[create-pull-request] automated change (#29003)

Co-authored-by: balhoff <[email protected]>
geneontology · Sep 28, 2024 · ad2794a · ad2794a
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diff --git a/docs/patterns/multi_organism_process.md b/docs/patterns/multi_organism_process.md
@@ -29,7 +29,7 @@ TODO
 
 ## Equivalent to
 
-`{process}`  and ([has characteristic](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0002486](http://purl.obolibrary.org/obo/PATO_0002486))
+`{process}`  and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0002486](http://purl.obolibrary.org/obo/PATO_0002486))
 
 
 

diff --git a/docs/patterns/protein_complex_by_activity.md b/docs/patterns/protein_complex_by_activity.md
@@ -29,7 +29,7 @@ TODO
 
 ## Equivalent to
 
-[protein-containing complex](http://purl.obolibrary.org/obo/GO_0032991)  and ([capable_of](http://purl.obolibrary.org/obo/RO_0002215) some `{function}`)
+[protein-containing complex](http://purl.obolibrary.org/obo/GO_0032991)  and ([capable of](http://purl.obolibrary.org/obo/RO_0002215) some `{function}`)
 
 
 

diff --git a/docs/patterns/single_organism_process.md b/docs/patterns/single_organism_process.md
@@ -29,7 +29,7 @@ TODO
 
 ## Equivalent to
 
-`{process}`  and ([has characteristic](http://purl.obolibrary.org/obo/RO_0000053) some [single organismal process quality](http://purl.obolibrary.org/obo/PATO_0002487))
+`{process}`  and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [single organismal process quality](http://purl.obolibrary.org/obo/PATO_0002487))
 
 
 

diff --git a/src/design_patterns/biosynthetic_process.tsv b/src/design_patterns/biosynthetic_process.tsv
@@ -306,8 +306,6 @@ http://purl.obolibrary.org/obo/GO_0016120	carotene biosynthetic process	http://p
 http://purl.obolibrary.org/obo/GO_0016117	carotenoid biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_23044	carotenoid
 http://purl.obolibrary.org/obo/GO_0009713	catechol-containing compound biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_33566	catechols
 http://purl.obolibrary.org/obo/GO_0042423	catecholamine biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_33567	catecholamine
-http://purl.obolibrary.org/obo/GO_0042398	cellular modified amino acid biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_83821	amino acid derivative
-http://purl.obolibrary.org/obo/GO_0052703	cellular modified histidine biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_24599	histidine derivative
 http://purl.obolibrary.org/obo/GO_0030244	cellulose biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_18246	(1->4)-beta-D-glucan
 http://purl.obolibrary.org/obo/GO_1901268	cephalosporin C biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_57511	cephalosporin C(1-)
 http://purl.obolibrary.org/obo/GO_0043646	cephalosporin biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_23066	cephalosporin
@@ -694,6 +692,8 @@ http://purl.obolibrary.org/obo/GO_0140877	mevastatin biosynthetic process	http:/
 http://purl.obolibrary.org/obo/GO_1901946	miltiradiene biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_65037	miltiradiene
 http://purl.obolibrary.org/obo/GO_0006705	mineralocorticoid biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_25354	mineralocorticoid
 http://purl.obolibrary.org/obo/GO_1901777	mitomycin C biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_194095	mitomycin C(1-)
+http://purl.obolibrary.org/obo/GO_0042398	modified amino acid biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_83821	amino acid derivative
+http://purl.obolibrary.org/obo/GO_0052703	modified histidine biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_24599	histidine derivative
 http://purl.obolibrary.org/obo/GO_0032324	molybdopterin cofactor biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_25372	molybdopterin cofactor
 http://purl.obolibrary.org/obo/GO_1901730	monensin A biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_27617	monensin A
 http://purl.obolibrary.org/obo/GO_0006640	monoacylglycerol biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_17408	monoacylglycerol

diff --git a/src/design_patterns/catabolic_process.tsv b/src/design_patterns/catabolic_process.tsv
@@ -196,6 +196,7 @@ http://purl.obolibrary.org/obo/GO_0046348	amino sugar catabolic process	http://p
 http://purl.obolibrary.org/obo/GO_0006579	amino-acid betaine catabolic process	http://purl.obolibrary.org/obo/CHEBI_22860	amino-acid betaine
 http://purl.obolibrary.org/obo/GO_0006026	aminoglycan catabolic process	http://purl.obolibrary.org/obo/CHEBI_22506	aminoglycan
 http://purl.obolibrary.org/obo/GO_0030649	aminoglycoside antibiotic catabolic process	http://purl.obolibrary.org/obo/CHEBI_22507	aminoglycoside antibiotic
+http://purl.obolibrary.org/obo/GO_0150094	amyloid-beta clearance by cellular catabolic process	http://purl.obolibrary.org/obo/CHEBI_64645	amyloid-beta
 http://purl.obolibrary.org/obo/GO_2000897	amylopectin catabolic process	http://purl.obolibrary.org/obo/CHEBI_28057	amylopectin
 http://purl.obolibrary.org/obo/GO_0006710	androgen catabolic process	http://purl.obolibrary.org/obo/GOCHE_50113	substance with androgen role
 http://purl.obolibrary.org/obo/GO_0046284	anthocyanin-containing compound catabolic process	http://purl.obolibrary.org/obo/CHEBI_35218	anthocyanin cation
@@ -279,8 +280,6 @@ http://purl.obolibrary.org/obo/GO_2000892	cellobiose catabolic process	http://pu
 http://purl.obolibrary.org/obo/GO_2000890	cellodextrin catabolic process	http://purl.obolibrary.org/obo/CHEBI_3523	cellodextrin
 http://purl.obolibrary.org/obo/GO_2000903	cellooligosaccharide catabolic process	http://purl.obolibrary.org/obo/CHEBI_62563	cellooligosaccharide
 http://purl.obolibrary.org/obo/GO_2000894	cellotriose catabolic process	http://purl.obolibrary.org/obo/CHEBI_3528	cellotriose
-http://purl.obolibrary.org/obo/GO_0042219	cellular modified amino acid catabolic process	http://purl.obolibrary.org/obo/CHEBI_83821	amino acid derivative
-http://purl.obolibrary.org/obo/GO_0052702	cellular modified histidine catabolic process	http://purl.obolibrary.org/obo/CHEBI_24599	histidine derivative
 http://purl.obolibrary.org/obo/GO_0030245	cellulose catabolic process	http://purl.obolibrary.org/obo/CHEBI_18246	(1->4)-beta-D-glucan
 http://purl.obolibrary.org/obo/GO_1901267	cephalosporin C catabolic process	http://purl.obolibrary.org/obo/CHEBI_57511	cephalosporin C(1-)
 http://purl.obolibrary.org/obo/GO_1901117	cephamycin C catabolic process	http://purl.obolibrary.org/obo/CHEBI_3543	cephamycin C
@@ -609,6 +608,8 @@ http://purl.obolibrary.org/obo/GO_0010587	miRNA catabolic process	http://purl.ob
 http://purl.obolibrary.org/obo/GO_1901945	miltiradiene catabolic process	http://purl.obolibrary.org/obo/CHEBI_65037	miltiradiene
 http://purl.obolibrary.org/obo/GO_0006712	mineralocorticoid catabolic process	http://purl.obolibrary.org/obo/CHEBI_25354	mineralocorticoid
 http://purl.obolibrary.org/obo/GO_1901776	mitomycin C catabolic process	http://purl.obolibrary.org/obo/CHEBI_194095	mitomycin C(1-)
+http://purl.obolibrary.org/obo/GO_0042219	modified amino acid catabolic process	http://purl.obolibrary.org/obo/CHEBI_83821	amino acid derivative
+http://purl.obolibrary.org/obo/GO_0052702	modified histidine catabolic process	http://purl.obolibrary.org/obo/CHEBI_24599	histidine derivative
 http://purl.obolibrary.org/obo/GO_0032325	molybdopterin cofactor catabolic process	http://purl.obolibrary.org/obo/CHEBI_25372	molybdopterin cofactor
 http://purl.obolibrary.org/obo/GO_1901729	monensin A catabolic process	http://purl.obolibrary.org/obo/CHEBI_27617	monensin A
 http://purl.obolibrary.org/obo/GO_0052651	monoacylglycerol catabolic process	http://purl.obolibrary.org/obo/CHEBI_17408	monoacylglycerol

diff --git a/src/design_patterns/metabolic_process.tsv b/src/design_patterns/metabolic_process.tsv
@@ -239,14 +239,18 @@ http://purl.obolibrary.org/obo/GO_0033535	ajugose metabolic process	http://purl.
 http://purl.obolibrary.org/obo/GO_0006522	alanine metabolic process	http://purl.obolibrary.org/obo/CHEBI_66916	alanine zwitterion
 http://purl.obolibrary.org/obo/GO_0006066	alcohol metabolic process	http://purl.obolibrary.org/obo/CHEBI_30879	alcohol
 http://purl.obolibrary.org/obo/GO_0019577	aldaric acid metabolic process	http://purl.obolibrary.org/obo/CHEBI_22289	aldaric acid anion
+http://purl.obolibrary.org/obo/GO_0006081	aldehyde metabolic process	http://purl.obolibrary.org/obo/CHEBI_17478	aldehyde
 http://purl.obolibrary.org/obo/GO_0019400	alditol metabolic process	http://purl.obolibrary.org/obo/CHEBI_17522	alditol
 http://purl.obolibrary.org/obo/GO_0052646	alditol phosphate metabolic process	http://purl.obolibrary.org/obo/CHEBI_22297	alditol phosphate
 http://purl.obolibrary.org/obo/GO_0019520	aldonic acid metabolic process	http://purl.obolibrary.org/obo/CHEBI_22299	aldonate
 http://purl.obolibrary.org/obo/GO_0032341	aldosterone metabolic process	http://purl.obolibrary.org/obo/CHEBI_27584	aldosterone
 http://purl.obolibrary.org/obo/GO_0019330	aldoxime metabolic process	http://purl.obolibrary.org/obo/CHEBI_22307	aldoxime
 http://purl.obolibrary.org/obo/GO_0042120	alginic acid metabolic process	http://purl.obolibrary.org/obo/CHEBI_58187	alginate
 http://purl.obolibrary.org/obo/GO_0009820	alkaloid metabolic process	http://purl.obolibrary.org/obo/CHEBI_22315	alkaloid
+http://purl.obolibrary.org/obo/GO_0043446	alkane metabolic process	http://purl.obolibrary.org/obo/CHEBI_18310	alkane
 http://purl.obolibrary.org/obo/GO_0019694	alkanesulfonate metabolic process	http://purl.obolibrary.org/obo/CHEBI_134249	alkanesulfonate oxoanion
+http://purl.obolibrary.org/obo/GO_0043449	alkene metabolic process	http://purl.obolibrary.org/obo/CHEBI_32878	alkene
+http://purl.obolibrary.org/obo/GO_0043452	alkyne metabolic process	http://purl.obolibrary.org/obo/CHEBI_22339	alkyne
 http://purl.obolibrary.org/obo/GO_1901831	all-trans-neoxanthin metabolic process	http://purl.obolibrary.org/obo/CHEBI_32446	all-trans-neoxanthin
 http://purl.obolibrary.org/obo/GO_0000255	allantoin metabolic process	http://purl.obolibrary.org/obo/CHEBI_15676	allantoin
 http://purl.obolibrary.org/obo/GO_1901605	alpha-amino acid metabolic process	http://purl.obolibrary.org/obo/CHEBI_78608	alpha-amino acid zwitterion
@@ -369,13 +373,6 @@ http://purl.obolibrary.org/obo/GO_2000891	cellobiose metabolic process	http://pu
 http://purl.obolibrary.org/obo/GO_2000889	cellodextrin metabolic process	http://purl.obolibrary.org/obo/CHEBI_3523	cellodextrin
 http://purl.obolibrary.org/obo/GO_2000902	cellooligosaccharide metabolic process	http://purl.obolibrary.org/obo/CHEBI_62563	cellooligosaccharide
 http://purl.obolibrary.org/obo/GO_2000893	cellotriose metabolic process	http://purl.obolibrary.org/obo/CHEBI_3528	cellotriose
-http://purl.obolibrary.org/obo/GO_0006081	cellular aldehyde metabolic process	http://purl.obolibrary.org/obo/CHEBI_17478	aldehyde
-http://purl.obolibrary.org/obo/GO_0043446	cellular alkane metabolic process	http://purl.obolibrary.org/obo/CHEBI_18310	alkane
-http://purl.obolibrary.org/obo/GO_0043449	cellular alkene metabolic process	http://purl.obolibrary.org/obo/CHEBI_32878	alkene
-http://purl.obolibrary.org/obo/GO_0043452	cellular alkyne metabolic process	http://purl.obolibrary.org/obo/CHEBI_22339	alkyne
-http://purl.obolibrary.org/obo/GO_0042180	cellular ketone metabolic process	http://purl.obolibrary.org/obo/CHEBI_17087	ketone
-http://purl.obolibrary.org/obo/GO_0006575	cellular modified amino acid metabolic process	http://purl.obolibrary.org/obo/CHEBI_83821	amino acid derivative
-http://purl.obolibrary.org/obo/GO_0052701	cellular modified histidine metabolic process	http://purl.obolibrary.org/obo/CHEBI_24599	histidine derivative
 http://purl.obolibrary.org/obo/GO_0030243	cellulose metabolic process	http://purl.obolibrary.org/obo/CHEBI_18246	(1->4)-beta-D-glucan
 http://purl.obolibrary.org/obo/GO_1901266	cephalosporin C metabolic process	http://purl.obolibrary.org/obo/CHEBI_57511	cephalosporin C(1-)
 http://purl.obolibrary.org/obo/GO_0043645	cephalosporin metabolic process	http://purl.obolibrary.org/obo/CHEBI_23066	cephalosporin
@@ -744,6 +741,7 @@ http://purl.obolibrary.org/obo/GO_0046400	keto-3-deoxy-D-manno-octulosonic acid
 http://purl.obolibrary.org/obo/GO_0019525	keto-D-gluconate metabolic process	http://purl.obolibrary.org/obo/CHEBI_24966	keto-D-gluconate
 http://purl.obolibrary.org/obo/GO_0019522	ketogluconate metabolic process	http://purl.obolibrary.org/obo/CHEBI_60978	ketogluconate
 http://purl.obolibrary.org/obo/GO_1902224	ketone body metabolic process	http://purl.obolibrary.org/obo/CHEBI_73693	ketone body
+http://purl.obolibrary.org/obo/GO_0042180	ketone metabolic process	http://purl.obolibrary.org/obo/CHEBI_17087	ketone
 http://purl.obolibrary.org/obo/GO_2001316	kojic acid metabolic process	http://purl.obolibrary.org/obo/CHEBI_43572	kojic acid
 http://purl.obolibrary.org/obo/GO_0034275	kynurenic acid metabolic process	http://purl.obolibrary.org/obo/CHEBI_58454	kynurenate
 http://purl.obolibrary.org/obo/GO_0070189	kynurenine metabolic process	http://purl.obolibrary.org/obo/CHEBI_28683	kynurenine
@@ -828,6 +826,8 @@ http://purl.obolibrary.org/obo/GO_0010586	miRNA metabolic process	http://purl.ob
 http://purl.obolibrary.org/obo/GO_1901944	miltiradiene metabolic process	http://purl.obolibrary.org/obo/CHEBI_65037	miltiradiene
 http://purl.obolibrary.org/obo/GO_0008212	mineralocorticoid metabolic process	http://purl.obolibrary.org/obo/CHEBI_25354	mineralocorticoid
 http://purl.obolibrary.org/obo/GO_1901775	mitomycin C metabolic process	http://purl.obolibrary.org/obo/CHEBI_194095	mitomycin C(1-)
+http://purl.obolibrary.org/obo/GO_0006575	modified amino acid metabolic process	http://purl.obolibrary.org/obo/CHEBI_83821	amino acid derivative
+http://purl.obolibrary.org/obo/GO_0052701	modified histidine metabolic process	http://purl.obolibrary.org/obo/CHEBI_24599	histidine derivative
 http://purl.obolibrary.org/obo/GO_0043545	molybdopterin cofactor metabolic process	http://purl.obolibrary.org/obo/CHEBI_25372	molybdopterin cofactor
 http://purl.obolibrary.org/obo/GO_1901728	monensin A metabolic process	http://purl.obolibrary.org/obo/CHEBI_27617	monensin A
 http://purl.obolibrary.org/obo/GO_0046462	monoacylglycerol metabolic process	http://purl.obolibrary.org/obo/CHEBI_17408	monoacylglycerol
@@ -898,6 +898,8 @@ http://purl.obolibrary.org/obo/GO_0006082	organic acid metabolic process	http://
 http://purl.obolibrary.org/obo/GO_1901376	organic heteropentacyclic compound metabolic process	http://purl.obolibrary.org/obo/CHEBI_38164	organic heteropentacyclic compound
 http://purl.obolibrary.org/obo/GO_1901615	organic hydroxy compound metabolic process	http://purl.obolibrary.org/obo/CHEBI_33822	organic hydroxy compound
 http://purl.obolibrary.org/obo/GO_0019634	organic phosphonate metabolic process	http://purl.obolibrary.org/obo/CHEBI_16215	phosphonate(2-)
+http://purl.obolibrary.org/obo/GO_0090346	organofluorine metabolic process	http://purl.obolibrary.org/obo/CHEBI_37143	organofluorine compound
+http://purl.obolibrary.org/obo/GO_0090345	organohalogen metabolic process	http://purl.obolibrary.org/obo/CHEBI_17792	organohalogen compound
 http://purl.obolibrary.org/obo/GO_0018942	organometal metabolic process	http://purl.obolibrary.org/obo/CHEBI_25707	organometallic compound
 http://purl.obolibrary.org/obo/GO_0019637	organophosphate metabolic process	http://purl.obolibrary.org/obo/CHEBI_25710	organophosphorus compound
 http://purl.obolibrary.org/obo/GO_0018945	organosilicon metabolic process	http://purl.obolibrary.org/obo/CHEBI_25713	organosilicon compound