From 6426dcfd34db105bd5348bb1eac688a2595c30f3 Mon Sep 17 00:00:00 2001 From: Edith Wong Date: Fri, 18 Oct 2024 13:05:33 -0700 Subject: [PATCH] Obsoleted rest of cellular metabolic process terms; Fixes #29021, #28908 --- src/ontology/go-edit.obo | 124 +++++++++++++++++++-------------------- 1 file changed, 61 insertions(+), 63 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index a0bc5b22e..e58d11dcf 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -167494,7 +167494,7 @@ synonym: "cell septum edging hydrolysis" EXACT [] synonym: "hydrolysis of cell septum edging" EXACT [] synonym: "hydrolysis of edging of cell septum" EXACT [] synonym: "septum edging hydrolysis" BROAD [] -is_a: GO:0071999 ! extracellular polysaccharide catabolic process +is_a: GO:0000272 ! polysaccharide catabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input GO:0043188 ! cell septum edging relationship: part_of GO:0000920 ! septum digestion after cytokinesis @@ -170747,56 +170747,48 @@ relationship: part_of GO:0031321 ! ascospore-type prospore assembly [Term] id: GO:0031323 -name: regulation of cellular metabolic process +name: obsolete regulation of cellular metabolic process namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate +def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] +comment: The reason for obsoletion is that this term is redundant to GO:0019222, regulation of metabolic process synonym: "regulation of cellular metabolism" EXACT [] -is_a: GO:0019222 ! regulation of metabolic process -is_a: GO:0050794 ! regulation of cellular process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0044237 ! cellular metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29021" xsd:anyURI +is_obsolete: true +replaced_by: GO:0019222 [Term] id: GO:0031324 -name: negative regulation of cellular metabolic process +name: obsolete negative regulation of cellular metabolic process namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate +def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] +comment: The reason for obsoletion is that term is redundant to GO:0009892, negative regulation of metabolic process synonym: "down regulation of cellular metabolic process" EXACT [] synonym: "down-regulation of cellular metabolic process" EXACT [] synonym: "downregulation of cellular metabolic process" EXACT [] synonym: "inhibition of cellular metabolic process" NARROW [] synonym: "negative regulation of cellular metabolism" EXACT [] -is_a: GO:0009892 ! negative regulation of metabolic process -is_a: GO:0031323 ! regulation of cellular metabolic process -is_a: GO:0048523 ! negative regulation of cellular process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0044237 ! cellular metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29021" xsd:anyURI +is_obsolete: true +replaced_by: GO:0009892 [Term] id: GO:0031325 -name: positive regulation of cellular metabolic process +name: obsolete positive regulation of cellular metabolic process namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate +def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] +comment: The reason for obsoletion is that this term is redundant to GO:0009893 synonym: "activation of cellular metabolic process" NARROW [] synonym: "positive regulation of cellular metabolism" EXACT [] synonym: "stimulation of cellular metabolic process" NARROW [] synonym: "up regulation of cellular metabolic process" EXACT [] synonym: "up-regulation of cellular metabolic process" EXACT [] synonym: "upregulation of cellular metabolic process" EXACT [] -is_a: GO:0009893 ! positive regulation of metabolic process -is_a: GO:0031323 ! regulation of cellular metabolic process -is_a: GO:0048522 ! positive regulation of cellular process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0044237 ! cellular metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29021" xsd:anyURI +is_obsolete: true +replaced_by: GO:0009893 [Term] id: GO:0031326 @@ -176928,7 +176920,7 @@ namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids." [GOC:mah] synonym: "regulation of glucocorticoid metabolism" EXACT [] is_a: GO:0019218 ! regulation of steroid metabolic process -is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0019222 ! regulation of metabolic process is_a: GO:0032350 ! regulation of hormone metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008211 ! glucocorticoid metabolic process @@ -176943,7 +176935,7 @@ synonym: "down-regulation of glucocorticoid metabolic process" EXACT [] synonym: "downregulation of glucocorticoid metabolic process" EXACT [] synonym: "inhibition of glucocorticoid metabolic process" NARROW [] synonym: "negative regulation of glucocorticoid metabolism" EXACT [] -is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0031943 ! regulation of glucocorticoid metabolic process is_a: GO:0032351 ! negative regulation of hormone metabolic process is_a: GO:0045939 ! negative regulation of steroid metabolic process @@ -176961,7 +176953,7 @@ synonym: "stimulation of glucocorticoid metabolic process" NARROW [] synonym: "up regulation of glucocorticoid metabolic process" EXACT [] synonym: "up-regulation of glucocorticoid metabolic process" EXACT [] synonym: "upregulation of glucocorticoid metabolic process" EXACT [] -is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0031943 ! regulation of glucocorticoid metabolic process is_a: GO:0032352 ! positive regulation of hormone metabolic process is_a: GO:0045940 ! positive regulation of steroid metabolic process @@ -181058,7 +181050,7 @@ synonym: "down-regulation of aldosterone metabolic process" EXACT [] synonym: "downregulation of aldosterone metabolic process" EXACT [] synonym: "inhibition of aldosterone metabolic process" NARROW [] synonym: "negative regulation of aldosterone metabolism" EXACT [] -is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0032344 ! regulation of aldosterone metabolic process is_a: GO:0032351 ! negative regulation of hormone metabolic process is_a: GO:0045939 ! negative regulation of steroid metabolic process @@ -181076,7 +181068,7 @@ synonym: "stimulation of aldosterone metabolic process" NARROW [] synonym: "up regulation of aldosterone metabolic process" EXACT [] synonym: "up-regulation of aldosterone metabolic process" EXACT [] synonym: "upregulation of aldosterone metabolic process" EXACT [] -is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0032344 ! regulation of aldosterone metabolic process is_a: GO:0032352 ! positive regulation of hormone metabolic process is_a: GO:0045940 ! positive regulation of steroid metabolic process @@ -247636,7 +247628,7 @@ id: GO:0043467 name: regulation of generation of precursor metabolites and energy namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances." [GOC:jl] -is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006091 ! generation of precursor metabolites and energy @@ -255793,15 +255785,15 @@ creation_date: 2010-01-07T04:07:24Z [Term] id: GO:0044237 -name: cellular metabolic process +name: obsolete cellular metabolic process namespace: biological_process -def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate +def: "OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] +comment: The reason for obsoletion is that this term is now redundant with GO:0008152, metabolic process synonym: "cellular metabolism" EXACT [] synonym: "intermediary metabolism" RELATED [GOC:mah] -is_a: GO:0008152 ! metabolic process -is_a: GO:0009987 ! cellular process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29021" xsd:anyURI +is_obsolete: true +replaced_by: GO:0008152 [Term] id: GO:0044238 @@ -277423,11 +277415,14 @@ intersection_of: has_primary_input_or_output CHEBI:73774 ! enterobacterial commo [Term] id: GO:0046379 -name: extracellular polysaccharide metabolic process +name: obsolete extracellular polysaccharide metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving polysaccharides used in extracellular structures." [GOC:ai] +def: "OBSOLETE. The chemical reactions and pathways involving polysaccharides used in extracellular structures." [GOC:ai] +comment: The reason for obsoletion is that this term is redundant with GO:0005976, polysaccharide metabolic process synonym: "extracellular polysaccharide metabolism" EXACT [] -is_a: GO:0005976 ! polysaccharide metabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29021" xsd:anyURI +is_obsolete: true +replaced_by: GO:0005976 [Term] id: GO:0046380 @@ -283508,13 +283503,14 @@ intersection_of: has_primary_output CHEBI:77636 ! fatty acyl-CoA(4-) [Term] id: GO:0046950 -name: cellular ketone body metabolic process +name: obsolete cellular ketone body metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism." [ISBN:0198506732] -subset: goslim_pir +def: "OBSOLETE. The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism." [ISBN:0198506732] +comment: The reason for obsoletion is that this term is redundant to GO:1902224, ketone body metabolic process synonym: "cellular ketone body metabolism" EXACT [] -is_a: GO:0008152 ! metabolic process -is_a: GO:0044281 ! small molecule metabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29021" xsd:anyURI +is_obsolete: true +replaced_by: GO:1902224 [Term] id: GO:0046951 @@ -283526,7 +283522,7 @@ synonym: "ketone body biosynthesis" EXACT [] synonym: "ketone body formation" EXACT [] synonym: "ketone body synthesis" EXACT [] is_a: GO:0044283 ! small molecule biosynthetic process -is_a: GO:0046950 ! cellular ketone body metabolic process +is_a: GO:1902224 ! ketone body metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:73693 ! ketone body @@ -283542,7 +283538,7 @@ synonym: "ketone body degradation" EXACT [] synonym: "utilization of ketone bodies" EXACT [] xref: MetaCyc:PWY66-368 is_a: GO:0044282 ! small molecule catabolic process -is_a: GO:0046950 ! cellular ketone body metabolic process +is_a: GO:1902224 ! ketone body metabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:73693 ! ketone body @@ -317118,7 +317114,7 @@ name: regulation of lipoprotein metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipoproteins, any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids." [GOC:ai] synonym: "regulation of lipoprotein metabolism" EXACT [] -is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042157 ! lipoprotein metabolic process @@ -317147,7 +317143,7 @@ synonym: "down-regulation of lipoprotein metabolic process" EXACT [] synonym: "downregulation of lipoprotein metabolic process" EXACT [] synonym: "inhibition of lipoprotein metabolic process" NARROW [] synonym: "negative regulation of lipoprotein metabolism" EXACT [] -is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042157 ! lipoprotein metabolic process @@ -388200,14 +388196,16 @@ creation_date: 2010-10-25T03:41:44Z [Term] id: GO:0071999 -name: extracellular polysaccharide catabolic process +name: obsolete extracellular polysaccharide catabolic process namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of polysaccharides used in extracellular structures." [GOC:mah, GOC:vw] +def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of polysaccharides used in extracellular structures." [GOC:mah, GOC:vw] +comment: The reason for obsoletion is that this term is now redundant with GO:0000272, polysaccharide catabolic process synonym: "extracellular polysaccharide breakdown" EXACT [GOC:mah] synonym: "extracellular polysaccharide catabolism" EXACT [GOC:mah] synonym: "extracellular polysaccharide degradation" EXACT [GOC:mah] -is_a: GO:0000272 ! polysaccharide catabolic process -is_a: GO:0046379 ! extracellular polysaccharide metabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI +is_obsolete: true +replaced_by: GO:0000272 created_by: mah creation_date: 2010-10-25T05:11:25Z @@ -542885,7 +542883,7 @@ namespace: biological_process def: "Any process that modulates the frequency, rate or extent of bile acid metabolic process." [GO_REF:0000058, GOC:bf, GOC:TermGenie] synonym: "regulation of bile acid metabolism" EXACT [GOC:TermGenie] is_a: GO:0019218 ! regulation of steroid metabolic process -is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008206 ! bile acid metabolic process created_by: bf @@ -542905,7 +542903,7 @@ synonym: "downregulation of bile acid metabolism" EXACT [GOC:TermGenie] synonym: "inhibition of bile acid metabolic process" NARROW [GOC:TermGenie] synonym: "inhibition of bile acid metabolism" NARROW [GOC:TermGenie] synonym: "negative regulation of bile acid metabolism" EXACT [GOC:TermGenie] -is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0045939 ! negative regulation of steroid metabolic process is_a: GO:1904251 ! regulation of bile acid metabolic process intersection_of: GO:0065007 ! biological regulation @@ -592296,7 +592294,7 @@ id: GO:2000609 name: regulation of thyroid hormone generation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of thyroid hormone generation." [GOC:obol] -is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0019222 ! regulation of metabolic process is_a: GO:0032350 ! regulation of hormone metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006590 ! thyroid hormone generation @@ -592308,7 +592306,7 @@ id: GO:2000610 name: negative regulation of thyroid hormone generation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of thyroid hormone generation." [GOC:obol] -is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0032351 ! negative regulation of hormone metabolic process is_a: GO:2000609 ! regulation of thyroid hormone generation intersection_of: GO:0065007 ! biological regulation @@ -592321,7 +592319,7 @@ id: GO:2000611 name: positive regulation of thyroid hormone generation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of thyroid hormone generation." [GOC:obol] -is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0032352 ! positive regulation of hormone metabolic process is_a: GO:2000609 ! regulation of thyroid hormone generation intersection_of: GO:0065007 ! biological regulation @@ -596219,7 +596217,7 @@ name: regulation of amylopectin metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of amylopectin metabolic process." [GOC:mengo_curators] synonym: "regulation of Amylopectin metabolism" EXACT [GOC:obol] -is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:2000896 ! amylopectin metabolic process created_by: tt @@ -596231,7 +596229,7 @@ name: negative regulation of amylopectin metabolic process namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of amylopectin metabolic process." [GOC:mengo_curators] synonym: "negative regulation of Amylopectin metabolism" EXACT [GOC:obol] -is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:2000896 ! amylopectin metabolic process created_by: tt @@ -596243,7 +596241,7 @@ name: positive regulation of amylopectin metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of amylopectin metabolic process." [GOC:mengo_curators] synonym: "positive regulation of Amylopectin metabolism" EXACT [GOC:obol] -is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:2000896 ! amylopectin metabolic process created_by: tt