From 02d18d9f23d533a62f204c6065a2079950eb7ffb Mon Sep 17 00:00:00 2001 From: balhoff Date: Thu, 11 Jul 2024 14:50:49 +0000 Subject: [PATCH] [create-pull-request] automated change --- docs/patterns/multi_organism_process.md | 2 +- docs/patterns/protein_complex_by_activity.md | 2 +- docs/patterns/single_organism_process.md | 2 +- src/design_patterns/catabolic_process.tsv | 2 -- ...ellular_anatomical_entity_organization.tsv | 2 +- src/design_patterns/metabolic_process.tsv | 2 -- src/design_patterns/negative_regulation.tsv | 3 +-- src/design_patterns/positive_regulation.tsv | 3 +-- src/design_patterns/regulation.tsv | 3 +-- .../imports/go-pattern-conformance.ttl | 27 +++---------------- 10 files changed, 10 insertions(+), 38 deletions(-) diff --git a/docs/patterns/multi_organism_process.md b/docs/patterns/multi_organism_process.md index 37b47b04a9..67d62e1692 100644 --- 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 index 85be12daf1..92888d3269 100644 --- 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 index 61a527175e..d8076858a2 100644 --- 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 index 675a8d92fd..ebf40a7409 100644 --- 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 index 97da3f6052..72c64529ab 100644 --- 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 index d5bf22a9e5..a881f89a60 100644 --- 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 index 24f0a792cc..5b0782c10c 100644 --- 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 index 28b976b8bd..c2916fcf39 100644 --- 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 index 8f8c02a041..baeed01178 100644 --- 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 index 72d08411df..c57731d52b 100644 --- a/src/ontology/imports/go-pattern-conformance.ttl +++ b/src/ontology/imports/go-pattern-conformance.ttl @@ -11304,12 +11304,6 @@ . - . - - - . - - . @@ -24520,12 +24514,6 @@ . - . - - - . - - , . @@ -39352,6 +39340,9 @@ . + . + + . @@ -53934,15 +53925,6 @@ . - . - - - . - - - . - - , . @@ -54938,9 +54920,6 @@ . - . - - .