Obsoleted rest of cellular metabolic process terms; Fixes #29021, #28908

[edwong57]

No description provided.

[github-actions]

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/2024-10-18/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/2024-10-18/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

cell septum edging catabolic process http://purl.obolibrary.org/obo/GO_0030995

Removed

• cell septum edging catabolic process SubClassOf obsolete extracellular polysaccharide catabolic process

Added

• cell septum edging catabolic process SubClassOf polysaccharide catabolic process

ketone body biosynthetic process http://purl.obolibrary.org/obo/GO_0046951

Removed

• ketone body biosynthetic process SubClassOf obsolete cellular ketone body metabolic process

ketone body catabolic process http://purl.obolibrary.org/obo/GO_0046952

Removed

• ketone body catabolic process SubClassOf obsolete cellular ketone body metabolic process

negative regulation of aldosterone metabolic process http://purl.obolibrary.org/obo/GO_0032345

Removed

• negative regulation of aldosterone metabolic process SubClassOf obsolete negative regulation of cellular metabolic process

negative regulation of amylopectin metabolic process http://purl.obolibrary.org/obo/GO_2000943

Removed

• negative regulation of amylopectin metabolic process SubClassOf obsolete negative regulation of cellular metabolic process

negative regulation of bile acid metabolic process http://purl.obolibrary.org/obo/GO_1904252

Removed

• negative regulation of bile acid metabolic process SubClassOf obsolete negative regulation of cellular metabolic process

negative regulation of glucocorticoid metabolic process http://purl.obolibrary.org/obo/GO_0031944

Removed

• negative regulation of glucocorticoid metabolic process SubClassOf obsolete negative regulation of cellular metabolic process

negative regulation of lipoprotein metabolic process http://purl.obolibrary.org/obo/GO_0050748

Removed

• negative regulation of lipoprotein metabolic process SubClassOf obsolete negative regulation of cellular metabolic process

negative regulation of thyroid hormone generation http://purl.obolibrary.org/obo/GO_2000610

Removed

• negative regulation of thyroid hormone generation SubClassOf obsolete negative regulation of cellular metabolic process

obsolete cellular ketone body metabolic process http://purl.obolibrary.org/obo/GO_0046950

Removed

• obsolete cellular ketone body metabolic process label "cellular ketone body metabolic process"

• obsolete cellular ketone body metabolic process in_subset goslim_pir

• obsolete cellular ketone body metabolic process definition "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."

  • database_cross_reference "ISBN:0198506732"

• obsolete cellular ketone body metabolic process SubClassOf small molecule metabolic process

Added

• obsolete cellular ketone body metabolic process label "obsolete cellular ketone body metabolic process"

• obsolete cellular ketone body metabolic process definition "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."

  • database_cross_reference "ISBN:0198506732"

• obsolete cellular ketone body metabolic process comment "The reason for obsoletion is that this term is redundant to GO:1902224, ketone body metabolic process"

• obsolete cellular ketone body metabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/29021"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete cellular ketone body metabolic process term replaced by "GO:1902224"

• obsolete cellular ketone body metabolic process deprecated true

obsolete cellular metabolic process http://purl.obolibrary.org/obo/GO_0044237

Removed

• obsolete cellular metabolic process definition "The chemical reactions and pathways by which individual cells transform chemical substances."

  • database_cross_reference "GOC:go_curators"

• obsolete cellular metabolic process in_subset gocheck_do_not_annotate

• obsolete cellular metabolic process label "cellular metabolic process"

• obsolete cellular metabolic process 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."

• obsolete cellular metabolic process SubClassOf metabolic process

Added

• obsolete cellular metabolic process term replaced by "GO:0008152"

• obsolete cellular metabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/29021"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete cellular metabolic process deprecated true

• obsolete cellular metabolic process label "obsolete cellular metabolic process"

• obsolete cellular metabolic process comment "The reason for obsoletion is that this term is now redundant with GO:0008152, metabolic process"

• obsolete cellular metabolic process definition "OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances."

  • database_cross_reference "GOC:go_curators"

obsolete extracellular polysaccharide catabolic process http://purl.obolibrary.org/obo/GO_0071999

Removed

• obsolete extracellular polysaccharide catabolic process definition "The chemical reactions and pathways resulting in the breakdown of polysaccharides used in extracellular structures."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "GOC:vw"

• obsolete extracellular polysaccharide catabolic process label "extracellular polysaccharide catabolic process"

• obsolete extracellular polysaccharide catabolic process SubClassOf polysaccharide catabolic process

• obsolete extracellular polysaccharide catabolic process SubClassOf obsolete extracellular polysaccharide metabolic process

Added

• obsolete extracellular polysaccharide catabolic process deprecated true

• obsolete extracellular polysaccharide catabolic process comment "The reason for obsoletion is that this term is now redundant with GO:0000272, polysaccharide catabolic process"

• obsolete extracellular polysaccharide catabolic process definition "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of polysaccharides used in extracellular structures."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "GOC:vw"

• obsolete extracellular polysaccharide catabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/28908"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete extracellular polysaccharide catabolic process label "obsolete extracellular polysaccharide catabolic process"

• obsolete extracellular polysaccharide catabolic process term replaced by "GO:0000272"

obsolete extracellular polysaccharide metabolic process http://purl.obolibrary.org/obo/GO_0046379

Removed

• obsolete extracellular polysaccharide metabolic process label "extracellular polysaccharide metabolic process"

• obsolete extracellular polysaccharide metabolic process definition "The chemical reactions and pathways involving polysaccharides used in extracellular structures."

  • database_cross_reference "GOC:ai"

• obsolete extracellular polysaccharide metabolic process SubClassOf polysaccharide metabolic process

Added

• obsolete extracellular polysaccharide metabolic process definition "OBSOLETE. The chemical reactions and pathways involving polysaccharides used in extracellular structures."

  • database_cross_reference "GOC:ai"

• obsolete extracellular polysaccharide metabolic process deprecated true

• obsolete extracellular polysaccharide metabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/29021"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete extracellular polysaccharide metabolic process comment "The reason for obsoletion is that this term is redundant with GO:0005976, polysaccharide metabolic process"

• obsolete extracellular polysaccharide metabolic process label "obsolete extracellular polysaccharide metabolic process"

• obsolete extracellular polysaccharide metabolic process term replaced by "GO:0005976"

obsolete negative regulation of cellular metabolic process http://purl.obolibrary.org/obo/GO_0031324

Removed

• obsolete negative regulation of cellular metabolic process in_subset gocheck_do_not_annotate

• obsolete negative regulation of cellular metabolic process definition "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."

  • database_cross_reference "GOC:mah"

• obsolete negative regulation of cellular metabolic process 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."

• obsolete negative regulation of cellular metabolic process label "negative regulation of cellular metabolic process"

• obsolete negative regulation of cellular metabolic process EquivalentTo biological regulation and (negatively regulates some obsolete cellular metabolic process)

• obsolete negative regulation of cellular metabolic process SubClassOf negative regulation of metabolic process

• obsolete negative regulation of cellular metabolic process SubClassOf obsolete regulation of cellular metabolic process

• obsolete negative regulation of cellular metabolic process SubClassOf negatively regulates some obsolete cellular metabolic process

Added

• obsolete negative regulation of cellular metabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/29021"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete negative regulation of cellular metabolic process term replaced by "GO:0009892"

• obsolete negative regulation of cellular metabolic process definition "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."

  • database_cross_reference "GOC:mah"

• obsolete negative regulation of cellular metabolic process comment "The reason for obsoletion is that term is redundant to GO:0009892, negative regulation of metabolic process"

• obsolete negative regulation of cellular metabolic process label "obsolete negative regulation of cellular metabolic process"

• obsolete negative regulation of cellular metabolic process deprecated true

obsolete positive regulation of cellular metabolic process http://purl.obolibrary.org/obo/GO_0031325

Removed

• obsolete positive regulation of cellular metabolic process 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."

• obsolete positive regulation of cellular metabolic process in_subset gocheck_do_not_annotate

• obsolete positive regulation of cellular metabolic process definition "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances."

  • database_cross_reference "GOC:mah"

• obsolete positive regulation of cellular metabolic process label "positive regulation of cellular metabolic process"

• obsolete positive regulation of cellular metabolic process EquivalentTo biological regulation and (positively regulates some obsolete cellular metabolic process)

• obsolete positive regulation of cellular metabolic process SubClassOf positive regulation of metabolic process

• obsolete positive regulation of cellular metabolic process SubClassOf obsolete regulation of cellular metabolic process

• obsolete positive regulation of cellular metabolic process SubClassOf positively regulates some obsolete cellular metabolic process

Added

• obsolete positive regulation of cellular metabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/29021"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete positive regulation of cellular metabolic process term replaced by "GO:0009893"

• obsolete positive regulation of cellular metabolic process deprecated true

• obsolete positive regulation of cellular metabolic process label "obsolete positive regulation of cellular metabolic process"

• obsolete positive regulation of cellular metabolic process definition "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."

  • database_cross_reference "GOC:mah"

• obsolete positive regulation of cellular metabolic process comment "The reason for obsoletion is that this term is redundant to GO:0009893"

obsolete regulation of cellular metabolic process http://purl.obolibrary.org/obo/GO_0031323

Removed

• obsolete regulation of cellular metabolic process label "regulation of cellular metabolic process"

• obsolete regulation of cellular metabolic process 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."

• obsolete regulation of cellular metabolic process definition "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances."

  • database_cross_reference "GOC:mah"

• obsolete regulation of cellular metabolic process in_subset gocheck_do_not_annotate

• obsolete regulation of cellular metabolic process EquivalentTo biological regulation and (regulates some obsolete cellular metabolic process)

• obsolete regulation of cellular metabolic process SubClassOf regulates some obsolete cellular metabolic process

• obsolete regulation of cellular metabolic process SubClassOf regulation of metabolic process

Added

• obsolete regulation of cellular metabolic process term replaced by "GO:0019222"

• obsolete regulation of cellular metabolic process label "obsolete regulation of cellular metabolic process"

• obsolete regulation of cellular metabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/29021"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete regulation of cellular metabolic process definition "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances."

  • database_cross_reference "GOC:mah"

• obsolete regulation of cellular metabolic process deprecated true

• obsolete regulation of cellular metabolic process comment "The reason for obsoletion is that this term is redundant to GO:0019222, regulation of metabolic process"

positive regulation of aldosterone metabolic process http://purl.obolibrary.org/obo/GO_0032346

Removed

• positive regulation of aldosterone metabolic process SubClassOf obsolete positive regulation of cellular metabolic process

positive regulation of amylopectin metabolic process http://purl.obolibrary.org/obo/GO_2000944

Removed

• positive regulation of amylopectin metabolic process SubClassOf obsolete positive regulation of cellular metabolic process

positive regulation of glucocorticoid metabolic process http://purl.obolibrary.org/obo/GO_0031945

Removed

• positive regulation of glucocorticoid metabolic process SubClassOf obsolete positive regulation of cellular metabolic process

positive regulation of thyroid hormone generation http://purl.obolibrary.org/obo/GO_2000611

Removed

• positive regulation of thyroid hormone generation SubClassOf obsolete positive regulation of cellular metabolic process

regulation of amylopectin metabolic process http://purl.obolibrary.org/obo/GO_2000942

Removed

• regulation of amylopectin metabolic process SubClassOf obsolete regulation of cellular metabolic process

regulation of bile acid metabolic process http://purl.obolibrary.org/obo/GO_1904251

Removed

• regulation of bile acid metabolic process SubClassOf obsolete regulation of cellular metabolic process

regulation of generation of precursor metabolites and energy http://purl.obolibrary.org/obo/GO_0043467

Removed

• regulation of generation of precursor metabolites and energy SubClassOf obsolete regulation of cellular metabolic process

Added

• regulation of generation of precursor metabolites and energy SubClassOf regulation of metabolic process

regulation of glucocorticoid metabolic process http://purl.obolibrary.org/obo/GO_0031943

Removed

• regulation of glucocorticoid metabolic process SubClassOf obsolete regulation of cellular metabolic process

regulation of lipoprotein metabolic process http://purl.obolibrary.org/obo/GO_0050746

Removed

• regulation of lipoprotein metabolic process SubClassOf obsolete regulation of cellular metabolic process

regulation of thyroid hormone generation http://purl.obolibrary.org/obo/GO_2000609

Removed

• regulation of thyroid hormone generation SubClassOf obsolete regulation of cellular metabolic process