: IC annotations require a With/From GO ID- column (with/from) is the same GOID
• Line 21872 – PomBase SPATRNATYR.01 SPATRNATYR.01 enables GO:0033410 GO_REF:0000111 IC GO:0033410 F tRNA Tyrosine tRNA taxon:4896 20150206 PomBase
  GORULE:0000016-With/From: IC annotations require a With/From GO ID- column (with/from) is the same GOID
• Line 32779 – PomBase SPBC31F10.07 lsb5 enables GO:0030674 GO_REF:0000111 IC F actin cortical patch component Lsb5 protein taxon:4896 20260713 PomBase
  GORULE:0000016-With/From: IC annotations require a With/From GO ID

✅ GORULE:0000017-IDA annotations must not have a With/From entry

• All checks passed - 0 violations

✅ GORULE:0000018-IPI annotations require a With/From entry

• All checks passed - 0 violations

⛔️ GORULE:0000020-Automatic repair of annotations to merged or obsoleted terms

• Total Violations: 9

• Line 7324 – PomBase SPAC1D4.06c csk1 involved_in GO:0007165 PMID:10226032 IC GO:0019912 P cyclin-dependent kinase activating kinase Csk1 protein taxon:4896 20090506 PomBase
  GORULE:0000020-Automatic repair of annotations to merged or obsoleted terms-Consider: GO:0004672|GO:0097472

✅ GORULE:0000022-Check for, and filter, annotations made to retracted publications

• All checks passed - 0 violations

⛔️ GORULE:0000027-Each identifier in GAF is valid

• Total Violations: 20

• Line 9344 – PomBase SPAC23A1.03 apt1 involved_in GO:0006166 GO_REF:0000024 ISO MGI:88061 P adenine phosphoribosyltransferase (APRT) Apt1 dap1 protein taxon:4896 20251218 PomBase
  GORULE:0000027-Each identifier in GAF is valid-Bad id syntax for MGI:88061
• Line 17073 – PomBase SPAC5D6.12 mtf2 enables GO:0008494 PMID:38499152 EXP F mitochondrial translational activator Mtf2 ppr12 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.01.1'
• Line 17074 – PomBase SPAC5D6.12 mtf2 contributes_to GO:0008494 PMID:29458562 EXP F mitochondrial translational activator Mtf2 ppr12 protein taxon:4896 20180307 PomBase has_input(SPMIT.01.1)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.01.1'
• Line 17075 – PomBase SPAC5D6.12 mtf2 contributes_to GO:0008494 PMID:34634819 EXP F mitochondrial translational activator Mtf2 ppr12 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.01.1'
• Line 19636 – PomBase SPAC8C9.06c ppr4 enables GO:0008494 PMID:38499152 EXP F mitochondrial PPR repeat protein, translation activator for Cox1 Ppr4 srd2 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.01.1'
• Line 19637 – PomBase SPAC8C9.06c ppr4 contributes_to GO:0008494 PMID:34634819 EXP F mitochondrial PPR repeat protein, translation activator for Cox1 Ppr4 srd2 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.01.1'
• Line 20966 – PomBase SPAP8A3.14c sls1 enables GO:0008494 PMID:38499152 EXP F mitochondrial translational activator Sls1 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.01.1'
• Line 20967 – PomBase SPAP8A3.14c sls1 contributes_to GO:0008494 PMID:34634819 EXP F mitochondrial translational activator Sls1 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.01.1'
• Line 22045 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general 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)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.05.1'
• Line 22046 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.01.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.01.1'
• Line 22047 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.11.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.11.1'
• Line 22048 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.04.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.04.1'
• Line 22049 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.07.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.07.1'
• Line 22050 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.08.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.08.1'
• Line 22051 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.09.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.09.1'
• Line 22052 – PomBase SPBC106.19 ppr10 enables GO:0008494 PMID:28334955 EXP F mitochondrial general translational activator, PPR repeat Ppr10 SPBC582.01|mpal10 protein taxon:4896 20170330 PomBase has_input(SPMIT.10.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.10.1'
• Line 30441 – PomBase SPBC25D12.02c dnt1 involved_in GO:0000183 GO_REF:0000024 ISO SGD: S000001718,SGD:S000003612 P nucleolar protein Dnt1 protein taxon:4896 20251022 PomBase
  GORULE:0000027-Each identifier in GAF is valid-Bad id syntax for SGD: S000001718
• Line 30520 – PomBase SPBC25D12.06 mrh5 enables GO:0008494 PMID:38499152 EXP F mitochondrial translation ATP-dependent RNA helicase Mrh5 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1),occurs_in(GO:0005759),part_of(GO:0070124)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.01.1'
• Line 30521 – PomBase SPBC25D12.06 mrh5 contributes_to GO:0008494 PMID:34634819 EXP F mitochondrial translation ATP-dependent RNA helicase Mrh5 protein taxon:4896 20250331 PomBase has_input(SPMIT.01.1)
  GORULE:0000027-Each identifier in GAF is valid-Bad CURIE syntax 'SPMIT.01.1'
• Line 34224 – 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:0000027-Each identifier in GAF is valid-Prefix not found in db-xrefs: PBQ

⚠️ GORULE:0000030-Obsolete GO_REFs are not allowed

• Total Violations: 3

• Line 21171 –
  GORULE:0000030-Obsolete GO_REFs are not allowed-GO_REF:0000025 reference is not allowed
• Line 21174 –
  GORULE:0000030-Obsolete GO_REFs are not allowed-GO_REF:0000025 reference is not allowed
• Line 21175 –
  GORULE:0000030-Obsolete GO_REFs are not allowed-GO_REF:0000025 reference is not allowed

✅ GORULE:0000033-Group-specific Reference IDs are not allowed, only public reference IDs (PMID, doi, or GO_REF)

• All checks passed - 0 violations

✅ GORULE:0000039-Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants

• All checks passed - 0 violations

✅ GORULE:0000042-Qualifier: IKR evidence code requires a NOT qualifier

• All checks passed - 0 violations

✅ GORULE:0000043-Check for valid combination of evidence code and GO_REF

• All checks passed - 0 violations

✅ 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.

• All checks passed - 0 violations

✅ GORULE:0000050-Annotations to ISS, ISA and ISO should not be self-referential

• All checks passed - 0 violations

⛔️ GORULE:0000053-'NOT' annotation should not have extension

• Total Violations: 5

• Line 13806 – PomBase SPAC31G5.13 rpn11 NOT|is_active_in GO:0034399 PMID:18504300 IDA C 19S proteasome regulatory subunit, ubiquitin-specific protease subunit Rpn11 bfr2|mts5|pad1|sks1 protein taxon:4896 20240417 PomBase existence_overlaps(GO:0044838)
  GORULE:0000053-'NOT' annotation should not have extension
• Line 13807 – PomBase SPAC31G5.13 rpn11 NOT|is_active_in GO:0034515 PMID:18504300 IDA C 19S proteasome regulatory subunit, ubiquitin-specific protease subunit Rpn11 bfr2|mts5|pad1|sks1 protein taxon:4896 20240417 PomBase existence_overlaps(GO:0000080)
  GORULE:0000053-'NOT' annotation should not have extension
• Line 14884 – PomBase SPAC3G9.07c hos2 NOT|is_active_in GO:0000792 PMID:27538348 IDA C histone deacetylase (class I) Hos2 hda1|phd1 protein taxon:4896 20240701 PomBase coincident_with(PomBase:SPBC428.08c)
  GORULE:0000053-'NOT' annotation should not have extension
• Line 14885 – PomBase SPAC3G9.07c hos2 NOT|is_active_in GO:0000792 PMID:27538348 IDA C histone deacetylase (class I) Hos2 hda1|phd1 protein taxon:4896 20240701 PomBase coincident_with(PomBase:SPCC11E10.08)
  GORULE:0000053-'NOT' annotation should not have extension
• Line 17771 – PomBase SPAC664.10 klp2 NOT|is_active_in GO:0097431 PMID:32327557 IDA C kinesin-14 family minus-end directed microtubule motor Klp2 protein taxon:4896 20220530 PomBase existence_overlaps(GO:0000087)
  GORULE:0000053-'NOT' annotation should not have extension

✅ GORULE:0000055-References should have only one ID per ID space

• All checks passed - 0 violations

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

• All checks passed - 0 violations

⚠️ GORULE:0000065-Term candidate for obsoletion

• Total Violations: 2274

• Line 11 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0098763
• Line 12 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0098762
• Line 36 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0007128
• Line 37 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0007128
• Line 39 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0007128
• Line 154 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0098763
• Line 164 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0098762
• Line 189 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0051329
• Line 192 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0098763
• Line 199 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0051329
• Line 207 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0051329
• Line 208 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0051329
• Line 211 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0000093
• Line 213 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0000092
• Line 214 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0000090
• Line 215 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0000089
• Line 221 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0000092
• Line 224 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0072690
• Line 254 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0044838
• Line 256 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0072690
• Line 258 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0044838
• Line 259 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0044838
• Line 321 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0000084
• Line 369 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0098762
• Line 370 –
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• Line 6807 – PomBase SPAC19G12.11 coq9 enables GO:0098772 PMID:38425362 TAS F ubiquinone biosynthesis protein Coq9 protein taxon:4896 20260630 PomBase
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0098772
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• Line 12217 – PomBase SPAC27F1.02c cdc8 involved_in GO:1904530 PMID:17452625 IDA P tropomyosin fus4 protein taxon:4896 20170811 PomBase
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:1904530
• Line 12221 – PomBase SPAC27F1.02c cdc8 enables GO:0098772 PMID:12796476 IDA F tropomyosin fus4 protein taxon:4896 20200317 PomBase has_input(PomBase:SPAC1F5.04c)
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0098772
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• Line 13796 –
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• Line 13797 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0044838
• Line 13800 –
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• Line 13801 –
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• Line 13805 –
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0044838
• Line 13806 – PomBase SPAC31G5.13 rpn11 NOT|is_active_in GO:0034399 PMID:18504300 IDA C 19S proteasome regulatory subunit, ubiquitin-specific protease subunit Rpn11 bfr2|mts5|pad1|sks1 protein taxon:4896 20240417 PomBase existence_overlaps(GO:0044838)
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0044838
• Line 13807 – PomBase SPAC31G5.13 rpn11 NOT|is_active_in GO:0034515 PMID:18504300 IDA C 19S proteasome regulatory subunit, ubiquitin-specific protease subunit Rpn11 bfr2|mts5|pad1|sks1 protein taxon:4896 20240417 PomBase existence_overlaps(GO:0000080)
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0000080
• Line 13887 –
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• Line 13965 –
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• Line 13977 –
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• Line 14110 –
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• Line 14123 –
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• Line 14570 –
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• Line 17500 –
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• Line 17771 – PomBase SPAC664.10 klp2 NOT|is_active_in GO:0097431 PMID:32327557 IDA C kinesin-14 family minus-end directed microtubule motor Klp2 protein taxon:4896 20220530 PomBase existence_overlaps(GO:0000087)
  GORULE:0000065-Term candidate for obsoletion-Obsolete term GO:0000087
• Line 17775 –
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• Line 17882 –
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• Line 17886 –
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• Line 18051 –
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• Line 18649 –
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• Line 18652 –
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• Line 18677 –
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• Line 18779 –
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• Line 18781 –
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• Line 18787 –
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• Line 19217 –
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• Line 27689 – PomBase SPBC17G9.11c pyr1 involved_in GO:0006090 GO_REF:0000033 IBA PANTHER:PTN001821692,RGD:3262 P pyruvate carboxylase Pyr1 protein taxon:4896 20260408 PomBase
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