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Eliminate use of GOCHE for biological roles except where these are guaranteed rigid #16511

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cmungall opened this issue Oct 14, 2018 · 2 comments
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Eliminate use of GOCHE for biological roles except where these are guaranteed rigid #16511

cmungall opened this issue Oct 14, 2018 · 2 comments
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@krchristie
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@cmungall
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We should examine all GOCHE classes that are bearers of biological roles. For any that are context-dependent, we should specify the context with the part-of pattern; e.g. instead of Rel some (bearer-of some X-Role) use part-of some X-Process.

If the classification is rigid, ie the chemicals always bear that role, then ok to keep.

Classes that reference a GOCHE biological role bearer:

Class Name Role Role Name
GO:0009672 auxin:proton symporter activity GOCHE:22676 substance with auxin role
GO:0009733 response to auxin GOCHE:22676 substance with auxin role
GO:0009850 auxin metabolic process GOCHE:22676 substance with auxin role
GO:0009851 auxin biosynthetic process GOCHE:22676 substance with auxin role
GO:0009852 auxin catabolic process GOCHE:22676 substance with auxin role
GO:0010011 auxin binding GOCHE:22676 substance with auxin role
GO:0010252 auxin homeostasis GOCHE:22676 substance with auxin role
GO:0010315 auxin efflux GOCHE:22676 substance with auxin role
GO:0010329 auxin efflux transmembrane transporter activity GOCHE:22676 substance with auxin role
GO:0038198 auxin receptor activity GOCHE:22676 substance with auxin role
GO:0060918 auxin transport GOCHE:22676 substance with auxin role
GO:0071365 cellular response to auxin stimulus GOCHE:22676 substance with auxin role
GO:0080161 auxin transmembrane transporter activity GOCHE:22676 substance with auxin role
GO:0009672 auxin:proton symporter activity GOCHE:22676 substance with auxin role
GO:0009733 response to auxin GOCHE:22676 substance with auxin role
GO:0009850 auxin metabolic process GOCHE:22676 substance with auxin role
GO:0009851 auxin biosynthetic process GOCHE:22676 substance with auxin role
GO:0009852 auxin catabolic process GOCHE:22676 substance with auxin role
GO:0010011 auxin binding GOCHE:22676 substance with auxin role
GO:0010252 auxin homeostasis GOCHE:22676 substance with auxin role
GO:0010315 auxin efflux GOCHE:22676 substance with auxin role
GO:0010329 auxin efflux transmembrane transporter activity GOCHE:22676 substance with auxin role
GO:0038198 auxin receptor activity GOCHE:22676 substance with auxin role
GO:0060918 auxin transport GOCHE:22676 substance with auxin role
GO:0071365 cellular response to auxin stimulus GOCHE:22676 substance with auxin role
GO:0080161 auxin transmembrane transporter activity GOCHE:22676 substance with auxin role
GO:0009672 auxin:proton symporter activity GOCHE:22676 substance with auxin role
GO:0009733 response to auxin GOCHE:22676 substance with auxin role
GO:0009850 auxin metabolic process GOCHE:22676 substance with auxin role
GO:0009851 auxin biosynthetic process GOCHE:22676 substance with auxin role
GO:0009852 auxin catabolic process GOCHE:22676 substance with auxin role
GO:0010011 auxin binding GOCHE:22676 substance with auxin role
GO:0010252 auxin homeostasis GOCHE:22676 substance with auxin role
GO:0010315 auxin efflux GOCHE:22676 substance with auxin role
GO:0010329 auxin efflux transmembrane transporter activity GOCHE:22676 substance with auxin role
GO:0038198 auxin receptor activity GOCHE:22676 substance with auxin role
GO:0060918 auxin transport GOCHE:22676 substance with auxin role
GO:0071365 cellular response to auxin stimulus GOCHE:22676 substance with auxin role
GO:0080161 auxin transmembrane transporter activity GOCHE:22676 substance with auxin role
GO:0006732 coenzyme metabolic process GOCHE:23354 substance with coenzyme role
GO:0009108 coenzyme biosynthetic process GOCHE:23354 substance with coenzyme role
GO:0009109 coenzyme catabolic process GOCHE:23354 substance with coenzyme role
GO:0050662 coenzyme binding GOCHE:23354 substance with coenzyme role
GO:0051182 coenzyme transport GOCHE:23354 substance with coenzyme role
GO:0051185 coenzyme transmembrane transporter activity GOCHE:23354 substance with coenzyme role
GO:0048037 cofactor binding GOCHE:23357 substance with cofactor role
GO:0051181 cofactor transport GOCHE:23357 substance with cofactor role
GO:0051184 cofactor transmembrane transporter activity GOCHE:23357 substance with cofactor role
GO:0051186 cofactor metabolic process GOCHE:23357 substance with cofactor role
GO:0051187 cofactor catabolic process GOCHE:23357 substance with cofactor role
GO:0051188 cofactor biosynthetic process GOCHE:23357 substance with cofactor role
GO:0009690 cytokinin metabolic process GOCHE:23530 substance with cytokinin role
GO:0009691 cytokinin biosynthetic process GOCHE:23530 substance with cytokinin role
GO:0009735 response to cytokinin GOCHE:23530 substance with cytokinin role
GO:0009823 cytokinin catabolic process GOCHE:23530 substance with cytokinin role
GO:0009884 cytokinin receptor activity GOCHE:23530 substance with cytokinin role
GO:0010184 cytokinin transport GOCHE:23530 substance with cytokinin role
GO:0044373 cytokinin binding GOCHE:23530 substance with cytokinin role
GO:0071368 cellular response to cytokinin stimulus GOCHE:23530 substance with cytokinin role
GO:0009690 cytokinin metabolic process GOCHE:23530 substance with cytokinin role
GO:0009691 cytokinin biosynthetic process GOCHE:23530 substance with cytokinin role
GO:0009735 response to cytokinin GOCHE:23530 substance with cytokinin role
GO:0009823 cytokinin catabolic process GOCHE:23530 substance with cytokinin role
GO:0009884 cytokinin receptor activity GOCHE:23530 substance with cytokinin role
GO:0010184 cytokinin transport GOCHE:23530 substance with cytokinin role
GO:0044373 cytokinin binding GOCHE:23530 substance with cytokinin role
GO:0071368 cellular response to cytokinin stimulus GOCHE:23530 substance with cytokinin role
GO:0009690 cytokinin metabolic process GOCHE:23530 substance with cytokinin role
GO:0009691 cytokinin biosynthetic process GOCHE:23530 substance with cytokinin role
GO:0009735 response to cytokinin GOCHE:23530 substance with cytokinin role
GO:0009823 cytokinin catabolic process GOCHE:23530 substance with cytokinin role
GO:0009884 cytokinin receptor activity GOCHE:23530 substance with cytokinin role
GO:0010184 cytokinin transport GOCHE:23530 substance with cytokinin role
GO:0044373 cytokinin binding GOCHE:23530 substance with cytokinin role
GO:0071368 cellular response to cytokinin stimulus GOCHE:23530 substance with cytokinin role
GO:0006775 fat-soluble vitamin metabolic process GOCHE:24020 substance with fat-soluble vitamin role
GO:0042362 fat-soluble vitamin biosynthetic process GOCHE:24020 substance with fat-soluble vitamin role
GO:0042363 fat-soluble vitamin catabolic process GOCHE:24020 substance with fat-soluble vitamin role
GO:0006775 fat-soluble vitamin metabolic process GOCHE:24020 substance with fat-soluble vitamin role
GO:0042362 fat-soluble vitamin biosynthetic process GOCHE:24020 substance with fat-soluble vitamin role
GO:0042363 fat-soluble vitamin catabolic process GOCHE:24020 substance with fat-soluble vitamin role
GO:0060992 response to fungicide GOCHE:24127 substance with fungicide role
GO:0009725 response to hormone GOCHE:24621 substance with hormone role
GO:0009914 hormone transport GOCHE:24621 substance with hormone role
GO:0032870 cellular response to hormone stimulus GOCHE:24621 substance with hormone role
GO:0042445 hormone metabolic process GOCHE:24621 substance with hormone role
GO:0042446 hormone biosynthetic process GOCHE:24621 substance with hormone role
GO:0042447 hormone catabolic process GOCHE:24621 substance with hormone role
GO:0042562 hormone binding GOCHE:24621 substance with hormone role
GO:0046879 hormone secretion GOCHE:24621 substance with hormone role
GO:0009725 response to hormone GOCHE:24621 substance with hormone role
GO:0009914 hormone transport GOCHE:24621 substance with hormone role
GO:0032870 cellular response to hormone stimulus GOCHE:24621 substance with hormone role
GO:0042445 hormone metabolic process GOCHE:24621 substance with hormone role
GO:0042446 hormone biosynthetic process GOCHE:24621 substance with hormone role
GO:0042447 hormone catabolic process GOCHE:24621 substance with hormone role
GO:0042562 hormone binding GOCHE:24621 substance with hormone role
GO:0046879 hormone secretion GOCHE:24621 substance with hormone role
GO:0010046 response to mycotoxin GOCHE:25442 substance with mycotoxin role
GO:0036146 cellular response to mycotoxin GOCHE:25442 substance with mycotoxin role
GO:0043385 mycotoxin metabolic process GOCHE:25442 substance with mycotoxin role
GO:0043386 mycotoxin biosynthetic process GOCHE:25442 substance with mycotoxin role
GO:0043387 mycotoxin catabolic process GOCHE:25442 substance with mycotoxin role
GO:0010046 response to mycotoxin GOCHE:25442 substance with mycotoxin role
GO:0036146 cellular response to mycotoxin GOCHE:25442 substance with mycotoxin role
GO:0043385 mycotoxin metabolic process GOCHE:25442 substance with mycotoxin role
GO:0043386 mycotoxin biosynthetic process GOCHE:25442 substance with mycotoxin role
GO:0043387 mycotoxin catabolic process GOCHE:25442 substance with mycotoxin role
GO:0010046 response to mycotoxin GOCHE:25442 substance with mycotoxin role
GO:0036146 cellular response to mycotoxin GOCHE:25442 substance with mycotoxin role
GO:0043385 mycotoxin metabolic process GOCHE:25442 substance with mycotoxin role
GO:0043386 mycotoxin biosynthetic process GOCHE:25442 substance with mycotoxin role
GO:0043387 mycotoxin catabolic process GOCHE:25442 substance with mycotoxin role
GO:0001504 neurotransmitter uptake GOCHE:25512 substance with neurotransmitter role
GO:0005326 neurotransmitter transporter activity GOCHE:25512 substance with neurotransmitter role
GO:0005328 neurotransmitter:sodium symporter activity GOCHE:25512 substance with neurotransmitter role
GO:0006836 neurotransmitter transport GOCHE:25512 substance with neurotransmitter role
GO:0007269 neurotransmitter secretion GOCHE:25512 substance with neurotransmitter role
GO:0015842 aminergic neurotransmitter loading into synaptic vesicle GOCHE:25512 substance with neurotransmitter role
GO:0042133 neurotransmitter metabolic process GOCHE:25512 substance with neurotransmitter role
GO:0042135 neurotransmitter catabolic process GOCHE:25512 substance with neurotransmitter role
GO:0042136 neurotransmitter biosynthetic process GOCHE:25512 substance with neurotransmitter role
GO:0042165 neurotransmitter binding GOCHE:25512 substance with neurotransmitter role
GO:0051583 dopamine uptake involved in synaptic transmission GOCHE:25512 substance with neurotransmitter role
GO:0051610 serotonin uptake GOCHE:25512 substance with neurotransmitter role
GO:0051933 amino acid neurotransmitter reuptake GOCHE:25512 substance with neurotransmitter role
GO:0051934 catecholamine uptake involved in synaptic transmission GOCHE:25512 substance with neurotransmitter role
GO:0051935 glutamate reuptake GOCHE:25512 substance with neurotransmitter role
GO:0051936 gamma-aminobutyric acid reuptake GOCHE:25512 substance with neurotransmitter role
GO:0098700 neurotransmitter loading into synaptic vesicle GOCHE:25512 substance with neurotransmitter role
GO:0098810 neurotransmitter reuptake GOCHE:25512 substance with neurotransmitter role
GO:0099528 G protein-coupled neurotransmitter receptor activity GOCHE:25512 substance with neurotransmitter role
GO:0005550 pheromone binding GOCHE:26013 substance with pheromone role
GO:0016503 pheromone receptor activity GOCHE:26013 substance with pheromone role
GO:0019236 response to pheromone GOCHE:26013 substance with pheromone role
GO:0042810 pheromone metabolic process GOCHE:26013 substance with pheromone role
GO:0042811 pheromone biosynthetic process GOCHE:26013 substance with pheromone role
GO:0042812 pheromone catabolic process GOCHE:26013 substance with pheromone role
GO:0071444 cellular response to pheromone GOCHE:26013 substance with pheromone role
GO:0052314 phytoalexin metabolic process GOCHE:26115 substance with phytoalexin role
GO:0052315 phytoalexin biosynthetic process GOCHE:26115 substance with phytoalexin role
GO:0052316 phytoalexin catabolic process GOCHE:26115 substance with phytoalexin role
GO:0052314 phytoalexin metabolic process GOCHE:26115 substance with phytoalexin role
GO:0052315 phytoalexin biosynthetic process GOCHE:26115 substance with phytoalexin role
GO:0052316 phytoalexin catabolic process GOCHE:26115 substance with phytoalexin role
GO:0052314 phytoalexin metabolic process GOCHE:26115 substance with phytoalexin role
GO:0052315 phytoalexin biosynthetic process GOCHE:26115 substance with phytoalexin role
GO:0052316 phytoalexin catabolic process GOCHE:26115 substance with phytoalexin role
GO:0009237 siderophore metabolic process GOCHE:26672 substance with siderophore role
GO:0015343 siderophore transmembrane transporter activity GOCHE:26672 substance with siderophore role
GO:0015891 siderophore transport GOCHE:26672 substance with siderophore role
GO:0019539 siderophore biosynthetic process from hydroxamic acid GOCHE:26672 substance with siderophore role
GO:0019540 siderophore biosynthetic process from catechol GOCHE:26672 substance with siderophore role
GO:0044718 siderophore transmembrane transport GOCHE:26672 substance with siderophore role
GO:0046215 siderophore catabolic process GOCHE:26672 substance with siderophore role
GO:0009237 siderophore metabolic process GOCHE:26672 substance with siderophore role
GO:0015343 siderophore transmembrane transporter activity GOCHE:26672 substance with siderophore role
GO:0015891 siderophore transport GOCHE:26672 substance with siderophore role
GO:0019539 siderophore biosynthetic process from hydroxamic acid GOCHE:26672 substance with siderophore role
GO:0019540 siderophore biosynthetic process from catechol GOCHE:26672 substance with siderophore role
GO:0044718 siderophore transmembrane transport GOCHE:26672 substance with siderophore role
GO:0046215 siderophore catabolic process GOCHE:26672 substance with siderophore role
GO:0009403 toxin biosynthetic process GOCHE:27026 substance with toxin role
GO:0009404 toxin metabolic process GOCHE:27026 substance with toxin role
GO:0009407 toxin catabolic process GOCHE:27026 substance with toxin role
GO:0019534 toxin transmembrane transporter activity GOCHE:27026 substance with toxin role
GO:1901998 toxin transport GOCHE:27026 substance with toxin role
GO:0009403 toxin biosynthetic process GOCHE:27026 substance with toxin role
GO:0009404 toxin metabolic process GOCHE:27026 substance with toxin role
GO:0009407 toxin catabolic process GOCHE:27026 substance with toxin role
GO:0019534 toxin transmembrane transporter activity GOCHE:27026 substance with toxin role
GO:1901998 toxin transport GOCHE:27026 substance with toxin role
GO:0006767 water-soluble vitamin metabolic process GOCHE:27314 substance with water-soluble vitamin role
GO:0042364 water-soluble vitamin biosynthetic process GOCHE:27314 substance with water-soluble vitamin role
GO:0042365 water-soluble vitamin catabolic process GOCHE:27314 substance with water-soluble vitamin role
GO:0006767 water-soluble vitamin metabolic process GOCHE:27314 substance with water-soluble vitamin role
GO:0042364 water-soluble vitamin biosynthetic process GOCHE:27314 substance with water-soluble vitamin role
GO:0042365 water-soluble vitamin catabolic process GOCHE:27314 substance with water-soluble vitamin role
GO:0006766 vitamin metabolic process GOCHE:33229 substance with vitamin role
GO:0009110 vitamin biosynthetic process GOCHE:33229 substance with vitamin role
GO:0009111 vitamin catabolic process GOCHE:33229 substance with vitamin role
GO:0019842 vitamin binding GOCHE:33229 substance with vitamin role
GO:0033273 response to vitamin GOCHE:33229 substance with vitamin role
GO:0035461 vitamin transmembrane transport GOCHE:33229 substance with vitamin role
GO:0051180 vitamin transport GOCHE:33229 substance with vitamin role
GO:0071295 cellular response to vitamin GOCHE:33229 substance with vitamin role
GO:0090482 vitamin transmembrane transporter activity GOCHE:33229 substance with vitamin role
GO:0006766 vitamin metabolic process GOCHE:33229 substance with vitamin role
GO:0009110 vitamin biosynthetic process GOCHE:33229 substance with vitamin role
GO:0009111 vitamin catabolic process GOCHE:33229 substance with vitamin role
GO:0019842 vitamin binding GOCHE:33229 substance with vitamin role
GO:0033273 response to vitamin GOCHE:33229 substance with vitamin role
GO:0035461 vitamin transmembrane transport GOCHE:33229 substance with vitamin role
GO:0051180 vitamin transport GOCHE:33229 substance with vitamin role
GO:0071295 cellular response to vitamin GOCHE:33229 substance with vitamin role
GO:0090482 vitamin transmembrane transporter activity GOCHE:33229 substance with vitamin role
GO:0016999 antibiotic metabolic process GOCHE:33281 substance with antimicrobial agent role
GO:0017000 antibiotic biosynthetic process GOCHE:33281 substance with antimicrobial agent role
GO:0017001 antibiotic catabolic process GOCHE:33281 substance with antimicrobial agent role
GO:0042891 antibiotic transport GOCHE:33281 substance with antimicrobial agent role
GO:0042895 antibiotic transmembrane transporter activity GOCHE:33281 substance with antimicrobial agent role
GO:0046677 response to antibiotic GOCHE:33281 substance with antimicrobial agent role
GO:0071236 cellular response to antibiotic GOCHE:33281 substance with antimicrobial agent role
GO:0007584 response to nutrient GOCHE:33284 substance with nutrient role
GO:0031670 cellular response to nutrient GOCHE:33284 substance with nutrient role
GO:0032094 response to food GOCHE:33290 substance with food role
GO:0071240 cellular response to food GOCHE:33290 substance with food role
GO:0097329 response to antimetabolite GOCHE:35221 substance with antimetabolite role
GO:0098649 response to peptidyl-dipeptidase A inhibitor GOCHE:35457 substance with EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitor role
GO:0098649 response to peptidyl-dipeptidase A inhibitor GOCHE:35457 substance with EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitor role
GO:0006805 xenobiotic metabolic process GOCHE:35703 substance with xenobiotic role
GO:0008559 xenobiotic transmembrane transporting ATPase activity GOCHE:35703 substance with xenobiotic role
GO:0009410 response to xenobiotic stimulus GOCHE:35703 substance with xenobiotic role
GO:0042178 xenobiotic catabolic process GOCHE:35703 substance with xenobiotic role
GO:0042908 xenobiotic transport GOCHE:35703 substance with xenobiotic role
GO:0042910 xenobiotic transmembrane transporter activity GOCHE:35703 substance with xenobiotic role
GO:0071466 cellular response to xenobiotic stimulus GOCHE:35703 substance with xenobiotic role
GO:0004903 growth hormone receptor activity GOCHE:37845 substance with growth hormone role
GO:0030252 growth hormone secretion GOCHE:37845 substance with growth hormone role
GO:0060416 response to growth hormone GOCHE:37845 substance with growth hormone role
GO:0071378 cellular response to growth hormone stimulus GOCHE:37845 substance with growth hormone role
GO:0004903 growth hormone receptor activity GOCHE:37845 substance with growth hormone role
GO:0030252 growth hormone secretion GOCHE:37845 substance with growth hormone role
GO:0060416 response to growth hormone GOCHE:37845 substance with growth hormone role
GO:0071378 cellular response to growth hormone stimulus GOCHE:37845 substance with growth hormone role
GO:0005497 androgen binding GOCHE:50113 substance with androgen role
GO:0005497 androgen binding GOCHE:50113 substance with androgen role
GO:0099130 estrogen binding GOCHE:50114 substance with estrogen role
GO:0099130 estrogen binding GOCHE:50114 substance with estrogen role
GO:0061477 response to aromatase inhibitor GOCHE:50790 substance with EC 1.14.14.14 (aromatase) inhibitor role
GO:0061477 response to aromatase inhibitor GOCHE:50790 substance with EC 1.14.14.14 (aromatase) inhibitor role
GO:0061479 response to reverse transcriptase inhibitor GOCHE:59897 substance with EC 2.7.7.49 (RNA-directed DNA polymerase) inhibitor role
GO:0061479 response to reverse transcriptase inhibitor GOCHE:59897 substance with EC 2.7.7.49 (RNA-directed DNA polymerase) inhibitor role
GO:0061479 response to reverse transcriptase inhibitor GOCHE:59897 substance with EC 2.7.7.49 (RNA-directed DNA polymerase) inhibitor role
GO:0004887 thyroid hormone receptor activity GOCHE:60311 substance with thyroid hormone role
GO:0015349 thyroid hormone transmembrane transporter activity GOCHE:60311 substance with thyroid hormone role
GO:0042403 thyroid hormone metabolic process GOCHE:60311 substance with thyroid hormone role
GO:0042404 thyroid hormone catabolic process GOCHE:60311 substance with thyroid hormone role
GO:0070324 thyroid hormone binding GOCHE:60311 substance with thyroid hormone role
GO:0070327 thyroid hormone transport GOCHE:60311 substance with thyroid hormone role
GO:0097066 response to thyroid hormone GOCHE:60311 substance with thyroid hormone role
GO:0097067 cellular response to thyroid hormone stimulus GOCHE:60311 substance with thyroid hormone role
GO:0004887 thyroid hormone receptor activity GOCHE:60311 substance with thyroid hormone role
GO:0015349 thyroid hormone transmembrane transporter activity GOCHE:60311 substance with thyroid hormone role
GO:0042403 thyroid hormone metabolic process GOCHE:60311 substance with thyroid hormone role
GO:0042404 thyroid hormone catabolic process GOCHE:60311 substance with thyroid hormone role
GO:0070324 thyroid hormone binding GOCHE:60311 substance with thyroid hormone role
GO:0070327 thyroid hormone transport GOCHE:60311 substance with thyroid hormone role
GO:0097066 response to thyroid hormone GOCHE:60311 substance with thyroid hormone role
GO:0097067 cellular response to thyroid hormone stimulus GOCHE:60311 substance with thyroid hormone role
GO:0009636 response to toxic substance GOCHE:64909 substance with poison role
GO:0097237 cellular response to toxic substance GOCHE:64909 substance with poison role
@cmungall cmungall mentioned this issue Oct 14, 2018
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@ukemi ukemi added this to Ontology meeting Oct 15 in ontology weekly meetings Oct 15, 2018
@ukemi ukemi moved this from Ontology meeting Oct 22 to Ontology meeting November 6 in ontology weekly meetings Nov 2, 2018
@ukemi ukemi moved this from Ontology meeting November 6 to Ontology meeting Oct 22 in ontology weekly meetings Nov 2, 2018
@ukemi ukemi self-assigned this Jan 14, 2019
@ukemi ukemi added this to Ontology meeting March 18th, 2019 in ontology weekly meetings Mar 15, 2019
@ukemi ukemi moved this from Ontology meeting April 1, 2019 to April 29, 2019 in ontology weekly meetings Apr 29, 2019
@pgaudet pgaudet removed this from May 6, 2019 in ontology weekly meetings May 6, 2019
@pgaudet
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pgaudet commented May 6, 2019

ontology editors agree to remove the ChEBI roles.

@ukemi ukemi added this to In progress in ChEBI Roles Jul 23, 2019
@krchristie krchristie moved this from In progress to To do in ChEBI Roles Jul 24, 2019
@ukemi ukemi removed their assignment Aug 22, 2019
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The plan has changed significantly since this ticket was opened and it is now supplanted by other tickets.

@krchristie krchristie moved this from To do to Done in ChEBI Roles Dec 13, 2020
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