Remove repair command from ontology build

[balhoff]

Fixes #27821.

[github-actions[bot]]

Here's a diff of how these changes impact the classified ontology:

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2024-11-06/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-master.owl/reasoned.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2024-11-06/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

1-phosphatidylinositol-3-kinase activity http://purl.obolibrary.org/obo/GO_0016303

Removed

• 1-phosphatidylinositol-3-kinase activity database_cross_reference "Wikipedia:Phosphoinositide_3-kinase"

15-oxoprostaglandin 13-oxidase [NAD(P)+] activity http://purl.obolibrary.org/obo/GO_0047522

Removed

• 15-oxoprostaglandin 13-oxidase [NAD(P)+] activity database_cross_reference "Reactome:R-HSA-2161692"
  • label "15k-PGE2/F2a is reduced to dhk-PGE2/F2a by PTGR1"

2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity http://purl.obolibrary.org/obo/GO_0008425

Removed

• 2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity database_cross_reference "Reactome:R-HSA-2162188"
  • label "MDMQ10H2 is methylated to DMQ10H2 by COQ5"

3,4-dihydroxy-5-polyprenylbenzoic acid O-methyltransferase activity http://purl.obolibrary.org/obo/GO_0010420

Removed

• 3,4-dihydroxy-5-polyprenylbenzoic acid O-methyltransferase activity database_cross_reference "Reactome:R-HSA-2162193"
  • label "DHDB is methylated to MHDB by COQ3"

3-demethylubiquinol-n 3-O-methyltransferase activity http://purl.obolibrary.org/obo/GO_0061542

Removed

• 3-demethylubiquinol-n 3-O-methyltransferase activity database_cross_reference "Reactome:R-HSA-2162186"
  • label "DeMQ10H2 is methylated to Q10H2 by COQ3"

4-hydroxybenzoate polyprenyltransferase activity http://purl.obolibrary.org/obo/GO_0008412

Removed

• 4-hydroxybenzoate polyprenyltransferase activity database_cross_reference "Reactome:R-HSA-2162192"
  • label "PHB and all-E-10PrP2 are combined into DHB by COQ2"

D-glucose transmembrane transporter activity http://purl.obolibrary.org/obo/GO_0055056

Removed

• D-glucose transmembrane transporter activity database_cross_reference "Reactome:R-HSA-499981"

  • label "Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2"

• D-glucose transmembrane transporter activity database_cross_reference "Reactome:R-HSA-5653873"

  • label "SLC2A1 tetramer transports Glc from cytosol to Golgi lumen"

GO_0004367 http://purl.obolibrary.org/obo/GO_0004367

Added

• GO_0004367 database_cross_reference "Reactome:R-HSA-75889"
  • label "DHAP is converted to G3P by GPD1/GPD1L"

N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity http://purl.obolibrary.org/obo/GO_0052903

Removed

• N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity database_cross_reference "Reactome:R-HSA-141348"

  • label "PAO:FAD oxidises NASPM to PTCN"

• N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity database_cross_reference "Reactome:R-HSA-141351"

  • label "PAOX:FAD oxidises NASPN to SPM"

N-acylsphingosine amidohydrolase activity http://purl.obolibrary.org/obo/GO_0017040

Removed

• N-acylsphingosine amidohydrolase activity database_cross_reference "Reactome:R-HSA-428262"
  • label "ACER3 hydrolyzes phytoceramide"

N-acylsphingosine galactosyltransferase activity http://purl.obolibrary.org/obo/GO_0003851

Removed

• N-acylsphingosine galactosyltransferase activity database_cross_reference "Reactome:R-HSA-6785933"
  • label "UGT8 transfers Gal from UDP-Gal to CERA"

NAD(P)HX epimerase activity http://purl.obolibrary.org/obo/GO_0052856

Removed

• NAD(P)HX epimerase activity database_cross_reference "Reactome:R-HSA-6806966"
  • label "APOA1BP dimer epimerises R-NAD(P)HX to S-NAD(P)HX"

NADP+ nucleosidase activity http://purl.obolibrary.org/obo/GO_0050135

Removed

• NADP+ nucleosidase activity database_cross_reference "Reactome:R-HSA-9637699"
  • label "CpnT hydrolyses NAD+"

alcohol dehydrogenase (NAD+) activity http://purl.obolibrary.org/obo/GO_0004022

Removed

• alcohol dehydrogenase (NAD+) activity database_cross_reference "Reactome:R-HSA-71707"
  • label "ethanol + NAD+ => acetaldehyde + NADH + H+"

biotin--[biotin carboxyl-carrier protein] ligase activity http://purl.obolibrary.org/obo/GO_0004077

Removed

• biotin--[biotin carboxyl-carrier protein] ligase activity database_cross_reference "Reactome:R-HSA-4167511"

  • label "HLCS biotinylates ACACB"

• biotin--[biotin carboxyl-carrier protein] ligase activity database_cross_reference "Reactome:R-HSA-2993814"

  • label "HLCS biotinylates ACACA:Mn2+"

• biotin--[biotin carboxyl-carrier protein] ligase activity database_cross_reference "Reactome:R-HSA-9035990"

  • label "Defective HLCS does not biotinylate 6x(PCCA:PCCB)"

• biotin--[biotin carboxyl-carrier protein] ligase activity database_cross_reference "Reactome:R-HSA-3323184"

  • label "Defective HLCS does not biotinylate ACACA:Mn2+"

• biotin--[biotin carboxyl-carrier protein] ligase activity database_cross_reference "Reactome:R-HSA-2993799"

  • label "HLCS biotinylates 6xMCCC1:6xMCCC2"

• biotin--[biotin carboxyl-carrier protein] ligase activity database_cross_reference "Reactome:R-HSA-9035988"

  • label "Defective HLCS does not biotinylate PC:Mn2+"

• biotin--[biotin carboxyl-carrier protein] ligase activity database_cross_reference "Reactome:R-HSA-2993447"

  • label "HLCS biotinylates 6x(PCCA:PCCB)"

• biotin--[biotin carboxyl-carrier protein] ligase activity database_cross_reference "Reactome:R-HSA-9035987"

  • label "Defective HLCS does not biotinylate 6xMCCC1:6xMCCC2"

• biotin--[biotin carboxyl-carrier protein] ligase activity database_cross_reference "Reactome:R-HSA-2993802"

  • label "HLCS biotinylates PC:Mn2+"

broad specificity oxidative DNA demethylase activity http://purl.obolibrary.org/obo/GO_0035516

Removed

• broad specificity oxidative DNA demethylase activity database_cross_reference "Reactome:R-HSA-112123"

  • label "Oxidative demethylation of 1-meA damaged DNA By ALKBH3"

• broad specificity oxidative DNA demethylase activity database_cross_reference "Reactome:R-HSA-112118"

  • label "Oxidative demethylation of 1-meA damaged DNA by ALKBH2"

cysteine-type endopeptidase activity http://purl.obolibrary.org/obo/GO_0004197

Removed

• cysteine-type endopeptidase activity database_cross_reference "Reactome:R-HSA-6800797"
  • label "The PIDDosome activates CASP2"

genomic imprinting http://purl.obolibrary.org/obo/GO_0071514

Removed

• genomic imprinting database_cross_reference "Wikipedia:Genomic_imprinting"

glycerol-3-phosphate dehydrogenase [NAD(P)+] activity http://purl.obolibrary.org/obo/GO_0047952

Removed

• glycerol-3-phosphate dehydrogenase [NAD(P)+] activity database_cross_reference "Reactome:R-HSA-75889"
  • label "DHAP is converted to G3P by GPD1/GPD1L"

intracellular pH elevation http://purl.obolibrary.org/obo/GO_0051454

Removed

• intracellular pH elevation EquivalentTo biological regulation and (positively regulates characteristic some cellular pH)

• intracellular pH elevation SubClassOf positively regulates characteristic some cellular pH

Added

• intracellular pH elevation EquivalentTo biological regulation and (positively regulates characteristic some OBA_0000050)

• intracellular pH elevation SubClassOf positively regulates characteristic some OBA_0000050

intracellular pH reduction http://purl.obolibrary.org/obo/GO_0051452

Removed

• intracellular pH reduction EquivalentTo biological regulation and (negatively regulates characteristic some cellular pH)

• intracellular pH reduction SubClassOf negatively regulates characteristic some cellular pH

Added

• intracellular pH reduction EquivalentTo biological regulation and (negatively regulates characteristic some OBA_0000050)

• intracellular pH reduction SubClassOf negatively regulates characteristic some OBA_0000050

medium-chain fatty acid-CoA ligase activity http://purl.obolibrary.org/obo/GO_0031956

Removed

• medium-chain fatty acid-CoA ligase activity database_cross_reference "Reactome:R-HSA-8875013"
  • label "ACSM3,ACSM6 ligate CoA to BUT"

negative regulation of brood size http://purl.obolibrary.org/obo/GO_0090728

Removed

• negative regulation of brood size EquivalentTo biological regulation and (negatively regulates characteristic some brood size)

• negative regulation of brood size SubClassOf negatively regulates characteristic some brood size

• negative regulation of brood size SubClassOf regulation of brood size

Added

• negative regulation of brood size EquivalentTo biological regulation and (negatively regulates characteristic some OBA_0000037)

• negative regulation of brood size SubClassOf negatively regulates characteristic some OBA_0000037

• negative regulation of brood size SubClassOf biological regulation

obsolete 13-prostaglandin reductase activity http://purl.obolibrary.org/obo/GO_0036132

Added

• obsolete 13-prostaglandin reductase activity database_cross_reference "Reactome:R-HSA-2161692"
  • label "15k-PGE2/F2a is reduced to dhk-PGE2/F2a by PTGR1"

obsolete 2-decaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity http://purl.obolibrary.org/obo/GO_0043430

Added

• obsolete 2-decaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity database_cross_reference "Reactome:R-HSA-2162188"
  • label "MDMQ10H2 is methylated to DMQ10H2 by COQ5"

obsolete 3-demethylubiquinol-10 3-O-methyltransferase activity http://purl.obolibrary.org/obo/GO_0044596

Added

• obsolete 3-demethylubiquinol-10 3-O-methyltransferase activity database_cross_reference "Reactome:R-HSA-2162186"
  • label "DeMQ10H2 is methylated to Q10H2 by COQ3"

obsolete 4-hydroxybenzoate decaprenyltransferase activity http://purl.obolibrary.org/obo/GO_0002083

Added

• obsolete 4-hydroxybenzoate decaprenyltransferase activity database_cross_reference "Reactome:R-HSA-2162192"
  • label "PHB and all-E-10PrP2 are combined into DHB by COQ2"

obsolete DNA-N1-methyladenine dioxygenase activity http://purl.obolibrary.org/obo/GO_0043734

Added

• obsolete DNA-N1-methyladenine dioxygenase activity database_cross_reference "Reactome:R-HSA-112118"

  • label "Oxidative demethylation of 1-meA damaged DNA by ALKBH2"

• obsolete DNA-N1-methyladenine dioxygenase activity database_cross_reference "Reactome:R-HSA-112123"

  • label "Oxidative demethylation of 1-meA damaged DNA By ALKBH3"

obsolete N-acylsphingosine galactosyltransferase activity http://purl.obolibrary.org/obo/GO_0047263

Added

• obsolete N-acylsphingosine galactosyltransferase activity database_cross_reference "Reactome:R-HSA-6785933"
  • label "UGT8 transfers Gal from UDP-Gal to CERA"

obsolete N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity http://purl.obolibrary.org/obo/GO_0052904

Added

• obsolete N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity database_cross_reference "Reactome:R-HSA-141348"

  • label "PAO:FAD oxidises NASPM to PTCN"

• obsolete N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity database_cross_reference "Reactome:R-HSA-141351"

  • label "PAOX:FAD oxidises NASPN to SPM"

obsolete NAD glycohydrolase activity http://purl.obolibrary.org/obo/GO_0061810

Added

• obsolete NAD glycohydrolase activity database_cross_reference "Reactome:R-HSA-9637699"
  • label "CpnT hydrolyses NAD+"

obsolete NADPHX epimerase activity http://purl.obolibrary.org/obo/GO_0052857

Added

• obsolete NADPHX epimerase activity database_cross_reference "Reactome:R-HSA-6806966"
  • label "APOA1BP dimer epimerises R-NAD(P)HX to S-NAD(P)HX"

obsolete acid-sensing ion channel activity http://purl.obolibrary.org/obo/GO_0044736

Added

• obsolete acid-sensing ion channel activity database_cross_reference "Wikipedia:Acid-sensing_ion_channel"

• obsolete acid-sensing ion channel activity database_cross_reference "Reactome:R-HSA-2671885"

  • label "ASIC trimers:H+ transport extracellular Na+ to cytosol"

obsolete alcohol dehydrogenase (NAD+) activity, zinc-dependent http://purl.obolibrary.org/obo/GO_0004024

Added

• obsolete alcohol dehydrogenase (NAD+) activity, zinc-dependent database_cross_reference "Reactome:R-HSA-71707"
  • label "ethanol + NAD+ => acetaldehyde + NADH + H+"

obsolete biotin-protein ligase activity http://purl.obolibrary.org/obo/GO_0018271

Added

• obsolete biotin-protein ligase activity database_cross_reference "Reactome:R-HSA-9035990"

  • label "Defective HLCS does not biotinylate 6x(PCCA:PCCB)"

• obsolete biotin-protein ligase activity database_cross_reference "Reactome:R-HSA-9035988"

  • label "Defective HLCS does not biotinylate PC:Mn2+"

• obsolete biotin-protein ligase activity database_cross_reference "Reactome:R-HSA-2993802"

  • label "HLCS biotinylates PC:Mn2+"

• obsolete biotin-protein ligase activity database_cross_reference "Reactome:R-HSA-4167511"

  • label "HLCS biotinylates ACACB"

• obsolete biotin-protein ligase activity database_cross_reference "Reactome:R-HSA-2993799"

  • label "HLCS biotinylates 6xMCCC1:6xMCCC2"

• obsolete biotin-protein ligase activity database_cross_reference "Reactome:R-HSA-2993447"

  • label "HLCS biotinylates 6x(PCCA:PCCB)"

• obsolete biotin-protein ligase activity database_cross_reference "Reactome:R-HSA-9035987"

  • label "Defective HLCS does not biotinylate 6xMCCC1:6xMCCC2"

• obsolete biotin-protein ligase activity database_cross_reference "Reactome:R-HSA-2993814"

  • label "HLCS biotinylates ACACA:Mn2+"

• obsolete biotin-protein ligase activity database_cross_reference "Reactome:R-HSA-3323184"

  • label "Defective HLCS does not biotinylate ACACA:Mn2+"

obsolete butyrate-CoA ligase activity http://purl.obolibrary.org/obo/GO_0047760

Added

• obsolete butyrate-CoA ligase activity database_cross_reference "Reactome:R-HSA-8875013"
  • label "ACSM3,ACSM6 ligate CoA to BUT"

obsolete cysteine-type endopeptidase activity involved in apoptotic process http://purl.obolibrary.org/obo/GO_0097153

Added

• obsolete cysteine-type endopeptidase activity involved in apoptotic process database_cross_reference "Reactome:R-HSA-6800797"
  • label "The PIDDosome activates CASP2"

obsolete decaprenyldihydroxybenzoate methyltransferase activity http://purl.obolibrary.org/obo/GO_0044595

Added

• obsolete decaprenyldihydroxybenzoate methyltransferase activity database_cross_reference "Reactome:R-HSA-2162193"
  • label "DHDB is methylated to MHDB by COQ3"

obsolete farnesyl-diphosphate farnesyltransferase activity http://purl.obolibrary.org/obo/GO_0004310

Added

• obsolete farnesyl-diphosphate farnesyltransferase activity database_cross_reference "Reactome:R-HSA-191405"

  • label "Two FPP molecules dimerize to form presqualene diphosphate"

• obsolete farnesyl-diphosphate farnesyltransferase activity database_cross_reference "Reactome:R-HSA-191402"

  • label "Reduction of presqualene diphosphate to form squalene"

obsolete glucose transmembrane transporter activity http://purl.obolibrary.org/obo/GO_0005355

Added

• obsolete glucose transmembrane transporter activity database_cross_reference "Reactome:R-HSA-499981"

  • label "Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2"

• obsolete glucose transmembrane transporter activity database_cross_reference "Reactome:R-HSA-5653873"

  • label "SLC2A1 tetramer transports Glc from cytosol to Golgi lumen"

obsolete induction by virus of host apoptotic process http://purl.obolibrary.org/obo/GO_0019051

Added

• obsolete induction by virus of host apoptotic process database_cross_reference "VZ:910"

  • label "Activation of host caspases by virus"

  • source "skos:narrowMatch"

obsolete peptidyl-arginine C5-methylation http://purl.obolibrary.org/obo/GO_0018181

Added

• obsolete peptidyl-arginine C5-methylation database_cross_reference "RESID:AA0272"

obsolete peptidyl-asparagine hydroxylation to form L-erythro-beta-hydroxyasparagine http://purl.obolibrary.org/obo/GO_0018376

Added

• obsolete peptidyl-asparagine hydroxylation to form L-erythro-beta-hydroxyasparagine database_cross_reference "RESID:AA0026"

obsolete perturbation by virus of host apoptosis http://purl.obolibrary.org/obo/GO_0039526

Added

• obsolete perturbation by virus of host apoptosis database_cross_reference "VZ:1581"
  • label "Apoptosis modulation"

obsolete phosphatidylinositol 3-kinase activity http://purl.obolibrary.org/obo/GO_0035004

Added

• obsolete phosphatidylinositol 3-kinase activity database_cross_reference "Wikipedia:Phosphoinositide_3-kinase"

obsolete phytoceramidase activity http://purl.obolibrary.org/obo/GO_0070774

Added

• obsolete phytoceramidase activity database_cross_reference "Reactome:R-HSA-428262"
  • label "ACER3 hydrolyzes phytoceramide"

obsolete regulation of gene expression by genomic imprinting http://purl.obolibrary.org/obo/GO_0006349

Added

• obsolete regulation of gene expression by genomic imprinting database_cross_reference "Wikipedia:Genomic_imprinting"

obsolete viral entry into host cell via pilus retraction http://purl.obolibrary.org/obo/GO_0039667

Added

• obsolete viral entry into host cell via pilus retraction database_cross_reference "VZ:981"

pH-gated monoatomic ion channel activity http://purl.obolibrary.org/obo/GO_0160128

Removed

• pH-gated monoatomic ion channel activity database_cross_reference "Reactome:R-HSA-2671885"

  • label "ASIC trimers:H+ transport extracellular Na+ to cytosol"

• pH-gated monoatomic ion channel activity database_cross_reference "Wikipedia:Acid-sensing_ion_channel"

peptidyl-aspartic acid 3-dioxygenase activity http://purl.obolibrary.org/obo/GO_0062101

Removed

• peptidyl-aspartic acid 3-dioxygenase activity database_cross_reference "RESID:AA0026"

positive regulation of brood size http://purl.obolibrary.org/obo/GO_0090727

Removed

• positive regulation of brood size EquivalentTo biological regulation and (positively regulates characteristic some brood size)

• positive regulation of brood size SubClassOf regulation of brood size

• positive regulation of brood size SubClassOf positively regulates characteristic some brood size

Added

• positive regulation of brood size EquivalentTo biological regulation and (positively regulates characteristic some OBA_0000037)

• positive regulation of brood size SubClassOf positively regulates characteristic some OBA_0000037

• positive regulation of brood size SubClassOf biological regulation

protein-arginine C-methyltransferase activity http://purl.obolibrary.org/obo/GO_0035244

Removed

• protein-arginine C-methyltransferase activity database_cross_reference "RESID:AA0272"

regulation of intracellular pH http://purl.obolibrary.org/obo/GO_0051453

Removed

• regulation of intracellular pH EquivalentTo biological regulation and (regulates characteristic some cellular pH)

• regulation of intracellular pH SubClassOf regulation of biological quality

• regulation of intracellular pH SubClassOf regulates characteristic some cellular pH

Added

• regulation of intracellular pH EquivalentTo biological regulation and (regulates characteristic some OBA_0000050)

• regulation of intracellular pH SubClassOf regulates characteristic some OBA_0000050

regulation of lysosomal lumen pH http://purl.obolibrary.org/obo/GO_0035751

Added

• regulation of lysosomal lumen pH SubClassOf regulation of biological quality

squalene synthase [NAD(P)H] activity http://purl.obolibrary.org/obo/GO_0051996

Removed

• squalene synthase [NAD(P)H] activity database_cross_reference "Reactome:R-HSA-191405"

  • label "Two FPP molecules dimerize to form presqualene diphosphate"

• squalene synthase [NAD(P)H] activity database_cross_reference "Reactome:R-HSA-191402"

  • label "Reduction of presqualene diphosphate to form squalene"

symbiont-mediated perturbation of host apoptosis http://purl.obolibrary.org/obo/GO_0052150

Removed

• symbiont-mediated perturbation of host apoptosis database_cross_reference "VZ:1581"
  • label "Apoptosis modulation"