From ad2794a99ad2e14705befbef19eaa4d468c1a7ae Mon Sep 17 00:00:00 2001 From: ontobot <52354757+ontobot@users.noreply.github.com> Date: Sat, 28 Sep 2024 16:23:59 -0400 Subject: [PATCH] [create-pull-request] automated change (#29003) Co-authored-by: balhoff --- 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/biosynthetic_process.tsv | 4 ++-- src/design_patterns/catabolic_process.tsv | 5 +++-- src/design_patterns/metabolic_process.tsv | 16 +++++++++------- src/design_patterns/negative_regulation.tsv | 7 ++++--- src/design_patterns/regulation.tsv | 10 +++++----- src/design_patterns/regulation_by.tsv | 10 +++++----- src/ontology/imports/go-pattern-conformance.ttl | 12 ++++++++++++ 10 files changed, 43 insertions(+), 27 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/biosynthetic_process.tsv b/src/design_patterns/biosynthetic_process.tsv index 7e10e7f95e..cb9afdb604 100644 --- 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 index 2178fcf334..1a1fa1acef 100644 --- 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 index 0829502522..30d88acd90 100644 --- a/src/design_patterns/metabolic_process.tsv +++ b/src/design_patterns/metabolic_process.tsv @@ -239,6 +239,7 @@ 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 @@ -246,7 +247,10 @@ http://purl.obolibrary.org/obo/GO_0032341 aldosterone metabolic process http://p 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 diff --git a/src/design_patterns/negative_regulation.tsv b/src/design_patterns/negative_regulation.tsv index 7be2ef0a94..f4586a9080 100644 --- a/src/design_patterns/negative_regulation.tsv +++ b/src/design_patterns/negative_regulation.tsv @@ -246,6 +246,7 @@ http://purl.obolibrary.org/obo/GO_1900492 negative regulation of [4Fe-4S] cluste http://purl.obolibrary.org/obo/GO_0090359 negative regulation of abscisic acid biosynthetic process http://purl.obolibrary.org/obo/GO_0009688 abscisic acid biosynthetic process http://purl.obolibrary.org/obo/GO_0009788 negative regulation of abscisic acid-activated signaling pathway http://purl.obolibrary.org/obo/GO_0009738 abscisic acid-activated signaling pathway http://purl.obolibrary.org/obo/GO_0045753 negative regulation of acetate catabolic process http://purl.obolibrary.org/obo/GO_0045733 acetate catabolic process +http://purl.obolibrary.org/obo/GO_0160218 negative regulation of acetyl-CoA biosynthetic process from pyruvate http://purl.obolibrary.org/obo/GO_0006086 acetyl-CoA biosynthetic process from pyruvate http://purl.obolibrary.org/obo/GO_1905922 negative regulation of acetylcholine biosynthetic process http://purl.obolibrary.org/obo/GO_0008292 acetylcholine biosynthetic process http://purl.obolibrary.org/obo/GO_0060410 negative regulation of acetylcholine metabolic process http://purl.obolibrary.org/obo/GO_0008291 acetylcholine metabolic process http://purl.obolibrary.org/obo/GO_0014058 negative regulation of acetylcholine secretion, neurotransmission http://purl.obolibrary.org/obo/GO_0014055 acetylcholine secretion, neurotransmission @@ -317,6 +318,7 @@ http://purl.obolibrary.org/obo/GO_0033242 negative regulation of amine catabolic http://purl.obolibrary.org/obo/GO_0033239 negative regulation of amine metabolic process http://purl.obolibrary.org/obo/GO_0009308 amine metabolic process http://purl.obolibrary.org/obo/GO_0051953 negative regulation of amine transport http://purl.obolibrary.org/obo/GO_0015837 amine transport http://purl.obolibrary.org/obo/GO_2000283 negative regulation of amino acid biosynthetic process http://purl.obolibrary.org/obo/GO_0008652 amino acid biosynthetic process +http://purl.obolibrary.org/obo/GO_0045763 negative regulation of amino acid metabolic process http://purl.obolibrary.org/obo/GO_0006520 amino acid metabolic process http://purl.obolibrary.org/obo/GO_0051956 negative regulation of amino acid transport http://purl.obolibrary.org/obo/GO_0006865 amino acid transport http://purl.obolibrary.org/obo/GO_0051942 negative regulation of amino acid uptake involved in synaptic transmission http://purl.obolibrary.org/obo/GO_0051933 amino acid neurotransmitter reuptake http://purl.obolibrary.org/obo/GO_2001249 negative regulation of ammonia assimilation cycle http://purl.obolibrary.org/obo/GO_0019676 ammonia assimilation cycle @@ -644,7 +646,6 @@ http://purl.obolibrary.org/obo/GO_2000937 negative regulation of cellotriose cat http://purl.obolibrary.org/obo/GO_2000934 negative regulation of cellotriose metabolic process http://purl.obolibrary.org/obo/GO_2000893 cellotriose metabolic process http://purl.obolibrary.org/obo/GO_1900286 negative regulation of cellotriose transport http://purl.obolibrary.org/obo/GO_2001096 cellotriose transport http://purl.obolibrary.org/obo/GO_1900420 negative regulation of cellular alcohol catabolic process http://purl.obolibrary.org/obo/GO_0046164 alcohol catabolic process -http://purl.obolibrary.org/obo/GO_0045763 negative regulation of cellular amino acid metabolic process http://purl.obolibrary.org/obo/GO_0006520 amino acid metabolic process http://purl.obolibrary.org/obo/GO_0031327 negative regulation of cellular biosynthetic process http://purl.obolibrary.org/obo/GO_0044249 cellular biosynthetic process http://purl.obolibrary.org/obo/GO_0031330 negative regulation of cellular catabolic process http://purl.obolibrary.org/obo/GO_0044248 cellular catabolic process http://purl.obolibrary.org/obo/GO_0051129 negative regulation of cellular component organization http://purl.obolibrary.org/obo/GO_0016043 cellular component organization @@ -653,8 +654,6 @@ http://purl.obolibrary.org/obo/GO_0002692 negative regulation of cellular extrav http://purl.obolibrary.org/obo/GO_2001030 negative regulation of cellular glucuronidation http://purl.obolibrary.org/obo/GO_0052695 cellular glucuronidation http://purl.obolibrary.org/obo/GO_1900070 negative regulation of cellular hyperosmotic salinity response http://purl.obolibrary.org/obo/GO_0071475 cellular hyperosmotic salinity response http://purl.obolibrary.org/obo/GO_0031324 negative regulation of cellular metabolic process http://purl.obolibrary.org/obo/GO_0044237 cellular metabolic process -http://purl.obolibrary.org/obo/GO_0090350 negative regulation of cellular organofluorine metabolic process http://purl.obolibrary.org/obo/GO_0090346 cellular organofluorine metabolic process -http://purl.obolibrary.org/obo/GO_0090349 negative regulation of cellular organohalogen metabolic process http://purl.obolibrary.org/obo/GO_0090345 cellular organohalogen metabolic process http://purl.obolibrary.org/obo/GO_0032848 negative regulation of cellular pH reduction http://purl.obolibrary.org/obo/GO_0051452 intracellular pH reduction http://purl.obolibrary.org/obo/GO_0048523 negative regulation of cellular process http://purl.obolibrary.org/obo/GO_0009987 cellular process http://purl.obolibrary.org/obo/GO_1901856 negative regulation of cellular respiration http://purl.obolibrary.org/obo/GO_0045333 cellular respiration @@ -1949,6 +1948,8 @@ http://purl.obolibrary.org/obo/GO_0046621 negative regulation of organ growth ht http://purl.obolibrary.org/obo/GO_1902116 negative regulation of organelle assembly http://purl.obolibrary.org/obo/GO_0070925 organelle assembly http://purl.obolibrary.org/obo/GO_0010639 negative regulation of organelle organization http://purl.obolibrary.org/obo/GO_0006996 organelle organization http://purl.obolibrary.org/obo/GO_0032891 negative regulation of organic acid transport http://purl.obolibrary.org/obo/GO_0015849 organic acid transport +http://purl.obolibrary.org/obo/GO_0090350 negative regulation of organofluorine metabolic process http://purl.obolibrary.org/obo/GO_0090346 organofluorine metabolic process +http://purl.obolibrary.org/obo/GO_0090349 negative regulation of organohalogen metabolic process http://purl.obolibrary.org/obo/GO_0090345 organohalogen metabolic process http://purl.obolibrary.org/obo/GO_1903267 negative regulation of ornithine catabolic process http://purl.obolibrary.org/obo/GO_0006593 ornithine catabolic process http://purl.obolibrary.org/obo/GO_0030279 negative regulation of ossification http://purl.obolibrary.org/obo/GO_0001503 ossification http://purl.obolibrary.org/obo/GO_0045668 negative regulation of osteoblast differentiation http://purl.obolibrary.org/obo/GO_0001649 osteoblast differentiation diff --git a/src/design_patterns/regulation.tsv b/src/design_patterns/regulation.tsv index 762120c638..cbe83d45ea 100644 --- a/src/design_patterns/regulation.tsv +++ b/src/design_patterns/regulation.tsv @@ -374,7 +374,9 @@ http://purl.obolibrary.org/obo/GO_0034248 regulation of amide metabolic process http://purl.obolibrary.org/obo/GO_0033241 regulation of amine catabolic process http://purl.obolibrary.org/obo/GO_0009310 amine catabolic process http://purl.obolibrary.org/obo/GO_0033238 regulation of amine metabolic process http://purl.obolibrary.org/obo/GO_0009308 amine metabolic process http://purl.obolibrary.org/obo/GO_0051952 regulation of amine transport http://purl.obolibrary.org/obo/GO_0015837 amine transport +http://purl.obolibrary.org/obo/GO_2000282 regulation of amino acid biosynthetic process http://purl.obolibrary.org/obo/GO_0008652 amino acid biosynthetic process http://purl.obolibrary.org/obo/GO_0010958 regulation of amino acid import across plasma membrane http://purl.obolibrary.org/obo/GO_0089718 amino acid import across plasma membrane +http://purl.obolibrary.org/obo/GO_0006521 regulation of amino acid metabolic process http://purl.obolibrary.org/obo/GO_0006520 amino acid metabolic process http://purl.obolibrary.org/obo/GO_1903789 regulation of amino acid transmembrane transport http://purl.obolibrary.org/obo/GO_0003333 amino acid transmembrane transport http://purl.obolibrary.org/obo/GO_0051955 regulation of amino acid transport http://purl.obolibrary.org/obo/GO_0006865 amino acid transport http://purl.obolibrary.org/obo/GO_0051941 regulation of amino acid uptake involved in synaptic transmission http://purl.obolibrary.org/obo/GO_0051933 amino acid neurotransmitter reuptake @@ -745,8 +747,6 @@ http://purl.obolibrary.org/obo/GO_2000936 regulation of cellotriose catabolic pr http://purl.obolibrary.org/obo/GO_2000933 regulation of cellotriose metabolic process http://purl.obolibrary.org/obo/GO_2000893 cellotriose metabolic process http://purl.obolibrary.org/obo/GO_1900285 regulation of cellotriose transport http://purl.obolibrary.org/obo/GO_2001096 cellotriose transport http://purl.obolibrary.org/obo/GO_1900419 regulation of cellular alcohol catabolic process http://purl.obolibrary.org/obo/GO_0046164 alcohol catabolic process -http://purl.obolibrary.org/obo/GO_2000282 regulation of cellular amino acid biosynthetic process http://purl.obolibrary.org/obo/GO_0008652 amino acid biosynthetic process -http://purl.obolibrary.org/obo/GO_0006521 regulation of cellular amino acid metabolic process http://purl.obolibrary.org/obo/GO_0006520 amino acid metabolic process http://purl.obolibrary.org/obo/GO_0031326 regulation of cellular biosynthetic process http://purl.obolibrary.org/obo/GO_0044249 cellular biosynthetic process http://purl.obolibrary.org/obo/GO_0031329 regulation of cellular catabolic process http://purl.obolibrary.org/obo/GO_0044248 cellular catabolic process http://purl.obolibrary.org/obo/GO_0044087 regulation of cellular component biogenesis http://purl.obolibrary.org/obo/GO_0044085 cellular component biogenesis @@ -755,11 +755,8 @@ http://purl.obolibrary.org/obo/GO_0010185 regulation of cellular defense respons http://purl.obolibrary.org/obo/GO_0002691 regulation of cellular extravasation http://purl.obolibrary.org/obo/GO_0045123 cellular extravasation http://purl.obolibrary.org/obo/GO_2001029 regulation of cellular glucuronidation http://purl.obolibrary.org/obo/GO_0052695 cellular glucuronidation http://purl.obolibrary.org/obo/GO_1900069 regulation of cellular hyperosmotic salinity response http://purl.obolibrary.org/obo/GO_0071475 cellular hyperosmotic salinity response -http://purl.obolibrary.org/obo/GO_0010565 regulation of cellular ketone metabolic process http://purl.obolibrary.org/obo/GO_0042180 cellular ketone metabolic process http://purl.obolibrary.org/obo/GO_0060341 regulation of cellular localization http://purl.obolibrary.org/obo/GO_0051641 cellular localization http://purl.obolibrary.org/obo/GO_0031323 regulation of cellular metabolic process http://purl.obolibrary.org/obo/GO_0044237 cellular metabolic process -http://purl.obolibrary.org/obo/GO_0090348 regulation of cellular organofluorine metabolic process http://purl.obolibrary.org/obo/GO_0090346 cellular organofluorine metabolic process -http://purl.obolibrary.org/obo/GO_0090347 regulation of cellular organohalogen metabolic process http://purl.obolibrary.org/obo/GO_0090345 cellular organohalogen metabolic process http://purl.obolibrary.org/obo/GO_0032847 regulation of cellular pH reduction http://purl.obolibrary.org/obo/GO_0051452 intracellular pH reduction http://purl.obolibrary.org/obo/GO_0050794 regulation of cellular process http://purl.obolibrary.org/obo/GO_0009987 cellular process http://purl.obolibrary.org/obo/GO_0043457 regulation of cellular respiration http://purl.obolibrary.org/obo/GO_0045333 cellular respiration @@ -1637,6 +1634,7 @@ http://purl.obolibrary.org/obo/GO_0051547 regulation of keratinocyte migration h http://purl.obolibrary.org/obo/GO_0010837 regulation of keratinocyte proliferation http://purl.obolibrary.org/obo/GO_0043616 keratinocyte proliferation http://purl.obolibrary.org/obo/GO_0010566 regulation of ketone biosynthetic process http://purl.obolibrary.org/obo/GO_0042181 ketone biosynthetic process http://purl.obolibrary.org/obo/GO_0010567 regulation of ketone catabolic process http://purl.obolibrary.org/obo/GO_0042182 ketone catabolic process +http://purl.obolibrary.org/obo/GO_0010565 regulation of ketone metabolic process http://purl.obolibrary.org/obo/GO_0042180 ketone metabolic process http://purl.obolibrary.org/obo/GO_0090183 regulation of kidney development http://purl.obolibrary.org/obo/GO_0001822 kidney development http://purl.obolibrary.org/obo/GO_2000356 regulation of kidney smooth muscle cell differentiation http://purl.obolibrary.org/obo/GO_0072195 kidney smooth muscle cell differentiation http://purl.obolibrary.org/obo/GO_0051709 regulation of killing of cells of another organism http://purl.obolibrary.org/obo/GO_0031640 killing of cells of another organism @@ -2209,6 +2207,8 @@ http://purl.obolibrary.org/obo/GO_1902115 regulation of organelle assembly http: http://purl.obolibrary.org/obo/GO_0033043 regulation of organelle organization http://purl.obolibrary.org/obo/GO_0006996 organelle organization http://purl.obolibrary.org/obo/GO_1902513 regulation of organelle transport along microtubule http://purl.obolibrary.org/obo/GO_0072384 organelle transport along microtubule http://purl.obolibrary.org/obo/GO_0032890 regulation of organic acid transport http://purl.obolibrary.org/obo/GO_0015849 organic acid transport +http://purl.obolibrary.org/obo/GO_0090348 regulation of organofluorine metabolic process http://purl.obolibrary.org/obo/GO_0090346 organofluorine metabolic process +http://purl.obolibrary.org/obo/GO_0090347 regulation of organohalogen metabolic process http://purl.obolibrary.org/obo/GO_0090345 organohalogen metabolic process http://purl.obolibrary.org/obo/GO_1903266 regulation of ornithine catabolic process http://purl.obolibrary.org/obo/GO_0006593 ornithine catabolic process http://purl.obolibrary.org/obo/GO_0090368 regulation of ornithine metabolic process http://purl.obolibrary.org/obo/GO_0006591 ornithine metabolic process http://purl.obolibrary.org/obo/GO_1904295 regulation of osmolarity-sensing cation channel activity http://purl.obolibrary.org/obo/GO_1990760 osmolarity-sensing monoatomic cation channel activity diff --git a/src/design_patterns/regulation_by.tsv b/src/design_patterns/regulation_by.tsv index eb8904f146..34d0bdf087 100644 --- a/src/design_patterns/regulation_by.tsv +++ b/src/design_patterns/regulation_by.tsv @@ -336,7 +336,9 @@ http://purl.obolibrary.org/obo/GO_0034248 regulation of amide metabolic process http://purl.obolibrary.org/obo/GO_0033241 regulation of amine catabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0009310 amine catabolic process http://purl.obolibrary.org/obo/GO_0033238 regulation of amine metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0009308 amine metabolic process http://purl.obolibrary.org/obo/GO_0051952 regulation of amine transport http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0015837 amine transport +http://purl.obolibrary.org/obo/GO_2000282 regulation of amino acid biosynthetic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0008652 amino acid biosynthetic process http://purl.obolibrary.org/obo/GO_0010958 regulation of amino acid import across plasma membrane http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0089718 amino acid import across plasma membrane +http://purl.obolibrary.org/obo/GO_0006521 regulation of amino acid metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0006520 amino acid metabolic process http://purl.obolibrary.org/obo/GO_1903789 regulation of amino acid transmembrane transport http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0003333 amino acid transmembrane transport http://purl.obolibrary.org/obo/GO_0051955 regulation of amino acid transport http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0006865 amino acid transport http://purl.obolibrary.org/obo/GO_0051941 regulation of amino acid uptake involved in synaptic transmission http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0051933 amino acid neurotransmitter reuptake @@ -691,8 +693,6 @@ http://purl.obolibrary.org/obo/GO_2000936 regulation of cellotriose catabolic pr http://purl.obolibrary.org/obo/GO_2000933 regulation of cellotriose metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_2000893 cellotriose metabolic process http://purl.obolibrary.org/obo/GO_1900285 regulation of cellotriose transport http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_2001096 cellotriose transport http://purl.obolibrary.org/obo/GO_1900419 regulation of cellular alcohol catabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0046164 alcohol catabolic process -http://purl.obolibrary.org/obo/GO_2000282 regulation of cellular amino acid biosynthetic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0008652 amino acid biosynthetic process -http://purl.obolibrary.org/obo/GO_0006521 regulation of cellular amino acid metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0006520 amino acid metabolic process http://purl.obolibrary.org/obo/GO_0031326 regulation of cellular biosynthetic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0044249 cellular biosynthetic process http://purl.obolibrary.org/obo/GO_0031329 regulation of cellular catabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0044248 cellular catabolic process http://purl.obolibrary.org/obo/GO_0044087 regulation of cellular component biogenesis http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0044085 cellular component biogenesis @@ -701,11 +701,8 @@ http://purl.obolibrary.org/obo/GO_0010185 regulation of cellular defense respons http://purl.obolibrary.org/obo/GO_0002691 regulation of cellular extravasation http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0045123 cellular extravasation http://purl.obolibrary.org/obo/GO_2001029 regulation of cellular glucuronidation http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0052695 cellular glucuronidation http://purl.obolibrary.org/obo/GO_1900069 regulation of cellular hyperosmotic salinity response http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0071475 cellular hyperosmotic salinity response -http://purl.obolibrary.org/obo/GO_0010565 regulation of cellular ketone metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0042180 cellular ketone metabolic process http://purl.obolibrary.org/obo/GO_0060341 regulation of cellular localization http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0051641 cellular localization http://purl.obolibrary.org/obo/GO_0031323 regulation of cellular metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0044237 cellular metabolic process -http://purl.obolibrary.org/obo/GO_0090348 regulation of cellular organofluorine metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0090346 cellular organofluorine metabolic process -http://purl.obolibrary.org/obo/GO_0090347 regulation of cellular organohalogen metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0090345 cellular organohalogen metabolic process http://purl.obolibrary.org/obo/GO_0032847 regulation of cellular pH reduction http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0051452 intracellular pH reduction http://purl.obolibrary.org/obo/GO_0050794 regulation of cellular process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0009987 cellular process http://purl.obolibrary.org/obo/GO_0043457 regulation of cellular respiration http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0045333 cellular respiration @@ -1526,6 +1523,7 @@ http://purl.obolibrary.org/obo/GO_0051547 regulation of keratinocyte migration h http://purl.obolibrary.org/obo/GO_0010837 regulation of keratinocyte proliferation http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0043616 keratinocyte proliferation http://purl.obolibrary.org/obo/GO_0010566 regulation of ketone biosynthetic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0042181 ketone biosynthetic process http://purl.obolibrary.org/obo/GO_0010567 regulation of ketone catabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0042182 ketone catabolic process +http://purl.obolibrary.org/obo/GO_0010565 regulation of ketone metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0042180 ketone metabolic process http://purl.obolibrary.org/obo/GO_0090183 regulation of kidney development http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0001822 kidney development http://purl.obolibrary.org/obo/GO_2000356 regulation of kidney smooth muscle cell differentiation http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0072195 kidney smooth muscle cell differentiation http://purl.obolibrary.org/obo/GO_0051709 regulation of killing of cells of another organism http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0031640 killing of cells of another organism @@ -2072,6 +2070,8 @@ http://purl.obolibrary.org/obo/GO_1902115 regulation of organelle assembly http: http://purl.obolibrary.org/obo/GO_0033043 regulation of organelle organization http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0006996 organelle organization http://purl.obolibrary.org/obo/GO_1902513 regulation of organelle transport along microtubule http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0072384 organelle transport along microtubule http://purl.obolibrary.org/obo/GO_0032890 regulation of organic acid transport http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0015849 organic acid transport +http://purl.obolibrary.org/obo/GO_0090348 regulation of organofluorine metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0090346 organofluorine metabolic process +http://purl.obolibrary.org/obo/GO_0090347 regulation of organohalogen metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0090345 organohalogen metabolic process http://purl.obolibrary.org/obo/GO_1903266 regulation of ornithine catabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0006593 ornithine catabolic process http://purl.obolibrary.org/obo/GO_0090368 regulation of ornithine metabolic process http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0006591 ornithine metabolic process http://purl.obolibrary.org/obo/GO_0030278 regulation of ossification http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0001503 ossification diff --git a/src/ontology/imports/go-pattern-conformance.ttl b/src/ontology/imports/go-pattern-conformance.ttl index 67cdb55476..bb59d8ad51 100644 --- a/src/ontology/imports/go-pattern-conformance.ttl +++ b/src/ontology/imports/go-pattern-conformance.ttl @@ -35723,6 +35723,12 @@ . + . + + + . + + , . @@ -38822,6 +38828,9 @@ . + . + + . @@ -39108,6 +39117,9 @@ . + . + + .