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Missing PR (Protein Ontology) axiomatization #11809

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gocentral opened this issue Apr 19, 2015 · 2 comments
Open

Missing PR (Protein Ontology) axiomatization #11809

gocentral opened this issue Apr 19, 2015 · 2 comments
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@cmungall
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enhancement logical definitions low priority
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Ontology jamboree January 2023

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@gocentral
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It seems there are various cases where we have a GO synonym derived from PR, but not equivalence axiom in GO. Many of these are candidates for missing logical defs, see attachment.

Columns:

  • scope
  • GO term
  • GO synonym (derived using PR)
  • PR ID (which is used as provenance for the synonym)

Example: FasL biosynthetic process should have axiom saying equiv to biosynthesis and has_output some PR:FasL

Reported by: cmungall

Original Ticket: geneontology/ontology-requests/11645
@gocentral gocentral self-assigned this Jul 26, 2015
@pgaudet pgaudet assigned cmungall and unassigned gocentral Aug 17, 2017
@pgaudet
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pgaudet commented Nov 13, 2020 •
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List of terms to axiomatize:

  •   exact GO:0001626 nociceptin receptor activity OFQ receptor activity PR:000012940
  •   exact GO:0005132 type I interferon receptor binding interferon-alpha/beta receptor binding PR:000008922
  •   exact GO:0005132 type I interferon receptor binding interferon-alpha/beta receptor binding PR:000008923
  •   exact GO:0007173 epidermal growth factor receptor signaling pathway ERBB1 signaling pathway PR:000006933
  •   exact GO:0007173 epidermal growth factor receptor signaling pathway receptor tyrosine-protein kinase erbB-1 signaling pathway PR:000006933
  •   exact GO:0010465 nerve growth factor receptor activity NGF receptor activity PR:000011194
  •   exact GO:0010465 nerve growth factor receptor activity beta-nerve growth factor receptor activity PR:000011194
  •   exact GO:0032455 nerve growth factor processing NGF processing PR:000011194
  •   exact GO:0032455 nerve growth factor processing beta-nerve growth factor processing PR:000011194
  •   exact GO:0032902 nerve growth factor production beta-nerve growth factor production PR:000011194
  •   exact GO:0033282 protein C inhibitor-acrosin complex PCI-ACR complex PR:000003652
  •   exact GO:0033282 protein C inhibitor-acrosin complex PCI-ACR complex PR:000014685
  •   exact GO:0033282 protein C inhibitor-acrosin complex PCI-acrosin complex PR:000014685
  •   exact GO:0033282 protein C inhibitor-acrosin complex SERPINA5-acrosin complex PR:000014685
  •   exact GO:0033282 protein C inhibitor-acrosin complex plasma serine protease inhibitor-acrosin complex PR:000014685
  •   exact GO:0033282 protein C inhibitor-acrosin complex serpin A5-acrosin complex PR:000014685
  •   exact GO:0035456 response to interferon-beta response to interferon beta PR:000008924
  •   exact GO:0035898 parathyroid hormone secretion PTH secretion PR:000013429
  •   exact GO:0035898 parathyroid hormone secretion parathormone secretion PR:000013429
  •   exact GO:0035898 parathyroid hormone secretion parathyrin secretion PR:000013429
  •   exact GO:0036024 protein C inhibitor-TMPRSS7 complex PCI-TMPRSS7 complex PR:000014685
  •   exact GO:0036024 protein C inhibitor-TMPRSS7 complex SERPINA5-TMPRSS7 complex PR:000014685
  •   exact GO:0036024 protein C inhibitor-TMPRSS7 complex plasma serine protease inhibitor-TMPRSS7 complex PR:000014685
  •   exact GO:0036024 protein C inhibitor-TMPRSS7 complex protein C inhibitor-matriptase-3 complex PR:000016461
  •   exact GO:0036024 protein C inhibitor-TMPRSS7 complex protein C inhibitor-transmembrane protease serine 7 complex PR:000016461
  •   exact GO:0036024 protein C inhibitor-TMPRSS7 complex serpin A5-TMPRSS7 complex PR:000014685
  •   exact GO:0036025 protein C inhibitor-TMPRSS11E complex PCI-TMPRSS11E complex PR:000014685
  •   exact GO:0036025 protein C inhibitor-TMPRSS11E complex SERPINA5-TMPRSS11E complex PR:000014685
  •   exact GO:0036025 protein C inhibitor-TMPRSS11E complex plasma serine protease inhibitor-TMPRSS11E complex PR:000014685
  •   exact GO:0036025 protein C inhibitor-TMPRSS11E complex protein C inhibitor-transmembrane protease serine 11E complex PR:000016451
  •   exact GO:0036025 protein C inhibitor-TMPRSS11E complex serpin A5-TMPRSS11E complex PR:000014685
  •   exact GO:0036026 protein C inhibitor-PLAT complex PCI-PLAT complex PR:000014685
  •   exact GO:0036026 protein C inhibitor-PLAT complex SERPINA5-PLAT complex PR:000014685
  •   exact GO:0036026 protein C inhibitor-PLAT complex plasma serine protease inhibitor-PLAT complex PR:000014685
  •   exact GO:0036026 protein C inhibitor-PLAT complex protein C inhibitor-tPA complex PR:000012825
  •   exact GO:0036026 protein C inhibitor-PLAT complex protein C inhibitor-tissue-type plasminogen activator complex PR:000012825
  •   exact GO:0036026 protein C inhibitor-PLAT complex serpin A5-PLAT complex PR:000014685
  •   exact GO:0036027 protein C inhibitor-PLAU complex PCI-PLAU complex PR:000014685
  •   exact GO:0036027 protein C inhibitor-PLAU complex SERPINA5-PLAU complex PR:000014685
  •   exact GO:0036027 protein C inhibitor-PLAU complex plasma serine protease inhibitor-PLAU complex PR:000014685
  •   exact GO:0036027 protein C inhibitor-PLAU complex protein C inhibitor-U-plasminogen activator complex PR:000012826
  •   exact GO:0036027 protein C inhibitor-PLAU complex protein C inhibitor-uPA complex PR:000012826
  •   exact GO:0036027 protein C inhibitor-PLAU complex protein C inhibitor-urokinase-type plasminogen activator complex PR:000012826
  •   exact GO:0036027 protein C inhibitor-PLAU complex serpin A5-PLAU complex PR:000014685
  •   exact GO:0036028 protein C inhibitor-thrombin complex PCI-thrombin complex PR:000014685
  •   exact GO:0036028 protein C inhibitor-thrombin complex SERPINA5-thrombin complex PR:000014685
  •   exact GO:0036028 protein C inhibitor-thrombin complex plasma serine protease inhibitor-thrombin complex PR:000014685
  •   exact GO:0036028 protein C inhibitor-thrombin complex protein C inhibitor-F2 complex PR:000007299
  •   exact GO:0036028 protein C inhibitor-thrombin complex protein C inhibitor-coagulation factor II complex PR:000007299
  •   exact GO:0036028 protein C inhibitor-thrombin complex serpin A5-thrombin complex PR:000014685
  •   exact GO:0036029 protein C inhibitor-KLK3 complex PCI-KLK3 complex PR:000014685
  •   exact GO:0036029 protein C inhibitor-KLK3 complex SERPINA5-KLK3 complex PR:000014685
  •   exact GO:0036029 protein C inhibitor-KLK3 complex plasma serine protease inhibitor-KLK3 complex PR:000014685
  •   exact GO:0036029 protein C inhibitor-KLK3 complex protein C inhibitor-kallikrein-3 complex PR:000003015
  •   exact GO:0036029 protein C inhibitor-KLK3 complex protein C inhibitor-prostate-specific antigen complex PR:000003015
  •   exact GO:0036029 protein C inhibitor-KLK3 complex serpin A5-KLK3 complex PR:000014685
  •   exact GO:0036030 protein C inhibitor-plasma kallikrein complex PCI-plasma kallikrein complex PR:000014685
  •   exact GO:0036030 protein C inhibitor-plasma kallikrein complex SERPINA5-plasma kallikrein complex PR:000014685
  •   exact GO:0036030 protein C inhibitor-plasma kallikrein complex plasma serine protease inhibitor-plasma kallikrein complex PR:000014685
  •   exact GO:0036030 protein C inhibitor-plasma kallikrein complex protein C inhibitor-KLKB1 complex PR:000009420
  •   exact GO:0036030 protein C inhibitor-plasma kallikrein complex serpin A5-plasma kallikrein complex PR:000014685
  •   exact GO:0036215 response to stem cell factor response to KIT ligand PR:000009345
  •   exact GO:0036215 response to stem cell factor response to SCF PR:000009345
  •   exact GO:0036215 response to stem cell factor response to hematopoietic growth factor KL PR:000009345
  •   exact GO:0036216 cellular response to stem cell factor stimulus cellular response to KIT ligand PR:000009345
  •   exact GO:0036216 cellular response to stem cell factor stimulus cellular response to SCF PR:000009345
  •   exact GO:0036216 cellular response to stem cell factor stimulus cellular response to hematopoietic growth factor KL PR:000009345
  •   exact GO:0036323 vascular endothelial growth factor receptor-1 signaling pathway FLT1 signaling pathway PR:000007563
  •   exact GO:0036323 vascular endothelial growth factor receptor-1 signaling pathway VEGFR-1 signaling pathway PR:000007563
  •   exact GO:0036324 vascular endothelial growth factor receptor-2 signaling pathway FLK-1 signaling pathway PR:000002112
  •   exact GO:0036324 vascular endothelial growth factor receptor-2 signaling pathway KDR signaling pathway PR:000002112
  •   exact GO:0036324 vascular endothelial growth factor receptor-2 signaling pathway VEGFR-2 signaling pathway PR:000002112
  •   exact GO:0036325 vascular endothelial growth factor receptor-3 signaling pathway FLT4 signaling pathway PR:000007565
  •   exact GO:0036326 VEGF-A-activated receptor activity vascular endothelial growth factor A-activated receptor activity PR:000017284
  •   exact GO:0036327 VEGF-B-activated receptor activity vascular endothelial growth factor B-activated receptor activity PR:000003096
  •   exact GO:0036328 VEGF-C-activated receptor activity VEGFC-activated receptor activity PR:000017285
  •   exact GO:0036328 VEGF-C-activated receptor activity vascular endothelial growth factor C-activated receptor activity PR:000017285
  •   exact GO:0036329 VEGF-D-activated receptor activity C-fos induced growth factor receptor activity PR:000007520
  •   exact GO:0036329 VEGF-D-activated receptor activity VEGFD-activated receptor activity PR:000017285
  •   exact GO:0036329 VEGF-D-activated receptor activity vascular endothelial growth factor D-activated receptor activity PR:000007520
  •   exact GO:0036363 transforming growth factor beta activation TGF-beta activation PR:000000046
  •   exact GO:0036364 transforming growth factor beta1 activation TGF-beta 1 activation PR:000000182
  •   exact GO:0036364 transforming growth factor beta1 activation TGFB1 activation PR:000000182
  •   exact GO:0036365 transforming growth factor beta2 activation TGF-beta 2 activation PR:000000183
  •   exact GO:0036365 transforming growth factor beta2 activation TGFB2 activation PR:000000183
  •   exact GO:0036366 transforming growth factor beta3 activation TGF-beta 3 activation PR:000000184
  •   exact GO:0036366 transforming growth factor beta3 activation TGFB3 activation PR:000000184
  •   exact GO:0038025 reelin receptor activity reeler receptor activity PR:000013879
  •   exact GO:0038026 reelin-mediated signaling pathway reeler-mediated signaling pathway PR:000013879
  •   exact GO:0038058 TNFSF11 receptor activity RANKL receptor activity PR:000002107
  •   exact GO:0038058 TNFSF11 receptor activity tumor necrosis factor ligand superfamily member 11 receptor activity PR:000002107
  •   exact GO:0038122 C-C motif chemokine 5 receptor activity CCL5 receptor activity PR:000002094
  •   exact GO:0038122 C-C motif chemokine 5 receptor activity small inducible cytokine A5 receptor activity PR:000002094
  •   exact GO:0038128 ERBB2 signaling pathway HER2 signaling pathway PR:000002082
  •   exact GO:0038128 ERBB2 signaling pathway receptor tyrosine-protein kinase erbB-2 signaling pathway PR:000002082
  •   exact GO:0038129 ERBB3 signaling pathway HER3 signaling pathway PR:000007159
  •   exact GO:0038129 ERBB3 signaling pathway receptor tyrosine-protein kinase erbB-3 signaling pathway PR:000007159
  •   exact GO:0038130 ERBB4 signaling pathway HER4 signaling pathway PR:000007160
  •   exact GO:0038130 ERBB4 signaling pathway receptor tyrosine-protein kinase erbB-4 signaling pathway PR:000007160
  •   exact GO:0038133 ERBB2-ERBB3 signaling pathway HER2-HER3 signaling pathway PR:000002082
  •   exact GO:0038133 ERBB2-ERBB3 signaling pathway HER2-HER3 signaling pathway PR:000007159
  •   exact GO:0038134 ERBB2-EGFR signaling pathway EGFR-HER2 signaling pathway PR:000002082
  •   exact GO:0038134 ERBB2-EGFR signaling pathway EGFR-HER2 signaling pathway PR:000006933
  •   exact GO:0038135 ERBB2-ERBB4 signaling pathway HER2-HER4 signaling pathway PR:000002082
  •   exact GO:0038135 ERBB2-ERBB4 signaling pathway HER2-HER4 signaling pathway PR:000007160
  •   exact GO:0038136 ERBB3-ERBB4 signaling pathway HER3-HER4 signaling pathway PR:000007159
  •   exact GO:0038136 ERBB3-ERBB4 signaling pathway HER3-HER4 signaling pathway PR:000007160
  •   exact GO:0038137 ERBB4-EGFR signaling pathway ERBB1-ERBB4 signaling pathway PR:000006933
  •   exact GO:0038137 ERBB4-EGFR signaling pathway ERBB1-ERBB4 signaling pathway PR:000007160
  •   exact GO:0038137 ERBB4-EGFR signaling pathway HER1-HER4 signaling pathway PR:000006933
  •   exact GO:0038137 ERBB4-EGFR signaling pathway HER1-HER4 signaling pathway PR:000007160
  •   exact GO:0038138 ERBB4-ERBB4 signaling pathway HER4-HER4 signaling pathway PR:000007160
  •   exact GO:0038146 chemokine (C-X-C motif) ligand 12 signaling pathway SDF1 signaling pathway PR:000006066
  •   exact GO:0038146 chemokine (C-X-C motif) ligand 12 signaling pathway stromal cell-derived factor-1 signaling pathway PR:000006066
  •   exact GO:0038147 C-X-C motif chemokine 12 receptor activity stromal cell-derived factor-1 receptor activity PR:000006066
  •   exact GO:0038150 C-C chemokine receptor CCR2 signaling pathway C-C chemokine receptor type 2 signaling pathway PR:000001199
  •   exact GO:0038152 C-C chemokine receptor CCR4 signaling pathway C-C chemokine receptor type 4 signaling pathway PR:000001200
  •   exact GO:0038157 granulocyte-macrophage colony-stimulating factor signaling pathway CSF2 signaling pathway PR:000005931
  •   exact GO:0038157 granulocyte-macrophage colony-stimulating factor signaling pathway GM-CSF signaling pathway PR:000005931
  •   exact GO:0038158 granulocyte colony-stimulating factor signaling pathway CSF3 signaling pathway PR:000005932
  •   exact GO:0038158 granulocyte colony-stimulating factor signaling pathway G-CSF signaling pathway PR:000005932
  •   exact GO:0038159 C-X-C chemokine receptor CXCR4 signaling pathway CXCR4 signaling pathway PR:000001208
  •   exact GO:0038161 prolactin signaling pathway PRL signaling pathway PR:000013246
  •   exact GO:0038163 thrombopoietin-mediated signaling pathway THPO signaling pathway PR:000016318
  •   exact GO:0038163 thrombopoietin-mediated signaling pathway thrombopoietin receptor signaling pathway PR:000001939
  •   exact GO:0038165 oncostatin-M-mediated signaling pathway OSM signaling pathway PR:000012059
  •   exact GO:0038172 interleukin-33-mediated signaling pathway IL33 signaling pathway PR:000001389
  •   exact GO:0038173 interleukin-17A-mediated signaling pathway IL17A signaling pathway PR:000001138
  •   exact GO:0038180 nerve growth factor signaling pathway NGF signaling pathway PR:000011194
  •   exact GO:0039545 suppression by virus of host MAVS activity suppression by virus of host mitochondrial antiviral-signaling protein PR:000010210
  •   exact GO:0039548 suppression by virus of host IRF3 activity suppression by virus of host interferon regulatory factor 3 PR:000002045
  •   exact GO:0039557 suppression by virus of host IRF7 activity suppression by virus of host interferon regulatory factor 7 activity PR:000002049
  •   exact GO:0039560 suppression by virus of host IRF9 activity suppression by virus of host interferon regulatory factor 9 activity PR:000002051
  •   exact GO:0039574 suppression by virus of host TYK2 activity suppression by virus of host non-receptor tyrosine-protein kinase TYK2 activity PR:000016874
  •   exact GO:0039576 suppression by virus of host JAK1 activity suppression by virus of host janus kinase 1 activity PR:000009196
  •   exact GO:0039580 suppression by virus of host PKR activity suppression by virus of host EIF2AK2 activity PR:000006959
  •   exact GO:0045210 FasL biosynthetic process fas ligand biosynthetic process PR:000000095
  •   exact GO:0072535 tumor necrosis factor (ligand) superfamily member 11 production RANKL production PR:000002107
  •   exact GO:0072535 tumor necrosis factor (ligand) superfamily member 11 production TNFSF11 production PR:000002107
  •   exact GO:0072535 tumor necrosis factor (ligand) superfamily member 11 production tumor necrosis factor ligand superfamily member 11 production PR:000002107
  •   exact GO:0097181 protein C inhibitor-coagulation factor V complex PCI-coagulation factor V complex PR:000014685
  •   exact GO:0097181 protein C inhibitor-coagulation factor V complex SERPINA5-coagulation factor V complex PR:000014685
  •   exact GO:0097181 protein C inhibitor-coagulation factor V complex plasma serine protease inhibitor-coagulation factor V complex PR:000014685
  •   exact GO:0097181 protein C inhibitor-coagulation factor V complex protein C inhibitor-F5 complex PR:000007300
  •   exact GO:0097181 protein C inhibitor-coagulation factor V complex serpin A5-coagulation factor V complex PR:000014685
  •   exact GO:0097182 protein C inhibitor-coagulation factor Xa complex PCI-coagulation factor Xa complex PR:000014685
  •   exact GO:0097182 protein C inhibitor-coagulation factor Xa complex SERPINA5-coagulation factor Xa complex PR:000014685
  •   exact GO:0097182 protein C inhibitor-coagulation factor Xa complex plasma serine protease inhibitor-coagulation factor Xa complex PR:000014685
  •   exact GO:0097182 protein C inhibitor-coagulation factor Xa complex serpin A5-coagulation factor Xa complex PR:000014685
  •   exact GO:0097183 protein C inhibitor-coagulation factor XI complex PCI-coagulation factor XI complex PR:000014685
  •   exact GO:0097183 protein C inhibitor-coagulation factor XI complex SERPINA5-coagulation factor XI complex PR:000014685
  •   exact GO:0097183 protein C inhibitor-coagulation factor XI complex plasma serine protease inhibitor-coagulation factor XI complex PR:000014685
  •   exact GO:0097183 protein C inhibitor-coagulation factor XI complex protein C inhibitor-F11 complex PR:000007295
  •   exact GO:0097183 protein C inhibitor-coagulation factor XI complex serpin A5-coagulation factor XI complex PR:000014685
  •   narrow GO:0005132 type I interferon receptor binding IFNAR1 binding PR:000008922
  •   narrow GO:0005132 type I interferon receptor binding IFNAR2 binding PR:000008923
  •   narrow GO:0034348 type III interferon receptor activity interferon-lambda receptor activity PR:000001362
  •   narrow GO:0038196 type III interferon signaling pathway interferon lambda signaling pathway PR:000001362
  •   related GO:0038115 chemokine (C-C motif) ligand 19 signaling pathway C-C chemokine receptor type 7 signaling pathway PR:000001203
  •   related GO:0038116 chemokine (C-C motif) ligand 21 signaling pathway C-C chemokine receptor type 7 signaling pathway PR:000001203
  •   related GO:0038118 C-C chemokine receptor CCR7 signaling pathway CCR7 signaling pathway PR:000001203
  •   related GO:0038121 C-C motif chemokine 21 receptor activity CCL21 receptor activity PR:000001993
  •   related GO:0038147 C-X-C motif chemokine 12 receptor activity SDF-1 receptor activity PR:000006066

@pgaudet pgaudet added this to To do in Ontology jamboree January 2023 via automation Jan 13, 2023
@pgaudet pgaudet moved this from To do to Chris in Ontology jamboree January 2023 Jan 13, 2023
@pgaudet pgaudet changed the title Missing PR axiomatization Missing PR (Protein Ontology) axiomatization Jan 18, 2023
@pgaudet
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pgaudet commented Jan 18, 2023

From @hdrabkin

Standard PRO definitions are something like "A protein that this the translation product of human xx or a human ortholog thereof" -- what does that mean if there is a 1-n ortholog relation? Would we need to check to check on the orthology before creating a LD ?

@cmungall Do we want to do this ?

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enhancement logical definitions low priority
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Ontology jamboree January 2023
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