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[create-pull-request] automated change (#29371)
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Co-authored-by: balhoff <[email protected]>
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ontobot and balhoff authored Dec 10, 2024
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2 changes: 1 addition & 1 deletion src/design_patterns/biosynthetic_process.tsv
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Expand Up @@ -140,6 +140,7 @@ http://purl.obolibrary.org/obo/GO_0055129 L-proline biosynthetic process http://
http://purl.obolibrary.org/obo/GO_0062143 L-propargylglycine biosynthetic process http://purl.obolibrary.org/obo/CHEBI_143285 L-propargylglycine zwitterion
http://purl.obolibrary.org/obo/GO_0006564 L-serine biosynthetic process http://purl.obolibrary.org/obo/CHEBI_33384 L-serine zwitterion
http://purl.obolibrary.org/obo/GO_0042849 L-sorbose biosynthetic process http://purl.obolibrary.org/obo/CHEBI_17266 L-sorbose
http://purl.obolibrary.org/obo/GO_0000162 L-tryptophan biosynthetic process http://purl.obolibrary.org/obo/CHEBI_57912 L-tryptophan zwitterion
http://purl.obolibrary.org/obo/GO_0009099 L-valine biosynthetic process http://purl.obolibrary.org/obo/CHEBI_57762 L-valine zwitterion
http://purl.obolibrary.org/obo/GO_0010493 Lewis a epitope biosynthetic process http://purl.obolibrary.org/obo/CHEBI_59295 beta-D-Galp-(1->3)-[alpha-L-Fucp-(1->4)]-beta-D-GlcpNAc
http://purl.obolibrary.org/obo/GO_0106402 Lewis x epitope biosynthetic process http://purl.obolibrary.org/obo/CHEBI_59294 alpha-L-Fucp-(1->3)-[beta-D-Galp-(1->4)]-beta-D-GlcpNAc
Expand Down Expand Up @@ -1044,7 +1045,6 @@ http://purl.obolibrary.org/obo/GO_0016104 triterpenoid biosynthetic process http
http://purl.obolibrary.org/obo/GO_0009710 tropane alkaloid biosynthetic process http://purl.obolibrary.org/obo/CHEBI_37332 tropane alkaloid
http://purl.obolibrary.org/obo/GO_0019342 trypanothione biosynthetic process http://purl.obolibrary.org/obo/CHEBI_58290 trypanothione(1+)
http://purl.obolibrary.org/obo/GO_0140654 tryprostatin A biosynthetic process http://purl.obolibrary.org/obo/CHEBI_72761 tryprostatin A
http://purl.obolibrary.org/obo/GO_0000162 tryptophan biosynthetic process http://purl.obolibrary.org/obo/CHEBI_64554 tryptophan zwitterion
http://purl.obolibrary.org/obo/GO_0035440 tuberculosinol biosynthetic process http://purl.obolibrary.org/obo/CHEBI_50387 tuberculosinol
http://purl.obolibrary.org/obo/GO_1901695 tyramine biosynthetic process http://purl.obolibrary.org/obo/CHEBI_327995 tyraminium
http://purl.obolibrary.org/obo/GO_1901904 tyrocidine biosynthetic process http://purl.obolibrary.org/obo/CHEBI_71947 tyrocidine
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2 changes: 1 addition & 1 deletion src/design_patterns/catabolic_process.tsv
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Expand Up @@ -122,6 +122,7 @@ http://purl.obolibrary.org/obo/GO_0006559 L-phenylalanine catabolic process http
http://purl.obolibrary.org/obo/GO_0019504 L-proline betaine catabolic process http://purl.obolibrary.org/obo/CHEBI_35280 L-proline betaine
http://purl.obolibrary.org/obo/GO_0006565 L-serine catabolic process http://purl.obolibrary.org/obo/CHEBI_33384 L-serine zwitterion
http://purl.obolibrary.org/obo/GO_0042850 L-sorbose catabolic process http://purl.obolibrary.org/obo/CHEBI_17266 L-sorbose
http://purl.obolibrary.org/obo/GO_0006569 L-tryptophan catabolic process http://purl.obolibrary.org/obo/CHEBI_57912 L-tryptophan zwitterion
http://purl.obolibrary.org/obo/GO_0032326 Mo-molybdopterin cofactor catabolic process http://purl.obolibrary.org/obo/CHEBI_21437 Mo-molybdopterin cofactor
http://purl.obolibrary.org/obo/GO_1900550 N',N'',N'''-triacetylfusarinine C catabolic process http://purl.obolibrary.org/obo/CHEBI_60481 N',N'',N'''-triacetylfusarinine C
http://purl.obolibrary.org/obo/GO_2001299 N(omega),N(omega)-dimethyl-L-arginine catabolic process http://purl.obolibrary.org/obo/CHEBI_58326 N(omega),N(omega)-dimethyl-L-argininium(1+)
Expand Down Expand Up @@ -883,7 +884,6 @@ http://purl.obolibrary.org/obo/GO_1901056 trimethylenediamine catabolic process
http://purl.obolibrary.org/obo/GO_0046260 trinitrotoluene catabolic process http://purl.obolibrary.org/obo/CHEBI_27135 trinitrotoluene
http://purl.obolibrary.org/obo/GO_0016105 triterpenoid catabolic process http://purl.obolibrary.org/obo/CHEBI_36615 triterpenoid
http://purl.obolibrary.org/obo/GO_0046207 trypanothione catabolic process http://purl.obolibrary.org/obo/CHEBI_58290 trypanothione(1+)
http://purl.obolibrary.org/obo/GO_0006569 tryptophan catabolic process http://purl.obolibrary.org/obo/CHEBI_64554 tryptophan zwitterion
http://purl.obolibrary.org/obo/GO_1901903 tyrocidine catabolic process http://purl.obolibrary.org/obo/CHEBI_71947 tyrocidine
http://purl.obolibrary.org/obo/GO_0006572 tyrosine catabolic process http://purl.obolibrary.org/obo/CHEBI_58315 L-tyrosine zwitterion
http://purl.obolibrary.org/obo/GO_0032322 ubiquinone catabolic process http://purl.obolibrary.org/obo/CHEBI_16389 ubiquinones
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16 changes: 0 additions & 16 deletions src/design_patterns/involved_in_x_y.tsv
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2 changes: 1 addition & 1 deletion src/design_patterns/metabolic_process.tsv
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Expand Up @@ -173,6 +173,7 @@ http://purl.obolibrary.org/obo/GO_0006558 L-phenylalanine metabolic process http
http://purl.obolibrary.org/obo/GO_0019502 L-proline betaine metabolic process http://purl.obolibrary.org/obo/CHEBI_35280 L-proline betaine
http://purl.obolibrary.org/obo/GO_0006563 L-serine metabolic process http://purl.obolibrary.org/obo/CHEBI_33384 L-serine zwitterion
http://purl.obolibrary.org/obo/GO_0019312 L-sorbose metabolic process http://purl.obolibrary.org/obo/CHEBI_17266 L-sorbose
http://purl.obolibrary.org/obo/GO_0006568 L-tryptophan metabolic process http://purl.obolibrary.org/obo/CHEBI_57912 L-tryptophan zwitterion
http://purl.obolibrary.org/obo/GO_1902759 Mo(VI)-molybdopterin cytosine dinucleotide metabolic process http://purl.obolibrary.org/obo/CHEBI_71308 Mo(VI)-molybdopterin cytosine dinucleotide(4-)
http://purl.obolibrary.org/obo/GO_0019720 Mo-molybdopterin cofactor metabolic process http://purl.obolibrary.org/obo/CHEBI_21437 Mo-molybdopterin cofactor
http://purl.obolibrary.org/obo/GO_1900549 N',N'',N'''-triacetylfusarinine C metabolic process http://purl.obolibrary.org/obo/CHEBI_60481 N',N'',N'''-triacetylfusarinine C
Expand Down Expand Up @@ -1212,7 +1213,6 @@ http://purl.obolibrary.org/obo/GO_0018973 trinitrotoluene metabolic process http
http://purl.obolibrary.org/obo/GO_0006722 triterpenoid metabolic process http://purl.obolibrary.org/obo/CHEBI_36615 triterpenoid
http://purl.obolibrary.org/obo/GO_0046448 tropane alkaloid metabolic process http://purl.obolibrary.org/obo/CHEBI_37332 tropane alkaloid
http://purl.obolibrary.org/obo/GO_0046206 trypanothione metabolic process http://purl.obolibrary.org/obo/CHEBI_58290 trypanothione(1+)
http://purl.obolibrary.org/obo/GO_0006568 tryptophan metabolic process http://purl.obolibrary.org/obo/CHEBI_57912 L-tryptophan zwitterion
http://purl.obolibrary.org/obo/GO_1901902 tyrocidine metabolic process http://purl.obolibrary.org/obo/CHEBI_71947 tyrocidine
http://purl.obolibrary.org/obo/GO_0006570 tyrosine metabolic process http://purl.obolibrary.org/obo/CHEBI_58315 L-tyrosine zwitterion
http://purl.obolibrary.org/obo/GO_0006743 ubiquinone metabolic process http://purl.obolibrary.org/obo/CHEBI_16389 ubiquinones
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5 changes: 0 additions & 5 deletions src/design_patterns/negative_regulation.tsv
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Expand Up @@ -71,9 +71,7 @@ http://purl.obolibrary.org/obo/GO_2000279 negative regulation of DNA biosyntheti
http://purl.obolibrary.org/obo/GO_1903625 negative regulation of DNA catabolic process http://purl.obolibrary.org/obo/GO_0006308 DNA catabolic process
http://purl.obolibrary.org/obo/GO_2000002 negative regulation of DNA damage checkpoint http://purl.obolibrary.org/obo/GO_0000077 DNA damage checkpoint signaling
http://purl.obolibrary.org/obo/GO_0043518 negative regulation of DNA damage response, signal transduction by p53 class mediator http://purl.obolibrary.org/obo/GO_0030330 DNA damage response, signal transduction by p53 class mediator
http://purl.obolibrary.org/obo/GO_1905463 negative regulation of DNA duplex unwinding http://purl.obolibrary.org/obo/GO_0032508 DNA duplex unwinding
http://purl.obolibrary.org/obo/GO_0032876 negative regulation of DNA endoreduplication http://purl.obolibrary.org/obo/GO_0042023 DNA endoreduplication
http://purl.obolibrary.org/obo/GO_0051107 negative regulation of DNA ligation http://purl.obolibrary.org/obo/GO_0006266 DNA ligation
http://purl.obolibrary.org/obo/GO_0051053 negative regulation of DNA metabolic process http://purl.obolibrary.org/obo/GO_0006259 DNA metabolic process
http://purl.obolibrary.org/obo/GO_0090310 negative regulation of DNA methylation-dependent heterochromatin formation http://purl.obolibrary.org/obo/GO_0006346 DNA methylation-dependent constitutive heterochromatin formation
http://purl.obolibrary.org/obo/GO_0062110 negative regulation of DNA recombinase disassembly http://purl.obolibrary.org/obo/GO_1990986 DNA recombinase disassembly
Expand Down Expand Up @@ -107,7 +105,6 @@ http://purl.obolibrary.org/obo/GO_2000245 negative regulation of FtsZ-dependent
http://purl.obolibrary.org/obo/GO_1904021 negative regulation of G protein-coupled receptor internalization http://purl.obolibrary.org/obo/GO_0002031 G protein-coupled receptor internalization
http://purl.obolibrary.org/obo/GO_0045744 negative regulation of G protein-coupled receptor signaling pathway http://purl.obolibrary.org/obo/GO_0007186 G protein-coupled receptor signaling pathway
http://purl.obolibrary.org/obo/GO_1905494 negative regulation of G-quadruplex DNA binding http://purl.obolibrary.org/obo/GO_0051880 G-quadruplex DNA binding
http://purl.obolibrary.org/obo/GO_1905466 negative regulation of G-quadruplex DNA unwinding http://purl.obolibrary.org/obo/GO_0044806 G-quadruplex DNA unwinding
http://purl.obolibrary.org/obo/GO_0070317 negative regulation of G0 to G1 transition http://purl.obolibrary.org/obo/GO_0045023 G0 to G1 transition
http://purl.obolibrary.org/obo/GO_1903451 negative regulation of G1 to G0 transition http://purl.obolibrary.org/obo/GO_0070314 G1 to G0 transition
http://purl.obolibrary.org/obo/GO_2000134 negative regulation of G1/S transition of mitotic cell cycle http://purl.obolibrary.org/obo/GO_0000082 G1/S transition of mitotic cell cycle
Expand Down Expand Up @@ -648,7 +645,6 @@ http://purl.obolibrary.org/obo/GO_1900286 negative regulation of cellotriose tra
http://purl.obolibrary.org/obo/GO_0051129 negative regulation of cellular component organization http://purl.obolibrary.org/obo/GO_0016043 cellular component organization
http://purl.obolibrary.org/obo/GO_0051245 negative regulation of cellular defense response http://purl.obolibrary.org/obo/GO_0006968 cellular defense response
http://purl.obolibrary.org/obo/GO_0002692 negative regulation of cellular extravasation http://purl.obolibrary.org/obo/GO_0045123 cellular extravasation
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_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
Expand Down Expand Up @@ -818,7 +814,6 @@ http://purl.obolibrary.org/obo/GO_2000958 negative regulation of cyclodextrin ca
http://purl.obolibrary.org/obo/GO_2000955 negative regulation of cyclodextrin metabolic process http://purl.obolibrary.org/obo/GO_2000900 cyclodextrin metabolic process
http://purl.obolibrary.org/obo/GO_1904042 negative regulation of cystathionine beta-synthase activity http://purl.obolibrary.org/obo/GO_0004122 cystathionine beta-synthase activity
http://purl.obolibrary.org/obo/GO_1901495 negative regulation of cysteine metabolic process http://purl.obolibrary.org/obo/GO_0006534 cysteine metabolic process
http://purl.obolibrary.org/obo/GO_2000117 negative regulation of cysteine-type endopeptidase activity http://purl.obolibrary.org/obo/GO_0004197 cysteine-type endopeptidase activity
http://purl.obolibrary.org/obo/GO_0060302 negative regulation of cytokine activity http://purl.obolibrary.org/obo/GO_0005125 cytokine activity
http://purl.obolibrary.org/obo/GO_0001818 negative regulation of cytokine production http://purl.obolibrary.org/obo/GO_0001816 cytokine production
http://purl.obolibrary.org/obo/GO_0002719 negative regulation of cytokine production involved in immune response http://purl.obolibrary.org/obo/GO_0002367 cytokine production involved in immune response
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9 changes: 1 addition & 8 deletions src/design_patterns/positive_regulation.tsv
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Expand Up @@ -73,11 +73,7 @@ http://purl.obolibrary.org/obo/GO_2000573 positive regulation of DNA biosyntheti
http://purl.obolibrary.org/obo/GO_1903626 positive regulation of DNA catabolic process http://purl.obolibrary.org/obo/GO_0006308 DNA catabolic process
http://purl.obolibrary.org/obo/GO_2000003 positive regulation of DNA damage checkpoint http://purl.obolibrary.org/obo/GO_0000077 DNA damage checkpoint signaling
http://purl.obolibrary.org/obo/GO_0043517 positive regulation of DNA damage response, signal transduction by p53 class mediator http://purl.obolibrary.org/obo/GO_0030330 DNA damage response, signal transduction by p53 class mediator
http://purl.obolibrary.org/obo/GO_1905464 positive regulation of DNA duplex unwinding http://purl.obolibrary.org/obo/GO_0032508 DNA duplex unwinding
http://purl.obolibrary.org/obo/GO_0032877 positive regulation of DNA endoreduplication http://purl.obolibrary.org/obo/GO_0042023 DNA endoreduplication
http://purl.obolibrary.org/obo/GO_1905776 positive regulation of DNA helicase activity http://purl.obolibrary.org/obo/GO_0003678 DNA helicase activity
http://purl.obolibrary.org/obo/GO_1904877 positive regulation of DNA ligase activity http://purl.obolibrary.org/obo/GO_0003909 DNA ligase activity
http://purl.obolibrary.org/obo/GO_0051106 positive regulation of DNA ligation http://purl.obolibrary.org/obo/GO_0006266 DNA ligation
http://purl.obolibrary.org/obo/GO_0051054 positive regulation of DNA metabolic process http://purl.obolibrary.org/obo/GO_0006259 DNA metabolic process
http://purl.obolibrary.org/obo/GO_1903934 positive regulation of DNA primase activity http://purl.obolibrary.org/obo/GO_0003896 DNA primase activity
http://purl.obolibrary.org/obo/GO_0045911 positive regulation of DNA recombination http://purl.obolibrary.org/obo/GO_0006310 DNA recombination
Expand Down Expand Up @@ -114,7 +110,6 @@ http://purl.obolibrary.org/obo/GO_1904022 positive regulation of G protein-coupl
http://purl.obolibrary.org/obo/GO_0045745 positive regulation of G protein-coupled receptor signaling pathway http://purl.obolibrary.org/obo/GO_0007186 G protein-coupled receptor signaling pathway
http://purl.obolibrary.org/obo/GO_1900129 positive regulation of G-protein activated inward rectifier potassium channel activity http://purl.obolibrary.org/obo/GO_0015467 G-protein activated inward rectifier potassium channel activity
http://purl.obolibrary.org/obo/GO_1905495 positive regulation of G-quadruplex DNA binding http://purl.obolibrary.org/obo/GO_0051880 G-quadruplex DNA binding
http://purl.obolibrary.org/obo/GO_1905467 positive regulation of G-quadruplex DNA unwinding http://purl.obolibrary.org/obo/GO_0044806 G-quadruplex DNA unwinding
http://purl.obolibrary.org/obo/GO_0070318 positive regulation of G0 to G1 transition http://purl.obolibrary.org/obo/GO_0045023 G0 to G1 transition
http://purl.obolibrary.org/obo/GO_1903452 positive regulation of G1 to G0 transition http://purl.obolibrary.org/obo/GO_0070314 G1 to G0 transition
http://purl.obolibrary.org/obo/GO_1900087 positive regulation of G1/S transition of mitotic cell cycle http://purl.obolibrary.org/obo/GO_0000082 G1/S transition of mitotic cell cycle
Expand Down Expand Up @@ -144,6 +139,7 @@ http://purl.obolibrary.org/obo/GO_1905010 positive regulation of L-lysine import
http://purl.obolibrary.org/obo/GO_1905626 positive regulation of L-methionine import across plasma membrane http://purl.obolibrary.org/obo/GO_1905544 L-methionine import across plasma membrane
http://purl.obolibrary.org/obo/GO_1905737 positive regulation of L-proline import across plasma membrane http://purl.obolibrary.org/obo/GO_1904271 L-proline import across plasma membrane
http://purl.obolibrary.org/obo/GO_1900928 positive regulation of L-threonine import across plasma membrane http://purl.obolibrary.org/obo/GO_1903807 L-threonine import across plasma membrane
http://purl.obolibrary.org/obo/GO_0090358 positive regulation of L-tryptophan metabolic process http://purl.obolibrary.org/obo/GO_0006568 L-tryptophan metabolic process
http://purl.obolibrary.org/obo/GO_1900931 positive regulation of L-tyrosine import across plasma membrane http://purl.obolibrary.org/obo/GO_1903808 L-tyrosine import across plasma membrane
http://purl.obolibrary.org/obo/GO_0140124 positive regulation of Lewy body formation http://purl.obolibrary.org/obo/GO_0140121 Lewy body formation
http://purl.obolibrary.org/obo/GO_1903007 positive regulation of Lys63-specific deubiquitinase activity http://purl.obolibrary.org/obo/GO_0061578 K63-linked deubiquitinase activity
Expand Down Expand Up @@ -651,7 +647,6 @@ http://purl.obolibrary.org/obo/GO_0044089 positive regulation of cellular compon
http://purl.obolibrary.org/obo/GO_0051130 positive regulation of cellular component organization http://purl.obolibrary.org/obo/GO_0016043 cellular component organization
http://purl.obolibrary.org/obo/GO_0010186 positive regulation of cellular defense response http://purl.obolibrary.org/obo/GO_0006968 cellular defense response
http://purl.obolibrary.org/obo/GO_0002693 positive regulation of cellular extravasation http://purl.obolibrary.org/obo/GO_0045123 cellular extravasation
http://purl.obolibrary.org/obo/GO_2001031 positive regulation of cellular glucuronidation http://purl.obolibrary.org/obo/GO_0052695 cellular glucuronidation
http://purl.obolibrary.org/obo/GO_0032849 positive regulation of cellular pH reduction http://purl.obolibrary.org/obo/GO_0051452 intracellular pH reduction
http://purl.obolibrary.org/obo/GO_0048522 positive regulation of cellular process http://purl.obolibrary.org/obo/GO_0009987 cellular process
http://purl.obolibrary.org/obo/GO_1901857 positive regulation of cellular respiration http://purl.obolibrary.org/obo/GO_0045333 cellular respiration
Expand Down Expand Up @@ -810,7 +805,6 @@ http://purl.obolibrary.org/obo/GO_0045737 positive regulation of cyclin-dependen
http://purl.obolibrary.org/obo/GO_2000959 positive regulation of cyclodextrin catabolic process http://purl.obolibrary.org/obo/GO_2000901 cyclodextrin catabolic process
http://purl.obolibrary.org/obo/GO_2000956 positive regulation of cyclodextrin metabolic process http://purl.obolibrary.org/obo/GO_2000900 cyclodextrin metabolic process
http://purl.obolibrary.org/obo/GO_1901496 positive regulation of cysteine metabolic process http://purl.obolibrary.org/obo/GO_0006534 cysteine metabolic process
http://purl.obolibrary.org/obo/GO_2001056 positive regulation of cysteine-type endopeptidase activity http://purl.obolibrary.org/obo/GO_0004197 cysteine-type endopeptidase activity
http://purl.obolibrary.org/obo/GO_1904960 positive regulation of cytochrome-c oxidase activity http://purl.obolibrary.org/obo/GO_0004129 cytochrome-c oxidase activity
http://purl.obolibrary.org/obo/GO_0060301 positive regulation of cytokine activity http://purl.obolibrary.org/obo/GO_0005125 cytokine activity
http://purl.obolibrary.org/obo/GO_0001819 positive regulation of cytokine production http://purl.obolibrary.org/obo/GO_0001816 cytokine production
Expand Down Expand Up @@ -2660,7 +2654,6 @@ http://purl.obolibrary.org/obo/GO_1905498 positive regulation of triplex DNA bin
http://purl.obolibrary.org/obo/GO_1904075 positive regulation of trophectodermal cell proliferation http://purl.obolibrary.org/obo/GO_0001834 trophectodermal cell proliferation
http://purl.obolibrary.org/obo/GO_1901165 positive regulation of trophoblast cell migration http://purl.obolibrary.org/obo/GO_0061450 trophoblast cell migration
http://purl.obolibrary.org/obo/GO_1905724 positive regulation of trypanothione biosynthetic process http://purl.obolibrary.org/obo/GO_0019342 trypanothione biosynthetic process
http://purl.obolibrary.org/obo/GO_0090358 positive regulation of tryptophan metabolic process http://purl.obolibrary.org/obo/GO_0006568 tryptophan metabolic process
http://purl.obolibrary.org/obo/GO_0090044 positive regulation of tubulin deacetylation http://purl.obolibrary.org/obo/GO_0090042 tubulin deacetylation
http://purl.obolibrary.org/obo/GO_2000309 positive regulation of tumor necrosis factor (ligand) superfamily member 11 production http://purl.obolibrary.org/obo/GO_0072535 tumor necrosis factor (ligand) superfamily member 11 production
http://purl.obolibrary.org/obo/GO_0032760 positive regulation of tumor necrosis factor production http://purl.obolibrary.org/obo/GO_0032640 tumor necrosis factor production
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