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geneontology · Dec 27, 2024 · cf35e55 · cf35e55
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diff --git a/docs/patterns/vesicle_mediated_transport_differentiated_by_cargo.md b/docs/patterns/vesicle_mediated_transport_differentiated_by_cargo.md
@@ -13,23 +13,23 @@ This pattern is for representing vesicle-mediated transport, differentiated by t
 
 | Variable name | Allowed type |
 |:--------------|:-------------|
-| `{target}` | [cellular anatomical structure](http://purl.obolibrary.org/obo/GO_0110165) |
+| `{cargo}` | [chemical entity](http://purl.obolibrary.org/obo/CHEBI_24431) |
 
 ## Name
 
-"`{target}` vesicle-mediated transport"^^[string](http://www.w3.org/2001/XMLSchema#string)
+"`{cargo}` vesicle-mediated transport"^^[string](http://www.w3.org/2001/XMLSchema#string)
 
 ## Annotations
 
 
 
 ## Definition
 
-"The directed movement of `{target}` into, out of or within a cell, or between cells, mediated by small transport vesicles."^^[string](http://www.w3.org/2001/XMLSchema#string)
+"The directed movement of `{cargo}` into, out of or within a cell, or between cells, mediated by small transport vesicles."^^[string](http://www.w3.org/2001/XMLSchema#string)
 
 ## Equivalent to
 
-[vesicle-mediated transport](http://purl.obolibrary.org/obo/GO_0016192)  and ([has primary input](http://purl.obolibrary.org/obo/RO_0004009) some `{target}`)
+[vesicle-mediated transport](http://purl.obolibrary.org/obo/GO_0016192)  and ([has primary input](http://purl.obolibrary.org/obo/RO_0004009) some `{cargo}`)
 
 
 

diff --git a/src/design_patterns/binding.tsv b/src/design_patterns/binding.tsv
@@ -559,7 +559,6 @@ http://purl.obolibrary.org/obo/GO_0031628	opioid receptor binding	http://purl.ob
 http://purl.obolibrary.org/obo/GO_0031854	orexigenic neuropeptide QRFP receptor binding	http://purl.obolibrary.org/obo/PR_000001498	pyroglutamylated RF-amide peptide receptor
 http://purl.obolibrary.org/obo/GO_0042324	orexin receptor binding	http://purl.obolibrary.org/obo/PR_000001499	orexin receptor
 http://purl.obolibrary.org/obo/GO_0043177	organic acid binding	http://purl.obolibrary.org/obo/CHEBI_64709	organic acid
-http://purl.obolibrary.org/obo/GO_0097159	organic cyclic compound binding	http://purl.obolibrary.org/obo/CHEBI_33832	organic cyclic compound
 http://purl.obolibrary.org/obo/GO_0019825	oxygen binding	http://purl.obolibrary.org/obo/CHEBI_15379	dioxygen
 http://purl.obolibrary.org/obo/GO_0008142	oxysterol binding	http://purl.obolibrary.org/obo/CHEBI_53030	oxysterol
 http://purl.obolibrary.org/obo/GO_0031855	oxytocin receptor binding	http://purl.obolibrary.org/obo/PR_000001635	oxytocin receptor

diff --git a/src/design_patterns/biosynthetic_process.tsv b/src/design_patterns/biosynthetic_process.tsv
@@ -753,7 +753,6 @@ http://purl.obolibrary.org/obo/GO_1901697	olivetolic acid biosynthetic process	h
 http://purl.obolibrary.org/obo/GO_0006727	ommochrome biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_25692	ommochrome
 http://purl.obolibrary.org/obo/GO_0046197	orcinol biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_16536	orcinol
 http://purl.obolibrary.org/obo/GO_0016053	organic acid biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_64709	organic acid
-http://purl.obolibrary.org/obo/GO_1901378	organic heteropentacyclic compound biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_38164	organic heteropentacyclic compound
 http://purl.obolibrary.org/obo/GO_0032923	organic phosphonate biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_16215	phosphonate(2-)
 http://purl.obolibrary.org/obo/GO_0090407	organophosphate biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_25710	organophosphorus compound
 http://purl.obolibrary.org/obo/GO_1900821	orlandin biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_145992	orlandin(1-)
@@ -1050,7 +1049,6 @@ http://purl.obolibrary.org/obo/GO_1901695	tyramine biosynthetic process	http://p
 http://purl.obolibrary.org/obo/GO_1901904	tyrocidine biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_71947	tyrocidine
 http://purl.obolibrary.org/obo/GO_0006571	tyrosine biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_58315	L-tyrosine zwitterion
 http://purl.obolibrary.org/obo/GO_0006744	ubiquinone biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_16389	ubiquinones
-http://purl.obolibrary.org/obo/GO_1901006	ubiquinone-6 biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_52971	ubiquinone-6
 http://purl.obolibrary.org/obo/GO_1902791	undecan-2-one biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_17700	undecan-2-one
 http://purl.obolibrary.org/obo/GO_0006636	unsaturated fatty acid biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_2580	unsaturated fatty acid anion
 http://purl.obolibrary.org/obo/GO_0046107	uracil biosynthetic process	http://purl.obolibrary.org/obo/CHEBI_17568	uracil

diff --git a/src/design_patterns/catabolic_process.tsv b/src/design_patterns/catabolic_process.tsv
@@ -83,7 +83,6 @@ http://purl.obolibrary.org/obo/GO_0019447	D-cysteine catabolic process	http://pu
 http://purl.obolibrary.org/obo/GO_0034194	D-galactonate catabolic process	http://purl.obolibrary.org/obo/CHEBI_12931	D-galactonate
 http://purl.obolibrary.org/obo/GO_0019698	D-galacturonate catabolic process	http://purl.obolibrary.org/obo/CHEBI_12952	aldehydo-D-galacturonate
 http://purl.obolibrary.org/obo/GO_0042838	D-glucarate catabolic process	http://purl.obolibrary.org/obo/CHEBI_30612	D-glucarate(2-)
-http://purl.obolibrary.org/obo/GO_0046177	D-gluconate catabolic process	http://purl.obolibrary.org/obo/CHEBI_18391	D-gluconate
 http://purl.obolibrary.org/obo/GO_0042840	D-glucuronate catabolic process	http://purl.obolibrary.org/obo/CHEBI_15748	D-glucuronate
 http://purl.obolibrary.org/obo/GO_1900832	D-leucine catabolic process	http://purl.obolibrary.org/obo/CHEBI_143079	D-leucine zwitterion
 http://purl.obolibrary.org/obo/GO_0019476	D-lysine catabolic process	http://purl.obolibrary.org/obo/CHEBI_32557	D-lysinium(1+)
@@ -660,7 +659,6 @@ http://purl.obolibrary.org/obo/GO_0009313	oligosaccharide catabolic process	http
 http://purl.obolibrary.org/obo/GO_0046153	ommochrome catabolic process	http://purl.obolibrary.org/obo/CHEBI_25692	ommochrome
 http://purl.obolibrary.org/obo/GO_0042209	orcinol catabolic process	http://purl.obolibrary.org/obo/CHEBI_16536	orcinol
 http://purl.obolibrary.org/obo/GO_0016054	organic acid catabolic process	http://purl.obolibrary.org/obo/CHEBI_64709	organic acid
-http://purl.obolibrary.org/obo/GO_1901377	organic heteropentacyclic compound catabolic process	http://purl.obolibrary.org/obo/CHEBI_38164	organic heteropentacyclic compound
 http://purl.obolibrary.org/obo/GO_0019700	organic phosphonate catabolic process	http://purl.obolibrary.org/obo/CHEBI_16215	phosphonate(2-)
 http://purl.obolibrary.org/obo/GO_0046434	organophosphate catabolic process	http://purl.obolibrary.org/obo/CHEBI_25710	organophosphorus compound
 http://purl.obolibrary.org/obo/GO_0046455	organosilicon catabolic process	http://purl.obolibrary.org/obo/CHEBI_25713	organosilicon compound
@@ -887,7 +885,6 @@ http://purl.obolibrary.org/obo/GO_0046207	trypanothione catabolic process	http:/
 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
-http://purl.obolibrary.org/obo/GO_1901005	ubiquinone-6 catabolic process	http://purl.obolibrary.org/obo/CHEBI_52971	ubiquinone-6
 http://purl.obolibrary.org/obo/GO_0006212	uracil catabolic process	http://purl.obolibrary.org/obo/CHEBI_17568	uracil
 http://purl.obolibrary.org/obo/GO_0019628	urate catabolic process	http://purl.obolibrary.org/obo/CHEBI_17775	7,9-dihydro-1H-purine-2,6,8(3H)-trione
 http://purl.obolibrary.org/obo/GO_0043419	urea catabolic process	http://purl.obolibrary.org/obo/CHEBI_16199	urea

diff --git a/src/design_patterns/involved_in_x_y.tsv b/src/design_patterns/involved_in_x_y.tsv
@@ -873,8 +873,6 @@ http://purl.obolibrary.org/obo/GO_0060084	synaptic transmission involved in mict
 http://purl.obolibrary.org/obo/GO_0016185	synaptic vesicle budding from presynaptic endocytic zone membrane	http://purl.obolibrary.org/obo/GO_0070142	synaptic vesicle budding	http://purl.obolibrary.org/obo/GO_0048488	synaptic vesicle endocytosis
 http://purl.obolibrary.org/obo/GO_0016081	synaptic vesicle docking	http://purl.obolibrary.org/obo/GO_0006904	vesicle docking involved in exocytosis	http://purl.obolibrary.org/obo/GO_0016079	synaptic vesicle exocytosis
 http://purl.obolibrary.org/obo/GO_0009862	systemic acquired resistance, salicylic acid mediated signaling pathway	http://purl.obolibrary.org/obo/GO_0009863	salicylic acid mediated signaling pathway	http://purl.obolibrary.org/obo/GO_0009627	systemic acquired resistance
-http://purl.obolibrary.org/obo/GO_0070413	trehalose metabolism in response to stress	http://purl.obolibrary.org/obo/GO_0005991	trehalose metabolic process	http://purl.obolibrary.org/obo/GO_0006950	response to stress
-http://purl.obolibrary.org/obo/GO_0070416	trehalose metabolism in response to water deprivation	http://purl.obolibrary.org/obo/GO_0005991	trehalose metabolic process	http://purl.obolibrary.org/obo/GO_0009414	response to water deprivation
 http://purl.obolibrary.org/obo/GO_1905420	vascular associated smooth muscle cell differentiation involved in phenotypic switching	http://purl.obolibrary.org/obo/GO_0035886	vascular associated smooth muscle cell differentiation	http://purl.obolibrary.org/obo/GO_0090677	reversible differentiation
 http://purl.obolibrary.org/obo/GO_0060851	vascular endothelial growth factor receptor signaling pathway involved in lymphatic endothelial cell fate commitment	http://purl.obolibrary.org/obo/GO_0048010	vascular endothelial growth factor receptor signaling pathway	http://purl.obolibrary.org/obo/GO_0060838	lymphatic endothelial cell fate commitment
 http://purl.obolibrary.org/obo/GO_0060979	vasculogenesis involved in coronary vascular morphogenesis	http://purl.obolibrary.org/obo/GO_0001570	vasculogenesis	http://purl.obolibrary.org/obo/GO_0060977	coronary vasculature morphogenesis

diff --git a/src/design_patterns/metabolic_process.tsv b/src/design_patterns/metabolic_process.tsv
@@ -897,7 +897,6 @@ http://purl.obolibrary.org/obo/GO_0009311	oligosaccharide metabolic process	http
 http://purl.obolibrary.org/obo/GO_0046152	ommochrome metabolic process	http://purl.obolibrary.org/obo/CHEBI_25692	ommochrome
 http://purl.obolibrary.org/obo/GO_0018940	orcinol metabolic process	http://purl.obolibrary.org/obo/CHEBI_16536	orcinol
 http://purl.obolibrary.org/obo/GO_0006082	organic acid metabolic process	http://purl.obolibrary.org/obo/CHEBI_64709	organic acid
-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_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
@@ -1216,7 +1215,6 @@ http://purl.obolibrary.org/obo/GO_0046206	trypanothione metabolic process	http:/
 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
-http://purl.obolibrary.org/obo/GO_1901004	ubiquinone-6 metabolic process	http://purl.obolibrary.org/obo/CHEBI_52971	ubiquinone-6
 http://purl.obolibrary.org/obo/GO_1902790	undecan-2-one metabolic process	http://purl.obolibrary.org/obo/CHEBI_17700	undecan-2-one
 http://purl.obolibrary.org/obo/GO_0033559	unsaturated fatty acid metabolic process	http://purl.obolibrary.org/obo/CHEBI_2580	unsaturated fatty acid anion
 http://purl.obolibrary.org/obo/GO_0019860	uracil metabolic process	http://purl.obolibrary.org/obo/CHEBI_17568	uracil

diff --git a/src/design_patterns/negative_regulation.tsv b/src/design_patterns/negative_regulation.tsv
@@ -168,7 +168,6 @@ http://purl.obolibrary.org/obo/GO_0046829	negative regulation of RNA import into
 http://purl.obolibrary.org/obo/GO_0051253	negative regulation of RNA metabolic process	http://purl.obolibrary.org/obo/GO_0016070	RNA metabolic process
 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_1903623	negative regulation of RNA polymerase III activity	http://purl.obolibrary.org/obo/GO_0001056	RNA polymerase III activity
 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_0035021	negative regulation of Rac protein signal transduction	http://purl.obolibrary.org/obo/GO_0016601	Rac protein signal transduction
@@ -468,6 +467,7 @@ http://purl.obolibrary.org/obo/GO_2000261	negative regulation of blood coagulati
 http://purl.obolibrary.org/obo/GO_2000264	negative regulation of blood coagulation, extrinsic pathway	http://purl.obolibrary.org/obo/GO_0007598	blood coagulation, extrinsic pathway
 http://purl.obolibrary.org/obo/GO_2000267	negative regulation of blood coagulation, intrinsic pathway	http://purl.obolibrary.org/obo/GO_0007597	blood coagulation, intrinsic pathway
 http://purl.obolibrary.org/obo/GO_2000333	negative regulation of blood microparticle formation	http://purl.obolibrary.org/obo/GO_0072564	blood microparticle formation
+http://purl.obolibrary.org/obo/GO_1905554	negative regulation of blood vessel branching	http://purl.obolibrary.org/obo/GO_0001569	branching involved in blood vessel morphogenesis
 http://purl.obolibrary.org/obo/GO_0110059	negative regulation of blood vessel endothelial cell differentiation	http://purl.obolibrary.org/obo/GO_0060837	blood vessel endothelial cell differentiation
 http://purl.obolibrary.org/obo/GO_0043537	negative regulation of blood vessel endothelial cell migration	http://purl.obolibrary.org/obo/GO_0043534	blood vessel endothelial cell migration
 http://purl.obolibrary.org/obo/GO_1903588	negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis	http://purl.obolibrary.org/obo/GO_0002043	blood vessel endothelial cell proliferation involved in sprouting angiogenesis
@@ -2687,7 +2687,6 @@ http://purl.obolibrary.org/obo/GO_0106021	negative regulation of vesicle docking
 http://purl.obolibrary.org/obo/GO_0031339	negative regulation of vesicle fusion	http://purl.obolibrary.org/obo/GO_0006906	vesicle fusion
 http://purl.obolibrary.org/obo/GO_0106215	negative regulation of vesicle fusion with Golgi apparatus	http://purl.obolibrary.org/obo/GO_0048280	vesicle fusion with Golgi apparatus
 http://purl.obolibrary.org/obo/GO_1901609	negative regulation of vesicle transport along microtubule	http://purl.obolibrary.org/obo/GO_0047496	vesicle transport along microtubule
-http://purl.obolibrary.org/obo/GO_1905554	negative regulation of vessel branching	http://purl.obolibrary.org/obo/GO_0001569	branching involved in blood vessel morphogenesis
 http://purl.obolibrary.org/obo/GO_1900714	negative regulation of violaceol I biosynthetic process	http://purl.obolibrary.org/obo/GO_1900590	violaceol I biosynthetic process
 http://purl.obolibrary.org/obo/GO_1900717	negative regulation of violaceol II biosynthetic process	http://purl.obolibrary.org/obo/GO_1900593	violaceol II biosynthetic process
 http://purl.obolibrary.org/obo/GO_1903773	negative regulation of viral budding via host ESCRT complex	http://purl.obolibrary.org/obo/GO_0039702	viral budding via host ESCRT complex

diff --git a/src/design_patterns/positive_regulation.tsv b/src/design_patterns/positive_regulation.tsv
@@ -74,7 +74,6 @@ http://purl.obolibrary.org/obo/GO_2000003	positive regulation of DNA damage chec
 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_0032877	positive regulation of DNA endoreduplication	http://purl.obolibrary.org/obo/GO_0042023	DNA endoreduplication
 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
 http://purl.obolibrary.org/obo/GO_0045739	positive regulation of DNA repair	http://purl.obolibrary.org/obo/GO_0006281	DNA repair
 http://purl.obolibrary.org/obo/GO_0045740	positive regulation of DNA replication	http://purl.obolibrary.org/obo/GO_0006260	DNA replication

diff --git a/src/design_patterns/response_to_stimulus_by_stimulus.tsv b/src/design_patterns/response_to_stimulus_by_stimulus.tsv
@@ -291,7 +291,6 @@ http://purl.obolibrary.org/obo/GO_0071873	response to norepinephrine	http://purl
 http://purl.obolibrary.org/obo/GO_0007584	response to nutrient	http://purl.obolibrary.org/obo/GOCHE_33284	substance with nutrient role
 http://purl.obolibrary.org/obo/GO_0097333	response to olanzapine	http://purl.obolibrary.org/obo/CHEBI_7735	olanzapine
 http://purl.obolibrary.org/obo/GO_0034201	response to oleic acid	http://purl.obolibrary.org/obo/CHEBI_30823	oleate
-http://purl.obolibrary.org/obo/GO_0014070	response to organic cyclic compound	http://purl.obolibrary.org/obo/CHEBI_33832	organic cyclic compound
 http://purl.obolibrary.org/obo/GO_0046683	response to organophosphorus	http://purl.obolibrary.org/obo/CHEBI_25710	organophosphorus compound
 http://purl.obolibrary.org/obo/GO_1905841	response to oxidopamine	http://purl.obolibrary.org/obo/CHEBI_78741	oxidopamine
 http://purl.obolibrary.org/obo/GO_0000305	response to oxygen radical	http://purl.obolibrary.org/obo/CHEBI_61073	oxygen radical

diff --git a/src/design_patterns/vesicle_mediated_transport_differentiated_by_cargo.tsv b/src/design_patterns/vesicle_mediated_transport_differentiated_by_cargo.tsv
@@ -1 +1 @@
-defined_class	defined_class_label	target	target_label
+defined_class	defined_class_label	cargo	cargo_label
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		defined_class defined_class_label target target_label
		defined_class defined_class_label cargo cargo_label