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geneontology · Jul 11, 2024 · 02d18d9 · 02d18d9
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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/catabolic_process.tsv b/src/design_patterns/catabolic_process.tsv
@@ -637,7 +637,6 @@ http://purl.obolibrary.org/obo/GO_0050899	nitrile catabolic process	http://purl.
 http://purl.obolibrary.org/obo/GO_1900998	nitrobenzene catabolic process	http://purl.obolibrary.org/obo/CHEBI_27798	nitrobenzene
 http://purl.obolibrary.org/obo/GO_0046263	nitrotoluene catabolic process	http://purl.obolibrary.org/obo/CHEBI_25566	nitrotoluene
 http://purl.obolibrary.org/obo/GO_0170044	non-proteinogenic amino acid catabolic process	http://purl.obolibrary.org/obo/CHEBI_83820	non-proteinogenic amino acid
-http://purl.obolibrary.org/obo/GO_0019468	nopaline catabolic process	http://purl.obolibrary.org/obo/CHEBI_58074	D-nopalinate(1-)
 http://purl.obolibrary.org/obo/GO_0046205	nor-spermidine catabolic process	http://purl.obolibrary.org/obo/CHEBI_57920	bis(3-azaniumylpropyl)azanium
 http://purl.obolibrary.org/obo/GO_0042422	norepinephrine catabolic process	http://purl.obolibrary.org/obo/CHEBI_72587	(R)-noradrenaline(1+)
 http://purl.obolibrary.org/obo/GO_0141188	nucleic acid catabolic process	http://purl.obolibrary.org/obo/CHEBI_33696	nucleic acid
@@ -658,7 +657,6 @@ http://purl.obolibrary.org/obo/GO_1900817	ochratoxin A catabolic process	http://
 http://purl.obolibrary.org/obo/GO_0046517	octamethylcyclotetrasiloxane catabolic process	http://purl.obolibrary.org/obo/CHEBI_25640	octamethylcyclotetrasiloxane
 http://purl.obolibrary.org/obo/GO_0046172	octanol catabolic process	http://purl.obolibrary.org/obo/CHEBI_16188	octan-1-ol
 http://purl.obolibrary.org/obo/GO_0046334	octopamine catabolic process	http://purl.obolibrary.org/obo/CHEBI_58025	octopaminium
-http://purl.obolibrary.org/obo/GO_0019469	octopine catabolic process	http://purl.obolibrary.org/obo/CHEBI_57520	D-octopine dizwitterion
 http://purl.obolibrary.org/obo/GO_0120256	olefinic compound catabolic process	http://purl.obolibrary.org/obo/CHEBI_78840	olefinic compound
 http://purl.obolibrary.org/obo/GO_0009313	oligosaccharide catabolic process	http://purl.obolibrary.org/obo/CHEBI_50699	oligosaccharide
 http://purl.obolibrary.org/obo/GO_0046153	ommochrome catabolic process	http://purl.obolibrary.org/obo/CHEBI_25692	ommochrome

diff --git a/src/design_patterns/cellular_anatomical_entity_organization.tsv b/src/design_patterns/cellular_anatomical_entity_organization.tsv
@@ -105,7 +105,6 @@ http://purl.obolibrary.org/obo/GO_0071763	nuclear membrane organization	http://p
 http://purl.obolibrary.org/obo/GO_0071764	nuclear outer membrane organization	http://purl.obolibrary.org/obo/GO_0005640	nuclear outer membrane
 http://purl.obolibrary.org/obo/GO_0035063	nuclear speck organization	http://purl.obolibrary.org/obo/GO_0016607	nuclear speck
 http://purl.obolibrary.org/obo/GO_0090143	nucleoid organization	http://purl.obolibrary.org/obo/GO_0009295	nucleoid
-http://purl.obolibrary.org/obo/GO_1990700	nucleolar chromatin organization	http://purl.obolibrary.org/obo/GO_0030874	nucleolar chromatin
 http://purl.obolibrary.org/obo/GO_0007000	nucleolus organization	http://purl.obolibrary.org/obo/GO_0005730	nucleolus
 http://purl.obolibrary.org/obo/GO_0006997	nucleus organization	http://purl.obolibrary.org/obo/GO_0005634	nucleus
 http://purl.obolibrary.org/obo/GO_0032122	oral apparatus organization	http://purl.obolibrary.org/obo/GO_0031912	oral apparatus
@@ -148,6 +147,7 @@ http://purl.obolibrary.org/obo/GO_0045231	slime layer organization	http://purl.o
 http://purl.obolibrary.org/obo/GO_0030721	spectrosome organization	http://purl.obolibrary.org/obo/GO_0045170	spectrosome
 http://purl.obolibrary.org/obo/GO_0007051	spindle organization	http://purl.obolibrary.org/obo/GO_0005819	spindle
 http://purl.obolibrary.org/obo/GO_0051300	spindle pole body organization	http://purl.obolibrary.org/obo/GO_0005816	spindle pole body
+http://purl.obolibrary.org/obo/GO_0160194	stereocilium bundle organization	http://purl.obolibrary.org/obo/GO_0032421	stereocilium bundle
 http://purl.obolibrary.org/obo/GO_1990255	subsynaptic reticulum organization	http://purl.obolibrary.org/obo/GO_0071212	subsynaptic reticulum
 http://purl.obolibrary.org/obo/GO_0097435	supramolecular fiber organization	http://purl.obolibrary.org/obo/GO_0099512	supramolecular fiber
 http://purl.obolibrary.org/obo/GO_0048499	synaptic vesicle membrane organization	http://purl.obolibrary.org/obo/GO_0030672	synaptic vesicle membrane

diff --git a/src/design_patterns/metabolic_process.tsv b/src/design_patterns/metabolic_process.tsv
@@ -870,7 +870,6 @@ http://purl.obolibrary.org/obo/GO_0018937	nitroglycerin metabolic process	http:/
 http://purl.obolibrary.org/obo/GO_0019326	nitrotoluene metabolic process	http://purl.obolibrary.org/obo/CHEBI_25566	nitrotoluene
 http://purl.obolibrary.org/obo/GO_0170041	non-proteinogenic amino acid metabolic process	http://purl.obolibrary.org/obo/CHEBI_83820	non-proteinogenic amino acid
 http://purl.obolibrary.org/obo/GO_1900876	nonadec-1-ene metabolic process	http://purl.obolibrary.org/obo/CHEBI_64503	nonadec-1-ene
-http://purl.obolibrary.org/obo/GO_0046418	nopaline metabolic process	http://purl.obolibrary.org/obo/CHEBI_58074	D-nopalinate(1-)
 http://purl.obolibrary.org/obo/GO_0046204	nor-spermidine metabolic process	http://purl.obolibrary.org/obo/CHEBI_57920	bis(3-azaniumylpropyl)azanium
 http://purl.obolibrary.org/obo/GO_0042415	norepinephrine metabolic process	http://purl.obolibrary.org/obo/CHEBI_72587	(R)-noradrenaline(1+)
 http://purl.obolibrary.org/obo/GO_0043641	novobiocin metabolic process	http://purl.obolibrary.org/obo/CHEBI_71339	novobiocin(1-)
@@ -893,7 +892,6 @@ http://purl.obolibrary.org/obo/GO_1900681	octadecene metabolic process	http://pu
 http://purl.obolibrary.org/obo/GO_0046518	octamethylcyclotetrasiloxane metabolic process	http://purl.obolibrary.org/obo/CHEBI_25640	octamethylcyclotetrasiloxane
 http://purl.obolibrary.org/obo/GO_0006070	octanol metabolic process	http://purl.obolibrary.org/obo/CHEBI_16188	octan-1-ol
 http://purl.obolibrary.org/obo/GO_0046333	octopamine metabolic process	http://purl.obolibrary.org/obo/CHEBI_58025	octopaminium
-http://purl.obolibrary.org/obo/GO_0046419	octopine metabolic process	http://purl.obolibrary.org/obo/CHEBI_57520	D-octopine dizwitterion
 http://purl.obolibrary.org/obo/GO_1900673	olefin metabolic process	http://purl.obolibrary.org/obo/CHEBI_33641	olefin
 http://purl.obolibrary.org/obo/GO_0120254	olefinic compound metabolic process	http://purl.obolibrary.org/obo/CHEBI_78840	olefinic compound
 http://purl.obolibrary.org/obo/GO_0009311	oligosaccharide metabolic process	http://purl.obolibrary.org/obo/CHEBI_50699	oligosaccharide

diff --git a/src/design_patterns/negative_regulation.tsv b/src/design_patterns/negative_regulation.tsv
@@ -162,7 +162,7 @@ http://purl.obolibrary.org/obo/GO_1904664	negative regulation of N-terminal pept
 http://purl.obolibrary.org/obo/GO_0060262	negative regulation of N-terminal protein palmitoylation	http://purl.obolibrary.org/obo/GO_0006500	N-terminal protein palmitoylation
 http://purl.obolibrary.org/obo/GO_1902689	negative regulation of NAD metabolic process	http://purl.obolibrary.org/obo/GO_0019674	NAD metabolic process
 http://purl.obolibrary.org/obo/GO_0033861	negative regulation of NAD(P)H oxidase activity	http://purl.obolibrary.org/obo/GO_0016174	NAD(P)H oxidase H2O2-forming activity
-http://purl.obolibrary.org/obo/GO_1901665	negative regulation of NAD+ ADP-ribosyltransferase activity	http://purl.obolibrary.org/obo/GO_0003950	NAD+ ADP-ribosyltransferase activity
+http://purl.obolibrary.org/obo/GO_1901665	negative regulation of NAD+ ADP-ribosyltransferase activity	http://purl.obolibrary.org/obo/GO_0003950	NAD+-protein poly-ADP-ribosyltransferase activity
 http://purl.obolibrary.org/obo/GO_0033671	negative regulation of NAD+ kinase activity	http://purl.obolibrary.org/obo/GO_0003951	NAD+ kinase activity
 http://purl.obolibrary.org/obo/GO_0051134	negative regulation of NK T cell activation	http://purl.obolibrary.org/obo/GO_0051132	NK T cell activation
 http://purl.obolibrary.org/obo/GO_0051137	negative regulation of NK T cell differentiation	http://purl.obolibrary.org/obo/GO_0001865	NK T cell differentiation
@@ -2625,7 +2625,6 @@ http://purl.obolibrary.org/obo/GO_1902948	negative regulation of tau-protein kin
 http://purl.obolibrary.org/obo/GO_0075258	negative regulation of teliospore formation	http://purl.obolibrary.org/obo/GO_0075255	teliospore formation
 http://purl.obolibrary.org/obo/GO_0075278	negative regulation of telium development	http://purl.obolibrary.org/obo/GO_0075275	telium development
 http://purl.obolibrary.org/obo/GO_1904873	negative regulation of telomerase RNA localization to Cajal body	http://purl.obolibrary.org/obo/GO_0090671	telomerase RNA localization to Cajal body
-http://purl.obolibrary.org/obo/GO_1905662	negative regulation of telomerase RNA reverse transcriptase activity	http://purl.obolibrary.org/obo/GO_0003721	telomerase RNA reverse transcriptase activity
 http://purl.obolibrary.org/obo/GO_0051974	negative regulation of telomerase activity	http://purl.obolibrary.org/obo/GO_0003720	telomerase activity
 http://purl.obolibrary.org/obo/GO_1904883	negative regulation of telomerase catalytic core complex assembly	http://purl.obolibrary.org/obo/GO_1904868	telomerase catalytic core complex assembly
 http://purl.obolibrary.org/obo/GO_1904354	negative regulation of telomere capping	http://purl.obolibrary.org/obo/GO_0016233	telomere capping

diff --git a/src/design_patterns/positive_regulation.tsv b/src/design_patterns/positive_regulation.tsv
@@ -165,7 +165,7 @@ http://purl.obolibrary.org/obo/GO_1904665	positive regulation of N-terminal pept
 http://purl.obolibrary.org/obo/GO_1902391	positive regulation of N-terminal peptidyl-serine acetylation	http://purl.obolibrary.org/obo/GO_0017198	N-terminal peptidyl-serine acetylation
 http://purl.obolibrary.org/obo/GO_1902690	positive regulation of NAD metabolic process	http://purl.obolibrary.org/obo/GO_0019674	NAD metabolic process
 http://purl.obolibrary.org/obo/GO_0033864	positive regulation of NAD(P)H oxidase activity	http://purl.obolibrary.org/obo/GO_0016174	NAD(P)H oxidase H2O2-forming activity
-http://purl.obolibrary.org/obo/GO_1901666	positive regulation of NAD+ ADP-ribosyltransferase activity	http://purl.obolibrary.org/obo/GO_0003950	NAD+ ADP-ribosyltransferase activity
+http://purl.obolibrary.org/obo/GO_1901666	positive regulation of NAD+ ADP-ribosyltransferase activity	http://purl.obolibrary.org/obo/GO_0003950	NAD+-protein poly-ADP-ribosyltransferase activity
 http://purl.obolibrary.org/obo/GO_0033672	positive regulation of NAD+ kinase activity	http://purl.obolibrary.org/obo/GO_0003951	NAD+ kinase activity
 http://purl.obolibrary.org/obo/GO_0051135	positive regulation of NK T cell activation	http://purl.obolibrary.org/obo/GO_0051132	NK T cell activation
 http://purl.obolibrary.org/obo/GO_0051138	positive regulation of NK T cell differentiation	http://purl.obolibrary.org/obo/GO_0001865	NK T cell differentiation
@@ -2617,7 +2617,6 @@ http://purl.obolibrary.org/obo/GO_0062090	positive regulation of taurine biosynt
 http://purl.obolibrary.org/obo/GO_0075257	positive regulation of teliospore formation	http://purl.obolibrary.org/obo/GO_0075255	teliospore formation
 http://purl.obolibrary.org/obo/GO_0075277	positive regulation of telium development	http://purl.obolibrary.org/obo/GO_0075275	telium development
 http://purl.obolibrary.org/obo/GO_1904874	positive regulation of telomerase RNA localization to Cajal body	http://purl.obolibrary.org/obo/GO_0090671	telomerase RNA localization to Cajal body
-http://purl.obolibrary.org/obo/GO_1905663	positive regulation of telomerase RNA reverse transcriptase activity	http://purl.obolibrary.org/obo/GO_0003721	telomerase RNA reverse transcriptase activity
 http://purl.obolibrary.org/obo/GO_0051973	positive regulation of telomerase activity	http://purl.obolibrary.org/obo/GO_0003720	telomerase activity
 http://purl.obolibrary.org/obo/GO_1904884	positive regulation of telomerase catalytic core complex assembly	http://purl.obolibrary.org/obo/GO_1904868	telomerase catalytic core complex assembly
 http://purl.obolibrary.org/obo/GO_1904355	positive regulation of telomere capping	http://purl.obolibrary.org/obo/GO_0016233	telomere capping

diff --git a/src/design_patterns/regulation.tsv b/src/design_patterns/regulation.tsv
@@ -187,7 +187,7 @@ http://purl.obolibrary.org/obo/GO_1902390	regulation of N-terminal peptidyl-seri
 http://purl.obolibrary.org/obo/GO_0060254	regulation of N-terminal protein palmitoylation	http://purl.obolibrary.org/obo/GO_0006500	N-terminal protein palmitoylation
 http://purl.obolibrary.org/obo/GO_1902688	regulation of NAD metabolic process	http://purl.obolibrary.org/obo/GO_0019674	NAD metabolic process
 http://purl.obolibrary.org/obo/GO_0033860	regulation of NAD(P)H oxidase activity	http://purl.obolibrary.org/obo/GO_0016174	NAD(P)H oxidase H2O2-forming activity
-http://purl.obolibrary.org/obo/GO_1901664	regulation of NAD+ ADP-ribosyltransferase activity	http://purl.obolibrary.org/obo/GO_0003950	NAD+ ADP-ribosyltransferase activity
+http://purl.obolibrary.org/obo/GO_1901664	regulation of NAD+ ADP-ribosyltransferase activity	http://purl.obolibrary.org/obo/GO_0003950	NAD+-protein poly-ADP-ribosyltransferase activity
 http://purl.obolibrary.org/obo/GO_0033670	regulation of NAD+ kinase activity	http://purl.obolibrary.org/obo/GO_0003951	NAD+ kinase activity
 http://purl.obolibrary.org/obo/GO_1902031	regulation of NADP metabolic process	http://purl.obolibrary.org/obo/GO_0006739	NADP metabolic process
 http://purl.obolibrary.org/obo/GO_0051133	regulation of NK T cell activation	http://purl.obolibrary.org/obo/GO_0051132	NK T cell activation
@@ -2976,7 +2976,6 @@ http://purl.obolibrary.org/obo/GO_0062089	regulation of taurine biosynthetic pro
 http://purl.obolibrary.org/obo/GO_0075256	regulation of teliospore formation	http://purl.obolibrary.org/obo/GO_0075255	teliospore formation
 http://purl.obolibrary.org/obo/GO_0075276	regulation of telium development	http://purl.obolibrary.org/obo/GO_0075275	telium development
 http://purl.obolibrary.org/obo/GO_1904872	regulation of telomerase RNA localization to Cajal body	http://purl.obolibrary.org/obo/GO_0090671	telomerase RNA localization to Cajal body
-http://purl.obolibrary.org/obo/GO_1905661	regulation of telomerase RNA reverse transcriptase activity	http://purl.obolibrary.org/obo/GO_0003721	telomerase RNA reverse transcriptase activity
 http://purl.obolibrary.org/obo/GO_0051972	regulation of telomerase activity	http://purl.obolibrary.org/obo/GO_0003720	telomerase activity
 http://purl.obolibrary.org/obo/GO_1904882	regulation of telomerase catalytic core complex assembly	http://purl.obolibrary.org/obo/GO_1904868	telomerase catalytic core complex assembly
 http://purl.obolibrary.org/obo/GO_1904353	regulation of telomere capping	http://purl.obolibrary.org/obo/GO_0016233	telomere capping

diff --git a/src/ontology/imports/go-pattern-conformance.ttl b/src/ontology/imports/go-pattern-conformance.ttl
@@ -11304,12 +11304,6 @@
 <http://purl.obolibrary.org/obo/GO_0019448> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/catabolic_process.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_0019468> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/catabolic_process.yaml> .
-
-
-<http://purl.obolibrary.org/obo/GO_0019469> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/catabolic_process.yaml> .
-
-
 <http://purl.obolibrary.org/obo/GO_0019470> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/catabolic_process.yaml> .
 
 
@@ -24520,12 +24514,6 @@
 <http://purl.obolibrary.org/obo/GO_0046417> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/metabolic_process.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_0046418> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/metabolic_process.yaml> .
-
-
-<http://purl.obolibrary.org/obo/GO_0046419> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/metabolic_process.yaml> .
-
-
 <http://purl.obolibrary.org/obo/GO_0046425> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/regulation.yaml> ,
                                                                                   <http://purl.obolibrary.org/obo/go/patterns/regulation_by.yaml> .
 
@@ -39352,6 +39340,9 @@
 <http://purl.obolibrary.org/obo/GO_0160181> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/biosynthetic_process.yaml> .
 
 
+<http://purl.obolibrary.org/obo/GO_0160194> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/cellular_anatomical_entity_organization.yaml> .
+
+
 <http://purl.obolibrary.org/obo/GO_0170033> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/metabolic_process.yaml> .
 
 
@@ -53934,15 +53925,6 @@
 <http://purl.obolibrary.org/obo/GO_1905660> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/cc_assembly.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_1905661> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/regulation.yaml> .
-
-
-<http://purl.obolibrary.org/obo/GO_1905662> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/negative_regulation.yaml> .
-
-
-<http://purl.obolibrary.org/obo/GO_1905663> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/positive_regulation.yaml> .
-
-
 <http://purl.obolibrary.org/obo/GO_1905664> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/regulation.yaml> ,
                                                                                   <http://purl.obolibrary.org/obo/go/patterns/regulation_by.yaml> .
 
@@ -54938,9 +54920,6 @@
 <http://purl.obolibrary.org/obo/GO_1990655> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/binding.yaml> .
 
 
-<http://purl.obolibrary.org/obo/GO_1990700> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/cellular_anatomical_entity_organization.yaml> .
-
-
 <http://purl.obolibrary.org/obo/GO_1990748> <http://purl.org/dc/terms/conformsTo> <http://purl.obolibrary.org/obo/go/patterns/occursIn.yaml> .