Merge pull request #28945 from geneontology/issue-28908

removed cellular metabolic process from child terms in prep for obsol…

src/ontology/go-edit.obo

@@ -13466,7 +13466,6 @@ def: "The chemical reactions and pathways involving compounds that contain selen
 synonym: "selenium compound metabolism" EXACT []
 synonym: "selenium metabolic process" EXACT []
 synonym: "selenium metabolism" EXACT []
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:26628 ! selenium molecular entity
 
@@ -58446,7 +58445,6 @@ synonym: "alkanal metabolic process" EXACT []
 synonym: "alkanal metabolism" EXACT []
 is_a: GO:0008152 ! metabolic process
 is_a: GO:0009987 ! cellular process
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:17478 ! aldehyde
 
@@ -58458,7 +58456,6 @@ def: "The chemical reactions and pathways involving organic acids, any acidic co
 subset: goslim_pir
 synonym: "organic acid metabolism" EXACT []
 is_a: GO:0009987 ! cellular process
-is_a: GO:0044237 ! cellular metabolic process
 is_a: GO:0044281 ! small molecule metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:64709 ! organic acid
@@ -58568,7 +58565,7 @@ subset: goslim_yeast
 synonym: "energy pathways" BROAD []
 synonym: "intermediary metabolism" RELATED [GOC:mah]
 synonym: "metabolic energy generation" RELATED []
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 
 [Term]
 id: GO:0006094
@@ -61950,7 +61947,7 @@ synonym: "biopolymerisation" BROAD []
 synonym: "biopolymerization" BROAD []
 synonym: "protein synthesis initiation" BROAD []
 synonym: "translation initiation" EXACT []
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 relationship: part_of GO:0006412 ! translation
 relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex
 
@@ -63621,7 +63618,7 @@ synonym: "cellular amino acid derivative metabolism" EXACT []
 synonym: "cellular modified amino acid metabolism" EXACT [GOC:mah]
 synonym: "modified amino acid metabolic process" EXACT [GOC:mah]
 synonym: "modified amino acid metabolism" EXACT [GOC:mah]
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:83821 ! amino acid derivative
 
@@ -65369,7 +65366,7 @@ synonym: "one-carbon metabolism" EXACT [GOC:mah]
 synonym: "one-carbon transfer metabolic process" EXACT [GOC:mah]
 synonym: "one-carbon transfer metabolism" EXACT [GOC:mah]
 xref: UM-BBD_pathwayID:C1cyc
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 is_a: GO:0044281 ! small molecule metabolic process
 
 [Term]
@@ -66043,7 +66040,6 @@ synonym: "sulfur metabolism" EXACT []
 synonym: "sulphur metabolic process" EXACT []
 synonym: "sulphur metabolism" EXACT []
 xref: Wikipedia:Sulfur_metabolism
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:26835 ! sulfur molecular entity
 
@@ -66073,7 +66069,6 @@ namespace: biological_process
 def: "The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus." [GOC:ai]
 subset: goslim_pir
 synonym: "phosphorus metabolism" EXACT []
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:26082 ! phosphorus molecular entity
 
@@ -66212,7 +66207,6 @@ synonym: "drug metabolism" RELATED []
 synonym: "xenobiotic metabolism" EXACT []
 xref: Wikipedia:Drug_metabolism
 xref: Wikipedia:Xenobiotic_metabolism
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output GOCHE:35703 ! substance with xenobiotic role
 relationship: part_of GO:0071466 ! cellular response to xenobiotic stimulus
@@ -76635,7 +76629,7 @@ def: "The production of light by certain enzyme-catalyzed reactions in cells." [
 subset: goslim_chembl
 subset: goslim_metagenomics
 xref: Wikipedia:Bioluminescence
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 
 [Term]
 id: GO:0008219
@@ -90770,7 +90764,6 @@ def: "The chemical reactions and pathways involving a toxin, a poisonous compoun
 subset: goslim_pir
 synonym: "toxin metabolism" EXACT []
 is_a: GO:0019748 ! secondary metabolic process
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output GOCHE:27026 ! substance with toxin role
 
@@ -95198,8 +95191,8 @@ name: auxin metabolic process
 namespace: biological_process
 def: "The chemical reactions and pathways involving auxins, a group of plant hormones that regulate aspects of plant growth." [GOC:lr]
 synonym: "auxin metabolism" EXACT []
+is_a: GO:0008152 ! metabolic process
 is_a: GO:0042445 ! hormone metabolic process
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output GOCHE:22676 ! substance with auxin role
 
@@ -98675,7 +98668,6 @@ namespace: biological_process
 def: "The chemical reactions and pathways involving mucilage, a gelatinous substance secreted by plants." [GOC:sm]
 subset: goslim_pir
 synonym: "mucilage metabolism" EXACT []
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:74969 ! mucilage
 
@@ -117719,7 +117711,7 @@ subset: goslim_plant_ribbon
 subset: goslim_prokaryote
 subset: goslim_prokaryote_ribbon
 xref: Wikipedia:Photosynthesis
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 
 [Term]
 id: GO:0015980
@@ -138472,7 +138464,6 @@ namespace: biological_process
 def: "The chemical reactions and pathways involving organometals, any metal-containing organic compound, especially one in which the metal atom is linked directly to one of more carbon atoms." [ISBN:0198506732]
 subset: goslim_pir
 synonym: "organometal metabolism" EXACT []
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:25707 ! organometallic compound
 
@@ -213573,7 +213564,6 @@ name: thioester metabolic process
 namespace: biological_process
 def: "The chemical reactions and pathways involving a thioester, a compound of general formula RC(=O)SR' in which the linking oxygen in an ester is replaced by a sulfur atom. They are the product of esterification between a carboxylic acid and a thiol." [GOC:bf, Wikipedia:Thioester]
 synonym: "thioester metabolism" EXACT []
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:51277 ! thioester
 created_by: bf
@@ -234807,7 +234797,6 @@ def: "The chemical reactions and pathways involving any of a class of organic co
 subset: goslim_pir
 synonym: "ketone metabolism" EXACT []
 is_a: GO:0009987 ! cellular process
-is_a: GO:0044237 ! cellular metabolic process
 is_a: GO:0044281 ! small molecule metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:17087 ! ketone
@@ -240972,7 +240961,6 @@ subset: goslim_pir
 synonym: "pheromone metabolism" EXACT []
 is_a: GO:0019748 ! secondary metabolic process
 is_a: GO:0042445 ! hormone metabolic process
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output GOCHE:26013 ! substance with pheromone role
 
@@ -243772,7 +243760,7 @@ name: cellular metabolic compound salvage
 namespace: biological_process
 def: "Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells." [GOC:mlg]
 subset: goslim_pir
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 
 [Term]
 id: GO:0043095
@@ -247389,7 +247377,6 @@ def: "The chemical reactions and pathways involving an alkane, any acyclic branc
 subset: goslim_pir
 synonym: "alkane metabolism" EXACT []
 is_a: GO:0008152 ! metabolic process
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:18310 ! alkane
 
@@ -247425,7 +247412,6 @@ namespace: biological_process
 def: "The chemical reactions and pathways involving an alkene, any acyclic branched or unbranched hydrocarbon having one carbon-carbon double bond and the general formula CnH2n, as carried out by individual cells." [GOC:jl, Wikipedia:Alkene]
 subset: goslim_pir
 synonym: "alkene metabolism" EXACT []
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:32878 ! alkene
 
@@ -247462,7 +247448,6 @@ def: "The chemical reactions and pathways involving an alkyne, any acyclic branc
 subset: goslim_pir
 synonym: "alkyne metabolism" EXACT []
 is_a: GO:0008152 ! metabolic process
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:22339 ! alkyne
 
@@ -255850,8 +255835,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of substanc
 synonym: "cellular breakdown" EXACT []
 synonym: "cellular catabolism" EXACT []
 synonym: "cellular degradation" EXACT []
+is_a: GO:0008152 ! metabolic process
 is_a: GO:0009056 ! catabolic process
-is_a: GO:0044237 ! cellular metabolic process
 
 [Term]
 id: GO:0044249
@@ -255864,8 +255849,8 @@ synonym: "cellular anabolism" EXACT []
 synonym: "cellular biosynthesis" EXACT []
 synonym: "cellular formation" EXACT []
 synonym: "cellular synthesis" EXACT []
+is_a: GO:0008152 ! metabolic process
 is_a: GO:0009058 ! biosynthetic process
-is_a: GO:0044237 ! cellular metabolic process
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI
 
 [Term]
@@ -255900,7 +255885,7 @@ def: "The chemical reactions and pathways involving lipids, as carried out by in
 subset: goslim_pir
 synonym: "cellular lipid metabolism" EXACT []
 is_a: GO:0006629 ! lipid metabolic process
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 
 [Term]
 id: GO:0044256
@@ -283478,7 +283463,7 @@ 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
 synonym: "cellular ketone body metabolism" EXACT []
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 is_a: GO:0044281 ! small molecule metabolic process
 
 [Term]
@@ -364424,7 +364409,7 @@ name: chemosynthesis
 namespace: biological_process
 def: "The cellular metabolic process in which organic chemical compounds are synthesized from carbon-containing molecules and nutrients using energy obtained from the oxidation of inorganic compounds or methane." [PMID:25050523]
 xref: Wikipedia:Chemosynthesis
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 created_by: dph
 creation_date: 2018-11-29T13:18:55Z
 
@@ -394602,7 +394587,6 @@ namespace: biological_process
 def: "The chemical reactions and pathways involving diatomic oxygen (O2)." [GOC:mah]
 synonym: "diatomic oxygen metabolic process" EXACT [CHEBI:33263]
 synonym: "oxygen metabolism" EXACT [GOC:mah]
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:15379 ! dioxygen
 created_by: mah
@@ -394615,7 +394599,6 @@ namespace: biological_process
 def: "The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers." [GOC:mah]
 synonym: "reactive oxygen species metabolism" EXACT [GOC:mah]
 synonym: "ROS metabolic process" EXACT [CHEBI:26523, GOC:mah]
-is_a: GO:0044237 ! cellular metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:26523 ! reactive oxygen species
 created_by: mah
@@ -407105,7 +407088,7 @@ id: GO:0090345
 name: cellular organohalogen metabolic process
 namespace: biological_process
 def: "The chemical reactions and pathways involving organohalogen compounds, as carried out by individual cells." [GOC:BHF]
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 created_by: tb
 creation_date: 2010-06-02T10:36:42Z
 
@@ -407688,7 +407671,7 @@ id: GO:0090398
 name: cellular senescence
 namespace: biological_process
 def: "A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest." [GOC:BHF, PMID:28682291]
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 relationship: part_of GO:0033554 ! cellular response to stress
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22788" xsd:anyURI
 created_by: tb
@@ -407699,7 +407682,7 @@ id: GO:0090399
 name: replicative senescence
 namespace: biological_process
 def: "A cell aging process associated with the dismantling of a cell as a response to telomere shortening and/or cellular aging." [GOC:BHF]
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22788" xsd:anyURI
 created_by: tb
 creation_date: 2011-01-05T02:32:29Z
@@ -415159,7 +415142,7 @@ id: GO:0097354
 name: prenylation
 namespace: biological_process
 def: "The covalent attachment of a prenyl group to a molecule; geranyl, farnesyl, or geranylgeranyl groups may be added." [GOC:di, PMID:18029206, PMID:21351751, PMID:22123822, PMID:22642693, PMID:22660767]
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 created_by: pr
 creation_date: 2012-07-03T01:12:19Z
 
@@ -444265,7 +444248,7 @@ id: GO:0110051
 name: metabolite repair
 namespace: biological_process
 def: "A cellular process that, through single- or multi-step enzymatic reactions, repairs useless or toxic endogenous compounds, formed as by-products of primary metabolism, by converting them into useful metabolites." [GOC:ka, PMID:23334546, PMID:28373563]
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 created_by: kmv
 creation_date: 2017-09-08T15:16:01Z
 
@@ -600021,7 +600004,7 @@ name: hydroperoxide metabolic process
 namespace: biological_process
 def: "The chemical reactions and pathways involving a hydroperoxide." [GOC:rs, PMID:15917183, PMID:18084891]
 synonym: "hydroperoxide metabolism" EXACT [GOC:obol]
-is_a: GO:0044237 ! cellular metabolic process
+is_a: GO:0008152 ! metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_primary_input_or_output CHEBI:35923 ! hydroperoxide
 created_by: pr