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Update design pattern docs #28433

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Update design pattern docs #28433

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2 changes: 1 addition & 1 deletion docs/patterns/multi_organism_process.md
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Expand Up @@ -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))



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2 changes: 1 addition & 1 deletion docs/patterns/protein_complex_by_activity.md
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Expand Up @@ -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}`)



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2 changes: 1 addition & 1 deletion docs/patterns/single_organism_process.md
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Expand Up @@ -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))



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2 changes: 0 additions & 2 deletions src/design_patterns/catabolic_process.tsv
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Expand Up @@ -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
Expand All @@ -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
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2 changes: 1 addition & 1 deletion src/design_patterns/cellular_anatomical_entity_organization.tsv
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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2 changes: 0 additions & 2 deletions src/design_patterns/metabolic_process.tsv
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Expand Up @@ -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-)
Expand All @@ -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
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3 changes: 1 addition & 2 deletions src/design_patterns/negative_regulation.tsv
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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3 changes: 1 addition & 2 deletions src/design_patterns/positive_regulation.tsv
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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3 changes: 1 addition & 2 deletions src/design_patterns/regulation.tsv
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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27 changes: 3 additions & 24 deletions src/ontology/imports/go-pattern-conformance.ttl
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Expand Up @@ -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> .


Expand Down Expand Up @@ -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> .

Expand Down Expand Up @@ -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> .


Expand Down Expand Up @@ -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> .

Expand Down Expand Up @@ -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> .


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