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balhoff authored Feb 11, 2025
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2 changes: 1 addition & 1 deletion docs/patterns/negative_regulation.md
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Expand Up @@ -48,7 +48,7 @@ This pattern is for classes representing types of negative regulation differenti
|:--|:--|:--|:--|
| [http://purl.obolibrary.org/obo/GO_0002085](http://purl.obolibrary.org/obo/GO_0002085) | inhibition of neuroepithelial cell differentiation | [http://purl.obolibrary.org/obo/GO_0060563](http://purl.obolibrary.org/obo/GO_0060563) | neuroepithelial cell differentiation |
| [http://purl.obolibrary.org/obo/GO_0140540](http://purl.obolibrary.org/obo/GO_0140540) | negative regulation melanotic encapsulation of foreign target | [http://purl.obolibrary.org/obo/GO_0035011](http://purl.obolibrary.org/obo/GO_0035011) | melanotic encapsulation of foreign target |
| [http://purl.obolibrary.org/obo/GO_1905013](http://purl.obolibrary.org/obo/GO_1905013) | negative regulation of 'de novo' NAD biosynthetic process from tryptophan | [http://purl.obolibrary.org/obo/GO_0034354](http://purl.obolibrary.org/obo/GO_0034354) | 'de novo' NAD biosynthetic process from tryptophan |
| [http://purl.obolibrary.org/obo/GO_1905013](http://purl.obolibrary.org/obo/GO_1905013) | negative regulation of 'de novo' NAD biosynthetic process from L-tryptophan | [http://purl.obolibrary.org/obo/GO_0034354](http://purl.obolibrary.org/obo/GO_0034354) | 'de novo' NAD biosynthetic process from L-tryptophan |
| [http://purl.obolibrary.org/obo/GO_1900693](http://purl.obolibrary.org/obo/GO_1900693) | negative regulation of (+)-kotanin biosynthetic process | [http://purl.obolibrary.org/obo/GO_1900596](http://purl.obolibrary.org/obo/GO_1900596) | (+)-kotanin biosynthetic process |
| [http://purl.obolibrary.org/obo/GO_0060636](http://purl.obolibrary.org/obo/GO_0060636) | negative regulation of (1->3)-beta-D-glucan biosynthetic process | [http://purl.obolibrary.org/obo/GO_0006075](http://purl.obolibrary.org/obo/GO_0006075) | (1->3)-beta-D-glucan biosynthetic process |

2 changes: 1 addition & 1 deletion docs/patterns/positive_regulation.md
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Expand Up @@ -47,7 +47,7 @@ This pattern is for classes representing types of positive regulation differenti
| defined_class | defined_class_label | entity | entity_label |
|:--|:--|:--|:--|
| [http://purl.obolibrary.org/obo/GO_0075294](http://purl.obolibrary.org/obo/GO_0075294) | positive regulation by symbiont of entry into host | [http://purl.obolibrary.org/obo/GO_0044409](http://purl.obolibrary.org/obo/GO_0044409) | symbiont entry into host |
| [http://purl.obolibrary.org/obo/GO_1905014](http://purl.obolibrary.org/obo/GO_1905014) | positive regulation of 'de novo' NAD biosynthetic process from tryptophan | [http://purl.obolibrary.org/obo/GO_0034354](http://purl.obolibrary.org/obo/GO_0034354) | 'de novo' NAD biosynthetic process from tryptophan |
| [http://purl.obolibrary.org/obo/GO_1905014](http://purl.obolibrary.org/obo/GO_1905014) | positive regulation of 'de novo' NAD biosynthetic process from L-tryptophan | [http://purl.obolibrary.org/obo/GO_0034354](http://purl.obolibrary.org/obo/GO_0034354) | 'de novo' NAD biosynthetic process from L-tryptophan |
| [http://purl.obolibrary.org/obo/GO_1900694](http://purl.obolibrary.org/obo/GO_1900694) | positive regulation of (+)-kotanin biosynthetic process | [http://purl.obolibrary.org/obo/GO_1900596](http://purl.obolibrary.org/obo/GO_1900596) | (+)-kotanin biosynthetic process |
| [http://purl.obolibrary.org/obo/GO_0060635](http://purl.obolibrary.org/obo/GO_0060635) | positive regulation of (1->3)-beta-D-glucan biosynthetic process | [http://purl.obolibrary.org/obo/GO_0006075](http://purl.obolibrary.org/obo/GO_0006075) | (1->3)-beta-D-glucan biosynthetic process |
| [http://purl.obolibrary.org/obo/GO_1902274](http://purl.obolibrary.org/obo/GO_1902274) | positive regulation of (R)-carnitine transmembrane transport | [http://purl.obolibrary.org/obo/GO_1902270](http://purl.obolibrary.org/obo/GO_1902270) | (R)-carnitine transmembrane transport |
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4 changes: 1 addition & 3 deletions src/design_patterns/biosynthetic_process.tsv
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Expand Up @@ -151,7 +151,7 @@ http://purl.obolibrary.org/obo/GO_0006045 N-acetylglucosamine biosynthetic proce
http://purl.obolibrary.org/obo/GO_0006052 N-acetylmannosamine biosynthetic process http://purl.obolibrary.org/obo/CHEBI_62164 N-acetylmannosamine
http://purl.obolibrary.org/obo/GO_0046380 N-acetylneuraminate biosynthetic process http://purl.obolibrary.org/obo/CHEBI_35418 N-acetylneuraminate
http://purl.obolibrary.org/obo/GO_0052709 N-alpha,N-alpha,N-alpha-trimethyl-L-histidine biosynthetic process http://purl.obolibrary.org/obo/CHEBI_15781 N(alpha),N(alpha),N(alpha)-trimethyl-L-histidine
http://purl.obolibrary.org/obo/GO_0009435 NAD biosynthetic process http://purl.obolibrary.org/obo/CHEBI_13389 NAD
http://purl.obolibrary.org/obo/GO_0009435 NAD biosynthetic process http://purl.obolibrary.org/obo/CHEBI_57540 NAD(1-)
http://purl.obolibrary.org/obo/GO_0006741 NADP biosynthetic process http://purl.obolibrary.org/obo/CHEBI_58349 NADP(3-)
http://purl.obolibrary.org/obo/GO_0140875 PR-toxin biosynthetic process http://purl.obolibrary.org/obo/CHEBI_7883 PR-toxin
http://purl.obolibrary.org/obo/GO_0006556 S-adenosylmethionine biosynthetic process http://purl.obolibrary.org/obo/CHEBI_59789 S-adenosyl-L-methionine zwitterion
Expand Down Expand Up @@ -322,7 +322,6 @@ http://purl.obolibrary.org/obo/GO_0033305 chlorophyll a biosynthetic process htt
http://purl.obolibrary.org/obo/GO_0015995 chlorophyll biosynthetic process http://purl.obolibrary.org/obo/CHEBI_28966 chlorophyll
http://purl.obolibrary.org/obo/GO_0006695 cholesterol biosynthetic process http://purl.obolibrary.org/obo/CHEBI_16113 cholesterol
http://purl.obolibrary.org/obo/GO_0042425 choline biosynthetic process http://purl.obolibrary.org/obo/CHEBI_15354 choline
http://purl.obolibrary.org/obo/GO_0030206 chondroitin sulfate biosynthetic process http://purl.obolibrary.org/obo/CHEBI_37397 chondroitin sulfate
http://purl.obolibrary.org/obo/GO_0050650 chondroitin sulfate proteoglycan biosynthetic process http://purl.obolibrary.org/obo/CHEBI_26349 proteochondroitin sulfate
http://purl.obolibrary.org/obo/GO_0009423 chorismate biosynthetic process http://purl.obolibrary.org/obo/CHEBI_29748 chorismate(2-)
http://purl.obolibrary.org/obo/GO_0042858 chrysobactin biosynthetic process http://purl.obolibrary.org/obo/CHEBI_61345 chrysobactin
Expand Down Expand Up @@ -399,7 +398,6 @@ http://purl.obolibrary.org/obo/GO_0006017 deoxyribose 1,5-bisphosphate biosynthe
http://purl.obolibrary.org/obo/GO_0046385 deoxyribose phosphate biosynthetic process http://purl.obolibrary.org/obo/CHEBI_19569 2-deoxyribose phosphate
http://purl.obolibrary.org/obo/GO_0046097 deoxyuridine biosynthetic process http://purl.obolibrary.org/obo/CHEBI_16450 2'-deoxyuridine
http://purl.obolibrary.org/obo/GO_0050763 depsipeptide biosynthetic process http://purl.obolibrary.org/obo/CHEBI_23643 depsipeptide
http://purl.obolibrary.org/obo/GO_0030208 dermatan sulfate biosynthetic process http://purl.obolibrary.org/obo/CHEBI_58465 dermatan sulfate polyanion
http://purl.obolibrary.org/obo/GO_0050651 dermatan sulfate proteoglycan biosynthetic process http://purl.obolibrary.org/obo/CHEBI_64602 dermatan sulfate proteoglycan
http://purl.obolibrary.org/obo/GO_0019351 dethiobiotin biosynthetic process http://purl.obolibrary.org/obo/CHEBI_57861 dethiobiotin(1-)
http://purl.obolibrary.org/obo/GO_0010132 dhurrin biosynthetic process http://purl.obolibrary.org/obo/CHEBI_27826 (S)-4-hydroxymandelonitrile beta-D-glucoside
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2 changes: 1 addition & 1 deletion src/design_patterns/catabolic_process.tsv
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Expand Up @@ -132,7 +132,7 @@ http://purl.obolibrary.org/obo/GO_0097173 N-acetylmuramic acid catabolic process
http://purl.obolibrary.org/obo/GO_0019262 N-acetylneuraminate catabolic process http://purl.obolibrary.org/obo/CHEBI_35418 N-acetylneuraminate
http://purl.obolibrary.org/obo/GO_0052710 N-alpha,N-alpha,N-alpha-trimethyl-L-histidine catabolic process http://purl.obolibrary.org/obo/CHEBI_15781 N(alpha),N(alpha),N(alpha)-trimethyl-L-histidine
http://purl.obolibrary.org/obo/GO_0042202 N-cyclopropylmelamine catabolic process http://purl.obolibrary.org/obo/CHEBI_30260 cyromazine
http://purl.obolibrary.org/obo/GO_0019677 NAD catabolic process http://purl.obolibrary.org/obo/CHEBI_13389 NAD
http://purl.obolibrary.org/obo/GO_0019677 NAD catabolic process http://purl.obolibrary.org/obo/CHEBI_57540 NAD(1-)
http://purl.obolibrary.org/obo/GO_0006742 NADP catabolic process http://purl.obolibrary.org/obo/CHEBI_58349 NADP(3-)
http://purl.obolibrary.org/obo/GO_0010304 PSII associated light-harvesting complex II catabolic process http://purl.obolibrary.org/obo/GO_0009517 PSII associated light-harvesting complex II
http://purl.obolibrary.org/obo/GO_0006401 RNA catabolic process http://purl.obolibrary.org/obo/CHEBI_33697 ribonucleic acid
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2 changes: 1 addition & 1 deletion src/design_patterns/cc_assembly.tsv
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Expand Up @@ -126,7 +126,7 @@ http://purl.obolibrary.org/obo/GO_0048041 focal adhesion assembly http://purl.ob
http://purl.obolibrary.org/obo/GO_0001732 formation of cytoplasmic translation initiation complex http://purl.obolibrary.org/obo/GO_0070992 translation initiation complex
http://purl.obolibrary.org/obo/GO_0001325 formation of extrachromosomal circular DNA http://purl.obolibrary.org/obo/GO_0005727 extrachromosomal circular DNA
http://purl.obolibrary.org/obo/GO_0001677 formation of translation initiation ternary complex http://purl.obolibrary.org/obo/GO_0044207 translation initiation ternary complex
http://purl.obolibrary.org/obo/GO_0001731 formation of translation preinitiation complex http://purl.obolibrary.org/obo/GO_0070993 translation preinitiation complex
http://purl.obolibrary.org/obo/GO_0001731 formation of translation preinitiation complex http://purl.obolibrary.org/obo/GO_0070993 cytosolic translation preinitiation complex
http://purl.obolibrary.org/obo/GO_0070649 formin-nucleated actin cable assembly http://purl.obolibrary.org/obo/GO_0070648 formin-nucleated actin cable
http://purl.obolibrary.org/obo/GO_0071940 fungal-type cell wall assembly http://purl.obolibrary.org/obo/GO_0009277 fungal-type cell wall
http://purl.obolibrary.org/obo/GO_1902481 gamma-tubulin complex assembly http://purl.obolibrary.org/obo/GO_0000930 gamma-tubulin complex
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4 changes: 1 addition & 3 deletions src/design_patterns/metabolic_process.tsv
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Expand Up @@ -187,7 +187,7 @@ http://purl.obolibrary.org/obo/GO_0070291 N-acylethanolamine metabolic process h
http://purl.obolibrary.org/obo/GO_0070292 N-acylphosphatidylethanolamine metabolic process http://purl.obolibrary.org/obo/CHEBI_62537 N-acylphosphatidylethanolamine(1-)
http://purl.obolibrary.org/obo/GO_0052708 N-alpha,N-alpha,N-alpha-trimethyl-L-histidine metabolic process http://purl.obolibrary.org/obo/CHEBI_15781 N(alpha),N(alpha),N(alpha)-trimethyl-L-histidine
http://purl.obolibrary.org/obo/GO_0042201 N-cyclopropylmelamine metabolic process http://purl.obolibrary.org/obo/CHEBI_30260 cyromazine
http://purl.obolibrary.org/obo/GO_0019674 NAD metabolic process http://purl.obolibrary.org/obo/CHEBI_13389 NAD
http://purl.obolibrary.org/obo/GO_0019674 NAD metabolic process http://purl.obolibrary.org/obo/CHEBI_57540 NAD(1-)
http://purl.obolibrary.org/obo/GO_0006734 NADH metabolic process http://purl.obolibrary.org/obo/CHEBI_57945 NADH(2-)
http://purl.obolibrary.org/obo/GO_0006739 NADP metabolic process http://purl.obolibrary.org/obo/CHEBI_58349 NADP(3-)
http://purl.obolibrary.org/obo/GO_0016070 RNA metabolic process http://purl.obolibrary.org/obo/CHEBI_33697 ribonucleic acid
Expand Down Expand Up @@ -392,7 +392,6 @@ http://purl.obolibrary.org/obo/GO_0052644 chlorophyllide a metabolic process htt
http://purl.obolibrary.org/obo/GO_0052643 chlorophyllide metabolic process http://purl.obolibrary.org/obo/CHEBI_38206 chlorophyllide
http://purl.obolibrary.org/obo/GO_0008203 cholesterol metabolic process http://purl.obolibrary.org/obo/CHEBI_16113 cholesterol
http://purl.obolibrary.org/obo/GO_0019695 choline metabolic process http://purl.obolibrary.org/obo/CHEBI_15354 choline
http://purl.obolibrary.org/obo/GO_0030204 chondroitin sulfate metabolic process http://purl.obolibrary.org/obo/CHEBI_37397 chondroitin sulfate
http://purl.obolibrary.org/obo/GO_0050654 chondroitin sulfate proteoglycan metabolic process http://purl.obolibrary.org/obo/CHEBI_26349 proteochondroitin sulfate
http://purl.obolibrary.org/obo/GO_0046417 chorismate metabolic process http://purl.obolibrary.org/obo/CHEBI_29748 chorismate(2-)
http://purl.obolibrary.org/obo/GO_0042857 chrysobactin metabolic process http://purl.obolibrary.org/obo/CHEBI_61345 chrysobactin
Expand Down Expand Up @@ -480,7 +479,6 @@ http://purl.obolibrary.org/obo/GO_0046389 deoxyribose 5-phosphate metabolic proc
http://purl.obolibrary.org/obo/GO_0019692 deoxyribose phosphate metabolic process http://purl.obolibrary.org/obo/CHEBI_19569 2-deoxyribose phosphate
http://purl.obolibrary.org/obo/GO_0046096 deoxyuridine metabolic process http://purl.obolibrary.org/obo/CHEBI_16450 2'-deoxyuridine
http://purl.obolibrary.org/obo/GO_0050761 depsipeptide metabolic process http://purl.obolibrary.org/obo/CHEBI_23643 depsipeptide
http://purl.obolibrary.org/obo/GO_0030205 dermatan sulfate metabolic process http://purl.obolibrary.org/obo/CHEBI_58465 dermatan sulfate polyanion
http://purl.obolibrary.org/obo/GO_0050655 dermatan sulfate proteoglycan metabolic process http://purl.obolibrary.org/obo/CHEBI_64602 dermatan sulfate proteoglycan
http://purl.obolibrary.org/obo/GO_0046450 dethiobiotin metabolic process http://purl.obolibrary.org/obo/CHEBI_57861 dethiobiotin(1-)
http://purl.obolibrary.org/obo/GO_0052778 diacetylchitobiose metabolic process http://purl.obolibrary.org/obo/CHEBI_28681 N,N'-diacetylchitobiose
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4 changes: 2 additions & 2 deletions src/design_patterns/negative_regulation.tsv
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@@ -1,7 +1,7 @@
defined_class defined_class_label entity entity_label
http://purl.obolibrary.org/obo/GO_0002085 inhibition of neuroepithelial cell differentiation http://purl.obolibrary.org/obo/GO_0060563 neuroepithelial cell differentiation
http://purl.obolibrary.org/obo/GO_0140540 negative regulation melanotic encapsulation of foreign target http://purl.obolibrary.org/obo/GO_0035011 melanotic encapsulation of foreign target
http://purl.obolibrary.org/obo/GO_1905013 negative regulation of 'de novo' NAD biosynthetic process from tryptophan http://purl.obolibrary.org/obo/GO_0034354 'de novo' NAD biosynthetic process from tryptophan
http://purl.obolibrary.org/obo/GO_1905013 negative regulation of 'de novo' NAD biosynthetic process from L-tryptophan http://purl.obolibrary.org/obo/GO_0034354 'de novo' NAD biosynthetic process from L-tryptophan
http://purl.obolibrary.org/obo/GO_1900693 negative regulation of (+)-kotanin biosynthetic process http://purl.obolibrary.org/obo/GO_1900596 (+)-kotanin biosynthetic process
http://purl.obolibrary.org/obo/GO_0060636 negative regulation of (1->3)-beta-D-glucan biosynthetic process http://purl.obolibrary.org/obo/GO_0006075 (1->3)-beta-D-glucan biosynthetic process
http://purl.obolibrary.org/obo/GO_1902273 negative regulation of (R)-carnitine transmembrane transport http://purl.obolibrary.org/obo/GO_1902270 (R)-carnitine transmembrane transport
Expand Down Expand Up @@ -169,7 +169,7 @@ http://purl.obolibrary.org/obo/GO_0051253 negative regulation of RNA metabolic p
http://purl.obolibrary.org/obo/GO_1903026 negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding http://purl.obolibrary.org/obo/GO_0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding
http://purl.obolibrary.org/obo/GO_0017055 negative regulation of RNA polymerase II transcription preinitiation complex assembly http://purl.obolibrary.org/obo/GO_0051123 RNA polymerase II preinitiation complex assembly
http://purl.obolibrary.org/obo/GO_0033119 negative regulation of RNA splicing http://purl.obolibrary.org/obo/GO_0008380 RNA splicing
http://purl.obolibrary.org/obo/GO_1900260 negative regulation of RNA-dependent RNA polymerase activity http://purl.obolibrary.org/obo/GO_0003968 RNA-dependent RNA polymerase activity
http://purl.obolibrary.org/obo/GO_1900260 negative regulation of RNA-dependent RNA polymerase activity http://purl.obolibrary.org/obo/GO_0003968 RNA-directed RNA polymerase activity
http://purl.obolibrary.org/obo/GO_0035021 negative regulation of Rac protein signal transduction http://purl.obolibrary.org/obo/GO_0016601 Rac protein signal transduction
http://purl.obolibrary.org/obo/GO_0046580 negative regulation of Ras protein signal transduction http://purl.obolibrary.org/obo/GO_0007265 Ras protein signal transduction
http://purl.obolibrary.org/obo/GO_0035024 negative regulation of Rho protein signal transduction http://purl.obolibrary.org/obo/GO_0007266 Rho protein signal transduction
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1 change: 0 additions & 1 deletion src/design_patterns/occursIn.tsv
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Expand Up @@ -184,7 +184,6 @@ http://purl.obolibrary.org/obo/GO_0007006 mitochondrial membrane organization ht
http://purl.obolibrary.org/obo/GO_0070155 mitochondrial methionyl-tRNA aminoacylation http://purl.obolibrary.org/obo/GO_0005739 mitochondrion http://purl.obolibrary.org/obo/GO_0006431 methionyl-tRNA aminoacylation
http://purl.obolibrary.org/obo/GO_0090144 mitochondrial nucleoid organization http://purl.obolibrary.org/obo/GO_0005739 mitochondrion http://purl.obolibrary.org/obo/GO_0090143 nucleoid organization
http://purl.obolibrary.org/obo/GO_0070156 mitochondrial phenylalanyl-tRNA aminoacylation http://purl.obolibrary.org/obo/GO_0005739 mitochondrion http://purl.obolibrary.org/obo/GO_0006432 phenylalanyl-tRNA aminoacylation
http://purl.obolibrary.org/obo/GO_0140040 mitochondrial polycistronic RNA processing http://purl.obolibrary.org/obo/GO_0005739 mitochondrion http://purl.obolibrary.org/obo/GO_0031426 polycistronic mRNA processing
http://purl.obolibrary.org/obo/GO_0070157 mitochondrial prolyl-tRNA aminoacylation http://purl.obolibrary.org/obo/GO_0005739 mitochondrion http://purl.obolibrary.org/obo/GO_0006433 prolyl-tRNA aminoacylation
http://purl.obolibrary.org/obo/GO_0035694 mitochondrial protein catabolic process http://purl.obolibrary.org/obo/GO_0005739 mitochondrion http://purl.obolibrary.org/obo/GO_0030163 protein catabolic process
http://purl.obolibrary.org/obo/GO_0034982 mitochondrial protein processing http://purl.obolibrary.org/obo/GO_0005739 mitochondrion http://purl.obolibrary.org/obo/GO_0016485 protein processing
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2 changes: 1 addition & 1 deletion src/design_patterns/positive_regulation.tsv
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@@ -1,6 +1,6 @@
defined_class defined_class_label entity entity_label
http://purl.obolibrary.org/obo/GO_0075294 positive regulation by symbiont of entry into host http://purl.obolibrary.org/obo/GO_0044409 symbiont entry into host
http://purl.obolibrary.org/obo/GO_1905014 positive regulation of 'de novo' NAD biosynthetic process from tryptophan http://purl.obolibrary.org/obo/GO_0034354 'de novo' NAD biosynthetic process from tryptophan
http://purl.obolibrary.org/obo/GO_1905014 positive regulation of 'de novo' NAD biosynthetic process from L-tryptophan http://purl.obolibrary.org/obo/GO_0034354 'de novo' NAD biosynthetic process from L-tryptophan
http://purl.obolibrary.org/obo/GO_1900694 positive regulation of (+)-kotanin biosynthetic process http://purl.obolibrary.org/obo/GO_1900596 (+)-kotanin biosynthetic process
http://purl.obolibrary.org/obo/GO_0060635 positive regulation of (1->3)-beta-D-glucan biosynthetic process http://purl.obolibrary.org/obo/GO_0006075 (1->3)-beta-D-glucan biosynthetic process
http://purl.obolibrary.org/obo/GO_1902274 positive regulation of (R)-carnitine transmembrane transport http://purl.obolibrary.org/obo/GO_1902270 (R)-carnitine transmembrane transport
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